bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of agricultural production outsourcing service and land fragmentation on agricultural non-point source pollution in China: Evidence from Jiangxi Province
Authors: Chen Su , Zhong Zeyun , Lu Hua
Published: January 2023

Agricultural production outsourcing service (APOS) are developing rapidly in China. In-depth research on whether the development of agricultural production outsourcing service can reduce agricultural non-point source pollution (ANSP) and the influencing mechanisms is still lacking. This study analyze the underlying mechanisms and empirically estimate the impact of agricultural production outsourcing service on agricultural non-point source pollution, explore the effect of land fragmentation on the relationship between them, and further empirically test these relationships with microsurvey data on farmers in China. The results reveal that agricultural production outsourcing service are negatively correlated with excess nitrogen and chemical fertilizer input. Agricultural production outsourcing service use can reduce excess nitrogen and an increase in the number of plots of land leads to an increase in excess nitrogen, and lower the negative effect of agricultural production outsourcing service on excess nitrogen. Agricultural production outsourcing service affect excess nitrogen by reducing farmers’ input of chemical fertilizers and increasing their adoption of green agricultural production technology. In the future, China should vigorously promote the development of agricultural production outsourcing service organizations, improve the standardization of outsourcing services to expand the scale of agricultural production outsourcing service. The government should also strengthen policy support for the construction of field roads, water conservation and irrigation, and should strive to centrally manage scattered land. It is necessary to encourage small-scale farmers to outsource agricultural production activities to the service organizations, thus reducing the negative effect of land fragmentation and increasing the positive effect of agricultural production outsourcing service in reducing agricultural non-point source pollution.
Evaluation and influencing factors of farmers’ sustainable livelihood response to ecocultural tourism in minority areas of China
Authors: Wu Jilin , Zuo Jinyou , Li Li , Liu Shuiliang
Published: January 2023

Ecocultural tourism plays an crucial role in promoting poverty reduction and farmers’ sustainable livelihood enhancement worldwide, which has attracted strong attention from scholars and society. However, the impact of ecological and cultural capital of farmers’ sustainable livelihoods have not been yet fully investigated. This paper modifies the sustainable livelihoods framework (SLF) and emphasizes the effects of ecological and cultural capital on farmers’ sustainable livelihoods. The modified SLF can be used as a possible theoretical model to comprehensively characterize farmers’ sustainable livelihoods in tourism destinations with rich ecological and cultural resources. By constructing an evaluation index system, principle component analysis and multiple linear regression are used to analyze the types and response levels of farmers’ sustainable livelihoods to ecocultural tourism and determine the factors influencing this response. The results show that farmers’ sustainable livelihood responses to ecocultural tourism can be classified into six types. The overall response values are low, and the responses are ranked by the degree of response in descending order as complete response, balanced development, cultural network, ecology-dominant, developmental delay, and resource advantage response. Farmers’ sustainable livelihoods respond strongly to cultural capital and ecological capital factors and relatively weakly to physical, natural, social, financial, and labor capital. Five main factors that influence farmers’ sustainable livelihood responses are then identified. Finally, strategies and suggestions for livelihood transformation, strategy selection, and improvement are proposed. This study provides case study examples for promoting the sustainable development of ecocultural tourism sites and improving farmers’ livelihoods in China and worldwide.
Spatial distribution of Dechlorane Plus and dechlorane related compounds in European background air
Authors: Skogeng Lovise P. , Lunder Halvorsen Helene , Breivik Knut , Eckhardt Sabine , Herzke Dorte , Moeckel Claudia , Krogseth Ingjerd S.
Published: January 2023

The highly chlorinated chemical Dechlorane Plus (DP) was introduced as a replacement flame retardant for Mirex, which is banned through the Stockholm Convention (SC) for its toxicity (T), environmental persistence (P), potential for bioaccumulation (B) and long-range environmental transport potential (LRETP). Currently, Dechlorane Plus is under consideration for listing under the Stockholm Convention and by the European Chemical Agency as it is suspected to also have potential for P, B, T and LRET. Knowledge of atmospheric concentrations of chemicals in background regions is vital to understand their persistence and long-range atmospheric transport but such knowledge is still limited for Dechlorane Plus. Also, knowledge on environmental occurrence of the less described Dechlorane Related Compounds (DRCs), with similar properties and uses as Dechlorane Plus, is limited. Hence, the main objective of this study was to carry out a spatial mapping of atmospheric concentrations of Dechlorane Plus and Dechlorane Related Compounds at background sites in Europe. Polyurethane foam passive air samplers were deployed at 99 sites across 33 European countries for 3 months in summer 2016 and analyzed for dechloranes. The study showed that syn- and anti-DP are present across the European continent (<MDL-2.6 pg/m3 and <MDL-12.3 pg/m3, respectively), including parts of the Arctic. This supports that these compounds have potential for long-range atmospheric transport to remote regions. The highest concentrations of Dechlorane Plus were observed in central continental Europe, with anti-DP fractions close to the commercial mixture of Dechlorane Plus. The only detected Dechlorane Related Compounds was Dechlorane-602, which was found in 27% of the samples (<MDL-0.33 pg/m3). The measured concentrations and spatial patterns of Dechlorane Plus and Dechlorane-602 in air across Europe indicate the influence of primary sources of these compounds on background concentrations in European air. Future air monitoring efforts targeting dechloranes is needed in both background and source areas, including consistent temporal trends.
Poly-γ-glutamic acid-producing bacteria reduce wheat Cd uptake by promoting Cd transfer from macro-to micro-aggregates in Cd-contaminated soil
Authors: Wang Xiaohan , Liu Xiaoyu , Ji Haikuan , Xia Tao
Published: January 2023

Heavy metal immobilization using poly-γ-glutamic acid-producing bacteria is a novel and environmentally friendly technique for the remediation of heavy metal-contaminated soil. However, only a few studies have investigated the effects of γ-PGA-producing bacteria on the Cd uptake of wheat plants and the Cd distribution in soil aggregates in Cd-polluted soils. In this study, solution culture and pot experiments were used to investigate the Cd immobilization effect and mechanism of the γ-PGA-producing bacteria Bacillus subtilis W7 and Bacillus amyloliquefaciens W25. In the two bacteria-inoculated culture media, the concentration of Cd decreased, whereas the pH, cell growth, γ-PGA production and cell-immobilized Cd significantly increased over time. Strain W25 exhibited a higher ability to produce γ-PGA and immobilize Cd than strain W7. In the pot experiments, the grain Cd content of wheat was reduced by 24–35% and the DTPA-Cd content was decreased by 22–37% in the rhizosphere soils inoculated with both strains compared to the control. Furthermore, strain W25 had a greater ability to decrease the grain Cd uptake than strain W7. Inoculation with the two strains significantly increased the pH, organic matter content, and urease activity and promoted the migration of Cd from large fractions (>0.25 mm) to small fractions (<0.048 mm) and the transformation of available Cd to unavailable Cd in wheat rhizosphere soil. Our results highlight the potential of γ-PGA-producing bacteria in remediating Cd-polluted soils for safe wheat producing.
Regional differences and dynamic evolution of urban land green use efficiency within the Yangtze river economic belt, China
Authors: Cui Xinghua , Lin Mingyu , Qiu Ying
Published: January 2023

In this study, we calculate the urban land green use efficiency (ULGUE) in the Yangtze River Economic Belt from 2005 to 2019 by using the epsilon-based measure (EBM) model. Further, the spatial-temporal distribution, regional differences and evolution trends of ULGUE in the Yangtze River Economic Belt are investigated in depth by using the Dagum Gini coefficient, Kernel Density estimation and Markov Chain method. The following results are obtained. 1) From the perspective of spatial-temporal evolution, the ULGUE in the Yangtze River Economic Belt show a fluctuating upward trend from 2005 to 2019, and it is manifested as diffusion from downstream to middle and upper reaches. 2) From the perspective of regional differences, there is a relatively obvious imbalance of ULGUE within the Yangtze River Economic Belt, but the differences narrow over time. 3) Considering the distribution dynamic evolution, the box diagram and distribution curve of ULGUE in the Yangtze River Economic Belt have a tendency to move to high values, but there is a more obvious phenomenon of spatial polarization. 4) For the part of time and space transfer, the ULGUE within the Yangtze River Economic Belt show the characteristic of “club convergence”, and the Spatial Markov Chain results show an obvious “spatial spillover” effect.
Application of textile (PAN-based) activated carbon fibers decorated with silver nanoparticles in water treatment
Authors: Martins Isabela M. , Sampaio Aline G. , Lima Gabriela M. G. , Oliveira e Campos Maria A. C. , Rodgher Suzelei , Rodrigues-Siqueli Aline C. , Baldan Maurício R. , Marcuzzo Jossano S. , Koga-Ito Cristiane Y.
Published: January 2023

Introduction: Water treatment deficit and poor health, hygiene and sanitation infrastructure can contribute to disease transmission by dissemination of contaminants and microorganisms. As an alternative, carbon-based materials coated with antimicrobial molecules have been proposed for water treatment, but few supporting data are available so far. Hence, this study investigates the potential use of PAN-based activated carbon fibers (ACF) decorated with silver nanoparticles in water treatment.

Methods: Silver nanoparticles were incorporated into the material using a cheap and electroless method. Field emission scanning electron microscopy (FEGSEM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) characterized the whole material. The textile was mounted on a water filter prototype and had its capacity to remove bacterial (Escherichia coli) and fungal (Candida albicans, Aspergillus niger and Penicillium funiculosum) cells evaluated. Composition and toxicity of the filtered water were determined.

Results: Water filtered by Ag@ACF for 2 and 24 h contained 0.254 mg/L and 0.964 mg/L Ag, respectively. Ag@ACF filtering successfully removed E. coli, C. albicans, and A. niger from the suspensions, but not P. funiculosum. Treated water was non-toxic for Vero cells and Drosophila melanogaster, but toxic for Raphidocelis subcapitata. Ag@ACF showed efficient microbial elimination when applied in water treatment. Silver nanoparticles released in aqueous medium may be responsible for R. subcapitata toxicity. Future studies should be conducted to reduce silver nanoparticles release from the carbon fiber.
Cognitive biases can play a role in extinction assessments: The case of the Caspian tiger
Authors: Can Özgün Emre , D’Cruze Neil
Published: January 2023

The premature declaration of a species as extinct has been reported across different taxonomic groups and is commonly referred to as Romeo’s error or the Lazarus effect. In this study, based on a review of historical records and testimonies from local communities, we review the case of Caspian tiger (Panthera tigris virgata), a species we consider was prematurely declared globally extinct in 1950s. Considering that compelling evidence which suggests that Caspian tigers existed in Turkey perhaps up until early 1990s (some 40 years after international scientific community considered the species extinct) it is reasonable to posit that conservationists missed a historical opportunity to save the species. The case of the Caspian tiger demonstrates the cognitive bias of the Dunning-Kruger effect in action and the potential implications for conservation experts who are engaged in remotely evaluating contemporary species distributions. To mitigate these factors when assessing the global status of species threatened by extinction, we suggest that increased awareness of this type of cognitive bias could facilitate the introduction of additional measures in relevant conservation initiatives and in IUCN Red List assessments. For example, the formation of independent and specific teams to unearth implicit assumptions and weaknesses in assessments, and to question the group thinking of the species assessors. Against the backdrop of the current unprecedented rapid biodiversity decline, we recommend that researchers should be alert of the cognitive biases involved in species assessments and in conservation at large.
The neglected potential of invertebrates in detecting disease via olfaction
Authors: Piqueret Baptiste , Sandoz Jean-Christophe , d’Ettorre Patrizia
Published: January 2023

Agents that cause disease alter the cell metabolism of their hosts. Cells with an altered metabolism produce particular profiles of biomolecules, which are different from those of healthy cells. Such differences may be detected by olfaction. Historically, physicians used olfactory cues to diagnose sickness by smelling the breath or the urine of patients. However, other species have been shown to possess excellent olfactory abilities. Dogs, for instance, have been frequently used as biodetectors of human diseases, including cancer, viral and bacterial infections. Other mammalian species, such as rats, have been trained to perform similar tasks, but their disease detection abilities remain poorly explored. Here, we focus on the overlooked potential of invertebrate species and we review the current literature on olfactory detection of diseases by these animals. We discuss the possible advantages of exploring further the abilities of invertebrates as detection tools for human disease.
Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches
Authors: Lydia Pramitha J. , Ganesan Jeeva , Francis Neethu , Rajasekharan Ravikesavan , Thinakaran Jenita
Published: January 2023

Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.
Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China
Authors: Li Guangzhen , Luo Jing , Wang Fuwen , Xu Donghui , Ahmed Zulfiqar , Chen Shengmei , Li Ruizhe , Ma Zhijie
Published: January 2023

The Qinghai Province of China is located in the northeast region of the Qinghai–Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. FST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and FST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.
Identification and validation of a TTN-associated immune prognostic model for skin cutaneous melanoma
Authors: Wang Qirui , Huang Xingtai , Zeng Siyi , Zhou Renpeng , Wang Danru
Published: January 2023

TTN is the most commonly mutated gene in skin cutaneous melanoma (SKCM). Tumor mutational burden (TMB) can generate new antigens that regulate the recognition of T cells, which will significantly affect the prognosis of patients. The TTN gene has a long coding sequence and a high number of mutant sites, which allows SKCM patients to produce higher TMB and may influence the immune response. It has been found that the overall survival (OS) of SKCM patients with TTN mutation was significantly higher than that of wild-type patients. However, the effect of TTN mutation on the immune microenvironment of SKCM has not been fully investigated. Here, we systematically explored the relationship and potential mechanisms between TTN mutation status and the immune response. We first revealed that TTN mutated SKCM were significantly associated with four immune-related biological processes. Next, 115 immune genes differentially expressed between TTN mutation and wild-type SKCM patients were found to significantly affect the OS of SKCM patients. Then, we screened four immune-related genes (CXCL9, PSMB9, CD274, and FCGR2A) using LASSO regression analysis and constructed a TTN mutation-associated immune prognostic model (TM-IPM) to distinguish the SKCM patients with a high or low risk of poor prognosis, independent of multiple clinical characteristics. SKCM in the low-risk group highly expressed a large number of immune-related genes, and functional enrichment analysis of these genes showed that this group was involved in multiple immune processes and pathways. Furthermore, the nomogram constructed by TM-IPM with other clinicopathological parameters can provide a predictive tool for clinicians. Moreover, we found that CD8+ T cells were significantly enriched in the low-risk group. The expression level of immune checkpoints was higher in the low-risk group than in the high-risk group. Additionally, the response to chemotherapeutic agents was higher in the low-risk group than in the high-risk group, which may be related to the long survival in the low-risk group. Collectively, we constructed and validated a TM-IPM using four immune-related genes and analyzed the potential mechanisms of TM-IPM to predict patient prognosis and response to immunotherapy from an immunological perspective.
PD-1 expression in transbronchial biopsies of lung transplant recipients is a possible early predictor of rejection
Authors: Righi Ilaria , Vaira Valentina , Morlacchi Letizia Corinna , Croci Giorgio Alberto , Rossetti Valeria , Blasi Francesco , Ferrero Stefano , Nosotti Mario , Rosso Lorenzo , Clerici Mario
Published: January 2023

Introduction

Chronic lung allograft dysfunction (CLAD) is the main cause of the reduced survival of lung transplanted (LTx) patients. The possible role of immune checkpoint molecules in establishing tolerance has been scarcely investigated in the setting of lung transplantation.

Methods

We conducted a retrospective, observational pilot study on a consecutive series of transbronchial cryobiopsies (TCB) obtained from 24 patients during LTx follow-up focusing on PD-1, one of the most investigated immune checkpoint molecules.

Results

Results showed that PD-1-expressing T lymphocytes were present in all TCB with a histological diagnosis of acute rejection (AR; 9/9), but not in most (11/15) of the TCB not resulting in a diagnosis of AR (p=0.0006). Notably, the presence of PD-1-expressing T lymphocytes in TCB resulted in a 10-times higher risk of developing chronic lung allograft dysfunction (CLAD), the main cause of the reduced survival of lung transplanted patients, thus being associated with a clearly worst clinical outcome.

Discussion

Results of this pilot study indicate a central role of PD-1 in the development of AR and its evolution towards CLAD and suggest that the evaluation of PD-1-expressing lymphocytes in TCB could offer a prognostic advantage in monitoring the onset of AR in patients who underwent lung transplantation.
Diagnostic challenge in a series of eleven patients with hyper IgE syndromes
Authors: Yaakoubi Roukaya , Mekki Najla , Ben-Mustapha Imen , Ben-Khemis Leila , Bouaziz Asma , Ben Fraj Ilhem , Ammar Jamel , Hamzaoui Agnès , Turki Hamida , Boussofara Lobna , Denguezli Mohamed , Haddad Samir , Ouederni Monia , Bejaoui Mohamed , Chan Koon Wing , Lau Yu Lung , Mellouli Fethi , Barbouche Mohamed-Ridha , Ben-Ali Meriem
Published: January 2023

Hyper IgE syndromes (HIES) is a heterogeneous group of Inborn Errors of Immunity characterized by eczema, recurrent skin and lung infections associated with eosinophilia and elevated IgE levels. Autosomal dominant HIES caused by loss of function mutations in Signal transducer and activator of transcription 3 (STAT3) gene is the prototype of these disorders. Over the past two decades, advent in genetic testing allowed the identification of ten other etiologies of HIES. Although Dedicator of Cytokinesis 8 (DOCK8) deficiency is no more classified among HIES etiologies but as a combined immunodeficiency, this disease, characterized by severe viral infections, food allergies, autoimmunity, and increased risk of malignancies, shares some clinical features with STAT3 deficiency. The present study highlights the diagnostic challenge in eleven patients with the clinical phenotype of HIES in a resource-limited region. Candidate gene strategy supported by clinical features, laboratory findings and functional investigations allowed the identification of two heterozygous STAT3 mutations in five patients, and a bi-allelic DOCK8 mutation in one patient. Whole Exome Sequencing allowed to unmask atypical presentations of DOCK8 deficiency in two patients presenting with clinical features reminiscent of STAT3 deficiency. Our study underlies the importance of the differential diagnosis between STAT3 and DOCK8 deficiencies in order to improve diagnostic criteria and to propose appropriate therapeutic approaches. In addition, our findings emphasize the role of NGS in detecting mutations that induce overlapping phenotypes.
Generation of bispecific antibodies by structure-guided redesign of IgG constant regions
Authors: Iwasaki Yordkhwan W. , Tharakaraman Kannan , Subramanian Vidya , Khongmanee Amnart , Hatas Andrew , Fleischer Eduardo , Rurak Troy T. , Ngok-ngam Patchara , Tit-oon Phanthakarn , Ruchirawat Mathuros , Satayavivad Jutamaad , Fuangthong Mayuree , Sasisekharan Ram
Published: January 2023

Bispecific antibodies (BsAbs) form an exciting class of bio-therapeutics owing to their multispecificity. Although numerous formats have been developed, generation of hetero-tetrameric IgG1-like BsAbs having acceptable safety and pharmacokinetics profiles from a single cell culture system remains challenging due to the heterogeneous pairing between the four chains. Herein, we employed a structure-guided approach to engineer mutations in the constant domain interfaces (CH1-CL and CH3-CH3) of heavy and κ light chains to prevent heavy-light mispairing in the antigen binding fragment (Fab) region and heavy-heavy homodimerization in the Fc region. Transient co-transfection of mammalian cells with heavy and light chains of pre-existing antibodies carrying the engineered constant domains generates BsAbs with percentage purity ranging from 78% to 85%. The engineered BsAbs demonstrate simultaneous binding of both antigens, while retaining the thermal stability, Fc-mediated effector properties and FcRn binding properties of the parental antibodies. Importantly, since the variable domains were not modified, the mutations may enable BsAb formation from antibodies belonging to different germline origins and isotypes. The rationally designed mutations reported in this work could serve as a starting point for generating optimized solutions required for large scale production.
Nintedanib in an elderly non-small-cell lung cancer patient with severe steroid-refractory checkpoint inhibitor-related pneumonitis: A case report and literature review
Authors: Pan Lei , Meng Fanqi , Wang Wei , Wang Xu-hao , Shen Hui , Bao Pengchen , Kang Jian , Kong Delei
Published: January 2023

Immune checkpoint inhibitors tremendously improve cancer prognosis; however, severe-grade immune-related adverse events may cause premature death. Current recommendations for checkpoint inhibitor-related pneumonitis (CIP) treatment are mainly about immunosuppressive therapy, and anti-fibrotic agents are also needed, especially for patients with poor response to corticosteroids and a longer pneumonitis course. This is because fibrotic changes play an important role in the pathological evolution of CIP. Here, we report a case demonstrating that nintedanib is a promising candidate drug for CIP management or prevention, as it has potent anti-fibrotic efficacy and a safety profile. Moreover, nintedanib could partially inhibit tumor growth in patients with non-small-cell lung cancer, and its efficacy can be improved in combination with other anti-tumor therapies.
Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV
Authors: Ghorbani Mahin , Al-Manei Khaled , Naud Sabrina , Healy Katie , Gabarrini Giorgio , Sobkowiak Michal Jacek , Chen Puran , Ray Shilpa , Akber Mira , Muschiol Sandra , Bogdanovic Gordana , Bergman Peter , Ljungman Per , Buggert Marcus , Ljunggren Hans-Gustaf , Pin Elisa , Nowak Piotr , Aleman Soo , Sällberg Chen Margaret
Published: January 2023

Coevolution of microbiome and immunity at mucosal sites is essential for our health. Whether the oral microbiome, the second largest community after the gut, contributes to the immunogenicity of COVID-19 vaccines is not known. We investigated the baseline oral microbiome in individuals in the COVAXID clinical trial receiving the BNT162b2 mRNA vaccine. Participants (n=115) included healthy controls (HC; n=57) and people living with HIV (PLHIV; n=58) who met the study selection criteria. Vaccine-induced Spike antibodies in saliva and serum from 0 to 6 months were assessed and comparative analyses were performed against the individual salivary 16S ASV microbiome diversity. High- versus low vaccine responders were assessed on general, immunological, and oral microbiome features. Our analyses identified oral microbiome features enriched in high- vs. low-responders among healthy and PLHIV participants. In low-responders, an enrichment of Gram-negative, anaerobic species with proteolytic activity were found including Campylobacter, Butyrivibrio, Selenomonas, Lachnoanaerobaculum, Leptotrichia, Megasphaera, Prevotella and Stomatobaculum. In high-responders, enriched species were mainly Gram-positive and saccharolytic facultative anaerobes: Abiotrophia, Corynebacterium, Gemella, Granulicatella, Rothia, and Haemophilus. Combining identified microbial features in a classifier using the area under the receiver operating characteristic curve (ROC AUC) yielded scores of 0.879 (healthy controls) to 0.82 (PLHIV), supporting the oral microbiome contribution in the long-term vaccination outcome. The present study is the first to suggest that the oral microbiome has an impact on the durability of mucosal immunity after Covid-19 vaccination. Microbiome-targeted interventions to enhance long-term duration of mucosal vaccine immunity may be exploited.
Single-cell RNA sequencing reveals the molecular features of peripheral blood immune cells in children, adults and centenarians
Authors: Zhong Jinjie , Ding Rong , Jiang Huimin , Li LongFei , Wan Junli , Feng Xiaoqian , Chen Miaomiao , Peng Liping , Li Xiaoqin , Lin Jing , Yang Haiping , Wang Mo , Li Qiu , Chen Qilin
Published: January 2023

Peripheral blood immune cells have different molecular characteristics at different stages of the whole lifespan. Knowledge of circulating immune cell types and states from children to centenarians remains incomplete. We profiled peripheral blood mononuclear cells (PBMCs) of multiple age groups with single-cell RNA sequencing (scRNA-seq), involving the age ranges of 1-12 (G1), 20-30(G2), 30-60(G3), 60-80(G4), and >110 years (G5). The proportion and states of myeloid cells change significantly from G1 to G2. We identified a novel CD8+CCR7+GZMB+ cytotoxic T cell subtype specific in G1, expressing naive and cytotoxic genes, and validated by flow cytometry. CD8+ T cells showed significant changes in the early stage (G1 to G2), while CD4+ T cells changed in the late stage (G4 to G5). Moreover, the intercellular crosstalk among PBMCs in G1 is very dynamic. Susceptibility genes for a variety of autoimmune diseases (AIDs) have different cell-specific expression localization, and the expression of susceptibility genes for AIDs changes with age. Notably, the CD3+ undefined T cells clearly expressed susceptibility genes for multiple AIDs, especially in G3. ETS1 and FLI1, susceptibility genes associated with systemic lupus erythematosus, were differentially expressed in CD4+ and CD8+ effector cells in G1 and G3. These results provided a valuable basis for future research on the unique immune system of the whole lifespan and AIDs.
Intestinal and blood lymphograms as new diagnostic tests for celiac disease
Authors: Roy Garbiñe , Fernández-Bañares Fernando , Corzo María , Gómez-Aguililla Sara , García-Hoz Carlota , Núñez Concepción
Published: January 2023

Accurate celiac disease (CD) diagnosis is still challenging for some specific patients or circumstances. Thus, much effort has been expended last decades focused on seronegative or low grade enteropathy CD and, especially, on enable early diagnosis of individuals on a gluten-free diet (GFD). We discuss here two diagnostic approaches based on immunophenotyping by flow cytometry that we expect to reduce the persistent low diagnostic rates and the common diagnostic delay. The intraepithelial lymphogram is based on determining the percentage of TCRγδ+ and surface CD3- lymphocytes in the intestinal epithelium. The concomitant increase in TCRγδ+ and decrease in surface CD3- intraepithelial lymphocytes has been termed the celiac lymphogram and has been proved to be discriminative in seronegative, low grade enteropathy and potential CD, as well as in most CD patients on a GFD. A blood lymphogram based on the analysis of activated gut-homing CD8+ T cells combined with a 3-day gluten challenge is also considered, which has shown high sensitivity and specificity to diagnose seropositive Marsh 1 and Marsh 3 CD in individuals following a GFD. In addition, flow cytometry can be extremely useful in cases of refractory CD type II to identify aberrant cells. Those approaches represent highly accurate methods for CD diagnosis, being simple, fast, highly reproducible and of easy implementation in clinical practice.
The detrimental effect of donor-specific antibodies is irrespective of its level in highly-immunized living donor kidney transplant recipients: A case-control series
Authors: Tramper T. , Roelen D. L. , Brand-Schaaf S. H. , Kal-van Gestel J. A. , Kho M. M. L. , Reinders M. E. J. , Roodnat J. I. , van de Wetering J. , Betjes M. G. H. , de Weerd A. E.
Published: January 2023

Background

The impact of donor-specific antibodies (DSA) in (highly-) immunized living donor kidney transplant recipients is reported differentially in various patient cohorts.

Methods

We have performed a retrospective analysis of all consecutive HLA-incompatible living donor kidney transplant recipients in our center between 2010-2019. Recipients who underwent plasmafiltration for a positive CDC-crossmatch were excluded. For each DSA+ recipient (DSA+), one immunized recipient without DSA (pPRA+) and two non-immunized recipients (pPRA-) were included. Patient and graft survival were analyzed and a subgroup analysis of DSA+ recipients was performed.

Results

For 63 DSA+ recipients, 63 PRA+ and 126 PRA- recipients were included. 26 (41%) had class I, 24 (38%) class II and 13 (21%) combined HLA class I and II DSA. Death-censored graft survival was inferior in DSA+ recipients compared to pPRA+ (HR 2.38 [95% CI 1.00-5.70]) as well as to pPRA- (HR 3.91 [1.86-8.22]). In multivariate analysis, DSA remained of negative influence on death-censored graft survival. Flowcytometric crossmatch, MFI value, HLA class and origin of DSA were not of significant impact.

Conclusion

In our cohort of (highly-) immunized recipients, pretransplant DSA led to inferior death-censored graft survival. There were no “safe” DSA characteristics since only DSA per se impacted death-censored graft survival.
Huwe1 supports B-cell development, B-cell-dependent immunity, somatic hypermutation and class switch recombination by regulating proliferation
Authors: Spanjaard Aldo , Stratigopoulou Maria , de Groot Daniël , Aslam Muhammad , van den Berk Paul C. M. , Stappenbelt Chantal , Ayidah Matilda , Catsman Joyce J. I. , Pardieck Iris N. , Kreft Maaike , Arens Ramon , Guikema Jeroen E. J. , Jacobs Heinz
Published: January 2023

The development and differentiation of B cells is intimately linked to cell proliferation and the generation of diverse immunoglobulin gene (Ig) repertoires. The ubiquitin E3 ligase HUWE1 controls proliferation, DNA damage responses, and DNA repair, including the base excision repair (BER) pathway. These processes are of crucial importance for B-cell development in the bone marrow, and the germinal center (GC) response, which results in the clonal expansion and differentiation of B cells expressing high affinity immunoglobulins. Here, we re-examined the role of HUWE1 in B-cell proliferation and Ig gene diversification, focusing on its involvement in somatic hypermutation (SHM) and class switch recombination (CSR). B-cell-specific deletion of Huwe1 resulted in impaired development, differentiation and maturation of B cells in the bone marrow and peripheral lymphoid organs. HUWE1 deficiency diminished SHM and CSR by impairing B-cell proliferation and AID expression upon activation in vitro and in vivo, and was unrelated to the HUWE1-dependent regulation of the BER pathway. Interestingly, we found that HUWE1-deficient B cells showed increased mRNA expression of Myc target genes upon in vitro activation despite diminished proliferation. Our results confirm that the E3 ligase HUWE1 is an important contributor in coordinating the rapid transition of antigen naïve, resting B cells into antigen-activated B cells and regulates mutagenic processes in B cells by controlling AID expression and the post-transcriptional output of Myc target genes.
Aspect processing across languages: A visual world eye-tracking study
Authors: Minor Serge , Mitrofanova Natalia , Guajardo Gustavo , Vos Myrte , Ramchand Gillian
Published: January 2023

The study employed a combination of a picture selection task and Visual World eye-tracking to investigate the processing ofgrammatical aspect(perfective vs. imperfective) in three languages: Russian, Spanish and English. In order to probe into the cognitive representations triggered by the aspectual forms we contrasted visual representations of different temporal portions of telic events—a snapshot of the process stage (ongoing event) and a snapshot of the immediate aftermath of the event/the result state (completed event). In all three languages, the gaze patterns and offline responses revealed a strong preference for representations of ongoing events in the imperfective condition. This confirms that the imperfective forms in all the three languages draw attention to the in-progress portion of a telic event. In the perfective condition, however, we found robust differences. Russian uses verbal prefixes to mark perfective aspect, and our results suggest that perfective telic verbs in Russian strongly highlight the result state of an event. In Spanish, the perfective past tense form (Preterite) also highlights event completion, but to a lesser extent than in Russian—in line with its less restrictive semantics in not requiring an inherent boundary. In contrast to Russian and Spanish, English speakers did not show a preference for representations of completed events in the perfective (Simple Past) condition. This suggests that the English Simple Past form does not encode a preferential cognitive salience for either the activity portion of an event or its result state, and lends support to the analysis of the English Simple Past as a non-aspectual tense form.
Wind effect on sediment suspensions over silt-dominated mixtures: An experimental study
Authors: Chen Yongping , Pu Jinshan , Zhu Qin , Su Min , Zhou Zeng , Qiao Zhongxing , Xu Chunyang , Yao Peng
Published: January 2023

A series of laboratory experiments have been conducted to explore the wind effect on Sediment Suspended Concentrations (SSCs) in fine-grained coastal systems. The paddle waves were overplayed with surface-blowing winds in a wind-wave flume to mimic offshore swells coupling with local wind waves during rough weather. Both SSCs and water turbulences under different wind and wave conditions have been investigated over two kinds of sediment beds (Sediment 1, S1, D50 = 52µm and Sediment 2, S2, D50 = 90µm). The High Concentration Layers (HCL) were formed under most of the wave-only conditions, while with the introduction of the stronger wind, more sediment suspensions were transported upward, increasing SSCs in upper water elevations. The finer sediment S1 is easier to suspend than S2 under the same conditions. The enhancement of the vertical turbulence intensity (σw) by winds is the main reason for the increase in SSCs. Meanwhile, because the wind-induced turbulence can hardly penetrate the HCL, the turbulence intensities outside the HCL can be further amplified compared to the experiment without a sediment bed. The wind contributes over 65% of the SSC enlargement above the HCL under a wind of 10m/s for S1, while less than 20% inside the HCL in most wind conditions. The sediment mixing coefficient (ϵs), a crucial parameter for suspended sediment modeling, was enhanced with stronger winds. Although the existing formulas for the vertical distribution of ϵs are valid under both wave-only and small winds (2.5 m/s) for both sediment beds, the enhancement of ϵs caused by strong winds cannot be captured, requiring further research.
Development of a novel sea surface temperature proxy based on bacterial 3-hydroxy fatty acids
Authors: Dong Zhengkun , Yang Yi , Wang Canfa , Bendle James A. , Ruan Xiaoyan , Lü Xiaoxia , Xie Shucheng
Published: January 2023

Gram-negative bacterial 3-hydroxy fatty acids (3-OH-FAs) have received recent attention for their potential as palaeoclimate proxies. A novel temperature proxy, the ratio of anteiso to normal C13 3-OH-FA (RAN13), has been proposed for sea surface temperature (SST) reconstruction in the North Pacific Ocean. However, whether this newly proposed temperature proxy is applicable to marginal seas with significant terrigenous input or tropical oligotrophic seas requires further investigation. Here, we analyzed the composition and distribution of 3-OH-FAs and evaluated the possible impact of various environmental parameters (SST, water depth, dissolved oxygen, salinity and nutrient concentration) on their distribution in marine surface sediments from the Bohai Sea (BS) and the South China Sea (SCS). In the BS, the potential source proxy, fractional abundance of anteiso 3-OH-FAs (average 17%), indicates 3-OH-FA geochemical signature are not greatly overprinted by terrigenous inputs. The relative abundance of long-chain 3-OH-FAs (C15-C18) are higher in the SCS (average 41%) compared to those in other seas (average 33% for all marine samples). Massive inputs of terrigenous organic matter to the BS likely result in overestimation of SSTs based on the RAN13 proxy, and limited abundance of anteiso and normal C13 3-OH-FAs in the oligotrophic SCS may increase the uncertainty of the RAN13 estimated SSTs. More importantly, we find that most short-chain 3-OH-FAs are temperature dependent, especially the fractional abundance of i-C12, a-C13, i-C14 and n-C14 with a high determination coefficient (R2 > 0.60). Based on these newly found correlations, we propose a novel proxy: RANs. The RANs index shows a strong linear relationship with SST (R2 = 0.92, p< 0.001, n = 85) and more accurate prediction than the RAN13, especially in tropical samples. Furthermore, the RANs proxy is significantly correlated with TEX86, and RANs-based SSTs are approximate to LDI derived temperature in the SCS, which support the reliability of RANs as a temperature proxy. These findings further suggest 3-OH-FA based proxies have potential for paleo-SST reconstruction, especially at higher and lower ends of the ocean temperature spectrum and even in cases where marginal inputs of terrestrial organic matter and nutrients are high.
Sexual dimorphism in corallite size and modularity of a broadcast spawning coral, Porites lobata
Authors: Pedraza-Pohlenz Ricardo M. , Balart Eduardo F. , Tortolero-Langarica J. J. Adolfo , Rodríguez-Troncoso Alma Paola , Hellberg Michael E. , Norzagaray-López Orión , Cabral-Tena Rafael A. , Cupul-Magaña Amílcar Leví , Paz-García David A.
Published: January 2023

Differences in selective pressures and the energetic cost of gametes in gonochoristic corals should vary with the sex of the colony, which may lead to sexual dimorphism. Coral colonies are composed of subunits (corallites) that create a complex morphological architecture. If corallite features are distinct between sexes, then the degree of coordinated change among these subunits may also vary (phenotypic modularity). This study tested for sexual dimorphism in the corallites of the reef-building coral Porites lobata, a gonochoric broadcast spawner, and compared this with previously demonstrated sexual dimorphism in its congener P. panamensis, a gonochoric brooder. Corallite area in P. lobata was 17% larger for males than for females (p < 0.05). Phenotypic modularity analysis showed that the integration of skeletal traits differs between sexes in both P. lobata and in P. panamensis. In P. lobata, females showed a higher trait integration than males, while the opposite pattern was observed in P. panamensis. Our results demonstrate corallite traits differentiate between sexes and suggest that between-sex differences in the degree of corallite integration may vary with reproductive mode.
Nitrogen mineralization and immobilization in surface sediments of coastal reclaimed aquaculture ecosystems
Authors: Lin Xianbiao , Lin Genmei , Zheng Yijie , Li Wenjing , Guo Peng , Fan Shiyuan , Kong Tiantian , Tian Dongfan , Sun Dongyao , Shen Zhuo
Published: January 2023

Sediment nitrogen (N) mineralization and immobilization are two crucial processes driven by microorganisms, which may play significant roles in the regulation of water quality in aquaculture ecosystems. However, limited information is available about the quantitative importance of sedimentary N mineralization and immobilization in coastal aquaculture systems. Here, a combination of incubation experiments with a 15N isotope dilution technique were employed, aiming to quantify N mineralization and immobilization processes in surface sediments (0–5 cm) of three types of aquaculture ecosystems (seabass, white shrimp, and green crab ponds) reclaimed within the western bank of the Pearl River Estuary. Our results showed that no significant difference in sediment N mineralization and immobilization rates, microbial abundances, and organic matter among different aquaculture types on small-scale range. Meanwhile, prolonged pond-drying significant reduced sediment N mineralization and immobilization rates, bacterial abundances, organic matter, moisture content, ferrous ion (Fe2+), Fe2+/Fe3+, and ammonium (NH4+), while not strongly altered sediment percentage of NH4+ mineralized per day (PAM), relative ammonium immobilization (RAI), fungal abundances, TOC/TN, nitrate (NO3−), and δ13Corg. N mineralization and immobilization rates were both significantly related to overlying water NO3−, as well as sediment moisture content, bulk density, organic matter, Fe2+, and microbial abundances. In addition, the total mineralized and immobilized N in aquaculture surface sediments from the Guangdong-Hong Kong-Macao Greater Bay Area were estimated to be approximately 4.55×104 and 3.68×104 t N yr-1, respectively. Higher N mineralization relative to N immobilized fluxes indicated that the sediment serves as an important source of eutrophication in reclaimed aquaculture system of coastal wetlands.