bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating basin-scale linkages of the food-energy-water nexus with reduced complexity modeling
Authors: Bokhari Hussain H. , Najafi Ehsan , Dawidowicz Jorin , Wuchen Liushan , Maxfield Nicolas , Vörösmarty Charles J. , Fekete Balazs M. , Corsi Fabio , Sanyal Swarnali , Lin Tzu-Shun , Miara Ariel , Tuler Seth P.
Published: May 2023

There is a rapidly growing need to communicate to the public and policymakers on the nature and impact of climate change and its associated extremes, which manifest themselves across essential Food-Energy-Water Systems (FEWS). The complexity of this nexus demands analytical tools that can capture the essence of FEWS with the climate system, which may be difficult to stage and implement from a computationally efficient point-of-view. Reduced Complexity Models (RCMs) can synthesize important facets of a system quickly and with less dependence on difficult-to-assign inputs. We report on the development of an RCM framework for the FEWS nexus, to serve as a basic research tool in facilitating parameter sensitivity experiments as well as a means to establish more insightful dialogue with stakeholders through joint scenario construction. Three stand-alone and coupled models at the basin scale have been configured using Stella Architect software to simulate: 1) major flows and storage of water, 2) power plant operations and subsequent impacts on river reaches; and 3) nitrogen (N) mobilization and transport from atmospheric and landmass sources to riverine receiving waters. The Delaware River Basin is chosen for a contemporary simulation test case. Modeled results are calibrated and validated using observed stream gauge data, indicating reliable model performance at the monthly and annual time steps (0.57 < NSE < 0.98). A set of single and multi-factor climate, technology, and policy experiments are then explored using the RCM framework. Basin-scale system sensitivities are investigated across a set of intensified climate extremes, revealing the crucial roles of sewage treatment and energy infrastructure for climate resilience, significant exacerbations as well as mitigations of thermal and N pollution under opposing climate extremes, and important tradeoffs between river temperature and electricity production that are explored with technology and policy scenarios.
The importance of groundwater for riverine fish faunas in a region of shale gas development in northern Australia
Authors: Davis Jenny , Garcia Erica A. , Gibb Karen S. , Kennard Mark J. , Rose Alea , Stromsoe Nicola , Wedd Dion
Published: May 2023

Northern Australia contains the continent’s largest number of intact river systems, but these are facing increasing pressure as the proposed development of multiple and large-scale industries, including onshore gas, mining, horticulture, and agriculture, accelerates. These developments will require the diversion or extraction of large amounts of water and increase the risk of contamination by industrial and agricultural chemicals. There is an urgent need to collect baseline biophysical information on these aquatic systems before major developments proceed. Much community concern has been expressed about the potential environmental impacts of a developing shale gas industry (fracking) in the Beetaloo Sub-basin and upper Roper River region of the Northern Territory. Here we describe the first major survey of the freshwater fish fauna of this region and an assessment of the importance of groundwater in supporting fish biodiversity. This region is remote from major human settlements and the waterbodies are often difficult to access. Accordingly, we maximised the information we collected from limited sampling sessions by using both traditional fish survey methods (netting and electrofishing) and eDNA analysis of water and benthic sediment samples. Water column eDNA doubled the number of species recorded to those obtained from traditional survey methods alone. We found that the fish fauna was richest at sites on northward-flowing groundwater-dependent rivers. More work is needed to fully understand the dependence of individual species on groundwater inflows. However, it is evident that conserving freshwater fish biodiversity in these rivers will require protection of the groundwater resources to ensure baseflows and aquatic refuges persist through the most extended of dry seasons.
Water depth modulates the species richness–biomass relationship in submerged macrophytes
Authors: Wen Zihao , Wang Hao , Shan Hang , Cao Yu , Tan Lu , Zhu Tianshun , Cai Qinghua , Ni Leyi , Zhang Xiaolin , Chou Qingchuan , Cao Te
Published: May 2023

The effect of biodiversity on ecosystem productivity has been a controversial issue in ecological research. The species richness–productivity relationship is highly variable in natural ecosystems, with a positive relationship being one of the most commonly observed relationships. Previous regional studies from terrestrial ecosystems have demonstrated that environmental gradients can regulate the species richness–productivity relationship. However, how this relationship varies in freshwater ecosystems across spatial environment gradients remains unclear. In this study, we propose that the species richness–productivity relationship can be modulated by the water depth. Here, we surveyed the submerged macrophyte community structure by establishing 24 transects and 642 quadrats in Erhai Lake, Yunnan Plateau, China. Our findings highlight that the species richness–productivity relationship gradually changed from slightly positive to strongly positive as the environment became more light-limited with the increasing water depth, supporting the stress-gradient hypothesis. The results from this study provide new insights into the biodiversity–ecosystem functioning relationships and in managing lake macrophyte communities and productivity.
An accurate fringe extraction model of small- and medium-sized urban areas using multi-source data
Authors: Li Jianfeng , Peng Biao , Liu Siqi , Ye Huping , Zhang Zhuoying , Nie Xiaowei
Published: May 2023

Urban fringes are of great significance to urban development as connecting hubs between urban and rural areas. However, there are many problems in urban fringes, including disorderly spatial layout, waste of social resources, and low quality of human settlements. Rapid and accurate identification of urban fringes has important practical significance for optimizing urban spatial layout, controlling urban unlimited expansion, and protecting land resources. Given the lack of suitable and high-quality fringe extraction models for small- and medium-sized urban areas, this study was based on Gaofen-2 (GF-2) imagery, Suomi National Polar-orbiting Partnership Visible Infrared Imager Radiometer Suite (NPP-VIIRS) imagery, point of interest (POI) data, and WorldPop data, taking the landscape disorder degree, POI kernel density, and night light intensity as urban feature factors and constructing a fringe extraction model of small- and medium-sized urban areas (FEM-SMU). Taking Hantai District in China as the study area, the results of the model were compared to the landscape disorder degree threshold method and POI kernel density breakpoint analysis method, while the generality of the model was further tested in Shangzhou and Hanbin Districts. The results show that the FEM-SMU model has evident improvements over the conventional methods in terms of accuracy, detail, and integrity, and has higher versatility, which can better meet the research needs of small- and medium-sized urban fringes.
Morphology and phase state of PM2.5 in urban and coastal-rural areas during summer
Authors: Gaikwad Sanjit , Kim Daeun , Jeong Rani , Lee Ji Yi , Lee Kwangyul , Ahn Junyoung , Jang Kyoung-Soon , Kim Changhyuk , Song Mijung
Published: May 2023

The morphology and phase state are critical physical properties of aerosol particles. However, studies related to the analysis of these properties primarily focus on laboratory experiments, and studies on real aerosol particles are limited. Herein, fine particulate matter (PM2.5) filter samples were obtained to investigate and compare the morphology and phase state of ambient aerosol particles in South Korea. The PM2.5 samples were collected in the summer of June 2021 from two different environments: Seoul (urban) and Seosan (coastal-rural). Optical microscopy was combined with the poke-and-flow technique to determine the morphology and phase state of the PM2.5 as a function of relative humidity (RH) at 293 ± 1 K. At both sites, the PM2.5 droplets, which were extracted in purified water, showed a multiphase nature that was dependent on the RH and chemical composition. Based on the results and ambient average RH in Seoul, most of the PM2.5 was observed in a liquid state on polluted days under an inorganic-dominant condition, but in a semisolid state on clean days under an organic carbon-rich condition. In Seosan, the PM2.5 predominantly existed in a liquid state, due to the high RH caused by proximity to the Yellow Sea. Our study provides fundamental physical properties of PM2.5 for both urban and coastal-rural environments. The results have strong applications for atmospheric chemistry and predicting particle size distributions.
BVLOS UAV missions for vegetation mapping in maritime Antarctic
Authors: Zmarz Anna , Karlsen Stein Rune , Kycko Marlena , Korczak-Abshire Małgorzata , Gołębiowska Izabela , Karsznia Izabela , Chwedorzewska Katarzyna
Published: May 2023

Polar areas are among the regions where climate change occurs faster than on most of the other areas on Earth. To study the effects of climate change on vegetation, there is a need for knowledge on its current status and properties. Both classic field observation methods and remote sensing methods based on manned aircraft or satellite image analysis have limitations. These include high logistic operation costs, limited research areas, high safety risks, direct human impact, and insufficient resolution of satellite images. Fixed-wing unmanned aerial vehicle beyond the visual line of sight (UAV BVLOS) missions can bridge the scale gap between field-based observations and full-scale airborne or satellite surveys. In this study the two operations of the UAV BVLOS, at an altitude of 350 m ASL, have been successfully performed in Antarctic conditions. Maps of the vegetation of the western shore of Admiralty Bay (King George Island, South Shetlands, Western Antarctic) that included the Antarctic Specially Protected Area No. 128 (ASPA 128) were designed. The vegetation in the 7.5 km2 area was mapped in ultra-high resolution (<5 cm and DEM of 0.25 m GSD), and from the Normalized Difference Vegetation Index (NDVI), four broad vegetation units were extracted: “dense moss carpets” (covering 0.14 km2, 0.8% of ASPA 128), “Sanionia uncinata moss bed” (0.31 km2, 1.7% of ASPA 128), “Deschampsia antarctica grass meadow” (0.24 km2, 1.3% of ASPA 128), and “Deschampsia antarctica–Usnea antarctica heath” (1.66 km2, 9.4% of ASPA 128). Our results demonstrate that the presented UAV BVLOS–based surveys are time-effective (single flight lasting 2.5 h on a distance of 300 km) and cost-effective when compared to classical field-based observations and are less invasive for the ecosystem. Moreover, unmanned airborne vehicles significantly improve security, which is of particular interest in polar region research. Therefore, their development is highly recommended for monitoring areas in remote and fragile environments.
Manure amendment acts as a recommended fertilization for improving carbon sequestration efficiency in soils of typical drylands of China
Authors: Liang Shuo , Sun Nan , Wang Shuhui , Colinet Gilles , Longdoz Bernard , Meersmans Jeroen , Wu Lianhai , Xu Minggang
Published: May 2023

It is generally known that soil organic carbon (SOC) stocks tend to increase with an increase in C input, whereas the C sequestration efficiency (CSE), i.e., the conversion ratio of C input to SOC, differs depending on the amount and type of C input. However, there is still a need to better understand the impact of various fertilization practices on CSE. We studied the data from eight long-term experiments located in the main dryland region of China in order to comprehensively assess the key drivers of CSE in the plow layer considering nearly four decades of various fertilizer treatments, i.e., no fertilizer (CK); chemical nitrogen, phosphorus, and potassium (NPK/NP); chemical fertilizers plus manure (NPKM/NPM/NM); and straw (NPKS/NPS/NS). Our results showed that manure amendment had the most significant fertilization effect on SOC sequestration with an average CSE of 14.9%, which was significantly higher than that of chemical fertilization (9.0%) and straw return treatments (7.9%). In addition, manure amendment also had the highest average SOC increase rate of 684 kg C ha-1 yr-1. Variance partitioning analysis (VPA) illustrated that the CSE of the main dryland region of China was mostly controlled by edaphic characteristics (32.2%), especially the soil C/N ratio and clay content. VPA and structural equation modeling revealed that the magnitude and influencing factors driving CSE varied among different fertilizer treatments. Soil total N was the limiting factor for CSE in the CK treatment, whereas the soil C/N ratio and pH were the main explanatory factors for CSE in the long-term chemical NPK fertilizer treatment. The negative impact of C input from straw was the main driver of CSE under straw return treatments, though C input had a positive effect on the improvement of soil physical properties. However, when considering manure amendments, the improvement of soil nutrients and clay content controlled CSE, underlining the main positive direct effect of soil chemical properties. In a nutshell, our results recommend manure plus chemical fertilizers as a sustainable practice for improving the C sequestration rate and efficiency in dryland cropping systems.
Toolkit for conducting citizen science activities in environmental epidemiology
Authors: Kocman David , Righi Valeria , Errandonea Lucia , Maccani Giovanni , Creus Javier , Froeling Frederique , Hoek Gerard , Andrusaityte Sandra , Grazuleviciene Regina , Ficorilli Antonella , De Marchi Bruna , Biggeri Annibale , Ftičar Jure , Gignac Florence , Toran Raul , Basagaña Xavier
Published: May 2023

Scientists and practitioners implementing citizen science projects, in which the involvement of citizens is key, often need ideas and tools that help in reaching citizens, engaging them in the project and maximizing their contributions. In this paper, we describe the creation of an open toolkit, a web-based portal citizensciencetoolkit.eu1 designed in the framework of the CitieS-Health project for the development and promotion of citizen science (CS) projects. The main focus is on projects linking urban environmental exposures and health, but it has applicability to other settings. The toolkit comprises the steps and phases during the implementation of CS activities in environmental epidemiology. A total of 28 tools are currently included, of which most were co-designed and tested within CitiesS-Health, as well as some resulting from external projects. For each tool, in addition to the details of its purpose and the specific challenges it poses, downloadable support content is available. To help facilitate inspiration and the adoption of tools provided, an illustrative step-by-step demonstration and description of its use in a CS project in a real-life setting is included, focusing on recommendations derived from the user experience. The portal is designed as a live inventory of tools, enabling interested CS practitioners not only to replicate, but also to continuously update and enrich it is content. To this end, the long-term objective of the portal is to act as a hub of resources that would enable the active inclusion of citizens in all the phases of the participatory research projects.
A numerical simulation of CCN impacts on weather modification efficiency
Authors: Lou Xiaofeng , Shi Yu , Shan Yunpeng
Published: May 2023

Aerosols affect development of clouds and precipitation by serving as cloud condensation nuclei (CCN) and ice nuclei (IN). Considering the dramatically changing ambient aerosol concentration, it is important to examine the potential “side effect” of aerosol pollution on precipitation enhancement by weather modification. In this study, the cloud seeding was performed on a precipitation event in Beijing in the summer of 2008, which is simulated by the NSSL two-moment cloud scheme of the Weather Research and Forecasting (WRF) model. Sensitivity tests were conducted by modifying the ambient aerosol concentration and the ice crystal seeding amount to investigate the cloud seeding efficacy in different CCN concentration scenarios. There was a slight difference in the precipitation distribution between the simulations with two ambient CCN concentrations: the northern precipitation center in polluted scenario was weaker and the southern center was stronger. Compared with normal CCN scenario, the cloud liquid water mass and ice crystal mass in the severe pollution scenario is larger, and the total contents of snow and graupel were not sensitive to the CCN concentration. With the same amount of man-made ice crystals seeding, the precipitation enhancement was quite different under different CCN conditions. The higher the CCN concentration usually leads to stronger precipitation suppression. As CCN concentration increase, the deposition growth of snow, auto-conversion and accretion of ice crystals to snow were weakened, as well as the conversion of melting snow and graupel into rainwater.
Modeling land susceptibility to wind erosion hazards using LASSO regression and graph convolutional networks
Authors: Gholami Hamid , Mohammadifar Aliakbar , Fitzsimmons Kathryn E. , Li Yue , Kaskaoutis Dimitris G.
Published: May 2023

Predicting land susceptibility to wind erosion is necessary to mitigate the negative impacts of erosion on soil fertility, ecosystems, and human health. This study is the first attempt to model wind erosion hazards through the application of a novel approach, the graph convolutional networks (GCNs), as deep learning models with Monte Carlo dropout. This approach is applied to Semnan Province in arid central Iran, an area vulnerable to dust storms and climate change. We mapped 15 potential factors controlling wind erosion, including climatic variables, soil characteristics, lithology, vegetation cover, land use, and a digital elevation model (DEM), and then applied the least absolute shrinkage and selection operator (LASSO) regression to discriminate the most important factors. We constructed a predictive model by randomly selecting 70% and 30% of the pixels, as training and validation datasets, respectively, focusing on locations with severe wind erosion on the inventory map. The current LASSO regression identified eight out of the 15 features (four soil property categories, vegetation cover, land use, wind speed, and evaporation) as the most important factors controlling wind erosion in Semnan Province. These factors were adopted into the GCN model, which estimated that 15.5%, 19.8%, 33.2%, and 31.4% of the total area is characterized by low, moderate, high, and very high susceptibility to wind erosion, respectively. The area under curve (AUC) and SHapley Additive exPlanations (SHAP) of game theory were applied to assess the performance and interpretability of GCN output, respectively. The AUC values for training and validation datasets were estimated at 97.2% and 97.25%, respectively, indicating excellent model prediction. SHAP values ranged between −0.3 and 0.4, while SHAP analyses revealed that the coarse clastic component, vegetation cover, and land use were the most effective features of the GCN output. Our results suggest that this novel suite of methods is highly recommended for future spatial prediction of wind erosion hazards in other arid environments around the globe.
Hydrogeochemical characterization and quality assessment of groundwater resources in the Upper-Doab region of Uttar Pradesh, India
Authors: Gautam Anant , Rai Suresh Chand
Published: May 2023

The present study tries to delineate groundwater zones in the Upper-Doab region of Uttar Pradesh, India based on its suitability for the use of domestic and irrigation purposes considering the physico-chemical parameters of groundwater samples (n ∼ 70) using Weighted Arithmetic Water Quality Index (WAWQI) and Composite Groundwater Quality Index for Irrigation (CGQII) methods, respectively. The Upper-Doab region of Uttar Pradesh is bounded by the mighty rivers of Ganga and Yamuna in the east and west respectively. In the southwest, the region shares the boundary with the national capital of Delhi, which has led to an increase in the growth of urbanization and industrialization in the region. These factors have a visible negative impact on the groundwater scenario of the region. Hydrogeochemical investigation reveals that the ionic dominance in the groundwater samples is in the order of HCO3 > Cl > SO4 > NO3 > F and Na > Mg > Ca > K. Chemical history of groundwater samples using piper-trilinear diagram shows that Ca-Mg-HCO3 and Ca-Na-HCO3 type of groundwater is mostly found in this region. Gibb’s plot reveals that rock-water interaction was dominantly controlling the ionic composition of the groundwater in the unconfined aquifer environment. Further, the bivariate plot of (SO4 + HCO3) vs. (Ca + Mg) reveals that the weathering of calcite and dolomite minerals present in the aquifer environment has largely attributed chemical character to the groundwater of the region. The groundwater zoning concerning its domestic and agricultural use reveals that the groundwater of Meerut, Muzaffarnagar, Baghpat, Ghaziabad, and Gautam Buddha Nagar districts have poorer quality of groundwater due to high electrical conductivity and higher concentration of nitrate which has a higher anthropogenic link. The evaluation of groundwater quality for irrigation using a single index value i.e., CGQII makes this study different from the other hydrochemical investigations under similar hydrogeolocal aquifer conditions in the region. The study suggests that corrective measures like, strict implementation of untreated discharge of industrial effluents to the water or groundwater directly, creating awareness among farmers for lesser use of chemical fertilizers, and regular groundwater monitoring systems for quality analysis must be considered for a sustainable future of the region.
Ecological water quality of the Three Gorges Reservoir and its relationship with land covers in the reservoir area: implications for reservoir management
Authors: Ye Lin , Chen Kefeng , Cheng Jingjing , Tan Lu , Zhang Min , Zhang Xiaoguang , Cai Qinghua
Published: May 2023

In this study, we evaluated the ecological water quality of the entire Three Gorges Reservoir (TGR) and further examined the relationship with changes in watershed land covers. Using the phytoplankton functional group-based Q index, we found that the ecological water quality in the mainstream (previously known as the Yangtze River) of TGR is good, with 84% of sites in the status above good. While the poor ecological water quality was generally observed in the backwater regions of TGR’s tributaries, with 79% of sites below the good status. Further investigating the potential impacts of the changes in land covers within the watershed on the tributary ecological water quality, we found that the percentage of urban and farmland areas had a significant (p < 0.05) negative correlation with the Q index-based ecological water quality of the tributary bays, and the forest cover had a marginally significant (p = 0.058) positive correlation with the ecological water quality. As a comparison, total nitrogen and total phosphorus in the tributary backwater regions of TGR had no reasonable correlation with the land covers within the watershed. Our study highlights that watershed management can enhance the ecological water quality in the backwater regions of TGR’s tributaries, but it likely to be a long-term process. This implies considerations of other rapid measures, such as the water level regulation approach, should also be considered in reservoir management. Our study underscores the importance of ecological water quality assessment in reservoir management and provides insights into the impacts of changes in watershed land covers on ecological water quality in backwater regions of TGR’s tributaries.
Hydrometeorological controls on net carbon dioxide exchange over a temperate desert steppe in Inner Mongolia, China
Authors: Song Jiaxin , Zhou Li , Zhou Guangsheng , Wang Yu , Zhang Sen , Yan Yujie
Published: May 2023

Understanding the effect of environmental factors on the net ecosystem CO2 exchange (NEE) and the response of NEE to rainfall events is of great significance for an accurate understanding of the carbon cycle for desert steppe ecosystems. Based on the long-term (2011–2018) eddy covariance flux data of a temperate desert steppe in Inner Mongolia, China, this study used path analysis to analyze the combined impact of the environmental factors on NEE. The results showed that during the growing season, vapor pressure deficit (VPD) and soil water content (SWC) was the most prominent environmental factor for the daytime NEE and nighttime NEE, respectively. NEE responds differently to individual environmental factors among multi-year climatic conditions. The size of rainfall event has significant impacts on NEE, it can effectively promote the CO2 uptake of the desert steppe ecosystem when rainfall event size is greater than 5 mm, and the NEE response increased with the rainfall event size. Moreover, NEE peaked approximately 1–3  days after a 5–10 mm rainfall event, while the rainfall event size >10 mm, it would take 3–5  days for NEE to reach a peak value; and yet, small rainfall events (< 5 mm) slightly increased CO2 emissions. During the growing season, carbon uptake increased with monthly rainfall, except in May. Our results are important for understanding the carbon cycle and its control mechanisms in the temperate desert steppe of Inner Mongolia.
Whole-exome identifies germline variants in families with obstructive sleep apnea syndrome
Authors: de Azevedo Pedro Guimarães , Guimarães Maria de Lourdes Rabelo , Albuquerque Anna Luiza Braga , Alves Rayane Benfica , Gomes Fernandes Bianca , Marques de Melo Flavia , Guimaraes Corrêa Do Carmo Lisboa Cardenas Raony , Friedman Eitan , De Marco Luiz , Bastos-Rodrigues Luciana
Published: May 2023

Background: Obstructive sleep apnea syndrome (OSAS) (OMIM #107650) is characterized by complete or partial obstruction of the upper airways, resulting in periods of sleep associated apnea. OSAS increases morbidity and mortality risk from cardiovascular and cerebrovascular diseases. While heritability of OSAS is estimated at ∼40%, the precise underlying genes remain elusive. Brazilian families with OSAS that follows as seemingly autosomal dominant inheritance pattern were recruited.

Methods: The study included nine individuals from two Brazilian families displaying a seemingly autosomal dominant inheritance pattern of OSAS. Whole exome sequencing of germline DNA were analyzed using Mendel, MD software. Variants selected were analyzed using Varstation® with subsequent analyses that included validation by Sanger sequencing, pathogenic score assessment by ACMG criteria, co-segregation analyses (when possible) allele frequency, tissue expression patterns, pathway analyses, effect on protein folding modeling using Swiss-Model and RaptorX.

Results: Two families (six affected patients and three unaffected controls) were analyzed. A comprehensive multistep analysis yielded variants in COX20 (rs946982087) (family A), PTPDC1 (rs61743388) and TMOD4 (rs141507115) (family B) that seemed to be strong candidate genes for being OSAS associated genes in these families.

Conclusion: Sequence variants in COX20, PTPDC1 and TMOD4 seemingly are associated with OSAS phenotype in these families. Further studies in more, ethnically diverse families and non-familial OSAS cases are needed to better define the role of these variants as contributors to OSAS phenotype.
CNVs in 8q24.3 do not influence gene co-expression in breast cancer subtypes
Authors: Hernández-Gómez Candelario , Hernández-Lemus Enrique , Espinal-Enríquez Jesús
Published: May 2023

Gene co-expression networks are a useful tool in the study of interactions that have allowed the visualization and quantification of diverse phenomena, including the loss of co-expression over long distances in cancerous samples. This characteristic, which could be considered fundamental to cancer, has been widely reported in various types of tumors. Since copy number variations (CNVs) have previously been identified as causing multiple genetic diseases, and gene expression is linked to them, they have often been mentioned as a probable cause of loss of co-expression in cancerous networks. In order to carry out a comparative study of the validity of this statement, we took 477 protein-coding genes from chromosome 8, and the CNVs of 101 genes, also protein-coding, belonging to the 8q24.3 region, a cytoband that is particularly active in the appearance of breast cancer. We created CNVS-conditioned co-expression networks of each of the 101 genes in the 8q24.3 region using conditional mutual information. The study was carried out using the four molecular subtypes of breast cancer (Luminal A, Luminal B, Her2, and Basal), as well as a case corresponding to healthy samples. We observed that in all cancer cases, the measurement of the Kolmogorov-Smirnov statistic shows that there are no significant differences between one and other values of the CNVs for any case. Furthermore, the co-expression interactions are stronger in all cancer subtypes than in the control networks. However, the control network presents a homogeneously distributed set of co-expression interactions, while for cancer networks, the highest interactions are more confined to specific cytobands, in particular 8q24.3 and 8p21.3. With this approach, we demonstrate that despite copy number alterations in the 8q24 region being a common trait in breast cancer, the loss of long-distance co-expression in breast cancer is not determined by CNVs.
Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest
Authors: Wang Zijie , Zhu Yuzhi , Liu Zhule , Li Hongfu , Tang Xinqiang , Jiang Yi
Published: May 2023

Introduction: With the advancement of RNA-seq technology and machine learning, training large-scale RNA-seq data from databases with machine learning models can generally identify genes with important regulatory roles that were previously missed by standard linear analytic methodologies. Finding tissue-specific genes could improve our comprehension of the relationship between tissues and genes. However, few machine learning models for transcriptome data have been deployed and compared to identify tissue-specific genes, particularly for plants.

Methods: In this study, an expression matrix was processed with linear models (Limma), machine learning models (LightGBM), and deep learning models (CNN) with information gain and the SHAP strategy based on 1,548 maize multi-tissue RNA-seq data obtained from a public database to identify tissue-specific genes. In terms of validation, V-measure values were computed based on k-means clustering of the gene sets to evaluate their technical complementarity. Furthermore, GO analysis and literature retrieval were used to validate the functions and research status of these genes.

Results: Based on clustering validation, the convolutional neural network outperformed others with higher V-measure values as 0.647, indicating that its gene set could cover as many specific properties of various tissues as possible, whereas LightGBM discovered key transcription factors. The combination of three gene sets produced 78 core tissue-specific genes that had previously been shown in the literature to be biologically significant.

Discussion: Different tissue-specific gene sets were identified due to the distinct interpretation strategy for machine learning models and researchers may use multiple methodologies and strategies for tissue-specific gene sets based on their goals, types of data, and computational resources. This study provided comparative insight for large-scale data mining of transcriptome datasets, shedding light on resolving high dimensions and bias difficulties in bioinformatics data processing.
Early activation and recruitment of invariant natural killer T cells during liver ischemia-reperfusion: the major role of the alarmin interleukin-33
Authors: Robin Aurélie , Mackowiak Claire , Bost Romain , Dujardin Fanny , Barbarin Alice , Thierry Antoine , Hauet Thierry , Pellerin Luc , Gombert Jean-Marc , Salamé Ephrem , Herbelin André , Barbier Louise
Published: May 2023

Over the past thirty years, the complexity of the αβ-T cell compartment has been enriched by the identification of innate-like T cells (ITCs), which are composed mainly of invariant natural killer T (iNKT) cells and mucosal-associated invariant T (MAIT) cells. Based on animal studies using ischemia-reperfusion (IR) models, a key role has been attributed to iNKT cells in close connection with the alarmin/cytokine interleukin (IL)-33, as early sensors of cell-stress in the initiation of acute sterile inflammation. Here we have investigated whether the new concept of a biological axis of circulating iNKT cells and IL-33 applies to humans, and may be extended to other ITC subsets, namely MAIT and γδ-T cells, in the acute sterile inflammation sequence occurring during liver transplant (LT). From a prospective biological collection of recipients, we reported that LT was accompanied by an early and preferential activation of iNKT cells, as attested by almost 40% of cells having acquired the expression of CD69 at the end of LT (i.e. 1-3 hours after portal reperfusion), as opposed to only 3-4% of conventional T cells. Early activation of iNKT cells was positively correlated with the systemic release of the alarmin IL-33 at graft reperfusion. Moreover, in a mouse model of hepatic IR, iNKT cells were activated in the periphery (spleen), and recruited in the liver in WT mice, as early as the first hour after reperfusion, whereas this phenomenon was virtually missing in IL-33-deficient mice. Although to a lesser degree than iNKT cells, MAIT and γδ-T cells also seemed targeted during LT, as attested by 30% and 10% of them acquiring CD69 expression, respectively. Like iNKT cells, and in clear contrast to γδ-T cells, activation of MAIT cells during LT was closely associated with both release of IL-33 immediately after graft reperfusion and severity of liver dysfunction occurring during the first three post-operative days. All in all, this study identifies iNKT and MAIT cells in connection with IL-33 as new key cellular factors and mechanisms of acute sterile inflammation in humans. Further investigations are required to confirm the implication of MAIT and iNKT cell subsets, and to precisely assess their functions, in the clinical course of sterile inflammation accompanying LT.
Substance P analogs devoid of key residues fail to activate human mast cells via MRGPRX2
Authors: Raj Shammy , Hlushak Stepan , Arizmendi Narcy , Kovalenko Andriy , Kulka Marianna
Published: May 2023

Mast cells play an important role in disease pathogenesis by secreting immunomodulatory molecules. Mast cells are primarily activated by the crosslinking of their high affinity IgE receptors (FcεRI) by antigen bound immunoglobulin (Ig)E antibody complexes. However, mast cells can also be activated by the mas related G protein-coupled receptor X2 (MRGPRX2), in response to a range of cationic secretagogues, such as substance P (SP), which is associated with pseudo-allergic reactions. We have previously reported that the in vitro activation of mouse mast cells by basic secretagogues is mediated by the mouse orthologue of the human MRGPRX2, MRGPRB2. To further elucidate the mechanism of MRGPRX2 activation, we studied the time-dependent internalization of MRGPRX2 by human mast cells (LAD2) upon stimulation with the neuropeptide SP. In addition, we performed computational studies to identify the intermolecular forces that facilitate ligand-MRGPRX2 interaction using SP. The computational predictions were tested experimentally by activating LAD2 with SP analogs, which were missing key amino acid residues. Our data suggest that mast cell activation by SP causes internalization of MRGPRX2 within 1 min of stimulation. Hydrogen bonds (h-bonds) and salt bridges govern the biding of SP to MRGPRX2. Arg1 and Lys3 in SP are key residues that are involved in both h-bonding and salt bridge formations with Glu164 and Asp184 of MRGPRX2, respectively. In accordance, SP analogs devoid of key residues (SP1 and SP2) failed to activate MRGPRX2 degranulation. However, both SP1 and SP2 caused a comparable release of chemokine CCL2. Further, SP analogs SP1, SP2 and SP4 did not activate tumor necrosis factor (TNF) production. We further show that SP1 and SP2 limit the activity of SP on mast cells. The results provide important mechanistic insight into the events that result in mast cell activation through MRGPRX2 and highlight the important physiochemical characteristics of a peptide ligand that facilitates ligand-MRGPRX2 interactions. The results are important in understanding activation through MRGPRX2, and the intermolecular forces that govern ligand-MRGPRX2 interaction. The elucidation of important physiochemical properties within a ligand that are needed for receptor interaction will aid in designing novel therapeutics and antagonists for MRGPRX2.
Case Report: The application of associating liver partition and portal vein ligation for staged hepatectomy in patients with hepatitis b virus-related hepatocellular carcinoma after undergoing treatment with an immune checkpoint inhibitor: a report of two cases
Authors: Ning Cong , Liu Guanmo , Zhang Junwei , Yang Xiaobo , Xu Yiyao , Zhao Haitao
Published: May 2023

Hepatocellular carcinoma (HCC) is often diagnosed at an unresectable stage without opportunities for curative therapy. Future liver remnant (FLR) insufficiency limits the range of patients who can undergo radical resection. Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) can ultimately achieve short-term hypertrophy of the FLR in patients with viral hepatitis-related fibrosis/cirrhosis and R0 resection. However, the influence of immune checkpoint inhibitors (ICIs) on liver regeneration remains unknown. We report two patients diagnosed with Barcelona Clinic Liver Cancer (BCLC)-B stage hepatitis B virus (HBV)-related HCC who underwent pioneering ALPPS after immunotherapy without posthepatectomy liver failure (PHLF). ALPPS has been shown to be safe and feasible in patients with HCC who underwent immunotherapy previously for the first time and might provide an alternative salvage option for future conversion therapy of HCC.
Pembrolizumab-induced optic neuropathy – a case report
Authors: Daetwyler Eveline , Zippelius Alfred , Meyer Peter , Läubli Heinz
Published: May 2023

Background

Immune checkpoint inhibitor (ICI) treatment has become important for treating various cancer types, including Hodgkin’s lymphoma. However, ICI can overstimulate the immune system, leading to a broad range of immunological side effects, known as immune-related adverse events (irAEs). Here, we report a case of optic neuropathy caused by pembrolizumab.

Case presentation

A patient with Hodgkin’s lymphoma received pembrolizumab every three weeks. Twelve days after the sixth cycle of pembrolizumab, the patient was admitted to the emergency department with blurred vision, visual field impairment and altered color perception affecting the right eye. The diagnosis of immune-related optic neuropathy was established. Pembrolizumab was stopped permanently and high-dose steroid treatment was immediately started. This emergency treatment led to a satisfactory binocular vision and an improvement of visual acuity testing results. After another 7 months, the left eye was affected with the same symptoms. At this time, only an extended immunosuppressive therapy consisting of high-dose steroid treatment, plasmapheresis, immunoglobulin treatment, retrobulbar injection of steroids and mycophenolate mofetil, successfully reduced the symptoms.

Conclusions

This case highlights the need for prompt recognition and treatment of rare irAEs, such as optic neuropathy. Urgent treatment with initial high-dose steroid treatment is required to avoid persistent loss of visual acuity. Options for further treatment are mainly based on small case series and case reports. In our case, a retrobulbar injection of steroids in combination with mycophenolate mofetil showed significant success in treating steroid-refractory optic neuropathy.
Preclinical models and evaluation criteria of prostatitis
Authors: He Hailan , Luo Hui , Xu Hui , Qian Biao , Zou Xiaofeng , Zhang Guoxi , Zeng Fei , Zou Junrong
Published: May 2023

Prostatitis is a common urological condition that affects almost half of all men at some point in their life. The prostate gland has a dense nerve supply that contributes to the production of fluid to nourish sperm and the mechanism to switch between urination and ejaculation. Prostatitis can cause frequent urination, pelvic pain, and even infertility. Long-term prostatitis increases the risk of prostate cancer and benign prostate hyperplasia. Chronic non-bacterial prostatitis presents a complex pathogenesis, which has challenged medical research. Experimental studies of prostatitis require appropriate preclinical models. This review aimed to summarize and compare preclinical models of prostatitis based on their methods, success rate, evaluation, and range of application. The objective of this study is to provide a comprehensive understanding of prostatitis and advance basic research.
African swine fever virus QP383R dampens type I interferon production by promoting cGAS palmitoylation
Authors: Hao Siyuan , Zheng Xiaojie , Zhu Yingqi , Yao Yao , Li Sihan , Xu Yangyang , Feng Wen-hai
Published: May 2023

Cyclic GMP-AMP synthase (cGAS) recognizes viral DNA and synthesizes cyclic GMP-AMP (cGAMP), which activates stimulator of interferon genes (STING/MITA) and downstream mediators to elicit an innate immune response. African swine fever virus (ASFV) proteins can antagonize host immune responses to promote its infection. Here, we identified ASFV protein QP383R as an inhibitor of cGAS. Specifically, we found that overexpression of QP383R suppressed type I interferons (IFNs) activation stimulated by dsDNA and cGAS/STING, resulting in decreased transcription of IFNβ and downstream proinflammatory cytokines. In addition, we showed that QP383R interacted directly with cGAS and promoted cGAS palmitoylation. Moreover, we demonstrated that QP383R suppressed DNA binding and cGAS dimerization, thus inhibiting cGAS enzymatic functions and reducing cGAMP production. Finally, the truncation mutation analysis indicated that the 284-383aa of QP383R inhibited IFNβ production. Considering these results collectively, we conclude that QP383R can antagonize host innate immune response to ASFV by targeting the core component cGAS in cGAS-STING signaling pathways, an important viral strategy to evade this innate immune sensor.
Development and validation of urinary exosomal microRNA biomarkers for the diagnosis of acute rejection in kidney transplant recipients
Authors: Seo Jung-Woo , Lee Yu Ho , Tae Dong Hyun , Kim Yang Gyun , Moon Ju-Young , Jung Su Woong , Kim Jin Sug , Hwang Hyeon Seok , Jeong Kyung-Hwan , Jeong Hye Yun , Lee So-Young , Chung Byung Ha , Kim Chan-Duck , Park Jae Berm , Seok Junhee , Kim Yeong Hoon , Lee Sang-Ho
Published: May 2023

Introduction

Acute rejection (AR) continues to be a significant obstacle for short- and long-term graft survival in kidney transplant recipients. Herein, we aimed to examine urinary exosomal microRNAs with the objective of identifying novel biomarkers of AR.

Materials and methods

Candidate microRNAs were selected using NanoString-based urinary exosomal microRNA profiling, meta-analysis of web-based, public microRNA database, and literature review. The expression levels of these selected microRNAs were measured in the urinary exosomes of 108 recipients of the discovery cohort using quantitative real-time polymerase chain reaction (qPCR). Based on the differential microRNA expressions, AR signatures were generated, and their diagnostic powers were determined by assessing the urinary exosomes of 260 recipients in an independent validation cohort.

Results

We identified 29 urinary exosomal microRNAs as candidate biomarkers of AR, of which 7 microRNAs were differentially expressed in recipients with AR, as confirmed by qPCR analysis. A three-microRNA AR signature, composed of hsa-miR-21-5p, hsa-miR-31-5p, and hsa-miR-4532, could discriminate recipients with AR from those maintaining stable graft function (area under the curve [AUC] = 0.85). This signature exhibited a fair discriminative power in the identification of AR in the validation cohort (AUC = 0.77).

Conclusion

We have successfully demonstrated that urinary exosomal microRNA signatures may form potential biomarkers for the diagnosis of AR in kidney transplantation recipients.
Racehorses from a breeding farm in Tropical Ecuador have a high seroprevalence of anti-Leptospira spp. antibodies: a paradigm for leptospirosis management from a One Health perspective
Authors: Orlando Solon Alberto , Paez Martinez Katherine , Sanchez Ericka , de la Cruz Carmen , Calderon Joselyn , Arcos Fabrizio , Torres-Lasso Pablo , Calvopiña Manuel , Garcia-Bereguiain Miguel Angel
Published: May 2023

Background

Leptospirosis is a zoonotic disease of worldwide distribution that affects humans and domestic and wild animals, and it is highly endemic in Ecuador. However, no reports of infections affecting horses have been published in the country.

Methods

This study evaluates the prevalence of anti-Leptospira spp. antibodies in racing horses from a breeding farm in the coastal Santa Elena province, southwest Ecuador. Sera were collected from 108 non-vaccinated horses and evaluated for 24 serovars of Leptospira spp. using the microscopic agglutination test (MAT).

Results

It was found that 100% of horses were reactive for Leptospira spp., most of them for multiple serovars. The most prevalent serovars were Leptospira kirschneri serovar Grippotyphosa (100%; 95% CI 99.9% to 100.1%); L. interrogans serovars Sejroe (96.3%; 95% CI 96.2% to 96.4%), Saxkoebing (95.4%; 95% CI 95.3% to 95.5%), Canicola (90.7%; 95% CI 90.5% to 90.9%), Icterohaemorrhagiae (80.5%; 95% CI 80.4% to 80.6%), Bataviae (73.1%; 95% CI 73.0% to 73.2%), Australis (75.0%; 95% CI 74.9% to 75.1%), and Bratislava (71.2%; 95% CI 71.1% to 71.4%); and L. borgpetersenii serovar Tarassovi (76.8%; 95% CI 76.6% to 77.0%).

Conclusions

We found a high prevalence of anti-Leptospira spp. seropositivity in racehorses from a breeding farm in Ecuador. This is the first serologic report for leptospirosis in horses in Ecuador. “One Health”-based sanitary practices for horse-breeding farms are recommended to improve animal and human health.