bluuebunny/crossref_metadata_2025 huggingface dataset:
Review on detection method, main source and geological application of diamondoids in crude oil
Authors: Fang Chenchen , Hu Guoyi , Yuan Yilin , Gong Deyu
Published: August 2023

Diamondoids are alkanes with cage-like structure. Their diamond-like structure makes them have high stability and anti-biodegradability, and can be preserved and enriched in complex and long geological processes. Therefore, the continuous development of quantitative detection methods for diamondoids in crude oil has deepened the research of these compounds and made them more widely used in crude oil cracking evaluation, maturity evaluation, biodegradation evaluation and other aspects.
Findings of pilot study following the implementation of point of care intraoperative PTH assay using whole blood during surgery for primary hyperparathyroidism
Authors: Mohan Kumar Rahul , Pannu Arslan , Metcalfe Emily , Senbeto Mesfin , Balasubramanian Saba P.
Published: August 2023

Objective

To report findings of pilot study using a novel point of care (POC) intraoperative parathyroid hormone (IOPTH) assay for parathyroid hormone (PTH) using whole blood during surgery for primary hyperparathyroidism (PHPT).

Methods

Patients undergoing surgery for primary hyperparathyroidism from March to November 2022 where intraoperative PTH assay was performed using the NBCL CONNECT IOPTH and the laboratory PTH assay were included (group 1). The biochemistry results were reviewed to determine concordance between NBCL and lab PTH values and diagnostic test parameters of the NBCL CONNECT assay. ‘In-theatre’ times were then compared with a historical cohort (group 2) where the lab-based IOPTH assay alone was used.

Results

Of the 141 paired samples in group I, correlation between NBCL and the lab assay was high (rho=0.82; p<0.001). PTH levels using the NBCL assay dropped satisfactorily (>50% of the basal or 0 min sample; whichever was lower – i.e. positive test) in 23 patients; giving a positive predictive value of 100%. Of the 9 patients that did not demonstrate a drop, two were true negative (negative predictive value of 22%) leading to cure after excision of another gland. Group 1 (150 mins) had a significantly shorter ‘in-theatre’ time compared to group 2 (167 mins) (p=0.007); despite much higher use of near infra-red autofluorescence (NIRAF) (72% vs 11.6% in group I and 2 respectively).

Conclusion

The NBCL CONNECT POC IOPTH assay gives comparable results to lab based PTH assays and can be performed without need for a centrifuge or qualified technicians. Surgeons, however, need to be aware of the potential for false-negative results.
Integration of clinical parameters and CT-based radiomics improves machine learning assisted subtyping of primary hyperaldosteronism
Authors: Mansour Nabeel , Mittermeier Andreas , Walter Roman , Schachtner Balthasar , Rudolph Jan , Erber Bernd , Schmidt Vanessa F. , Heinrich Daniel , Bruedgam Denise , Tschaidse Lea , Nowotny Hanna , Bidlingmaier Martin , Kunz Sonja L. , Adolf Christian , Ricke Jens , Reincke Martin , Reisch Nicole , Wildgruber Moritz , Ingrisch Michael
Published: August 2023

Objectives

The aim of this study was to investigate an integrated diagnostics approach for prediction of the source of aldosterone overproduction in primary hyperaldosteronism (PA).

Methods

269 patients from the prospective German Conn Registry with PA were included in this study. After segmentation of adrenal glands in native CT images, radiomic features were calculated. The study population consisted of a training (n = 215) and a validation (n = 54) cohort. The k = 25 best radiomic features, selected using maximum-relevance minimum-redundancy (MRMR) feature selection, were used to train a baseline random forest model to predict the result of AVS from imaging alone. In a second step, clinical parameters were integrated. Model performance was assessed via area under the receiver operating characteristic curve (ROC AUC). Permutation feature importance was used to assess the predictive value of selected features.

Results

Radiomics features alone allowed only for moderate discrimination of the location of aldosterone overproduction with a ROC AUC of 0.57 for unilateral left (UL), 0.61 for unilateral right (UR), and 0.50 for bilateral (BI) aldosterone overproduction (total 0.56, 95% CI: 0.45-0.65). Integration of clinical parameters into the model substantially improved ROC AUC values (0.61 UL, 0.68 UR, and 0.73 for BI, total 0.67, 95% CI: 0.57-0.77). According to permutation feature importance, lowest potassium value at baseline and saline infusion test (SIT) were the two most important features.

Conclusion

Integration of clinical parameters into a radiomics machine learning model improves prediction of the source of aldosterone overproduction and subtyping in patients with PA.
Numerical investigation on the blade load distribution in a pump as turbine
Authors: Bai Xiaobang , Yang Junhu , Wang Xiaohui , Li Jicheng
Published: August 2023

Pump as turbine plays an important role in modern industrial process. One of the major goals of turbine design and optimization is to maximize its efficiency. Therefore, it is of great importance to connect force with work in the analysis process. In the present study, the three-dimensional flow field of the pump as a hydraulic turbine has been investigated in the steady-state mode. The load distribution along three captured streamlines (i.e., the shroud, hub and middle streamline) on both the pressure and the suction surface is observed, and the relationship between the load distribution and the working capability is systematically analyzed. The results show that the load distribution on the pressure surface of the hydraulic turbine blade gradually transitions from the reverse “S” shape to the “S” shape in the process of increasing flow rate, while the load distribution on the suction surface keeps increasing with a concave trend. The main work area of the fluid medium on the hydraulic turbine impeller is in the middle section of the blade. As the flow rate increases, the loads on the blade depict a linear decreasing trend from the inlet to the outlet. The net load acting on the blade is distributed in a concave parabola profile along the radial position of the blade. Focusing on the inlet and middle section of the blade profile in the design or optimization process of the hydraulic turbines will be more useful. This study provides a new analysis method for the design or optimization of hydraulic turbine impellers.
Arthropod communities of rice agroecosystems can be shaped both by local agricultural practices and the surrounding landscape
Authors: Chen Jia-Hsuan , Liao Yi-Chang , Chiu Ming-Chi , Yang Man-Miao
Published: August 2023

Both intensive farming of paddy field crops and conventional farm management techniques have been a major cause of environmental issues in recent years. A more ecosystem-based, sustainable agricultural methodology should be utilized to help solve this dilemma. However, the joint effects of landscape and farming on arthropod communities in paddy fields are unexplored. In eco-friendly paddy fields, we postulate the arthropod diversity to be higher in fields that use ecosystem-based methods. In this study, we collected arthropods monthly using a blower-vac during the first rice crop of 2019 in Taiwan. A total of 53,522 individuals of 14 orders, 96 families, and 445 morphospecies were collected. All arthropods were identified into four functional groups. The result showed that insect communities are different between sustainable and conventional fields. Results showed that sustainable fields had a higher abundance of arthropod fauna than conventional fields. It was also apparent that the arthropod community changed along with the developmental growth of rice and in different areas. Three functional groups, viz., herbivores, parasitoids, and detritivores, present the best model when the farming type was assigned as the fixed effect, while the predator reveal the best model when the farming type, landscape, and their interaction were assigned as the fixed effects. The arthropod communities have also been affected by the surrounding landscape. This study reveals that both agricultural management and landscape can have a joint effect on arthropod communities in paddy fields.
Anthropogenic disturbance modifies tree functional traits in the only remnant swamp forest of Bangladesh
Authors: Khan Ariful , Karim Md Rezaul , Mohammed  , Kibria Mohammad Golam , Sinha Karishma , Sultana Fahmida , Mukul Sharif A. , Arfin-Khan Mohammed A. S.
Published: August 2023

The relationship between ecosystem functions and plant functional traits has been well documented and is considered to be one of the most vital topics in ecology. However, the correlation between anthropogenic disturbance and tree functional trait diversity remains largely unclear. The present study investigates the role of anthropogenic disturbance on selected tree functional traits in Ratargul Swamp Forest (RSF) – the only remnant tropical freshwater swamp forest ecosystem in Bangladesh. We established 50 plots and collected six plant traits, i.e., tree height, specific leaf area (SLA), wood density (WD), leaf dry matter content (LDMC), seed mass, and bark thickness. A two-way analysis of variance (ANOVA) was carried out to test the interaction between plant functional traits and anthropogenic disturbance in RSF. Our study found that anthropogenic disturbance has a significant (p< 0.05) influence on deciduous swamp forest tree species’ functional traits but none on evergreen tree species’ functional traits. For deciduous trees, disturbance has a significant positive effect on CWM.SLA (p< 0.05) and CWM.Height (p< 0.05) and a negative impact on CWM.Bark-thickness and CWM.Seed-mass (p< 0.05). There were no significant effects of disturbance on CWM.WD and CWM.LDMC. We believe the present study will contribute toward improving our understanding of the effect of disturbances on tree functional trait diversity in tropical human-dominated landscapes where anthropogenic pressure is increasing at an unprecedented rate. It will also function as an essential conservation for related decision-making of Ratargul Swamp Forest in northeastern Bangladesh and elsewhere in the tropics with a similar context.
Small immunological clocks identified by deep learning and gradient boosting
Authors: Kalyakulina Alena , Yusipov Igor , Kondakova Elena , Bacalini Maria Giulia , Franceschi Claudio , Vedunova Maria , Ivanchenko Mikhail
Published: August 2023

Background

The aging process affects all systems of the human body, and the observed increase in inflammatory components affecting the immune system in old age can lead to the development of age-associated diseases and systemic inflammation.

Results

We propose a small clock model SImAge based on a limited number of immunological biomarkers. To regress the chronological age from cytokine data, we first use a baseline Elastic Net model, gradient-boosted decision trees models, and several deep neural network architectures. For the full dataset of 46 immunological parameters, DANet, SAINT, FT-Transformer and TabNet models showed the best results for the test dataset. Dimensionality reduction of these models with SHAP values revealed the 10 most age-associated immunological parameters, taken to construct the SImAge small immunological clock. The best result of the SImAge model shown by the FT-Transformer deep neural network model has mean absolute error of 6.94 years and Pearson ρ = 0.939 on the independent test dataset. Explainable artificial intelligence methods allow for explaining the model solution for each individual participant.

Conclusions

We developed an approach to construct a model of immunological age based on just 10 immunological parameters, coined SImAge, for which the FT-Transformer deep neural network model had proved to be the best choice. The model shows competitive results compared to the published studies on immunological profiles, and takes a smaller number of features as an input. Neural network architectures outperformed gradient-boosted decision trees, and can be recommended in the further analysis of immunological profiles.
Exosomes from osteoarthritic fibroblast-like synoviocytes promote cartilage ferroptosis and damage via delivering microRNA-19b-3p to target SLC7A11 in osteoarthritis
Authors: Kong Ruina , Ji Lianmei , Pang Yafei , Zhao Dongbao , Gao Jie
Published: August 2023

Objective

Our previous studies revealed that normal synovial exosomes promoted chondrogenesis, and microRNA (miR)-19b-3p independently related to osteoarthritis (OA) risk. Subsequently, this study intended to further explore the effect of OA fibroblast-like synoviocyte (OA-FLS) exosomal miR-19b-3p on OA ferroptosis and its potential mechanisms.

Methods

Interleukin (IL)-1β-stimulated chondrocytes and medial meniscus surgery were used to construct the OA cellular model and the OA rat model, respectively. OA-FLS exosomes with/without miR-19b-3p modification were added to the IL-1β-stimulated chondrocytes and OA rat models, followed by direct miR-19b-3p mimic/inhibitor transfection with/without SLC7A11 overexpression plasmids. miR-19b-3p, ferroptosis-related markers (malondialdehyde (MDA), glutathione (GSH)/oxidized glutathione (GSSG), ferrous ion (Fe2+), glutathione peroxidase 4 (GPX4), solute carrier family 7 member 11 (SLC7A11), and acyl-CoA synthetase long-chain family member 4 (ACSL4)), mitochondrial membrane potential (MMP), and reactive oxygen species (ROS) levels were detected.

Results

Enhanced ferroptosis reflected by dysregulated ferroptosis-related markers, a reduced MMP, and an increased ROS was observed in cartilage tissues from OA patients vs. controls, IL-1β-stimulated chondrocytes vs. normal ones, and OA rat models vs. sham, so did miR-19b-3p. OA-FLS exosomes promoted MDA, Fe2+, ACSL4, and ROS but reduced cell viability, GSH/GSSG, GPX4, SLC7A11, and MMP in IL-1β-stimulated chondrocytes, whose effect was enhanced by miR-19b-3p mimics and attenuated by miR-19b-3p inhibitors. miR-19b-3p negatively regulated SLC7A11 and directly bound to SLC7A11 via luciferase reporter gene assay. Furthermore, SLC7A11 overexpression weakened miR-19b-3p mimics’ effect on ferroptosis-related markers, MMP, or ROS in IL-1β-stimulated chondrocytes. OA-FLS exosomes also induced cartilage damage and ferroptosis in OA rats whose influence was tempered by miR-19b-3p inhibitors.

Conclusion

OA-FLS exosomal miR-19b-3p enhances cartilage ferroptosis and damage by sponging SLC7A11 in OA, indicating a potential linkage among synovium, cartilage, and ferroptosis during the OA process.
HEV-associated dendritic cells are observed in metastatic tumor-draining lymph nodes of cutaneous melanoma patients with longer distant metastasis-free survival after adjuvant immunotherapy
Authors: Bravo Alicia Inés , Aris Mariana , Panouillot Marylou , Porto Martina , Dieu-Nosjean Marie-Caroline , Teillaud Jean-Luc , Barrio María Marcela , Mordoh José
Published: August 2023

Introduction

Tissue biomarkers that aid in identifying cutaneous melanoma (CM) patients who will benefit from adjuvant immunotherapy are of crucial interest. Metastatic tumor-draining lymph nodes (mTDLN) are the first encounter site between the metastatic CM cells and an organized immune structure. Therefore, their study may reveal mechanisms that could influence patients´ outcomes.

Methods

Twenty-nine stage-III CM patients enrolled in clinical trials to study the vaccine VACCIMEL were included in this retrospective study. After radical mTDLN dissection, patients were treated with VACCIMEL (n=22) or IFNα-2b (n=6), unless rapid progression (n=1). Distant Metastasis-Free Survival (DMFS) was selected as an end-point. Two cohorts of patients were selected: one with a good outcome (GO) (n=17; median DMFS 130.0 months), and another with a bad outcome (BO) (n=12; median DMFS 8.5 months). We analyzed by immunohistochemistry and immunofluorescence the expression of relevant biomarkers to tumor-cell biology and immune cells and structures in mTDLN, both in the tumor and peritumoral areas.

Results

In BO patients, highly replicating Ki-67+ tumor cells, low tumor HLA-I expression and abundant FoxP3+ lymphocytes were found (p=0.037; p=0.056 and p=0.021). In GO patients, the most favorable biomarkers for prolonged DMFS were the abundance of peri- and intra-tumoral CD11c+ cells (p=0.0002 and p=0.001), peri-tumoral DC-LAMP+ dendritic cells (DCs) (p=0.001), and PNAd+ High Endothelial Venules (HEVs) (p=0.004). Most strikingly, we describe in GO patients a peculiar, heterogeneous structure that we named FAPS (Favoring Antigen-Presenting Structure), a triad composed of DC, HEV and CD62L+ naïve lymphocytes, whose postulated role would be to favor tumor antigen (Ag) priming of incoming naïve lymphocytes. We also found in GO patients a preferential tumor infiltration of CD8+ and CD20+ lymphocytes (p=0.004 and p=0.027), as well as peritumoral CD20+ aggregates, with no CD21+ follicular dendritic cells detected (p=0.023). Heterogeneous infiltration with CD64+CD68-CD163-, CD64+CD68+CD163- and CD64+CD68+CD163+ macrophages were observed in both cohorts.

Discussion

The analysis of mTDLN in GO and BO patients revealed marked differences. This work highlights the importance of analyzing resected mTDLN from CM patients and suggests a correlation between tumor and immune characteristics that may be associated with a spontaneous or vaccine-induced long DMFS. These results should be confirmed in prospective studies.
Ontogeny, functions and reprogramming of Kupffer cells upon infectious disease
Authors: Musrati Mohamed Amer , De Baetselier Patrick , Movahedi Kiavash , Van Ginderachter Jo A.
Published: August 2023

The liver is a vital metabolic organ that also performs important immune-regulatory functions. In the context of infections, the liver represents a target site for various pathogens, while also having an outstanding capacity to filter the blood from pathogens and to contain infections. Pathogen scavenging by the liver is primarily performed by its large and heterogeneous macrophage population. The major liver-resident macrophage population is located within the hepatic microcirculation and is known as Kupffer cells (KCs). Although other minor macrophages reside in the liver as well, KCs remain the best characterized and are the best well-known hepatic macrophage population to be functionally involved in the clearance of infections. The response of KCs to pathogenic insults often governs the overall severity and outcome of infections on the host. Moreover, infections also impart long-lasting, and rarely studied changes to the KC pool. In this review, we discuss current knowledge on the biology and the various roles of liver macrophages during infections. In addition, we reflect on the potential of infection history to imprint long-lasting effects on macrophages, in particular liver macrophages.
CSF-1 and Notch signaling cooperate in macrophage instruction and tissue repair during peripheral limb ischemia
Authors: Kapanadze Tamar , Gamrekelashvili Jaba , Sablotny Stefan , Kijas Dustin , Haller Hermann , Schmidt-Ott Kai , Limbourg Florian P.
Published: August 2023

Ischemia causes an inflammatory response featuring monocyte-derived macrophages (MF) involved in angiogenesis and tissue repair. Angiogenesis and ischemic macrophage differentiation are regulated by Notch signaling via Notch ligand Delta-like 1 (Dll1). Colony stimulating factor 1 (CSF-1) is an essential MF lineage factor, but its role in ischemic macrophage development and the interaction with Notch signaling is so far unclear. Using a mouse model of hind limb ischemia with CSF-1 inhibitor studies and Dll1 heterozygous mice we show that CSF-1 is induced in the ischemic niche by a subpopulation of stromal cells expressing podoplanin, which was paralleled by the development of ischemic macrophages. Inhibition of CSF-1 signaling with small molecules or blocking antibodies impaired macrophage differentiation but prolonged the inflammatory response, resulting in impaired perfusion recovery and tissue regeneration. Yet, despite high levels of CSF-1, macrophage maturation and perfusion recovery were impaired in mice with Dll1 haploinsufficiency, while inflammation was exaggerated. In vitro, CSF-1 was not sufficient to induce full MF differentiation from donor monocytes in the absence of recombinant DLL1, while the presence of DLL1 in a dose-dependent manner stimulated MF differentiation in combination with CSF-1. Thus, CSF-1 is an ischemic niche factor that cooperates with Notch signaling in a non-redundant fashion to instruct macrophage cell fate and maturation, which is required for ischemic perfusion recovery and tissue repair.
BNT162b2 COVID-19 vaccination in children alters cytokine responses to heterologous pathogens and Toll-like receptor agonists
Authors: Noé Andrés , Dang Thanh D. , Axelrad Christine , Burrell Emma , Germano Susie , Elia Sonja , Burgner David , Perrett Kirsten P. , Curtis Nigel , Messina Nicole L.
Published: August 2023

Background

Vaccines can have beneficial off-target (heterologous) effects that alter immune responses to, and protect against, unrelated infections. The heterologous effects of COVID-19 vaccines have not been investigated in children.

Aim

To investigate heterologous and specific immunological effects of BNT162b2 COVID-19 vaccination in children.

Methods

A whole blood stimulation assay was used to investigate in vitro cytokine responses to heterologous stimulants (killed pathogens, Toll-like receptor ligands) and SARS-CoV-2 antigens. Samples from 29 children, aged 5-11 years, before and 28 days after a second BNT162b2 vaccination were analysed (V2 + 28). Samples from eight children were analysed six months after BNT162b2 vaccination.

Results

At V2 + 28, interferon-γ and monocyte chemoattractant protein-1 responses to S. aureus, E. coli, L. monocytogenes, BCG vaccine, H. influenzae, hepatitis B antigen, poly(I:C) and R848 stimulations were decreased compared to pre-vaccination. For most of these heterologous stimulants, IL-6, IL-15 and IL-17 responses were also decreased. There were sustained decreases in cytokine responses to viral, but not bacterial, stimulants six months after BNT162b2 vaccination. Cytokine responses to irradiated SARS-CoV-2, and spike glycoprotein subunits (S1 and S2) were increased at V2 + 28 for most cytokines and remained higher than pre-vaccination responses 6 months after BNT162b2 vaccination for irradiated SARS-CoV-2 and S1. There was no correlation between BNT162b2 vaccination-induced anti-SARS-CoV2-receptor binding domain IgG antibody titre at V2 + 28 and cytokine responses.

Conclusions

BNT162b2 vaccination in children alters cytokine responses to heterologous stimulants, particularly one month after vaccination. This study is the first to report the immunological heterologous effects of COVID-19 vaccination in children.
Impact of SARS-CoV-2 mRNA vaccine on arthritis condition in rheumatoid arthritis
Authors: Takatani Ayuko , Iwamoto Naoki , Koto Serina , Aramaki Toshiyuki , Terada Kaoru , Ueki Yukitaka , Kawakami Atsushi , Eguchi Katsumi
Published: August 2023

Background

The SARS-CoV-2 mRNA vaccine has been reported to cause various adverse reactions, including the development or exacerbation of autoimmune diseases, but the adverse reactions and the effects of the vaccines on disease activity in patients with rheumatoid arthritis (RA) remain unknown. We therefore investigated the arthritis condition in RA patients after SARS-CoV-2 vaccination.

Methods

RA patients who visited our hospital from January to April 2022 completed a questionnaire regarding adverse reactions to the SARS-CoV-2 vaccine. We compared the frequency and duration of post-vaccination arthralgia between RA patients and health care workers in our hospital. For the RA patients who reported post-vaccination arthralgia, we collected medical records for the 6 months after vaccination.

Results

Of the 1198 vaccinated RA patients, 256 (21.4%) had systemic inflammatory symptoms, 18 (1.5%) had allergies including urticaria and asthma, and 37 (3.1%) had arthralgia. A few patients had extra-articular manifestations such as acute exacerbation of interstitial lung disease. Compared with health care workers, RA patients more frequently developed arthralgia, and the arthralgia was longer lasting than that in controls: only 9 (0.8%) of the 1117 health care workers reported arthralgia, and all cases resolved within 3 days. Data from 31 of the 37 RA patients with post-vaccination arthralgia were further analyzed; in these patients, disease activity was highest after 2 months, and 10 patients required additional DMARDs within 6 months. The proportion of concomitant use of PSL at vaccination was higher in these patients. No patients on biological DMARDs or targeted synthetic DMARDs prior to vaccination needed additional DMARDs or a change of regimen.

Conclusion

RA patients had more frequent and longer-lasting arthralgia after vaccination than healthy subjects, and one-third of patients with post-vaccination arthralgia required additional DMARDs. Although the SARS-CoV-2 mRNA vaccine was administered safely in most RA patients, in some patients RA symptoms may worsen after vaccination.
Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine
Authors: Peng Ouyang , Xia Yu , Wei Ying , Zeng Siying , Zou Chuangchao , Hu Fangyu , Xu Qiuping , Huang Yihui , Geng Rui , Hu Guangli , Cao Yongchang , Zhang Hao
Published: August 2023

Introduction

The porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV’s intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated.

Methods

In this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs).

Results

Differentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data.

Discussion

This study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing.
A decision-support framework for the restoration of Cystoseira sensu lato forests
Authors: Smith Christopher J. , Verdura Jana , Papadopoulou Nadia , Fraschetti Simonetta , Cebrian Emma , Fabbrizzi Erika , Monserrat Margalida , Drake Matilde , Bianchelli Silvia , Danovaro Roberto , Malak Dania Abdul , Ballesteros Enric , Benjumea Tesouro Tatí , Boissery Pierre , D’Ambrosio Paolo , Galobart Cristina , Javel Fabrice , Laurent Didier , Orfanidis Sotiris , Mangialajo Luisa
Published: August 2023

Macroalgal forests characterised by species of the genus Cystoseira sensu lato form important shallow coastal rocky habitats in the Mediterranean Sea. These forests support a high biodiversity and provide important ecosystem services and societal benefits. Currently these habitats are often in a poor condition in many areas, due to loss and degradation from both anthropogenic and climate stressors. Restoration has recently moved to the forefront of the United Nations and European Union agendas to reverse this trend, particularly in the last decade with the implementation of various international policies. However, this has been in the form of generic targets (e.g., restoration of 30% of degraded habitats by 2030) and has not been linked to specifically what habitat or species to restore, where and how. Initial targets have been missed, new targets are expected through the proposed EU Nature Restoration Law, but overall guidance is still lacking. There are few specific guides to marine habitat restoration limited to mostly seagrass, corals and shellfish. As a priority action for the recovery of coastal marine ecosystems a decision-support framework has been developed for the restoration of Mediterranean macroalgal forests, comprising a stepwise decision tree with additional descriptions of key elements to be considered for a restoration action. The decision tree includes steps concerning current and historical forest presence, site local condition assessment and choice of actions. Key considerations include restoration implementation (competence, society and support, finance and governance), success evaluation (at the target species and the ecosystem level) and long-term management. The framework builds on existing work on Cystoseira s.l. restoration, the work carried out in the EU AFRIMED project, but also on principles and guidelines in place for both generic and specific marine habitats. The work reported here has involved the expertise of scientists and information from stakeholders. Gaps were identified and recommendations were made, dealing with stressors, coordinating and networking stakeholders, integrating top down policy and bottom up initiatives, funding of restoration actions, establishing synergies between restoration, conservation and marine spatial planning and finally communication and publicity.
Distinctive sedimentary processes on two contrasting tidal flats of the Yellow River Delta
Authors: Xie Weiming , Sun Jianwei , Guo Leicheng , Xu Fan , Wang Xianye , Ji Hongyu , Fan Yaoshen , Wang Zheng Bing , He Qing
Published: August 2023

Coastal tidal flats provide valuable ecosystems, but are highly sensitive to tidal dynamics, sea-level rise, and human activities. Tidal inundation depth and frequency are known to affect tidal flat morphodynamics. However, the causes, processes and extent remain uncertain, particularly given the associated changes in sediment availability. In this study, we monitored the hydrodynamics, sediment transport, and morphological changes on two tidal flats in the northern and southern parts of the Yellow River Delta, with contrasting tidal regimes. The data showed that longer inundation periods under diurnal tides gained additional sediment and deposition than under semi-diurnal tides, because of the associated increase in water depth and sediment availability. The wave impact increased at the site with a semi-diurnal tidal regime owing to the lower water depth, where a larger bed shear stress led to tidal flat erosion. These results indicated that the combination of tidal regime and the occurrence of powerful waves played a joint role in controlling bed erosion, sediment availability, and short-term tidal flat evolution. This has implications for coping with delta erosion by enhancing local sediment availability in diurnal tidal regions and restoring vegetation to attenuate waves in semi-diurnal regions of the Yellow River Delta.
Effect of heat-clearing and dampness-eliminating Chinese medicine for high-risk cervical cancer papillomavirus infection: a systematic review and meta-analysis of randomized controlled trials
Authors: Huang Shan , Qi Yuanjie , Chen Shouzhen , He Baochang , Chen Xueli , Xu Jinbang
Published: August 2023

Background

Heat-clearing and dampness-eliminating Chinese medicine (HDCM) has been studied in clinical trials for cervical HPV infection for decades. However, there has been little comprehensive assessment of the strength and quality of the evidence. Therefore, this study conducted a systematic review and meta-analysis to assess the effectiveness and safety of HDCM in high-risk cervical HPV-infected patients.

Methods

The research focus questions were constructed in accordance with the criteria of participants, intervention, comparison, and outcomes (PICO), and a protocol was registered in PROSPERO. Comprehensive and systematic searches and inquiries in eight electronic databases were conducted from their inception to 30th June 2022. Further, a systematic review and meta-analysis of all randomized controlled trials (RCTs) were conducted to evaluate the HDCM therapy methods.

Results

A total of 12 studies were eligible for inclusion, including 1,574 patients. Data synthesis showed that the HPV clearance rate of HDCM groups was superior to both interferon and follow-up groups (RR = 1.40,95% CI:1.15, 1.71, P < 0.01) and (RR = 3.15, 95% CI:2.43,4.08, P < 0.01), respectively. HDCM was proven to exhibit greater potential in reducing HPV-DNA virus load (MD = −5.16, 95% CI: −5.91, −4.41, P < 0.01). The reversal rate of cervical intraepithelial neoplasia (CIN) for HDCM groups was approximately 2.8 times (RR = 2.80, 95% CI: 2.19, 3.57, P < 0.01), as high as the follow-up groups. Additionally, the recurrence rate of HR-HPV at the end of follow-up in this meta-analysis was reported to be lower in HDCM groups compared to follow-up groups [6.81% (16/235) and 14.65% (29/198), respectively]. The most commonly used Chinese herbal remedies were as follows: Huangbai (Phellodendron chinense var.Glabriusculum C.K. Schneid.), Kushen (Sophora flavescens Aiton), Daqingye (Isatis indigotica Fortune), Zicao (Arnebia hi-spidissima DC.), Baihuasheshecao (Hedyotis diffusa Spreng.), Banlangen (Isatis tinctoria subsp.tinctoria L.), Huzhang (Reynoutria japonica Houtt.), and Huangqi (Orobanche astragali Mouterde).

Conclusion

HDCM interventions appeared to generate significant effects on enhancing the rate of HR-HPV clearance, reducing the HPV-DNA virus load, and increasing the CIN regression rate. Some active components were confirmed to be responsible for this efficacy, which deserves further exploration.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022333226.
Guardians of the gut: influence of the enteric nervous system on the intestinal epithelial barrier
Authors: Bubeck Marvin , Becker Christoph , Patankar Jay V.
Published: August 2023

The intestinal mucosal surface forms one of the largest areas of the body, which is in direct contact with the environment. Co-ordinated sensory functions of immune, epithelial, and neuronal cells ensure the timely detection of noxious queues and potential pathogens and elicit proportional responses to mitigate the threats and maintain homeostasis. Such tuning and maintenance of the epithelial barrier is constantly ongoing during homeostasis and its derangement can become a gateway for systemic consequences. Although efforts in understanding the gatekeeping functions of immune cells have led the way, increasing number of studies point to a crucial role of the enteric nervous system in fine-tuning and maintaining this delicate homeostasis. The identification of immune regulatory functions of enteric neuropeptides and glial-derived factors is still in its infancy, but has already yielded several intriguing insights into their important contribution to the tight control of the mucosal barrier. In this review, we will first introduce the reader to the current understanding of the architecture of the enteric nervous system and the epithelial barrier. Next, we discuss the key discoveries and cellular pathways and mediators that have emerged as links between the enteric nervous, immune, and epithelial systems and how their coordinated actions defend against intestinal infectious and inflammatory diseases. Through this review, the readers will gain a sound understanding of the current neuro-immune-epithelial mechanisms ensuring intestinal barrier integrity and maintenance of intestinal homeostasis.
Mango anthracnose disease: the current situation and direction for future research
Authors: Dofuor Aboagye Kwarteng , Quartey Naa Kwarley-Aba , Osabutey Angelina Fathia , Antwi-Agyakwa Akua Konadu , Asante Kwasi , Boateng Belinda Obenewa , Ablormeti Fred Kormla , Lutuf Hanif , Osei-Owusu Jonathan , Osei Joseph Harold Nyarko , Ekloh William , Loh Seyram Kofi , Honger Joseph Okani , Aidoo Owusu Fordjour , Ninsin Kodwo Dadzie
Published: August 2023

Mango anthracnose disease (MAD) is a destructive disease of mangoes, with estimated yield losses of up to 100% in unmanaged plantations. Several strains that constitute Colletotrichum complexes are implicated in MAD worldwide. All mangoes grown for commercial purposes are susceptible, and a resistant cultivar for all strains is not presently available on the market. The infection can widely spread before being detected since the disease is invincible until after a protracted latent period. The detection of multiple strains of the pathogen in Mexico, Brazil, and China has prompted a significant increase in research on the disease. Synthetic pesticide application is the primary management technique used to manage the disease. However, newly observed declines in anthracnose susceptibility to many fungicides highlight the need for more environmentally friendly approaches. Recent progress in understanding the host range, molecular and phenotypic characterization, and susceptibility of the disease in several mango cultivars is discussed in this review. It provides updates on the mode of transmission, infection biology and contemporary management strategies. We suggest an integrated and ecologically sound approach to managing MAD.
Role of the gut microbiota in hematologic cancer
Authors: Guevara-Ramírez Patricia , Cadena-Ullauri Santiago , Paz-Cruz Elius , Tamayo-Trujillo Rafael , Ruiz-Pozo Viviana A. , Zambrano Ana Karina
Published: August 2023

Hematologic neoplasms represent 6.5% of all cancers worldwide. They are characterized by the uncontrolled growth of hematopoietic and lymphoid cells and a decreased immune system efficacy. Pathological conditions in hematologic cancer could disrupt the balance of the gut microbiota, potentially promoting the proliferation of opportunistic pathogens. In this review, we highlight studies that analyzed and described the role of gut microbiota in different types of hematologic diseases. For instance, myeloma is often associated with Pseudomonas aeruginosa and Clostridium leptum, while in leukemias, Streptococcus is the most common genus, and Lachnospiraceae and Ruminococcaceae are less prevalent. Lymphoma exhibits a moderate reduction in microbiota diversity. Moreover, certain factors such as delivery mode, diet, and other environmental factors can alter the diversity of the microbiota, leading to dysbiosis. This dysbiosis may inhibit the immune response and increase susceptibility to cancer. A comprehensive analysis of microbiota-cancer interactions may be useful for disease management and provide valuable information on host-microbiota dynamics, as well as the possible use of microbiota as a distinguishable marker for cancer progression.
Antimicrobial susceptibility of Escherichia coli isolated from diabetic patients in Mogadishu, Somalia
Authors: Hassan Shafie Abdulkadir , Ahmed Yousif Mousa Alobaid , Hassan Gallad Dahir
Published: August 2023

Background

Urinary tract infections (UTIs) are a major concern for diabetic patients due to the impact of diabetes on the urinary tract and immune system. Escherichia coli is the most common pathogen causing UTIs in diabetic patients and is known for its resistance. This study aimed to assess the antimicrobial susceptibility of Escherichia coli strains isolated from diabetic patients in Mogadishu, Somalia.

Methods

This descriptive cross-sectional study was conducted at Ummah Hospital in Mogadishu, Somalia, from November 2021 to April 2022. Clean catch mid-stream urine specimens were collected from each participant and uropathogens were identified using standard techniques. The samples were cultured on CLED agar and antibiotic susceptibility patterns were determined using the Kirby-Bauer disk diffusion method. Data analysis was performed using SPSS version 20.

Results

The overall prevalence of uropathogens among diabetic patients was 236/350 (67.5%) with Escherichia coli being the most common organism. According to multivariate logistic regression, the results showed that Female diabetic patients had a significantly higher likelihood of developing UTIs compared to males (AOR = 2.5, 95% CI: 1.357–4.522, p = 0.003). The duration of diabetes, history of previous UTIs, and previous antibiotic use were also significantly associated with UTIs. All isolates were found to be resistant to Cefotaxime (100%). In addition, high resistance rates were observed with ofloxacin (91%), ciprofloxacin (77.8%), amikacin (60.9%), ceftriaxone (58.3%), and cefepime (51.8%). The most sensitive antibiotics were colistin and imipenem (99.6 and 88.6%, respectively), followed by gentamycin (70%).

Conclusion

This study found a high prevalence of uropathogens and increased multi-drug resistance. Continuous surveillance is needed to monitor uropathogen prevalence and resistance rates, guiding treatment recommendations, rational prescription programs, and policy decisions.
Intestinal acetic acid regulates the synthesis of sex pheromones in captive giant pandas
Authors: Zhang Ming-yue , Zhang Xiao-hui , Wang Xue-ying , Liu Yu-liang , An Jun-hui , Wang Dong-hui , Cai Zhi-gang , Hou Rong
Published: August 2023

As a typical solitary animal, adult giant pandas rely on chemical signals (sex pheromones) to transmit reproductive information during oestrous. Although researchers have confirmed that the gut microbiota is related to the emission and reception of sex pheromones, there is no clear correlation between the gut microbes and the synthesis of sex pheromone of giant pandas, that is, which gut microbes and microbial metabolites are participate in the synthesis of giant panda’s sex pheromone. As a mirror of gut microbiota, fecal microbiota can reflect the composition of gut microbiota and its interaction with host to some extent. The purpose of this study is to explore how the gut microbes affect the synthesis of sex pheromones in captive giant pandas by combining analysis of the fecal microbiome and metabolomics. The results of correlation and microbial function analysis show that intestinal microorganisms such as Veillonellaceae and Lactobacillilaceae are associated with the synthesis of short chain fatty acid (acetic acid) and volatile ester metabolites, such as 1-butanol, 3-methyl, acetate, acetic acid, hexyl ester and 3-hexen-1-ol, acetate, (Z). In summary, based on this study, we believe that volatile metabolites such as fecal acetate participate in the process of mate preference of captive giant pandas and affect their expression of natural mating behavior. The possible mechanism is that the gut microbes can promote the synthesis of key chemical signaling substances in perianal glands through mediated intermediate fecal metabolites, thus affecting the normal information exchange between giant pandas individuals. The results of this study have greatly enriched our understanding of gut microbes regulating the synthesis of sex pheromones in giant pandas.
Infectivity and stress tolerance traits affect community assembly of plant pathogenic fungi
Authors: Choi Soyoung , Yang Jung Wook , Kim Jung-Eun , Jeon Hosung , Shin Soobin , Wui Dayoun , Kim Lee Seul , Kim Byung Joo , Son Hokyoung , Min Kyunghun
Published: August 2023

Understanding how ecological communities assemble is an urgent research priority. In this study, we used a community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of plant pathogenic fungi, Fusarium graminearum and F. asiaticum. High-throughput screening revealed that the isolates had a wide range of phenotypic variation in stress tolerance traits. Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) values were computed based on stress-tolerant distance matrices. Certain local regions exhibited positive values of NRI and NTI, indicating phenotypic clustering within the fungal communities. Competition assays of the pooled strains were conducted to investigate the cause of clustering. During stress conditions and wheat colonization, only a few strains dominated the fungal communities, resulting in reduced diversity. Overall, our findings support the modern coexistence theory that abiotic stress and competition lead to phenotypic similarities among coexisting organisms by excluding large, low-competitive clades. We suggest that agricultural environments and competition for host infection lead to locally clustered communities of plant pathogenic fungi in the field.
Root microbiota alters response to root rot in Rhododendron delavayi Franch
Authors: Tang Jing , Xiao Yufeng , Xu Xiaorong , Tang Ming , Zhang Ximin , Yi Yin
Published: August 2023

Root microbiota have a significant effect on plant health. However, the role of root microbiota in the resistance of Rhododendron against root rot is not known. In this study, we employed amplicon 16S and ITS sequencing to investigate the bacterial and fungal communities associated with four distinct niches (bulk soil, rhizosphere, rhizoplane, and endosphere) of both healthy and diseased Rhododendron plants in the Baili Rhododendron nature reserve in China. The amplicon data analysis identified 182 bacterial genera and 141 fungal genera that were impacted by root rot across all niches. Specifically, the rhizoplane appeared to exert a selective gating effect, resulting in a reduction in the complexity of bacterial communities, but not fungal communities, in wild Rhododendron delavayi Franch roots. Nevertheless, the stress induced by root rot led to alterations in the root microbiota and compromised the gating function of the rhizoplane, thereby significantly increasing the complexity of the bacterial community within the plant root. In the root tissue following root rot outbreak, the relative abundance of the pathogenic species Pezicula brunnea and Diaporthe helianthi was enriched by as much as 6.13% and 1.71%, respectively. These findings provide novel insights into the contribution of enrichment of root-associated microbiota to wild plant hosts under the disease stress of root rot. The root rot-causing pathogenic fungi may interact with beneficial bacteria and induce plants to send out “cry for help” signals, which may encourage the specific assembly of microbiota. In the Rhododendron delavayi Franch root microbiota, we found 23 potentially beneficial microbes. Notably, certain beneficial bacteria, such as Sporolactobacillus and Stenotrophomonas, were found to accumulate in the rhizoplane and endosphere under root rot disease stress. Overall, our results lend support to our hypothesis that Rhododendron recruits protective microbes as a strategy to suppress root rot outbreaks. Future endeavors in isolating beneficial microbes capable of mitigating root rot have the potential to enhance plant resilience against root diseases.