bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive evaluation and reservoir classification in the Quan 3 Member of the Cretaceous Quantou Formation in the Fuxin Uplift, Songliao Basin
Authors: Zhang Qin , Zhang Ya-Xiong , Wang Bo-Han , Yin Shuai , Wu Xin-Song , Yuan Cheng-Shuai
Published: September 2022

Continental tight oil sandstone reservoirs are developed in the Cretaceous Quentou Formation in the Songliao Basin, China. At present, there is still a lack of research on the reservoir microstructures, reservoir physical properties, and the division scheme of reservoir types in the Quan 3 Member of the Quanzhou Formation. Therefore, in this paper, taking the Quan 3 Member in the Fuxin Uplift Belt of the Songliao Basin as an example, the microscopic pore structure characteristics of tight oil sandstones have been systematically studied, and the classification standard of tight sandstones has been formulated. Furthermore, the sweet spots of the main production layers are predicted. The results show that the I sandstone group in the Quan 3 Member in the study area belongs to shallow water delta facies. Feldspar lithic fine sandstones are developed in the target layer, and calcareous sandstone is locally developed. Moreover, the mian pore types of the target layer include dissolved intergranular and intragranular pores, followed by primary intergranular pores, while micro-fractures are occasionally seen. According to the mercury intrusion test results, the pore-throat structures of the reservoir in the Quan 3 Member are divided into four types: 1) small-pore medium-throat type (point bar and delta distributary channel), 2) small-pore micro-throat type (point bar), 3) small-pore micro-throat type (natural levee), 4) micro-pore micro-throat type (river floodplain and inter-tributary bay). The lower limits of the physical properties of the effective reservoirs in the Quan 3 Member has been determined: the porosity is 10% and the permeability is 0.1 mD. Finally, combined with the study of the mercury intrusion curves, the physical properties and the sedimentary facies, the classification standard of the Quan 3 Member reservoirs was formulated. For the I sandstone group, the sweet spots of the Type I reservoirs are mainly developed in the Fuyu Oilfield in the southeast areas. The sandstones in this area suffered less compaction, and primary and secondary pores suffered from late dissolution are mainly developed.
Experimental study on the effect of prefabricated fissures on the creep mechanical properties and acoustic emission characteristics of sandstone under uniaxial compression
Authors: Yu Huaichang , Wang Guanqiang , Zhang Zhongyu , Niu Rui , Cheng Guangli
Published: September 2022

This study investigates the effect of prefabricated fissures on the creep mechanical strength and acoustic emission (AE) characteristics of sandstone. Under the same test conditions, indoor uniaxial compression creep AE tests were performed on intact and artificially fissured sandstone specimens using a rock rheometer and a PCI-Ⅱ AE tester controlled with an RLJW-2000 microcomputer. The variation characteristics of strain, long-term strength, number of AE events, AE ringing count, AE energy, and RA value of the two specimens were then analyzed to determine the effect of prefabricated fissures on the creep mechanical properties and AE characteristics of sandstone. The results show that under the same stress level, the instantaneous strain, creep strain, and total strain of the prefabricated fissures specimen was larger than the corresponding values of the intact specimen. The prefabricated fissures exhibited the most significant influence on the creep strain of the specimen, followed by the total strain. The fissures showed the least influence on the instantaneous strain of the specimen. Furthermore, the long-term strength of the prefabricated fissures specimen was only 37.5% of that of the intact specimen. Owing to the influence of the prefabricated fissures, the long-term strength of the sandstone was significantly reduced. In engineering practice, fissures should be noted and analyzed for the potential failure of a formation. Moreover, as the stress level increases, the number of AE events of the specimen also increases. The number of AE events and cumulative AE events generated by the prefabricated fissures specimen at various stress levels is significantly higher than the corresponding values of the intact specimen. The maximum ringing count of the prefabricated fissures specimen was 7.3 times that of the intact specimen, and the maximum AE energy was 3.8 times that of the intact specimen. The cumulative AE ringing count was 1.5 times that of the intact specimen, and the cumulative energy was 4.5 times that of the intact specimen. The prefabricated fissures significantly affect the maximum AE ringing count, maximum AE energy, cumulative AE ringing count, and cumulative AE energy of the specimen. Finally, tensile fissures were the main microcracks generated inside the intact specimen during creep, and shear cracks were secondary. The microcracks generated inside the prefabricated fissures specimen consisted of mixed tension-shear cracks, but mainly consisted of shear cracks with fewer tension cracks. The RA value correlates well with the observed internal microcracks, indicating that the RA value can be used to characterize fractures in sandstone specimens. The RA value has a guiding significance for characterizing the type of internal microcracks in the process of rock creep.
QEMSCAN® automated mineralogical analysis of PM2.5 and PM4: A preliminary study of underground coal mine dust from Poland and Slovenia
Authors: Johnson Diane , Rollinson Gavyn. K. , Arif Ali Talib , Moreno Teresa , Ruiz Pedro Trechera , Lah Robert , Lubosik Zbigniew , Pindel Thomas , Gminsk Richard , Williamson Ben J.
Published: September 2022

Determining the physical and chemical properties of airborne dusts in occupational settings is essential for assessing their potential toxicity as well as the effectiveness of respiratory protective equipment and dust mitigation measures. Here, we report the first successful QEMSCAN® automated mineralogical analysis of potentially toxic PM4 and PM2.5 dust from deep coal mines in Poland and Slovenia. QEMSCAN® was setup to automatically delimit 100,000 ‘particles’ per sample, based on average atomic number contrast, subject these to X-ray elemental analysis at points in a grid pattern (0.5 µm spacing), assign a mineral name to each point and then output the results as particle size, shape, mineralogy and mineral associations data and as mineral maps. The dusts were prepared as dispersions on a polyethylene sheet so that coal particles, with a slightly higher BSE signal, could be recognized from their substrate. Samples were analyzed repeatedly and in different orientations to determine the effects of sample geometry and topography. QEMSCAN® mineral identifications were manually checked using standard SEM X-ray elemental analysis. From a pilot study of Polish and Slovenian coal dust samples, PM4 and PM2.5 contain varying proportions of coal, quartz and other silicates, sulphides, sulphates, carbonates, oxides and other minerals, and notable concentrations of fly-ash particles. That some of these components may be toxic when inhaled, particularly the quartz and fly-ash, highlights the need for larger scale and wider ranging studies. The further potential of the newly developed QEMSCAN® methodology is discussed.
Formation of calcium chloride brines in volcaniclastic-rich sediments
Authors: Sena Clara , Parkhurst David L. , Tepley ||| Frank J. , Jiang Fuqing , van der Land Cees , Coelho Francisco JRC , Oliveira Vanessa , Lever Mark A. , Ishizuka Osamu , Arculus Richard
Published: September 2022

The Amami-Sankaku Basin, located in the Philippine Sea, records approximately 50 million years of sediment accumulation and diagenesis of volcanic ash derived from the Kyushu-Palau and Kyushu-Ryukyu arcs. Analyses of porewater and sediment samples from the 1461-m core recovered at IODP Expedition 351, Site U1438, included major and trace elements, strontium radiogenic isotope ratio (87Sr/86Sr), and taxonomic identification of archaeal classes and bacterial orders. Sediment X-ray diffraction and thin section analyses show that smectite, zeolites and chlorite are the main authigenic minerals. A multicomponent solute diffusion and reaction numerical model was developed to simulate the long-term diagenesis that took place in this sedimentary sequence and to account for the transition to a calcium chloride brine at about 670 mbsf. Numerical results indicate that 45% of the initial amount of volcanic ash has been dissolved at 750 mbsf. At this depth, 13% of the initial water (H2O) in the pore space is estimated to have been transferred to the solid phase by the formation of zeolites, which accounts for an increase in porewater chloride concentration. In contrast, dissolution of anorthite and volcanic ash combined with sodium uptake by zeolites accounts for the predominance of calcium in the brine. In the upper 160 m of the sedimentary column, the electrochemical migration of solutes causes chloride to move in the opposite direction of the concentration gradient, i.e., uphill diffusion, sustaining downward diffusion of seawater chloride into the sediments.
A novel prognostic 6-gene signature for osteoporosis
Authors: Zhao Yu , Yan Jieping , Zhu Yimiao , Han Zhenping , Li Tingting , Wang Lijuan
Published: September 2022

Introduction

The incidence of osteoporosis (OP) keeps increasing due to global aging of the population. Therefore, identifying the diagnostic and prognostic biomarkers of OP is of great significance.

Methods

mRNA data from OP and non-OP samples were obtained from GEO database, which were divided into training set (GSE35959) and testing sets (GSE7158, GSE62402, GSE7429 and GSE56815). Gene modules most significantly related to OP were revealed using weighted gene co-expression network analysis (WGCNA) and differentially expressed genes (DEGs) between OP and normal samples in training set were identified using limma R package. Thereafter, above two gene sets were intersected to obtain the genes potentially related to OP. Protein-protein interaction (PPI) pairs were screened by STRING database and visualized using Cytoscape, while the plug-in cytoHubba was used to screen hub genes by determining their topological parameters. Afterwards, a diagnostic model was constructed using those hub genes, whose creditability was further evaluated by testing sets.

Results

The results of WGCNA analysis found the Black module was most significantly related to OP, which included altogether 1286 genes. Meanwhile, 2771 DEGs were discovered between OP patients and the normal controls. After taking the intersection, 479 genes were identified potentially correlated with the development of OP. Subsequently, six hub genes were discovered through PPI network construction and node topological analysis. Finally, we constructed a support vector machine model based on these six genes, which can accurately classified training and testing set samples into OP and normal groups.

Conclusion

Our current study constructed a six hub genes-based diagnostic model for OP. Our findings may shed some light on the research of the early diagnosis for OP and had certain practical significance.
Research on optimized SOC estimation algorithm based on extended kalman filter
Authors: Yang Bo , Li Guanjun , Tang Wencheng , Li Haoyuan
Published: September 2022

The paper studies the estimation of state of charge (SOC) of batteries. Firstly, the research status of battery management system, battery equivalent model and SOC estimation algorithm is introduced, and the performance of common equivalent circuit model and SOC estimation algorithm in complexity and accuracy is compared and analyzed. On this basis, this paper proposes an extended Kalman filter (EKF) algorithm based on the first-order RC model, and optimizes it by piecewise fitting. The accuracy of the optimized EKF algorithm is greatly improved. Finally, the modeling and simulation are completed through MATLAB/SIMULINK, and the experimental platform is designed and built to test the SOC estimation algorithm based on EKF. The simulation and experimental results verify the accuracy of the estimation algorithm.
Instance-based transfer learning for soil organic carbon estimation
Authors: Bursać Petar , Kovačević Miloš , Bajat Branislav
Published: September 2022

Soil organic carbon (SOC) is a vital component for sustainable agricultural production. This research investigates the transfer learning-based neural network model to improve classical machine learning estimation of SOC values from other geochemical and physical soil parameters. The results on datasets based on LUCAS data from 2015 showed that the Instance-based transfer learning model captured the valuable information contained in different source domains (cropland and grassland) of soil samples when estimating the SOC values in arable cropland areas. The effects of using transfer learning are more pronounced in the case of different source (grassland) and target (cropland) domains. Obtained results indicate that the transfer learning (TL) approach provides better or at least equal output results compared to the classical machine learning procedure. The proposed TL methodology could be used to generate a pedotransfer function (PTF) for target domains with described samples and unknown related PTF outputs if the described samples with known related PTF outputs from a different geographic or similar land class source domain are available.
The environmental effects of regional economic cooperation: Evidence from the Belt and Road Initiative
Authors: Li Baoxi , Hu Jiemei , Chen Guo , Xiao De , Cheng Shixiong
Published: September 2022

China’s Belt and Road Initiative is a significant regional economic cooperation. This paper uses the Belt and Road Initiative (BRI) as a quasi-natural experiment to investigate the impact of regional economic cooperation on environmental quality. Using difference-in-differences (DID) and a series of robustness checks, we find that regional economic cooperation like BRI deteriorates environmental quality in countries along the Belt and Road. The main reason is that the improving effects on environmental quality in the BRI countries are smaller than in the non-BRI countries after the BRI. The ecological impacts of the BRI exist differences in different countries. The results show that the BRI improves environmental quality in South Asia, and Europe and Central Asia. However, the BRI negatively affects environmental quality in East Asia and Pacific, developing and non-OECD countries. We found that, unlike the BRI, the Green BRI improves environmental quality in countries along the Belt and Road. We also discuss the mechanism of the BRI on environmental quality from foreign direct investment (FDI).
Prevention of radioactive pollution: A comparative simulation study on the reduction of several important radionuclides by pyrite and magnetite
Authors: Yu Haoqi , Yu Tao , Zeng Kai
Published: September 2022

In order to ensure the long-term effective isolation of radionuclides from human beings to the environment, pyrite and magnetite, which exist widely and stably in the geological environment, can be considered to reduce the strong mobility of high-valence redox-sensitive nuclides to the low-valence nuclides with low mobility. In this work, the reducing reaction between pyrite, magnetite, and redox-sensitive radionuclides (U, Se, Tc, and Np) in the Gansu proposed-treatment plant area was under simulation by PHREEQC. Due to the considerable existence of quartz and calcite in the Gansu proposed-treatment plant area surrounding the rock of interest, the influence of the dissolved Ca2+ and SiO32- should be taken into account. The corresponding precipitation saturation index of the complex (UOX, Se(s), and TcO2) and species of interest was calculated, and the results suggested that pyrite can significantly reduce the high-valence radionuclides (U, Se, Tc, and Np), and their corresponding precipitation saturation indexes (SIs) were usually positive. However, magnetite, in a given condition, showed a certain reducing effect against Se and Np and a poor effect on U and Tc. It was worth noting that the aqueous pH in the system always remained constant because of the CO2 partial pressure of the underground biosphere under this long-term time scale. These conclusions have an important guiding significance for the prevention and retention of radioactive pollution released into the biological environment.
Space-time perception and behavioral response of farmers to climate change: Evidence from Sichuan Province, China
Authors: Ma Junqiao , Zhou Wenfeng , Guo Shili , Deng Xin , Song Jiahao , Xu Dingde
Published: September 2022

It is of great significance for global environmental governance to guide farmers to effectively perceive climate change. Based on the survey data of 540 farmers in Sichuan Province, China, this study used binary Logit model and Multinomial Logistic Regression model to explore the effects of farmers’ space-time perception of climate change and their interaction effects on farmers’ adaptation behavior to climate change. The results showed that: (1) 88.51% of farmers took adaptation measures to climate change, and 61.11% of them took both passive and active adaptation measures. Among the 7 measures, the highest rate of “Increase irrigation” is 23%, and the lowest rate of “Migrant work” is only 5%. (2) The scale difference of farmers’ time perception of climate change has a significant positive impact on their adaptive behavior of climate change. In terms of time: climate change perception in the next 5 years > in the next 10 years > in the next 15 years. (3) The scale difference of farmers’ space perception of climate change has a significant positive impact on their adaptation behavior to climate change. In other words, spatially, farmers’ perception of climate change is global > national > local village (the perception of local province is not significant). (4) Farmers’ space-time perception of climate change significantly affects farmers’ adaptive behavior. Among them, “farmers’ perception of climate change in the next 5 years” and their own “village’s perception of climate change” play an important role. This study will help deepen the understanding of farmers’ perception of climate change and their adaptive behavior, and provide reference for national policy making.
You Can’t Have AI Both Ways: Balancing Health Data Privacy and Access Fairly
Authors: Bak Marieke , Madai Vince Istvan , Fritzsche Marie-Christine , Mayrhofer Michaela Th. , McLennan Stuart
Published: September 2022

Artificial intelligence (AI) in healthcare promises to make healthcare safer, more accurate, and more cost-effective. Public and private actors have been investing significant amounts of resources into the field. However, to benefit from data-intensive medicine, particularly from AI technologies, one must first and foremost have access to data. It has been previously argued that the conventionally used “consent or anonymize approach” undermines data-intensive medicine, and worse, may ultimately harm patients. Yet, this is still a dominant approach in European countries and framed as an either-or choice. In this paper, we contrast the different data governance approaches in the EU and their advantages and disadvantages in the context of healthcare AI. We detail the ethical trade-offs inherent to data-intensive medicine, particularly the balancing of data privacy and data access, and the subsequent prioritization between AI and other effective health interventions. If countries wish to allocate resources to AI, they also need to make corresponding efforts to improve (secure) data access. We conclude that it is unethical to invest significant amounts of public funds into AI development whilst at the same time limiting data access through strict privacy measures, as this constitutes a waste of public resources. The “AI revolution” in healthcare can only realise its full potential if a fair, inclusive engagement process spells out the values underlying (trans) national data governance policies and their impact on AI development, and priorities are set accordingly.
Genetic variant of ADH1C for predicting survival in esophageal squamous cell cancer patients who underwent postoperative radiotherapy
Authors: Xu Xin , Sun Zhiyong , Rong Ling , Wang Xiaohang , Xu Lei , Lu Jun , Ye Qing , Zhang Lei , Bai Yongrui , Ma Xiumei
Published: September 2022

Background: Single nucleotide polymorphisms (SNPs) of essential enzymes for alcohol metabolism ADH1B, ADH1C, and ALDH2 are commonly regarded as genetic biomarkers for esophageal squamous cell carcinoma (ESCC) susceptibility. However, there have not been any reports on relations between SNPs of these genes and the prognosis of postoperative radiotherapy in ESCC. The current study aimed to understand the associations between gene variants of alcohol metabolism and adjuvant radiotherapy’s prognosis in ESCC.

Methods: This study retrospectively analyzed 110 ESCC patients from our institution who received adjuvant radiotherapy after surgery. The SNPs of ADH1B rs1229984, ADH1C rs1789924, and ALDH2 rs671 were detected by Sanger sequencing using formalin-fixed paraffin-embedded tumor samples. A nomogram was drawn based on prognostic factors associated with overall survival (OS).

Results: ADH1C rs1789924 (C>T) was associated with poor DFS and OS in ESCC patients undergoing adjuvant radiotherapy. Multivariate analysis showed that ADH1C rs1789924 (C>T) was one of the independent prognosis factors of DFS and OS. However, the genotypes of ADH1B SNP rs1229984 and ALDH2 rs671 were not associated with differences in the PFS and OS of these patients. Compared with the AJCC staging system, the nomogram containing the ADH1C genotype can more effectively and accurately predict the survival time of ESCC after surgery and adjuvant radiotherapy.

Conclusion: ADH1C rs1789924 might be a prognostic genetic biomarker for ESCC patients undergoing surgery and postoperative radiotherapy.
You are what you eat: How to best fuel your immune system
Authors: Hellmich Charlotte , Wojtowicz Edyta E.
Published: September 2022

Normal bone marrow (BM) homeostasis ensures consistent production of progenitor cells and mature blood cells. This requires a reliable supply of nutrients in particular free fatty acids, carbohydrates and protein. Furthermore, rapid changes can occur in response to stress such as infection which can alter the demand for each of these metabolites. In response to infection the haematopoietic stem cells (HSCs) must respond and expand rapidly to facilitate the process of emergency granulopoiesis required for the immediate immune response. This involves a shift from the use of glycolysis to oxidative phosphorylation for energy production and therefore an increased demand for metabolites. Thus, the right balance of each dietary component helps to maintain not only normal homeostasis but also the ability to quickly respond to systemic stress. In addition, some dietary components can drive chronic inflammatory changes in the absence of infection or immune stress, which in turn can impact on overall immune function. The optimal nutrition for the best immunological outcomes would therefore be a diet that supports the functions of immune cells allowing them to initiate effective responses against pathogens but also to resolve the response rapidly when necessary and to avoid any underlying chronic inflammation. In this review we discuss how these key dietary components can alter immune function, what is their impact on bone marrow metabolism and how changes in dietary intake of each of these can improve the outcomes of infections.
The impact of pre-transplant donor specific antibodies on the outcome of kidney transplantation – Data from the Swiss transplant cohort study
Authors: Frischknecht Lukas , Deng Yun , Wehmeier Caroline , de Rougemont Olivier , Villard Jean , Ferrari-Lacraz Sylvie , Golshayan Déla , Gannagé Monique , Binet Isabelle , Wirthmueller Urs , Sidler Daniel , Schachtner Thomas , Schaub Stefan , Nilsson Jakob ,   the Swiss Transplant Cohort Study
Published: September 2022

Background

Pre-transplant donor specific antibodies (DSA), directed at non-self human leukocyte antigen (HLA) protein variants present in the donor organ, have been associated with worse outcomes in kidney transplantation. The impact of the mean fluorescence intensity (MFI) and the target HLA antigen of the detected DSA has, however, not been conclusively studied in a large cohort with a complete virtual cross-match (vXM).

Methods

We investigated the effect of pre-transplant DSA on the risk of antibody-mediated rejection (ABMR), graft loss, and the rate of eGFR decline in 411 DSA positive transplants and 1804 DSA negative controls.

Results

Pre-transplant DSA were associated with a significantly increased risk of ABMR, graft loss, and accelerated eGFR decline. DSA directed at Class I and Class II HLA antigens were strongly associated with increased risk of ABMR, but only DSA directed at Class II associated with graft loss. DSA MFI markedly affected outcome, and Class II DSA were associated with ABMR already at 500-1000 MFI, whereas Class I DSA did not affect outcome at similar low MFI values. Furthermore, isolated DSA against HLA-DP carried comparable risks for ABMR, accelerated eGFR decline, and graft loss as DSA against HLA-DR.

Conclusion

Our results have important implications for the construction and optimization of vXM algorithms used within organ allocation systems. Our data suggest that both the HLA antigen target of the detected DSA as well as the cumulative MFI should be considered and that different MFI cut-offs could be considered for Class I and Class II directed DSA.
Physical activity and risk of multiple sclerosis: A Mendelian randomization study
Authors: Li Chunyu , Lin Junyu , Yang Tianmi , Xiao Yi , Jiang Qirui , Shang Huifang
Published: September 2022

Multiple evidence from epidemiological studies has suggested association between physical activity and risk of multiple sclerosis (MS). However, the conclusion was still controversial between studies, and whether the association was causal or confounded is elusive. To evaluate the role of physical activity with different intensities in the risk of MS, we first estimated their genetic correlation, and then conducted two-sample and multivariable Mendelian randomization analyses based on summary statistics from previous large genome-wide association studies. A significant genetic correlation was identified between moderate physical activity and the risk of MS (genetic correlation: -0.15, SE=0.05, P=2.9E-03). Meanwhile, higher moderate physical activity was significantly associated with a reduced risk of MS (OR:0.87, 95% CI:0.80-0.96, P=3.45E-03). Such association was further verified using summary statistics from another study on overall physical activity (OR:0.36, 95% CI:0.17-0.76, P=6.82E-03). The results were robust under all sensitivity analyses. Current results suggested moderate physical activity could reduce the risk of MS. These findings help better understand the role of physical activity in MS, and provide some lifestyle recommendations for individuals susceptible to MS.
Experimental and genetic evidence for the impact of CD5 and CD6 expression and variation in inflammatory bowel disease
Authors: Casadó-Llombart Sergi , Velasco-de Andrés María , Català Cristina , Leyton-Pereira Alejandra , Gutiérrez-Cózar Rebeca , Suárez Belén , Armiger Noelia , Carreras Esther , Esteller Miriam , Ricart Elena , Ordás Ingrid , Gisbert Javier P. , Chaparro María , Esteve María , Márquez Lucía , Busquets David , Iglesias Eva , García-Planella Esther , Martín-Arranz María Dolores , Lohmann Juliane , Ayata C. Korcan , Niess Jan Hendrik , Engel Pablo , Panés Julián , Salas Azucena , Domènech Eugeni , Lozano Francisco ,   ENEIDA Project of GETECCU
Published: September 2022

Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) resulting from the interaction of multiple environmental, genetic and immunological factors. CD5 and CD6 are paralogs encoding lymphocyte co-receptors involved in fine-tuning intracellular signals delivered upon antigen-specific recognition, microbial pattern recognition and cell adhesion. While CD5 and CD6 expression and variation is known to influence some immune-mediated inflammatory disorders, their role in IBD remains unclear. To this end, Cd5- and Cd6-deficient mice were subjected to dextran sulfate sodium (DSS)-induced colitis, the most widely used experimental animal model of IBD. The two mouse lines showed opposite results regarding body weight loss and disease activity index (DAI) changes following DSS-induced colitis, thus supporting Cd5 and Cd6 expression involvement in the pathophysiology of this experimental IBD model. Furthermore, DNA samples from IBD patients of the ENEIDA registry were used to test association of CD5 (rs2241002 and rs2229177) and CD6 (rs17824933, rs11230563, and rs12360861) single nucleotide polymorphisms with susceptibility and clinical parameters of CD (n=1352) and UC (n=1013). Generalized linear regression analyses showed association of CD5 variation with CD ileal location (rs2241002CC) and requirement of biological therapies (rs2241002C-rs2229177T haplotype), and with poor UC prognosis (rs2241002T-rs2229177T haplotype). Regarding CD6, association was observed with CD ileal location (rs17824933G) and poor prognosis (rs12360861G), and with left-sided or extensive UC, and absence of ankylosing spondylitis in IBD (rs17824933G). The present experimental and genetic evidence support a role for CD5 and CD6 expression and variation in IBD’s clinical manifestations and therapeutic requirements, providing insight into its pathophysiology and broadening the relevance of both immunomodulatory receptors in immune-mediated disorders.
Wind-wave forecasting in enclosed basins using statistically downscaled global wind forcing
Authors: Barbariol Francesco , Pezzutto Paolo , Davison Silvio , Bertotti Luciana , Cavaleri Luigi , Papa Alvise , Favaro Marco , Sambo Enrico , Benetazzo Alvise
Published: September 2022

Accurate wind-wave forecasting in enclosed and semi-enclosed basins is a challenging task, demanding primarily for high-resolution wind forcing at regional scale. This is generally obtained with dynamical downscaling from a low-to-mid resolution atmospheric model. In this context, a new wave forecasting system for the marginal Adriatic Sea is herein presented aimed at proposing an alternative strategy for accurate wind-wave forecasting in (semi-) enclosed basins that does not require an ad-hoc regional atmospheric model. The system is based on the state-of-the-art WAVEWATCH III® spectral wave model forced by the global IFS-ECMWF forecast. At first, wind speed is quantile-corrected to account for the systematic underestimation over the Adriatic Sea. Then, the significant wave height in the target region and for regimes associated with marine storms is calibrated following standard procedure. Wind and wave observations from different sources are used for calibration and validation of the wave forecasts, which achieve satisfactory scores. We also compare results with those of other forecasting systems in the area, highlighting the importance of the wind forcing accuracy and the wave model calibration. Doing so, we discuss the challenges that characterise (semi-) enclosed environments in order to propose effective solutions for them and future developments.
Multi-year acoustic tracking reveals transient movements, recurring hotspots, and apparent seasonality in the coastal-offshore presence of Greenland sharks (Somniosus microcephalus)
Authors: Edwards Jena E. , Hedges Kevin J. , Kessel Steven T. , Hussey Nigel E.
Published: September 2022

Variable movement strategies can complicate the conservation and management of mobile species. Given its extreme life history traits as a long-lived, deep-water species, the Greenland shark (Somniosus microcephalus) is vulnerable to fisheries bycatch, but little is known over its long-term movements across a spatially and seasonally variable Arctic environment. To address this knowledge gap, the movements of Greenland sharks in coastal fjords and offshore waters of Baffin Bay were examined using seven years of acoustic telemetry data. Seasonal patterns in broad-scale movements and inshore-offshore connectivity were compared among 155 sharks (101 males, 54 females [mean LT = 2.65 ± 0.48 m, range 0.93-3.5 m]) tagged in 6 discrete coastal locations spanning from Grise Fiord to Cumberland Sound (Nunavut). Sharks exhibited transient movements throughout coastal and offshore regions with some evidence of seasonally recurring hotspots revealed by repeat detections of individuals at sites over multiple years. Shark presence in coastal fjords occurred exclusively during the coastal ice-free period (July to November), regardless of the location of tagging or detection, while presence in the offshore was recorded during the period of ice re-formation and cover (November to July). Through multi-year telemetry, it was possible to reveal repetitive patterns in broad-scale habitat use for a complex marine predator with direct relevance for understanding the seasonal distribution of mobile Arctic consumers and informing regional fisheries management.
The presence of silver nanoparticles reduces demand for dissolved phosphorus to the benefit of biological nitrogen fixation in the coastal eastern Mediterranean Sea
Authors: Rees Andrew P. , Faraggiana Eleonora , Tait Karen , Celussi Mauro , Dafnomilli Eleni , Manna Vincenzo , Manning Andrew , Pitta Paraskevi , Tsiola Anastasia , Živanović Snežana
Published: September 2022

The release of silver into the marine environment is of growing concern as its impact on marine life is not fully understood. Despite previous experiments that have shown toxic effects of silver as nanoparticles (AgNPs) and as free ions (Ag+) on microbial organisms, the impact on important biogeochemical processes, such as marine nitrogen fixation, remains relatively unexplored. The present study investigated the impact of AgNPs and Ag+ on nitrogen fixation activity in oligotrophic coastal ecosystems. Nine mesocosm enclosures were set-up in Crete, Greece, for twelve days during May 2019. Three mesocosms were left unamended at ambient light and temperature; three were manipulated with 50 ng AgNPs L-1d-1 and three were amended with 50 ng Ag+ L-1d-1. Over the duration of the experiment, mean nitrogen fixation rates proved higher in treated waters; 0.28 ± 0.24 nmol N L-1d-1 and 0.21 ± 0.19 nmol N L-1d-1 in AgNP and Ag+ which were 2.2 (p< 0.001) and 1.6 (not significant) times higher than control rates of 0.13 ± 0.07 nmol N L-1d-1 respectively. Changes in nitrogen fixation rates were paralleled by significantly higher concentrations of phosphate and silicate in treated versus control mesocosms, suggesting an inhibition of the uptake of these nutrients by non-diazotrophic groups. Sequencing of 16S and 18S rRNA genes showed shifts in community composition over time but only very minor changes could be linked to the Ag treatments. Decreases to the relative abundance of three diatom species were observed in the Ag treatments but these were considered insufficient to support the relative differences in nutrient concentration. It is therefore speculated that there was physiological disruption of nutrient uptake mechanisms of the non-diazotrophic community. A number of potential diazotrophs were detected and the relative sequence abundance of a number of known nitrogen fixing taxa, including Burkholderiaceae, Oceanospirillales and Pseudomonadales correlated with measured nitrogen fixation rates. Phosphorus limitation of diazotrophic activity was therefore lowered relative to other microbial groups in silver amended treatments and significant increases in particulate nitrogen for both Ag treatments indicate an enhancement in cellular N for the nitrogen fixing communities.
Coastal seascape variability in the intensifying East Australian Current Southern Extension
Authors: Phillips Lachlan R. , Malan Neil , Roughan Moninya , Harcourt Robert , Jonsen Ian , Cox Martin , Brierley Andrew S. , Slip David , Wilkins Adam , Carroll Gemma
Published: September 2022

Coastal pelagic ecosystems are highly variable in space and time, with environmental conditions and the distribution of biomass being driven by complex processes operating at multiple scales. The emergent properties of these processes and their interactive effects result in complex and dynamic environmental mosaics referred to as “seascapes”. Mechanisms that link large-scale oceanographic processes and ecological variability in coastal environments remain poorly understood, despite their importance for predicting how ecosystems will respond to climate change. Here we assessed seascape variability along the path of the rapidly intensifying East Australian Current (EAC) Southern Extension in southeast Australia, a hotspot of ocean warming and ecosystem tropicalisation. Using satellite and in situ measures of temperature, salinity and current velocity coupled with contemporaneous measurements of pelagic biomass distribution from nine boat-based active acoustic surveys in five consecutive years, we investigated relationships between the physical environment and the distribution of pelagic biomass (zooplankton and fish) at multiple timescales. Survey periods were characterised by high variability in oceanographic conditions, with variation in coastal conditions influenced by meso-to-large scale processes occurring offshore, including the position and strength of eddies. Intra-annual variability was often of a similar or greater magnitude to inter-annual variability, suggesting highly dynamic conditions with important variation occurring at scales of days to weeks. Two seascape categories were identified being characterised by (A) warmer, less saline water and (B) cooler, more saline water, with the former indicating greater influence of the EAC on coastal processes. Warmer waters were also associated with fewer, deeper and less dense biological aggregations. As the EAC continues to warm and penetrate further south, it is likely that this will have substantial effects on biological activity in coastal pelagic ecosystems, including a potential reduction in the accessibility of prey aggregations to surface-feeding predators and to fisheries. These results highlight the import role of offshore oceanographic processes in driving coastal seascape variability and biological activity in a region undergoing rapid oceanic warming and ecological change.
Apparent shifts in the microplankton community in response to zinc and iron enrichments in the Northeastern Subarctic Pacific
Authors: Crawford David W. , Purdie Duncan A. , Lohan Maeve C. , Statham Peter J. , Peterson Tawnya D. , Kennedy Hilary A. , Lipsen Michael S. , Putland Jennifer N. , Whitney Frank A.
Published: September 2022

The offshore Gulf of Alaska—in the northeastern subarctic Pacific—is a high-nitrate, low-chlorophyll (HNLC) oceanic region where concentrations of dissolved iron (DFe) and zinc (DZn) are of the order ~0.1 nmol kg−1 in surface waters. At the average winter mixed layer depth of ~120 m, DFe and DZn are of the orders ~0.1–0.2 nmol kg−1 and ~1–2 nmol kg−1, respectively. Vertical supply of Fe to surface waters is therefore limited, with phytoplankton blooms driven by episodic atmospheric and lateral inputs of Fe. In contrast, DZn is presumably replenished through seasonal vertical mixing, though maintained at low levels in surface waters, even in winter, implying that removal processes are in operation. Previous supplementation experiments have demonstrated that phytoplankton biomass (chl-a), growth, and drawdown of nitrate (NO3-) are stimulated strongly by Fe but only minimally, if at all, by Zn alone. Using on-deck bioassay incubations of surface waters, we confirm that the addition of Fe stimulates significant increases in chl-a and large diatoms, and drawdown of NO3- and silicic acid [Si(OH)4]. Associated drawdown of DZn and dissolved cadmium (DCd) indicated Zn stress in the control and +Fe treatment. Supplementation with Zn alone had no significant impact on NO3- and commonly monitored pigments such as chl-a and fucoxanthin. However, in the +Zn treatment, DFe and coccolithophore abundance were significantly lower, and the concentration of particulate organic carbon (POC) and that of the pigments alloxanthin and chlorophyll c1+2 were significantly higher than those in control incubations. Our experiment corroborates previously observed relationships between DZn and alloxanthin and chlorophyll c across the subarctic north Pacific and Bering Sea and could help to explain the low or undetectable concentrations of alloxanthin frequently observed in this region. Alloxanthin is a pigment specific to the cryptophytes, either within free-living cells or within functional plastids retained by mixotrophic protists. Both cryptophytes and mixotrophic ciliates, such as Laboea sp. and Strombidium spp., make a variable but significant contribution to phytoplankton biomass in this area. In the absence of Fe supply to surface waters, Zn could play a hitherto unsuspected role in shaping plankton communities in the HNLC Gulf of Alaska.
Irreversibility of regime shifts in the North Sea
Authors: Sguotti Camilla , Blöcker Alexandra M. , Färber Leonie , Blanz Benjamin , Cormier Roland , Diekmann Rabea , Letschert Jonas , Rambo Henrike , Stollberg Nicole , Stelzenmüller Vanessa , Stier Adrian C. , Möllmann Christian
Published: September 2022

Human impacts can induce ecosystems to cross tipping points and hence unexpected and sudden changes in ecosystem services that are difficult or impossible to reverse. The world´s oceans suffer from cumulative anthropogenic pressures like overexploitation and climate change and are especially vulnerable to such regime shifts. Yet an outstanding question is whether regime changes in marine ecosystems are irreversible. Here we first review the evidence for regime shifts in the North Sea ecosystem, one of the heaviest impacted and best studied marine ecosystems in the world. We then used catastrophe theory to show that fishing and warming have caused a previously undetected and potentially irreversible regime shift. Our study emphasizes the combined effects of local and global human impacts in driving significant ecosystem shifts and suggests that adaptation is likely the central avenue forward for maintaining services in the face of global climate change.
Influence of the phytoplankton community composition on the in situ fluorescence signal: Implication for an improved estimation of the chlorophyll-a concentration from BioGeoChemical-Argo profiling floats
Authors: Petit Flavien , Uitz Julia , Schmechtig Catherine , Dimier Céline , Ras Joséphine , Poteau Antoine , Golbol Melek , Vellucci Vincenzo , Claustre Hervé
Published: September 2022

In-situ fluorescence is a widely used method to estimate the chlorophyll-a (Chla) concentration, a proxy of the phytoplankton biomass. With the emergence of autonomous platforms such as BioGeoChemical-Argo (BGC-Argo) profiling floats, its use has expanded to global scale observations. However, the relationship between in-situ fluorescence and Chla may vary significantly, leading to major discrepancies between oceanic regions. This study aims to investigate the main sources of the natural variability in the in-situ fluorescence signal in the global open ocean, specifically the influence of the phytoplankton community composition. In this view, we analyzed a combination of three datasets comprising concomitant measurements of in-situ fluorescence, pigment concentrations and phytoplankton absorption spectra. Two datasets cover several contrasted bioregions of the global ocean whereas the third one consists of a regional time series in the northwestern Mediterranean Sea, which allows to examine the effect of phytoplankton community composition on the fluorescence signal on the global, seasonal and vertical scales. We studied the variability of the two major drivers of the natural variability of the fluorescence process, i.e. the light absorption and the fluorescence quantum yield of phytoplankton, in regards of the variability of the pigment composition of the communities. The community composition correlates substantially with the Chla-to-fluorescence ratio, with high fluorescence values associated with phytoplankton communities dominated by large cells. This trend may be explained by the combined effects of the community composition on the phytoplankton absorption coefficient and the fluorescence quantum yield, and is consistently observed globally, seasonally and vertically. Non-photosynthetic pigments also appear to play a critical role in oligotrophic surface waters, leading to a reduction of the quantum yield of fluorescence. The results indicate that the phytoplankton community composition plays a key role in the relationship between the in-situ fluorescence signal and Chla concentration. Therefore, we suggest that taking into account the composition of phytoplankton communities in the retrieval of the Chla concentration from current in-situ fluorometers, those mounted on BGC-Argo floats in particular, would lead to a better estimation of the phytoplankton biomass on a wide range of spatial and temporal scales.
Benthic community zonation from mesophotic to deep sea: Description of first deep-water kelp forest and coral gardens in the Madeira archipelago (central NE Atlantic)
Authors: Braga-Henriques Andreia , Buhl-Mortensen Pål , Tokat Erdal , Martins Ana , Silva Teresa , Jakobsen Joachim , Canning-Clode João , Jakobsen Kirsten , Delgado João , Voirand Thibaut , Biscoito Manuel
Published: September 2022

The Madeira archipelago has a unique underwater landscape that is characterised by narrow shelves, steep slopes and a large submarine tributary system that boosts primary productivity in oligotrophic waters and thus offers a potential for hotspots of biodiversity. Despite this, there have been limited deep-water exploration activities with less than five expeditions since the 1960s. Here, we investigated the seabed on the southern side of the Madeira-Desertas Ridge using a manned submersible along a 3.8 km long transect starting at 366 m depth up the ridge shelf until its top at 73 m. Benthic habitats and community composition were documented with video along a depth gradient from mesophotic to deep sea. Six distinct biotopes were recognised (three deeper, and three shallower than 115 m depth). Our results showed a rich biodiversity with deep biotopes characterised by sponges and non-reef-building corals (e.g., Pachastrella monilifera, Viminella flagellum, Eunicella verrucosa) and shallow biotopes comprising macroalgae and the gorgonian Paramuricea cf. grayi. The pronounced benthic zonation reflects the steep environmental gradient that includes high topographic variation, heterogeneous substrates, and bidirectional regular wave-motion at the shallow mesophotic part. Together with biotic factors, such as low density of sea urchins and presence of predatory fish, this environment with unusual deep light penetration, a mesoscale cyclonic eddy, and deep wave-motion, has allowed the establishment of a mature deep-water kelp population of Laminaria ochroleuca in the plateau (max. >100 individuals p/100 m2). At the same time, a conspicuous coral fauna was observed on a wide range of soft to hard bottoms with several species taking advantage of the favourable hydrodynamic regime and seawater properties together with substratum availability to create coral gardens. These habitats were previously not known from Madeira, and their newfound discovery in the archipelago merit further investigation and protection.