bluuebunny/crossref_metadata_2025 huggingface dataset:
Taxonomic revision of Sobralia section Racemosae Brieger (Sobralieae, Orchidaceae)
Authors: Baranow Przemyslaw , Szlachetko Dariusz , Kindlmann Pavel
Published: January 2023

Sobralia Ruiz & Pav. is a large and morphologically diverse neotropical orchid genus. It can be divided into four sections and some informal groups of species based mainly on the inflorescence architecture. While most of the species have strongly abbreviated, compact raceme, the section Racemosae is characterized by an elongated inflorescence with distinct internodes between flowers. Although the group is well-defined and easily distinguishable in terms of morphology, its species are often similar to each other and may be easily misidentified. Identification is especially difficult when considering herbarium specimens. Here, a taxonomic revision of Sobralia section Racemosae is presented. Apart from particular species’ morphological characteristics, keys for identification, ecological data, and distribution maps are presented. Sobralia gambitana is described as a species new to science. A neotype for S. hoppii Schltr. is proposed.
Male’s influence on the primary sex ratio bias in Ryukyu drywood termite
Authors: Agarie Ayaka , Miyaguni Yasushi , Sugio Koji , Tsuji Kazuki , Kobayashi Kazuya
Published: January 2023

Selfish genetic elements (SGEs) increase their transmission efficiency relative to the rest of the individual genome, which is often deleterious to individual fitness. Theoretical studies have suggested that intragenomic conflict over the sex ratio distortion between SGEs and the rest of the genome should lead to the evolution of sex-determining systems. However, in insects, there are relatively few studies other than those on Dipterans, which makes it difficult to understand the role of SGEs in the evolution of insect sex determination. This is partially due to the difficulties in observing SGEs under field conditions. The effect of SGEs is often masked by the counter-evolution of the resistance genes. Interpopulation cross-breeding experiments are effective to detect the SGEs and their resistance genes. If these populations have different SGEs and resistance genes, cross-breeding experiments reveal their existence by collapsing the evolutionary antagonistic state. The Ryukyu drywood termites Neotermes sugioi, distributed in the Ryukyu Islands, show male-biased sex ratios in pseudergates, nymphs, alates and soldiers both in Okinawa and Ishigaki Islands, but different degrees of bias have been reported between the islands. Male-specific microsatellite alleles have been reported in this species, which allowed us to identify the sex of the eggs and young larvae. In this study, we used the microsatellite locus with male-specific alleles to investigate the primary sex ratio of field colonies on Okinawa and Ishigaki islands and the sex ratio of offspring obtained through cross-breeding experiments between the islands. The primary sex ratios of field colonies were male-biased in Okinawa but not in Ishigaki. Cross-breeding experiments showed that Okinawa males tend to have a male-biased sex ratio in their offspring, but Ishigaki males do not. This result is consistent with the hypothesis that the male bias in this species is caused by SGEs, even though termites are phylogenetically distant from Diptera. Accumulation of knowledge on genetic conflicts in a wide range of taxa might be an important step toward elucidating the mechanisms of diversification of sex determination systems in insects.
Transcriptomic analysis of the upper lip and primary palate development in mice
Authors: Cai Sini , Si Nuo , Wang Yanyang , Yin Ningbei
Published: January 2023

Background: Normal fusion of the upper lip and primary palate is a complex process involving a series of characteristic and orderly regulated cellular events. Cleft lip with or without palate (CL/P), one of the most common congenital malformations, may be induced by abnormalities in any of these events. However, less is known about the precise regulatory process in the fusion of the upper lip and primary palate.

Methods: Lambdoidal junction tissues of mice from embryonic days 10.5, 11.5, and 12.5— three key fusion stages—were acquired for RNA sequencing.

Results: Gene expression profiles in distinct fusion stages of mice were identified. Some of the differentially expressed genes (DEGs) have been reported to affect upper lip and primary palate development. However, other DEGs, such as Krt5, Pax1, Ambn, Hey2, and Tnmd, have not previously been investigated. Gene set enrichment analysis (GSEA) of these DEGs revealed the sequential intensification of Wnt, PI3K-Akt, MAPK, Hippo, and TGF-beta signaling pathways and identified relatively highly expressed genes including Tnn, Wnt3a, and Wnt16. We also observed substantial alternative splicing events during the fusion of the upper lip and primary palate and identified potentially important genes including Gtpbp8, Armcx1, Tle3, and Numa1. Protein-protein interaction (PPI) network analysis identified a series of hub genes, including Col1a2, Fos, Bmp2, Shh, Col1a1, Wnt3a, Anxa1, Gem, etc.

Conclusion: Overall, the results of this study provided a comprehensive analysis of the development of the upper lip and primary palate. Our work provides insight into future studies of normal upper lip and primary palate development and the etiology of CL/P.
Fc gamma receptor IIb in tumor-associated macrophages and dendritic cells drives poor prognosis of recurrent glioblastoma through immune-associated signaling pathways
Authors: Jin Xiong , Kang Jianlei , Lu Qing , Guo Shuang-Lei , Liu Meichen , Zhang Yue , Cui Can , Liu Hong-Lin , Xu Xin , Yin Jinlong
Published: January 2023

Background: Among central nervous system tumors, glioblastoma (GBM) is considered to be the most destructive malignancy. Recurrence is one of the most fatal aspects of GBM. However, the driver molecules that trigger GBM recurrence are currently unclear.

Methods: The mRNA expression data and clinical information of GBM and normal tissues were collected from the Chinese Glioma Genome Atlas The Cancer Genome Atlas (TCGA), and REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) cohorts. The DESeq2 R package was used to identify the differentially expressed genes between primary and recurrent GBM. ClueGO, Kyoto Encyclopedia of Genes and Genomes (KEGG), Biological Process in Gene ontology (GO-BP), and the Protein ANalysis THrough Evolutionary Relationships (PANTHER) pathway analyses were performed to explore the enriched signaling pathways in upregulated DEGs in recurrent GBM. A gene list that contained potential oncogenes that showed a significant negative correlation with patient survival from The Cancer Genome Atlas was used to further screen driver candidates for recurrent GBM. Univariate Cox proportional hazards regression analyses were used to investigate the risk score for the mRNA expression of the candidates. Single-cell RNA sequencing (scRNA-Seq) analyses were used to determine the cell type-specific distribution of Fc gamma receptor II b (FcγRIIb) in GBM. Immunohistochemistry (IHC) was used to confirm the FcγRIIb-positive cell populations in primary and paired recurrent GBM.

Results: Through DEG analysis and overlap analysis, a total of 10 genes that are upregulated in recurrent GBM were screened. Using validation databases, FcγRIIb was identified from the 10 candidates that may serve as a driver for recurrent GBM. FCGR2B expression, not mutation, further showed a highly negative correlation with the poor prognosis of patients with recurrent GBM. Furthermore, scRNA-Seq analyses revealed that tumor-associated macrophage- and dendritic cell-specific FCGR2B was expressed. Moreover, FcγRIIb also showed a strong positive correlation coefficient with major immune-associated signaling pathways. In clinical specimens, FcγRIIb-positive cell populations were higher in recurrent GBM than in primary GBM.

Conclusion: This study provides novel insights into the role of FcγRIIb in recurrent GBM and a promising strategy for treatment as an immune therapeutic target.
Exploration of comorbidity mechanisms and potential therapeutic targets of rheumatoid arthritis and pigmented villonodular synovitis using machine learning and bioinformatics analysis
Authors: Heng Hongquan , Li Dazhuang , Su Wenxing , Liu Xinyue , Yu Daojiang , Bian Zhengjun , Li Jian
Published: January 2023

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disease. Pigmented villonodular synovitis (PVNS) is a tenosynovial giant cell tumor that can involve joints. The mechanisms of co-morbidity between the two diseases have not been thoroughly explored. Therefore, this study focused on investigating the functions, immunological differences, and potential therapeutic targets of common genes between RA and PVNS.

Methods: Through the dataset GSE3698 obtained from the Gene Expression Omnibus (GEO) database, the differentially expressed genes (DEGs) were screened by R software, and weighted gene coexpression network analysis (WGCNA) was performed to discover the modules most relevant to the clinical features. The common genes between the two diseases were identified. The molecular functions and biological processes of the common genes were analyzed. The protein-protein interaction (PPI) network was constructed using the STRING database, and the results were visualized in Cytoscape software. Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) logistic regression and random forest (RF) were utilized to identify hub genes and predict the diagnostic efficiency of hub genes as well as the correlation between immune infiltrating cells.

Results: We obtained a total of 107 DEGs, a module (containing 250 genes) with the highest correlation with clinical characteristics, and 36 common genes after taking the intersection. Moreover, using two machine learning algorithms, we identified three hub genes (PLIN, PPAP2A, and TYROBP) between RA and PVNS and demonstrated good diagnostic performance using ROC curve and nomogram plots. Single sample Gene Set Enrichment Analysis (ssGSEA) was used to analyze the biological functions in which three genes were mostly engaged. Finally, three hub genes showed a substantial association with 28 immune infiltrating cells.

Conclusion: PLIN, PPAP2A, and TYROBP may influence RA and PVNS by modulating immunity and contribute to the diagnosis and therapy of the two diseases.
Is an SV caller compatible with sequencing data? An online recommendation tool to automatically recommend the optimal caller based on data features
Authors: Wang Shenjie , Liu Yuqian , Wang Juan , Zhu Xiaoyan , Shi Yuzhi , Wang Xuwen , Liu Tao , Xiao Xiao , Wang Jiayin
Published: January 2023

A lot of bioinformatics tools were released to detect structural variants from the sequencing data during the past decade. For a data analyst, a natural question is about the selection of a tool fits for the data. Thus, this study presents an automatic tool recommendation method to facilitate data analysis. The optimal variant calling tool was recommended from a set of state-of-the-art bioinformatics tools by given a sequencing data. This recommendation method was implemented under a meta-learning framework, identifying the relationships between data features and the performance of tools. First, the meta-features were extracted to characterize the sequencing data and meta-targets were identified to pinpoint the optimal caller for the sequencing data. Second, a meta-model was constructed to bridge the meta-features and meta-targets. Finally, the recommendation was made according to the evaluation from the meta-model. A series of experiments were conducted to validate this recommendation method on both the simulated and real sequencing data. The results revealed that different SV callers often fit different sequencing data. The recommendation accuracy averaged more than 80% across all experimental configurations, outperforming the random- and fixed-pick strategy. To further facilitate the research community, we incorporated the recommendation method into an online cloud services for genomic data analysis, which is available at https://c.solargenomics.com/via a simple registration. In addition, the source code and a pre-trained model is available at https://github.com/hello-json/CallerRecommendation for academic usages only.
Coding roles of long non-coding RNAs in breast cancer: Emerging molecular diagnostic biomarkers and potential therapeutic targets with special reference to chemotherapy resistance
Authors: Kashyap Dharambir , Sharma Riya , Goel Neelam , Buttar Harpal S. , Garg Vivek Kumar , Pal Deeksha , Rajab Khairan , Shaikh Asadullah
Published: January 2023

Dysregulation of epigenetic mechanisms have been depicted in several pathological consequence such as cancer. Different modes of epigenetic regulation (DNA methylation (hypomethylation or hypermethylation of promotor), histone modifications, abnormal expression of microRNAs (miRNAs), long non-coding RNAs, and small nucleolar RNAs), are discovered. Particularly, lncRNAs are known to exert pivot roles in different types of cancer including breast cancer. LncRNAs with oncogenic and tumour suppressive potential are reported. Differentially expressed lncRNAs contribute a remarkable role in the development of primary and acquired resistance for radiotherapy, endocrine therapy, immunotherapy, and targeted therapy. A wide range of molecular subtype specific lncRNAs have been assessed in breast cancer research. A number of studies have also shown that lncRNAs may be clinically used as non-invasive diagnostic biomarkers for early detection of breast cancer. Such molecular biomarkers have also been found in cancer stem cells of breast tumours. The objectives of the present review are to summarize the important roles of oncogenic and tumour suppressive lncRNAs for the early diagnosis of breast cancer, metastatic potential, and chemotherapy resistance across the molecular subtypes.
Explaining recently arrived refugees' labor market participation: The role of policy characteristics among Syrians in the Netherlands
Authors: Damen Roxy Elisabeth Christina , Huijnk Willem , Dagevos Jaco
Published: January 2023

Various studies have indicated the disadvantaged positions of refugees on the labor market and studied various characteristics explaining this. Yet, little is known about the impact of settlement policy characteristics on recent arrivals' labor market participation, despite them being heavily subject to such policies. We argue such policies, next to individual characteristics, can serve as a means to gather resources relevant to the host country and consequently labor market positions, but can also serve as a post-migration stressor obstructing this. Using the Netherlands as an example, we contribute to studies on the refugee gap and provide insight into key policy characteristics explaining recently arrived refugees' (finding) employment. We use two-wave panel data of 2,379 recently arrived Syrian refugees in the Netherlands, including data on key policy and individual characteristics combined with administrative data. Employing a hybrid model, we show both within- and between-person variation. Results indicate policy matters: short and active stays in reception, complying with the civic integration obligation and a lower unemployment rate in the region refugees are randomly assigned to are beneficial for Syrians' (finding) employment. Like for other migrants, various forms of individual human capital also play a role.
Heterogeneity in making: Findings, approaches, and reflections on inclusivity in making and makerspaces
Authors: Fuchsberger Verena , Smit Dorothé , Campreguer França Nathalia , Gerdenitsch Cornelia , Jaques Olivia , Kowolik Joanna , Regal Georg , Roodbergen Emma
Published: January 2023

Making, that is, the hobbyist and technologically based creation of things, has been associated with many benefits. It is considered to contribute to the development of skills and to enable participation in innovation, and even democracy. At the same time, institutionalized making (in makerspaces, FabLabs) is known to be exclusive as members of such spaces are very often young well-educated white men. This is in contradiction to the promise and self-understanding of the maker culture, which aims to be open and inclusive. In the past 3 years, we, a group of researchers, makers, fablab employees, hackerspace operators, and artists, have engaged with such disparities in a collaborative research project. We inquired into barriers that women*and other underrepresented groups experience, created visions to change the status quo, and implemented smaller and bigger interventions in different spaces (fablab, hackerspace, and makers' homes) to explore their impacts. This article discusses findings, approaches, and foremost, reflections and experiences. In addition to presenting selected insights from our explorations, we pay particular attention to the tensions and challenges that we encountered during our research endeavors. Many of those are rooted in our own roles, perspectives, and backgrounds, which are multiple, sometimes conflicting, troubling, frustrating, yet enriching, and rewarding. In the form of a written conversation among project members, we present those different viewpoints, connect them where possible, and oppose them where needed. We conclude by articulating tensions that we see as characteristic regarding making and the research around it.
A new natural killer cell-specific gene signature predicting recurrence in colorectal cancer patients
Authors: Shembrey Carolyn , Foroutan Momeneh , Hollande Frédéric
Published: January 2023

The protective role of Natural Killer (NK) cell tumour immunosurveillance has long been recognised in colorectal cancer (CRC). However, as most patients show limited intra-tumoral NK cell infiltration, improving our ability to identify those with high NK cell activity might aid in dissecting the molecular features which underlie NK cell sensitivity. Here, a novel CRC-specific NK cell gene signature that infers NK cell load in primary tissue samples was derived and validated in multiple patient CRC cohorts. In contrast with other NK cell gene signatures that have several overlapping genes across different immune cell types, our NK cell signature has been extensively refined to be specific for CRC-infiltrating NK cells. The specificity of the signature is substantiated in tumour-infiltrating NK cells from primary CRC tumours at the single cell level, and the signature includes genes representative of NK cells of different maturation states, activation status and anatomical origin. Our signature also accurately discriminates murine NK cells, demonstrating the applicability of this geneset when mining datasets generated from preclinical studies. Differential gene expression analysis revealed tumour-intrinsic features associated with NK cell inclusion versus exclusion in CRC patients, with those tumours with predicted high NK activity showing strong evidence of enhanced chemotactic and cytotoxic transcriptional programs. Furthermore, survival modelling indicated that NK signature expression is associated with improved survival outcomes in CRC patients. Thus, scoring CRC samples with this refined NK cell signature might aid in identifying patients with high NK cell activity who could be prime candidates for NK cell directed immunotherapies.
Comparing the pertussis antibody levels of healthy children immunized with four doses of DTap-IPV/Hib (Pentaxim) combination vaccine and DTaP vaccine in Quzhou, China
Authors: Yin Zhiying , Zheng Canjie , Fang Quanjun , Wen Tingcui , Wang Shuangqing , Li Junji , Gong Xiaoying , Xiang Ziling
Published: January 2023

Despite the high coverage of pertussis vaccines in high-income countries, pertussis resurgence has been reported in recent years, and has stimulated interest in the effects of vaccines and vaccination strategies. Immunoglobulin G (IgG) antibodies against pertussis toxoid (PT), filamentous hemagglutinin (FHA), and pertactin (PRN) after immunization with four doses of co-purified or component vaccines were determined by enzyme-linked immunosorbent assay (ELISA). Serological data of PT-IgG geometric mean concentrations (GMCs) over time since vaccination were used to fit the mathematical models. A total of 953 children were included in this study; 590 participants received four doses of the component acellular vaccine and 363 participants received four doses of the co-purified acellular vaccine. The GMCs and the seropositivity rate of pertussis IgG were significantly influenced by the production methods, and the immunogenicity of the component acellular vaccine was superior to that of the co-purified acellular vaccine. The fitted mathematical models for the component acellular vaccine and the co-purified acellular vaccine were Y=91.20e-0.039x and Y=37.71x-0.493, respectively. The initial GMCs of the component acellular vaccine was higher than that of the co-purified acellular vaccine, but both were similar at 72 months after immunization. Pertussis IgG levels waned over time after four doses of acellular pertussis vaccine, regardless of whether component or co-purified vaccine was used. The development and promotion of component acellular pertussis vaccines should be accelerated in China, and booster doses of pertussis vaccine in adolescents, adults, and pregnant women should be employed.
Inflammatory markers and pulmonary function in adolescents and young adults 6 months after mild COVID-19
Authors: Sommen Silke Lauren , Havdal Lise Beier , Selvakumar Joel , Einvik Gunnar , Leegaard Truls Michael , Lund-Johansen Fridtjof , Michelsen Annika E. , Mollnes Tom E. , Stiansen-Sonerud Tonje , Tjade Trygve , Wyller Vegard Bruun Bratholm , Berven Lise Lund
Published: January 2023

Introduction

Both public and scientific attention have shifted from the acute COVID-19 illness to the chronic disability experienced by a proportion of COVID-19 convalescents. Post COVID-19 condition, a term used for long-lasting symptoms after COVID-19, can affect individuals across all disease severity and age groups. Data on post-COVID-19 symptomatology, epidemiology and pathophysiology in adolescents and young adults are scarce. To date, little is known on the immunological and pulmonary trends in these patients after COVID-19. This study investigated immunological markers and pulmonary function in non-hospitalized patients in this group at 6 months after initial mild COVID-19 infection.

Methods

Non-hospitalized SARS-CoV-2 positive (n = 405) and SARS-CoV-2 negative (n = 111) adolescents and young adults (aged 12-25 years) were followed prospectively for six months after SARS-CoV-2 PCR testing. At baseline and at six months follow-up, all participants underwent an assessment including clinical examination, questionnaires, spirometry, and blood sampling. Cross-sectional comparisons of blood biomarkers; including white blood cell counts, CRP, GDF-15, a 27-multiplex cytokine assay, complement activation products and SARS-CoV-2 antibodies; and spirometry measures were performed after classification of all participants according to their COVID-19 status and adherence to post-COVID-19 case criteria. Associations between biomarkers and COVID-19 symptoms were explored.

Results

No difference in pulmonary function was detected between the groups. COVID-19 convalescents had higher levels of chemokines eotaxin, MCP-1 and IP-10 than non-infected controls. The increase was modest and not associated with long-lasting COVID-19 symptoms.

Discussion

Elevated inflammatory mediators were found in adolescents and young adults six months after mild COVID-19, but there was no association with post-COVID-19 condition.
The role of Akkermansia muciniphila in inflammatory bowel disease: Current knowledge and perspectives
Authors: Zheng Mengyu , Han Ran , Yuan Yali , Xing Yunqi , Zhang Wenji , Sun Zhongmei , Liu Yuyue , Li Junxiang , Mao Tangyou
Published: January 2023

Inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis, is a chronic relapsing gastrointestinal inflammatory disease mediated by dysregulated immune responses to resident intestinal microbiota. Current conventional approaches including aminosalicylates, corticosteroids, immunosuppressive agents, and biological therapies are focused on reducing intestinal inflammation besides inducing and maintaining disease remission, and managing complications. However, these therapies are not curative and are associated with various limitations, such as drug resistance, low responsiveness and adverse events. Recent accumulated evidence has revealed the involvement of mucin-degrading bacterium Akkermansia muciniphila (A. muciniphila) in the regulation of host barrier function and immune response, and how reduced intestinal colonisation of probiotic A. muciniphila can contribute to the process and development of inflammatory bowel diseases, suggesting that it may be a potential target and promising strategy for the therapy of inflammatory bowel disease. In this review, we summarise the current knowledge of the role of A. muciniphila in IBD, especially focusing on the related mechanisms, as well as the strategies based on supplementation with A. muciniphila, probiotics and prebiotics, natural diets, drugs, and herbs to promote its colonisation in the gut, and holds promise for A. muciniphila-targeted and -based therapies in the treatment of inflammatory bowel disease.
High-resolution wave data for improving marine habitat suitability models
Authors: Bertelli Chiara M. , Bennett William G. , Karunarathna Harshinie , Reeve Dominic E. , Unsworth Richard K. F. , Bull James C.
Published: January 2023

Habitat suitability modelling (HSM) is a tool that is increasingly being used to help guide decision making for conservation management. It can also be used to focus efforts of restoration in our oceans. To improve on model performance, the best available environmental data along with species distribution data are needed. Marine habitats tend to have ecological niches defined by physical environmental conditions and of particular importance for shallow water species is wave energy. In this study we examined the relative improvements to HSM outputs that could be achieved by producing high-resolution Delft-3D modelled wave height data to see if model predictions at a fine-scale can be improved. Seagrasses were used as an exemplar and comparisons at fine-scale showed considerable differences in the area predicted suitable for seagrass growth and greatly increased the importance of waves as a predictor variable when compared with open-source low resolution wave energy data.
Geochemical-mineralogical analysis of ferromanganese oxide precipitated on porifera in the Magellan seamount, western Pacific
Authors: Park Kyuyoung , Jung Jaewoo , Park Jinsub , Ko Youngtak , Lee Yongmoon , Yang Kiho
Published: January 2023

This study investigated ferromanganese oxide (Fe-Mn oxide) precipitated on porifera located on the tabletop of the Magellan seamount (OSM17, 1571 m depth) in the western Pacific. As the growth rate of Fe-Mn oxide is several mm/Myr and porifera skeletons are difficult to preserve posthumously, geochemical and mineralogical studies have not yet been conducted on this topic. Fe-Mn oxides from porifera have a morphological differentiation from general ferromanganese deposits because porifera act as substrates for the Fe-Mn oxide. The thickness of Fe-Mn oxide cannot be visually confirmed because it thinly precipitates on the skeletons of porifera. Therefore, high-resolution fluctuations are reflected in marine environmental factors, such as redox conditions and surface productivity over tens of thousands of years, compared to ferromanganese deposits representing tens of millions of years. Hence, the geochemical and mineralogical characteristics were investigated. Porifera skeletons were confirmed, displaying a stratified lattice-like structure, thickness of Fe-Mn oxide of up to 110 μm, and age of approximately 55,000 years. Irregular distribution of major elements of Fe-Mn oxide, Mn, Fe, Ni, and Co was due to the characteristics of the structures. The presence of Fe-vernadite, identified by quantitative and mineralogical analysis, indicates oxidative environmental conditions at the tabletop of OSM17. Biomineralization was identified by confirming the presence of Fe-Mn oxides with a globular, sheath-like structure. Because of its conservation state, species identification of porifera was not based on the shape of the spicule, but was confirmed to beFarrea occa. This study verified that the tabletop of OSM17 has been in an oxidative environment for approximately 55,000 years, and through species identification, high dissolved silica (DSi) concentrations provide appropriate conditions forFarrea occato survive. The sample in this study can be used as a new indicator in paleo-environment research.
Aggregation process of two disaster-causing jellyfish species, Nemopilema nomurai and Aurelia coerulea, at the intake area of a nuclear power cooling-water system in Eastern Liaodong Bay, China
Authors: Wang Xiaocheng , Jin Qingqing , Yang Lu , Jia Chuan , Guan Chunjiang , Wang Haining , Guo Hao
Published: January 2023

The intake safety of nuclear power cooling-water systems (NPCSs) is an important aspect of operational safety of nuclear power plants (NPPs). The blockages caused by aberrant outbreaks of various aquatic organisms have seriously affected operational safety. Large jellyfish constitute the main groups of marine organisms responsible for these blockages. The processes of aggregation and the relationships of two major disaster-causing scyphozoan jellyfish species, Nemopilema nomurai and Aurelia coerulea, with four environmental factors at the intake area of an NPCS in Eastern Liaodong Bay, China, were investigated in 2019 and 2020. The findings revealed that A. coerulea ephyrae were present in the surrounding ports in mid-May; however, N. nomurai ephyrae were absent during the survey period in this study, and the medusae of N. nomurai started appearing from late May. The individual growth and relative biomass (RB) of the jellyfish increased rapidly from late June to July and decreased rapidly thereafter, in September. The RB of N. nomurai was highly correlated to the sea surface temperature (SST) and levels of dissolved oxygen (DO) in the region. The RB increased with increasing SST and decreased at increasing DO levels. The RB of A. coerulea was significantly negatively correlated with that of N. nomurai, and the peak biomass of the two species alternated over time, which could be attributed to the fact that the jellyfish species share similar ecological niches. The bell diameters were significantly positively correlated with the individual wet weights, and the value of one could be inferred from the value of the other. Although the processes of jellyfish aggregation are attributed to several factors, including interactions with environmental factors and human activities, such as fishing, the results obtained in this study would serve as an important reference and provide a basis for the prevention of jellyfish blooms in waters adjacent to NPPs. The prevention and control of jellyfish disasters at the intake area of NPCSs are not only local concerns. Therefore, remediation from the source combined with the maximum utilization of social resources for monitoring and early warning would immensely improve the efficacy of such preventive strategies.
Beluga whale (Delphinapterus leucas) behaviour in the presence of whale-watching vessels
Authors: Westdal Kristin H. , Richard Pierre R. , Sportelli Jessica , Gillis Erica , Ferguson Steve H.
Published: January 2023

Beluga whales (Delphinapterus leucas) are social animals that return to the same estuaries each summer season. The Western Hudson Bay belugas in the Churchill River estuary appear to be attracted to boats, resulting in whale-watching being a popular tourism activity for the area. However, regulators have raised concerns about whether this activity has negative consequences on the beluga population. We hypothesized that more vulnerable groups, such as groups containing calves, would avoid whale-watching vessels, while juvenile groups, who appear to have a more developed curiosity, would be more likely to interact with vessels. To test these hypotheses, behavioural observations were conducted in 2019, 2020, and 2021, in the estuary using a similar methodology to a study conducted in 2005 and 2006. An increase in tourism since that initial study offered a unique opportunity to compare potential change over time. In this study, a group of whales was randomly selected; the group type, initial behaviour type, distance to vessel, and observed behaviour with distance to vessel during three-minute focal follows were recorded. The same method was also applied from shore and we compared frequencies of whale behaviour during experimental (vessels present) and control (vessels greater than 300m away) periods. Results showed that there was a significant difference in the mean group size of belugas in the presence of vessels compared to those observed in the absence of vessels. There was also a significant difference in beluga behaviour as well as a significant behavioural difference between age class of belugas in the presence of vessels, compared to their behaviour in absence of vessels. During focal follows from vessels, belugas spent 63% of their time interacting with vessels, when within 25 m of a vessel, an increase from the 48% observed from the previous study conducted 15 years previous. Our results overall showed beluga behaviour differed in the experimental compared to control settings but suggest that those belugas’ reactions to vessels are not necessarily deleterious to them, in that direct interactions with wildlife are low and unlikely to carry risk, and that they may have habituated to whale-watching vessels over the last two decades.
Identifying trade-offs and reference points in support of ecosystem approaches to managing Gulf of Mexico menhaden
Authors: Berenshtein Igal , Sagarese Skyler R. , Lauretta Matthew V. , Schueller Amy M. , Chagaris David D.
Published: January 2023

Gulf menhaden (Brevoortia patronus) support the largest fishery by yield in the Gulf of Mexico (GoM) and are a key forage species for many marine predators. While menhaden stock assessments indicated that overfishing was not likely to have occurred in the past, concerns have been raised regarding the possible effects of menhaden fishing on their predators. In this study, we used a US Gulfwide Ecopath with Ecosim (EwE) model to explore the predicted effects of increased menhaden harvest on the GoM ecosystem and focused our analyses on Gulf menhaden predators. Key menhaden predators identified included king mackerel (Scomberomorus cavalla), Spanish mackerel (Scomberomorus maculatus), sea trout (Cynoscion spp.), red drum (Sciaenops ocellatus), and pelagic coastal piscivores [e.g., bluefish (Pomatomus saltatrix)]. As expected, these predators exhibited reduced biomass in response to increased Gulf menhaden harvest, with a predicted 11% decrease in predator biomass at simulated fishing levels near historical highs. Our results indicate strong relationships between the effects of menhaden fishing and the predator fishing mortality for king mackerel and intermediate relationships for Spanish mackerel, blacktip shark (Carcharhinus limbatus), red drum, large coastal sharks, and pelagic coastal piscivores. Biomass of predator groups such as demersal coastal invertebrate feeders [e.g., drums and croakers (Sciaenidae)] are more affected by menhaden harvest (through trophodynamics interactions and bycatch removal) compared to the isolated effect of their fishing mortality. For almost all the groups examined in the trade-off analysis, with the exception of sea trout, current biomass (2016) was higher than their target biomass representing 75% of their biomass at maximum sustainable yield. In comparison to the time series of fishing mortality rates estimated by the most recent Gulf menhaden stock assessment, the mean ecological reference point (ERP) of 0.862 was exceeded in all but 1 year from 1977 to 2007; however, neither the target nor threshold upper ERP value has been exceeded since 2008. The observed Gulf menhaden landings from 2003 to the present were generally within the range of the projected equilibrium landings (i.e., within confidence intervals) at both the ERP target and threshold values except for three recent years.
On the effect of water content on fatigue mechanical behaviors of mud-shale under stress disturbance conditions
Authors: Li Xuguang , Wu Jihuan , Yang Haonan , Wang Yu
Published: January 2023

This paper aims to reveal the fatigue damage and instability behaviors of mud-shale under multistage increasing-amplitude fatigue loading. The fatigue loading tests combined with real-time acoustic emission (AE) monitoring technique were employed to investigate the influence of water content on the deformation, damage, and fracture characteristics. Testing results show that rock fatigue life decreases with the increase of water content, and the hysteresis curve changes regularly with time. The failure process can be divided into three stages: initial stage, stable development stage and acceleration stage. The acoustic emission output activities were also influenced by the water content. The acoustic emission ring count and acoustic emission energy both decrease with increasing water ratio and the accumulative count and energy are the least for a sample having high water ratio. The acoustic emission activity shows a sudden increase trend at the amplitude-increasing moment, indicating the occurrence of strong damage within rock sample. The damage propagation within a cyclic loading stage is relatively small compared to the stress-increasing moment. The results are helpful to understand the fatigue mechanical responses of water-sensitive soft rock, as well as the slope stability of the open-pit mine. The research results have important theoretical and practical significance for promoting slope treatment and disaster prevention.
Application of machine learning algorithms to evaluate the influence of various parameters on the flexural strength of ultra-high-performance concrete
Authors: Qian Yunfeng , Sufian Muhammad , Hakamy Ahmad , Farouk Deifalla Ahmed , El-said Amr
Published: January 2023

The effect of various parameters on the flexural strength (FS) of ultra-high-performance concrete (UHPC) is an intricate mechanism due to the involvement of several inter-dependent raw ingredients. In this digital era, novel artificial intelligence (AI) approaches, especially machine learning (ML) techniques, are gaining popularity for predicting the properties of concrete composites due to their better precision than typical regression models. In addition, the developed ML models in the literature for FS of UHPC are minimal, with limited input parameters. Hence, this research aims to predict the FS of UHPC considering extensive input parameters (21) and evaluate each their effect on its strength by applying advanced ML approaches. Consequently, this paper involves the application of ML approaches, i.e., Support Vector Machine (SVM), Multi-Layer Perceptron (MLP), and Gradient Boosting (GB), to predict the FS of UHPC. The GB approach is more effective in predicting the FS of UHPC precisely than the SVM and MLP algorithms, as evident from the outcomes of the current study. The ensembled GB model determination coefficient (R2) is 0.91, higher than individual SVM with 0.75 and individual MLP with 0.71. Moreover, the precision of applied models is validated by employing the k-fold cross-validation technique. The validity of algorithms is ensured by statistical means, i.e., mean absolute error and root mean square errors. The exploration of input parameters (raw materials) impact on FS of UHPC is also made with the help of SHAP analysis. It is revealed from the SHAP analysis that the steel fiber content feature has the highest influence on the FS of UHPC.
TRACK-CF prospective cohort study: Understanding early cystic fibrosis lung disease
Authors: Steinke Eva , Sommerburg Olaf , Graeber Simon Y. , Joachim Cornelia , Labitzke Christiane , Nissen Gyde , Ricklefs Isabell , Rudolf Isa , Kopp Matthias V. , Dittrich Anna-Maria , Mall Marcus A. , Stahl Mirjam
Published: January 2023

Background

Lung disease as major cause for morbidity in patients with cystic fibrosis (CF) starts early in life. Its large phenotypic heterogeneity is partially explained by the genotype but other contributing factors are not well delineated. The close relationship between mucus, inflammation and infection, drives morpho-functional alterations already early in pediatric CF disease, The TRACK-CF cohort has been established to gain insight to disease onset and progression, assessed by lung function testing and imaging to capture morpho-functional changes and to associate these with risk and protective factors, which contribute to the variation of the CF lung disease progression.

Methods and design

TRACK-CF is a prospective, longitudinal, observational cohort study following patients with CF from newborn screening or clinical diagnosis throughout childhood. The study protocol includes monthly telephone interviews, quarterly visits with microbiological sampling and multiple-breath washout and as well as a yearly chest magnetic resonance imaging. A parallel biobank has been set up to enable the translation from the deeply phenotyped cohort to the validation of relevant biomarkers. The main goal is to determine influencing factors by the combined analysis of clinical information and biomaterials. Primary endpoints are the lung clearance index by multiple breath washout and semi-quantitative magnetic resonance imaging scores. The frequency of pulmonary exacerbations, infection with pro-inflammatory pathogens and anthropometric data are defined as secondary endpoints.

Discussion

This extensive cohort includes children after diagnosis with comprehensive monitoring throughout childhood. The unique composition and the use of validated, sensitive methods with the attached biobank bears the potential to decisively advance the understanding of early CF lung disease.

Ethics and trial registration

The study protocol was approved by the Ethics Committees of the University of Heidelberg (approval S-211/2011) and each participating site and is registered at clinicaltrials.gov (NCT02270476).
A simple marking system for accurate intraoperative monitoring and adjustment of cyclotorsion strabismus surgery
Authors: Lee Lung-Chi , Chang Hsu-Chieh , Chen Yi-Hao , Chien Ke-Hung
Published: January 2023

Ocular cyclotorsion is treatable only with surgery. The surgical procedure must be tailored individually to the specific etiologies causing the horizontal and vertical strabismus and its torsional components. An adjustable surgical approach is often used for postoperative or intraoperative adjustments. However, the methods currently used have some limitations. In this study, we propose a simple intraoperative marking system for all cyclotorsion correction surgery. The proposed marking system used three sets of surface markers: external horizontal markings, ocular horizontal markings, and surgical torsion markings, drawn in sequence. We retrospectively analyzed the surgical results using this novel marking system in this single-center, single-surgeon study. Fifteen patients with cyclotorsion who underwent treatment using the proposed marking system as an intraoperative aid between August 2019 and August 2021 were included. The medical charts were thoroughly reviewed, and the pre-and postoperative subjective and objective cyclotorsion were analyzed. Among the study subjects (10 males, 5 females; age range: 6–89 years), 13 had excyclotorsion and 2 incyclotorsion. Preoperative mean net subjective cyclotorsion measured by the double Maddox rod (DMR) test was 6.0° (standard deviation: 10.8°) and mean net disc-to-fovea angle (DFA) was 20.23° (13.21°). The postoperative net DMR and DFA were 0.2° (2.1°) and 14.09° (5.97°), respectively. The mean absolute net DMR and DFA being treated were 9.8° (4.8°) and 9.76° (4.61°). Overall, the proposed intraoperative marking system is a simple and quantitative method to assess, monitor, and adjust the torsional aspect for all strabismus surgeries.
Plastic biodegradation by in vitro environmental microorganisms and in vivo gut microorganisms of insects
Authors: Yang Xian-Guang , Wen Ping-Ping , Yang Yi-Fan , Jia Pan-Pan , Li Wei-Guo , Pei De-Sheng
Published: January 2023

Traditional plastics, such as polyethylene (PE), polystyrene (PS), polypropylene (PP), polyvinyl chloride (PVC), polyethylene terephthalate (PET), polyurethane (PUR), and other plastic polymers, are difficult to degrade and are gradually accumulated in the environment to cause a serious environmental problem, which is urgently needed to develop novel treatments or control technology. The biodegradation of plastics has gained great attention due to the advantages of green and safe characteristics. Microorganisms play a vital role in the biodegradation of plastics, including environmental microbes (in vitro) and gut microbes of insects (in vivo). Microbial degradation in environmental conditions in vitro is extremely slow for major plastics at degradation rates on the basis of a month or even a year time, but recent discoveries show that the fast biodegradation of specific plastics, such as PS, PE, and PUR, in some invertebrates, especially insects, could be enhanced at rates on basis of hours; the biodegradation in insects is likely to be gut microbial-dependent or synergetic bioreactions in animal digestive systems. This review comprehensively summarizes the latest 7-year (2016–2022) publications on plastic biodegradation by insects and microorganisms, elucidates the mechanism of plastic degradation in insects and environmental microbes, and highlights the cutting-edge perspectives for the potential applications of plastic biodegradation.
How methanotrophs respond to pH: A review of ecophysiology
Authors: Yao Xiangwu , Wang Jiaqi , Hu Baolan
Published: January 2023

Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure–function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.