bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic parameters of color phenotypes of black tiger shrimp (Penaeus monodon)
Authors: Hasan Md. Mehedi , Raadsma Herman W. , Thomson Peter C. , Wade Nicholas M. , Jerry Dean R , Khatkar Mehar S.
Published: October 2022

Black tiger shrimp (Penaeus monodon) is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams. The color of uncooked shrimp was subjectively scored on a scale from 1 to 4, with “1” being the lightest/pale color and “4” being the darkest color. For cooked shrimp color, shrimp were graded firstly by subjective scoring using a commercial grading score card, where the score ranged from 1 to 12 representing light to deep coloration which was subsequently found to not be sufficiently reliable with poor repeatability of measurement (r= 0.68–0.78) Therefore, all images of cooked color were regraded on a three-point scale from brightest and lightest colored cooked shrimp, to darkest and most color-intense, with a high repeatability (r= 0.80–0.92). Objective color of both cooked and uncooked color was obtained by measurement of RGB intensities (values range from 0 to 255) for each pixel from each shrimp. Using the “convertColor” function in “R”, the RGB values were converted toL*a*b* (CIE Lab) systems of color properties. This system of color space was established in 1976, by the International Commission of Illumination (CIE) where “L*” represents the measure of degree of lightness, values range from 0 to 100, where 0 = pure black and 100 = pure white. The value “a*” represents red to green coloration, where a positive value represents the color progression towards red and a negative value towards green. The value “b*” represents blue to yellow coloration, where a positive value refers to more yellowish and negative towards the blue coloration. In total, eight color-related traits were investigated. An ordinal mixed (threshold) model was adopted for manually (subjectively) scored color phenotypes, whereas all other traits were analyzed by linear mixed models using ASReml software to derive variance components and estimated breeding values (EBVs). Moderate to low heritability estimates (0.05–0.35) were obtained for body color traits. For subjectively scored cooked and uncooked color, EBV-based selection would result in substantial genetic improvement in these traits. The genetic correlations among cooked, uncooked and body weight traits were high and ranged from −0.88 to 0.81. These suggest for the first time that 1) cooked color can be improved indirectly by genetic selection based on color of uncooked/live shrimp, and 2) intensity of coloration is positively correlated with body weight traits and hence selection for body weight will also improve color traits in this population.
Expression pattern and clinical value of Key RNA methylation modification regulators in ischemic stroke
Authors: Zhang Xinyue , Wang Yuanlin , Dong Beibei , Jiang Yi , Liu Dan , Xie Keliang , Yu Yonghao
Published: October 2022

Ischemic stroke (IS) is one of the major causes of death and disability worldwide, and effective diagnosis and treatment methods are lacking. RNA methylation, a common epigenetic modification, plays an important role in disease progression. However, little is known about the role of RNA methylation modification in the regulation of IS. The aim of this study was to investigate RNA methylation modification patterns and immune infiltration characteristics in IS through bioinformatics analysis. We downloaded gene expression profiles of control and IS model rat brain tissues from the Gene Expression Omnibus database. IS profiles were divided into two subtypes based on RNA methylation regulators, and functional enrichment analyses were conducted to determine the differentially expressed genes (DEGs) between the subtypes. Weighted gene co-expression network analysis was used to explore co-expression modules and genes based on DEGs. The IS clinical diagnosis model was successfully constructed and four IS characteristic genes (GFAP, GPNMB, FKBP9, and CHMP5) were identified, which were significantly upregulated in IS samples. Characteristic genes were verified by receiver operating characteristic curve and real-time quantitative PCR analyses. The correlation between characteristic genes and infiltrating immune cells was determined by correlation analysis. Furthermore, GPNMB was screened using the protein-protein interaction network, and its regulatory network and the potential therapeutic drug chloroquine were predicted. Our finding describes the expression pattern and clinical value of key RNA methylation modification regulators in IS and novel diagnostic and therapeutic targets of IS from a new perspective.
Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat
Authors: Gohar Sasha , Sajjad Muhammad , Zulfiqar Sana , Liu Jiajun , Wu Jiajie , Rahman Mehboob-ur-
Published: October 2022

Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.
Histone deacetylases modulate resistance to the therapy in lung cancer
Authors: Contreras-Sanzón Estefanía , Prado-Garcia Heriberto , Romero-Garcia Susana , Nuñez-Corona David , Ortiz-Quintero Blanca , Luna-Rivero Cesar , Martínez-Cruz Victor , Carlos-Reyes Ángeles
Published: October 2022

The acetylation status of histones located in both oncogenes and tumor suppressor genes modulate cancer hallmarks. In lung cancer, changes in the acetylation status are associated with increased cell proliferation, tumor growth, migration, invasion, and metastasis. Histone deacetylases (HDACs) are a group of enzymes that take part in the elimination of acetyl groups from histones. Thus, HDACs regulate the acetylation status of histones. Although several therapies are available to treat lung cancer, many of these fail because of the development of tumor resistance. One mechanism of tumor resistance is the aberrant expression of HDACs. Specific anti-cancer therapies modulate HDACs expression, resulting in chromatin remodeling and epigenetic modification of the expression of a variety of genes. Thus, HDACs are promising therapeutic targets to improve the response to anti-cancer treatments. Besides, natural compounds such as phytochemicals have potent antioxidant and chemopreventive activities. Some of these compounds modulate the deregulated activity of HDACs (e.g. curcumin, apigenin, EGCG, resveratrol, and quercetin). These phytochemicals have been shown to inhibit some of the cancer hallmarks through HDAC modulation. The present review discusses the epigenetic mechanisms by which HDACs contribute to carcinogenesis and resistance of lung cancer cells to anticancer therapies.
A machine learning approach for missing persons cases with high genotyping errors
Authors: Huang Meng , Liu Muyi , Li Hongmin , King Jonathan , Smuts Amy , Budowle Bruce , Ge Jianye
Published: October 2022

Estimating the relationships between individuals is one of the fundamental challenges in many fields. In particular, relationship.ip estimation could provide valuable information for missing persons cases. The recently developed investigative genetic genealogy approach uses high-density single nucleotide polymorphisms (SNPs) to determine close and more distant relationships, in which hundreds of thousands to tens of millions of SNPs are generated either by microarray genotyping or whole-genome sequencing. The current studies usually assume the SNP profiles were generated with minimum errors. However, in the missing person cases, the DNA samples can be highly degraded, and the SNP profiles generated from these samples usually contain lots of errors. In this study, a machine learning approach was developed for estimating the relationships with high error SNP profiles. In this approach, a hierarchical classification strategy was employed first to classify the relationships by degree and then the relationship types within each degree separately. As for each classification, feature selection was implemented to gain better performance. Both simulated and real data sets with various genotyping error rates were utilized in evaluating this approach, and the accuracies of this approach were higher than individual measures; namely, this approach was more accurate and robust than the individual measures for SNP profiles with genotyping errors. In addition, the highest accuracy could be obtained by providing the same genotyping error rates in train and test sets, and thus estimating genotyping errors of the SNP profiles is critical to obtaining high accuracy of relationship estimation.
Case Report:Pregnancy and birth in a mild phenotype of Alström syndrome
Authors: Marozio Luca , Dassie Francesca , Bertschy Gianluca , Canuto Emilie M. , Milan Gabriella , Cosma Stefano , Maffei Pietro , Benedetto Chiara
Published: October 2022

Background: Alström syndrome (AS) is an ultrarare multisystemic progressive disease caused by autosomal recessive variations of the ALMS1 gene (2p13). AS is characterized by double sensory impairment, cardiomyopathy, childhood obesity, extreme insulin resistance, early nonalcoholic fatty liver disease, renal dysfunction, respiratory disease, endocrine and urologic disorders. In female AS patients, hyperandrogenism has been described but fertility issues and conception have not been investigated so far.

Case: This case report describes the spontaneous conception, pregnancy, and birth in a 27-year-old woman with AS, characterized by a mild phenotype with late onset of visual impairment, residual perception of light, and hypertension. Before pregnancy, menses were regular with increased levels of dihydrotestosterone and androstanediol glucuronide in the follicular phase, and the ovaries and endometrium were normal during vaginal ultrasound. A thorough clinical follow-up of the maternal and fetal conditions was carried out. A weight gain of 10 kg during pregnancy was recorded, and serial blood and urine tests were all within the normal range, except for mild anemia. The course of pregnancy was uneventful up to 34 weeks of gestation when preeclampsia developed with an abnormally high level of blood pressure and edema in the lower limbs. At 35 weeks + 3 days of gestation, an urgent cesarean section was performed, and a healthy male weighing 1,950 g was born. Histological examination of the placenta showed partial signs of flow obstruction, limited abruption areas, congested fetal vessels and villi, and a small single infarcted area.

Conclusion: The present case demonstrates for the first time that conceiving is possible for patients with ALMS. Particular attention should be given to the management of AS systemic comorbidities through the course of pregnancy.
Next generation L2-based HPV vaccines cross-protect against cutaneous papillomavirus infection and tumor development
Authors: Ahmels Melinda , Mariz Filipe C. , Braspenning-Wesch Ilona , Stephan Sonja , Huber Bettina , Schmidt Gabriele , Cao Rui , Müller Martin , Kirnbauer Reinhard , Rösl Frank , Hasche Daniel
Published: October 2022

Licensed L1-VLP-based immunizations against high-risk mucosal human papillomavirus (HPV) types have been a great success in reducing anogenital cancers, although they are limited in their cross-protection against HPV types not covered by the vaccine. Further, their utility in protection against cutaneous HPV types, of which some contribute to non-melanoma skin cancer (NMSC) development, is rather low. Next generation vaccines achieve broadly cross-protective immunity against highly conserved sequences of L2. In this exploratory study, we tested two novel HPV vaccine candidates, HPV16 RG1-VLP and CUT-PANHPVAX, in the preclinical natural infection model Mastomys coucha. After immunization with either vaccines, a mock control or MnPV L1-VLPs, the animals were experimentally infected and monitored. Besides vaccine-specific seroconversion against HPV L2 peptides, the animals also developed cross-reactive antibodies against the cutaneous Mastomys natalensis papillomavirus (MnPV) L2, which were cross-neutralizing MnPV pseudovirions in vitro. Further, both L2-based vaccines also conferred in vivo protection as the viral loads in plucked hair after experimental infection were lower compared to mock-vaccinated control animals. Importantly, the formation of neutralizing antibodies, whether directed against L1-VLPs or L2, was able to prevent skin tumor formation and even microscopical signs of MnPV infection in the skin. For the first time, our study shows the proof-of-principle of next generation L2-based vaccines even across different PV genera in an infection animal model with its genuine PV. It provides fundamental insights into the humoral immunity elicited by L2-based vaccines against PV-induced skin tumors, with important implications to the design of next generation HPV vaccines.
A humanized mouse model for in vivo evaluation of invariant Natural Killer T cell responses
Authors: Saavedra-Avila Noemi Alejandra , Dellabona Paolo , Casorati Giulia , Veerapen Natacha , Besra Gurdyal S. , Howell Amy R. , Porcelli Steven A.
Published: October 2022

Invariant natural killer T (iNKT) cells mediate immune responses when stimulated by glycolipid agonists presented by CD1d. In extensive studies of synthetic analogues of α-galactosyl ceramides, we identified numerous examples of significant differences in the recognition of specific glycolipids in wild type mice versus human iNKT cell clones or PBMC samples. To predict human iNKT cell responses more accurately in a mouse model, we derived a mouse line in which compound genetic modifications were used to express a human-like iNKT cell TCR along with human CD1d in place of the endogenous mouse proteins. Detailed transcriptional and phenotypic profiling demonstrated that these partially humanized mice developed an expanded population of T cells recognizing CD1d-presented glycolipid antigens, among which a subset characterized by expression of chemokine receptor CXCR6 had features characteristic of authentic iNKT cells. Responses to iNKT cell activating glycolipids in these mice generated cytokine production in vitro and in vivo that showed a pattern of fine specificity that closely resembled that of cultured human iNKT cell clones. Anti-tumor responses to variants of α-galactosyl ceramide in VαKI mice also correlated with their potency for stimulating human iNKT cells. This genetically modified mouse line provides a practical model for human presentation and recognition of iNKT cell activators in the context of a normally functioning immune system, and may furnish valuable opportunities for preclinical evaluation of iNKT cell-based therapies.
T-cell deficiency and hyperinflammatory monocyte responses associate with Mycobacterium avium complex lung disease
Authors: Lindestam Arlehamn Cecilia S. , Benson Basilin , Kuan Rebecca , Dill-McFarland Kimberly A. , Peterson Glenna J. , Paul Sinu , Nguyen Felicia K. , Gilman Robert H. , Saito Mayuko , Taplitz Randy , Arentz Matthew , Goss Christopher H. , Aitken Moira L. , Horne David J. , Shah Javeed A. , Sette Alessandro , Hawn Thomas R.
Published: October 2022

Immunological mechanisms of susceptibility to nontuberculous mycobacterial (NTM) disease are poorly understood. To understand NTM pathogenesis, we evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex (MAC) in asymptomatic individuals with a previous history of MAC lung disease (MACDZ). We hypothesized that Mav-specific immune responses are associated with susceptibility to MAC lung disease. We measured MAC-, NTM-, or MAC/Mtb-specific T-cell responses by cytokine production, expression of surface markers, and analysis of global gene expression in 27 MACDZ individuals and 32 healthy controls. We also analyzed global gene expression in Mycobacterium avium-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls. We were unable to detect increased T-cell responses against MAC-specific reagents in MACDZ compared to controls, while the responses to non-mycobacteria derived antigens were preserved. MACDZ individuals had a lower frequency of Th1 and Th1* T-cell populations. In addition, MACDZ subjects had lower transcriptional responses in PBMCs stimulated with a mycobacterial peptide pool (MTB300). By contrast, global gene expression analysis demonstrated upregulation of proinflammatory pathways in uninfected and M. avium-infected monocytes, i.e. a hyperinflammatory in vitro response, derived from MACDZ subjects compared to controls. Together, these data suggest a novel immunologic defect which underlies MAC pathogenesis and includes concurrent innate and adaptive dysregulation which persists years after completion of treatment.
Natural killer cell-related prognosis signature characterizes immune landscape and predicts prognosis of HNSCC
Authors: Chi Hao , Xie Xixi , Yan Yingjie , Peng Gaoge , Strohmer Dorothee Franziska , Lai Guichuan , Zhao Songyun , Xia Zhijia , Tian Gang
Published: October 2022

Background

Head and neck squamous cell carcinoma (HNSCC), the most common head and neck cancer, is highly aggressive and heterogeneous, resulting in variable prognoses and immunotherapeutic outcomes. Natural killer (NK) cells play essential roles in malignancies’ development, diagnosis, and prognosis. The purpose of this study was to establish a reliable signature based on genes related to NK cells (NRGs), thus providing a new perspective for assessing immunotherapy response and prognosis of HNSCC patients.

Methods

In this study, NRGs were used to classify HNSCC from the TCGA-HNSCC and GEO cohorts. The genes were evaluated using univariate cox regression analysis based on the differential analysis of normal and tumor samples in TCGA-HNSCC conducted using the “limma” R package. Thereafter, we built prognostic gene signatures using LASSO-COX analysis. External validation was carried out in the GSE41613 cohort. Immunity analysis based on NRGs was performed via several methods, such as CIBERSORT, and immunotherapy response was evaluated by TIP portal website.

Results

With the TCGA-HNSCC data, we established a nomogram based on the 17-NRGs signature and a variety of clinicopathological characteristics. The low-risk group exhibited a better effect when it came to immunotherapy.

Conclusions

17-NRGs signature and nomograms demonstrate excellent predictive performance and offer new perspectives for assessing pre-immune efficacy, which will facilitate future precision immuno-oncology research.
Single center blind testing of a US multi-center validated diagnostic algorithm for Kawasaki disease in Taiwan
Authors: Kuo Ho-Chang , Hao Shiying , Jin Bo , Chou C. James , Han Zhi , Chang Ling-Sai , Huang Ying-Hsien , Hwa Kuoyuan , Whitin John C. , Sylvester Karl G. , Reddy Charitha D. , Chubb Henry , Ceresnak Scott R. , Kanegaye John T. , Tremoulet Adriana H. , Burns Jane C. , McElhinney Doff , Cohen Harvey J. , Ling Xuefeng B.
Published: October 2022

Background

Kawasaki disease (KD) is the leading cause of acquired heart disease in children. The major challenge in KD diagnosis is that it shares clinical signs with other childhood febrile control (FC) subjects. We sought to determine if our algorithmic approach applied to a Taiwan cohort.

Methods

A single center (Chang Gung Memorial Hospital in Taiwan) cohort of patients suspected with acute KD were prospectively enrolled by local KD specialists for KD analysis. Our previously single-center developed computer-based two-step algorithm was further tested by a five-center validation in US. This first blinded multi-center trial validated our approach, with sufficient sensitivity and positive predictive value, to identify most patients with KD diagnosed at centers across the US. This study involved 418 KDs and 259 FCs from the Chang Gung Memorial Hospital in Taiwan.

Findings

Our diagnostic algorithm retained sensitivity (379 of 418; 90.7%), specificity (223 of 259; 86.1%), PPV (379 of 409; 92.7%), and NPV (223 of 247; 90.3%) comparable to previous US 2016 single center and US 2020 fiver center results. Only 4.7% (15 of 418) of KD and 2.3% (6 of 259) of FC patients were identified as indeterminate. The algorithm identified 18 of 50 (36%) KD patients who presented 2 or 3 principal criteria. Of 418 KD patients, 157 were infants younger than one year and 89.2% (140 of 157) were classified correctly. Of the 44 patients with KD who had coronary artery abnormalities, our diagnostic algorithm correctly identified 43 (97.7%) including all patients with dilated coronary artery but one who found to resolve in 8 weeks.

Interpretation

This work demonstrates the applicability of our algorithmic approach and diagnostic portability in Taiwan.
A population of dermal Langerin+ dendritic cells promote the inflammation in mouse model of atopic dermatitis
Authors: Xiao Chunying , Zhu Zhenlai , Zhang Chen , Gao Jixin , Luo Yixin , Fang Hui , Qiao Hongjiang , Li Wei , Wang Gang , Fu Meng
Published: October 2022

Cutaneous dendritic cells (DCs) have been implicated in the pathogenesis of atopic dermatitis (AD). However, the specific role of different subsets of DCs has not been well defined. This study aimed to investigate the contributions of Langerhans cells (LCs), resident dermal Langerin+ DCs (r-Langerin+ dDCs), and newly infiltrated inflammatory dermal Langerin+ DCs (i-Langerin+ dDCs) in an AD mouse model induced by the topical application of MC903. The result showed that depletion of i-Langerin+ dDCs in DTR mice after multiple diphtheria toxin (DT) injection significantly reduced thymic stromal lymphopoietin (TSLP) production in lesions and skin inflammation alleviation. However, depletion of LCs or r-Langerin+ dDCs didn’t resulted in significant changes in skin inflammation of DTA or single DT injection-treated DTR mice compared with the wild-type (WT) mice. DT-treated DTR-WT chimeric mice with the depletion of bone marrow (BM)-derived i-Langerin+ dDCs resulted in markedly decreased skin inflammation than controls, while PBS-treated chimeric mice (DTR-WT) with only the depletion of r-Langerin+ dDCs showed inflammation comparable to that in WT mice. Furthermore, TSLP contributed to the upregulation of Langerin expression in BM-derived DCs and promoted the maturation of Langerin+ DCs. In summary, the present study demonstrated that the newly infiltrated inflammatory dermal Langerin+ DCs were essential for AD development and local TSLP production, and TSLP further promoted the production of BM-derived i-Langerin+ dDCs, which might maintain AD inflammation.
Fluorine labelling of therapeutic human tolerogenic dendritic cells for 19F-magnetic resonance imaging
Authors: Cooke Fiona , Neal Mary , Wood Matthew J. , de Vries I. Jolanda M. , Anderson Amy E. , Diboll Julie , Pratt Arthur G. , Stanway James , Nicorescu Ioana , Moyse Nicholas , Hiles Dawn , Caulfield David , Dickinson Anne M. , Blamire Andrew M. , Thelwall Pete , Isaacs John D. , Hilkens Catharien M. U.
Published: October 2022

Tolerogenic dendritic cell (tolDC) therapies aim to restore self-tolerance in patients suffering from autoimmune diseases. Phase 1 clinical trials with tolDC have shown the feasibility and safety of this approach, but have also highlighted a lack of understanding of their distribution in vivo. Fluorine-19 magnetic resonance imaging (19F-MRI) promises an attractive cell tracking method because it allows for detection of 19F-labelled cells in a non-invasive and longitudinal manner. Here, we tested the suitability of nanoparticles containing 19F (19F-NP) for labelling of therapeutic human tolDC for detection by 19F-MRI. We found that tolDC readily endocytosed 19F-NP with acceptable effects on cell viability and yield. The MRI signal-to-noise ratios obtained are more than sufficient for detection of the administered tolDC dose (10 million cells) at the injection site in vivo, depending on the tissue depth and the rate of cell dispersal. Importantly, 19F-NP labelling did not revert tolDC into immunogenic DC, as confirmed by their low expression of typical mature DC surface markers (CD83, CD86), low secretion of pro-inflammatory IL-12p70, and low capacity to induce IFN-γ in allogeneic CD4+ T cells. In addition, the capacity of tolDC to secrete anti-inflammatory IL-10 was not diminished by 19F-NP labelling. We conclude that 19F-NP is a suitable imaging agent for tolDC. With currently available technologies, this imaging approach does not yet approach the sensitivity required to detect small numbers of migrating cells, but could have important utility for determining the accuracy of injecting tolDC into the desired target tissue and their efflux rate.
Deficiency of MST1 in endometriosis related peritoneal macrophages promoted the autophagy of ectopic endometrial stromal cells by IL-10
Authors: Huang Yufei , Yan Shumin , Dong Xiaoyu , Jiao Xue , Wang Shuang , Li Dong , Wang Guoyun
Published: October 2022

Changes in the function of peritoneal macrophages contribute to the homeostasis of the peritoneal immune microenvironment in endometriosis. The mechanism by which ectopic tissues escape phagocytic clearance by macrophages to achieve ectopic colonization and proliferation is unknown. The expression of CD163 in peritoneal macrophages in patients with endometriosis is increased, with the overexpression of MAPK, which can promote the M2-type polarization of macrophages and reduce their ability to phagocytose ectopic endometrial cells. As an upstream regulator of MAPK, MST1 expression is deficient in peritoneal macrophages of patients with endometriosis. This process is regulated by miR-887-5p, a noncoding RNA targeting MST1. Moreover, MST1-knockout macrophages secrete anti-inflammatory factor IL-10, which promotes autophagy of ectopic endometrial stromal cells. These results suggest that MST1 deficient macrophages may accelerate the autophagy of ectopic endometrium via IL-10 which was regulated by miR-887-5p.
Comprehensive analysis of the clinical significance, immune infiltration, and biological role of MARCH ligases in HCC
Authors: Cao Jun , Tu Dao-yuan , Zhou Jie , Jiang Guo-qing , Jin Sheng-jie , Su Bing-bing , Tang Hao , Tang Yu-hong , Wang Ao-qing , Wang Qian , Liu Ren-jie , Zhang Chi , Bai Dou-sheng
Published: October 2022

The membrane‐associated RING‐CH (MARCH) family, a member of the E3 ubiquitin ligases, has been confirmed by a growing number of studies to be associated with immune function and has been highlighted as a potential immunotherapy target. In our research, hepatocellular carcinoma (HCC) patients were divided into C1 and C2 MARCH ligase-related patterns by the non-negative matrix factorization (NMF) algorithm. Multiple analyses revealed that the MARCH ligase-related cluster was related to prognosis, clinicopathological characteristics, and the tumor immune microenvironment (TIME). Next, the signature (risk score) of the MARCH prognosis was constructed, including eight genes associated with the MARCH ligase (CYP2C9, G6PD, SLC1A5, SPP1, ANXA10, CDC20, PON1, and FTCD). The risk score showed accuracy and stability. We found that the correlations between risk score and TIME, tumor mutation burden (TMB), prognosis, and clinicopathological characteristics were significant. Additionally, the risk score also had important guiding significance for HCC treatment, including chemotherapy, immunotherapy, and transarterial chemoembolization (TACE).
A 17-year time-series of diatom populations‘ flux and composition in the Mauritanian coastal upwelling
Authors: Romero Oscar E. , Ramondenc Simon
Published: October 2022

Understanding seasonal and multiyear variability of primary producers’ populations in the Mauritanian coastal upwelling system along the northwestern African margin may help to predict future impact of climate change (e.g., nutrient availability, productivity, and phyto- and zooplankton dynamics). For this, continuous, long time-series are required. A major challenge in obtaining these time-series is the logistics associated with the uninterrupted, in-situ sampling over several years. Sediment traps represent a reliable alternative. In this study, we assess the variations of the diatom community in samples almost continuously collected between June 2003 and March 2020 with 17 sediment traps deployed at site CBeu (=Cape Blanc eutrophic), located at c. 20°N-18°45’W, offshore Mauritania in the Canary Current Eastern Boundary Upwelling Ecosystems (CC-EBUE). In addition to describing the multiyear dynamics of the total diatom flux and major shifts in the species-specific composition of the populations, our study addresses questions such as (i) how constant is the intrannual pattern of populations’ occurrence, (ii) what the amplitude of annual changes is, and (iii) how populations’ shifts relate to physical setting dynamics. Matching the occurrence of most intense seasonal upwelling, highest diatom flux maxima mainly occur in spring and summer between 2003 and 2020. The diverse diatom community (e.g., benthic, coastal upwelling, coastal planktonic, and open-ocean diatoms) closely follows the annual cycle of atmospheric and hydrologic conditions. Benthic diatoms dominate during spring and summer (e.g., upwelling season), while open-ocean diatoms contribute the most in fall and winter when the upper water column stratifies. As no persistent –either decreasing or increasing trend of diatom productivity over the 17 sampled years, our results are at odds with Bakun’s hypothesis of upwelling intensification. Anchoring temporal changes of diatoms in a wider environmental frame allows for insights into the complex dynamics of the Mauritanian upwelling ecosystem and the populations’ response to climate forcing. This helps in establishing the scientific basis for modeling future states of the CC-EBUE and/or comparable environments.
Impact of and recovery from seabed trawling in soft-bottom benthic communities under natural disturbance of summer hypoxia: A case study in subtropical Hong Kong
Authors: Xu Wenzhe , Fleddum Anne Lise , Shin Paul K. S. , Sun Jun
Published: October 2022

Bottom trawling has widespread impact on the structure and composition of benthic communities. In this study, soft-bottom macrofauna in a heavily trawled area and an adjacent marine park that has been closed to bottom trawling for more than ten years were sampled, allowing to investigate the impact of and recovery from trawling. Both areas were equally affected by seasonal summer hypoxia. Polychaetes were the most abundant at trawled (78-86%) and non-trawled (85-94%) sites in both summer and winter. The non-trawled sites inside the marine park area had a lower level of species composition and abundance as compared to the trawled sites in summer, whereas in winter the benthic communities at these trawled and non-trawled sites appeared much similar with the majority of the identified taxa being dominated by new recruiting juveniles in both sampling areas. Results of permutational multivariate analysis of variance (PERMANOVA) on transformed infaunal abundance and biomass data revealed significant differences (p<0.05) between trawled and non-trawled treatments and seasons, as well as their interactions. Pair-wise a posteriori PERMANOVA further indicated significant differences for the abundance and biomass data in summer but insignificant differences in winter. PERMANOVA of the biological traits of infauna weighted with transformed biomass also confirmed significant difference for seasons only. Such findings imply that the effect of season was more important than that of trawling especially on the biological trait structure of the benthic communities. In addition, bottom trawling may contribute to a higher level of dissolved oxygen when the area suffered from hypoxia, resulting a higher biodiversity in the trawled area in summer. By comparing data taken prior to closure of the marine park from trawling, the recovery of infaunal community has been slow over the 12 years as a trawl-free area. Apart from natural disturbance of summer hypoxia, such recovery could also be complicated with the presence of artificial reefs deployed within the marine park, which may affect the hydrodynamics of the benthic environment and modify the community structure and function.
A significant wave height prediction method based on deep learning combining the correlation between wind and wind waves
Authors: Song Tao , Han Runsheng , Meng Fan , Wang Jiarong , Wei Wei , Peng Shiqiu
Published: October 2022

Accurate wave height prediction is significant in ports, energy, fisheries, and other offshore operations. In this study, a regional significant wave height prediction model with a high spatial and temporal resolution is proposed based on the ConvLSTM algorithm. The model learns the intrinsic correlations of the data generated by the numerical model, making it possible to combine the correlations between wind and wind waves to improve the predictions. In addition, this study also optimizes the long-term prediction ability of the model through the proposed Mask method and Replace mechanism. The experimental results show that the introduction of the wind field can significantly improve the significant wave height prediction results. The research on the prediction effect of the entire study area and two separate stations shows that the prediction performance of the proposed model is better than the existing methods. The model makes full use of the physical correlation between wind and wind waves, and the validity is up to 24 hours. The 24-hour forecast R² reached 0.69.
Evaluating the effects of a symmetric instability parameterization scheme in the Xisha-Zhongsha waters, South China Sea in winter
Authors: Jiang Yifei , Dong Jihai , Zhang Xiaojiang , Zhang Wenjing , Wang Huizan , Zhang Weimin
Published: October 2022

As one of the important submesoscale instabilities, symmetric instability (SI) widely exists in the ocean surface mixed layer (SML), which enhances the vertical material transport in the SML and also the exchanges between the SML and the ocean interior. Due to the small spatial scales of SI, O (10 m–1 km), which are not resolved by most current ocean models, the application of SI parameterization is an alternative choice in the coming decades to include the SI effects in ocean models and improve the model performance. In this study, we evaluate the impacts of SI in a realistic configuration with the SI parameterization scheme applied in the Xisha-Zhongsha waters, South China Sea in winter by using the Coastal and Regional Ocean Community Model (CROCO) version of the Regional Ocean Modeling System. Compared to the SI-lacking case, the SI energy source, the geostrophic shear production, is increased and elimination of anticyclonic potential vorticity is revealed in the SI-parameterized case. According to the energy analysis, multi-scale interactions are also influenced by the SI. The effective wind energy input is reduced, and the potential energy release in the SML is suppressed. Moreover, the SI scheme makes the SML depth shallower and closer to the reanalysis one. This work demonstrates a good performance of the SI scheme applied in regional models in representing SI effects.
A scientometric analysis of international publication trends in oyster research
Authors: Azra Mohamad Nor , Mohd Noor Mohd Iqbal , Zekker Ivar
Published: October 2022

Oysters form extraordinary ecosystems (e.g. oyster reefs) with a high economic importance (e.g. aquaculture) to the world’s aquatic ecological systems. Shellfish, especially mollusks, have a significant contribution towards the future global food security. However, to the best of our knowledge, there are no bibliometric studies on oyster-related topics. In the present study, we queried the Web of Science Core Collection (WOSCC) database to selectively identify the scope of oyster publications. Citespace was used as a tool for the co-citation analysis and Microsoft Excel software for the handling of descriptive datasets. A total of 19,202 papers available from WOSCC between 1975 and 2021 were extracted and analyzed. Our data indicated that the number of publications increased two-fold between 2010 (654) and 2021 (1309). Our study also revealed that almost 70% of the publications were published by the five countries that lead oyster research in the world, USA, China, France, Australia, and Japan. Over the last five decades, there are a total of 7,905 participating institutions, a tremendous 40,939 authors involved, and 2,319 different journals published about oyster related studies. To the best of our knowledge, this is the first scientometric review to identify the scope of oyster research and publications. These findings show the emergence of oyster research and could attract various stakeholders, especially the early career researchers in various fields to collaborate in oyster research in the future.
Staphylococcus aureus lipoproteins in infectious diseases
Authors: Mohammad Majd , Ali Abukar , Nguyen Minh-Thu , Götz Friedrich , Pullerits Rille , Jin Tao
Published: October 2022

Infections with the Gram-positive bacterial pathogen Staphylococcus aureus remain a major challenge for the healthcare system and demand new treatment options. The increasing antibiotic resistance of S. aureus poses additional challenges, consequently inflicting a huge strain in the society due to enormous healthcare costs. S. aureus expresses multiple molecules, including bacterial lipoproteins (Lpps), which play a role not only in immune response but also in disease pathogenesis. S. aureus Lpps, the predominant ligands of TLR2, are important for bacterial survival as they maintain the metabolic activity of the bacteria. Moreover, Lpps possess many diverse properties that are of vital importance for the bacteria. They also contribute to host cell invasion but so far their role in different staphylococcal infections has not been fully defined. In this review, we summarize the current knowledge about S. aureus Lpps and their distinct roles in various infectious disease animal models, such as septic arthritis, sepsis, and skin and soft tissue infections. The molecular and cellular response of the host to S. aureus Lpp exposure is also a primary focus.
The active functional microbes contribute differently to soil nitrification and denitrification potential under long-term fertilizer regimes in North-East China
Authors: Wang Feng , Liang Xiaolong , Ding Fan , Ren Lingling , Liang Minjie , An Tingting , Li Shuangyi , Wang Jingkuan , Liu Lingzhi
Published: October 2022

Nitrogen (N) cycling microorganisms mediate soil nitrogen transformation processes, thereby affecting agricultural production and environment quality. However, it is not fully understood how active N-cycling microbial community in soil respond to long-term fertilization, as well as which microorganisms regulate soil nitrogen cycling in agricultural ecosystem. Here, we collected the soils from different depths and seasons at a 29-year fertilization experimental field (organic/chemical fertilizer), and investigated the transcriptions of N-cycling functional genes and their contribution to potential nitrification and denitrification. We found that long-term fertilization exerted significant impacts on the transcript abundances of nitrifiers (AOA amoA, AOB amoA and hao) and denitrifiers (narG and nosZ), which was also notably influenced by season variation. The transcriptions of AOA amoA, hao, and narG genes were lowest in autumn, and AOB amoA and nosZ transcript abundances were highest in autumn. Compared to no fertilization, soil potential nitrification rate (PNR) was reduced in fertilization treatments, while soil potential denitrification rate (PDR) was significantly enhanced in organic combined chemical fertilizer treatment. Both PNR and PDR were highest in 0–20 cm among the tested soil depths. Path model indicated active nitrifiers and denitrifiers had significant impact on soil PNR and PDR, respectively. The transcriptions of AOA amoA and nxr genes were significantly correlated with soil PNR (Pearson correlation, r > 0.174, p < 0.05). Significant correlation of napA and nosZ transcriptions with soil PDR (Pearson correlation, r > 0.234, p < 0.05) was also revealed. Random forest analysis showed that SOC content and soil pH were the important factors explaining the total variance of active nitrifers and denitrifiers, respectively. Taken together, long-term fertilization regimes reduced soil PNR and enhanced PDR, which could be attributed to the different responses of active N-cycling microorganisms to soil environment variations. This work provides new insight into the nitrogen cycle, particularly microbial indicators in nitrification and denitrification of long-term fertilized agricultural ecosystems.
Comparative study on the microbiota of colostrum and nipple skin from lactating mothers separated from their newborn at birth in China
Authors: Du Yanli , Qiu Qing , Cheng Jing , Huang Zhili , Xie Ruixia , Wang Lu , Wang Xiangyu , Han Zongli , Jin Gang
Published: October 2022

Increasing studies have found breast milk (BM) contains its own microbiota. However, the route through which microbes enter the BM is still unclear. In order to verify the entero-mammary pathway of BM, we designed a rigorous study that prevented oral bacteria from contaminating the breast and nipple skin (NS) during baby nursing. Thirty-one healthy, postpartum mothers living in southern China who were immediately separated from their newborn after delivery were enrolled in this study. Using an aseptic protocol for sampling, sterile water was used to wash the NS and was then collected. Then the first drop of BM was discarded and colostrum was collected manually. Amplicon sequencing was performed targeting the V3–V4 region of the bacterial 16S rRNA gene, and the differences between the microbiota of the colostrum and NS were analyzed. Additionally, the effects of environmental factors, such as the delivery mode and intrapartum antibiotic exposure, on the diversity of the colostrum microbiota were also analyzed. We found significant differences in the α diversity and richness between the BM and NS as evidenced by richness, Chao1, and Simpson indices. There were 170 operational taxonomic units (OTUs) shared by colostrum and NS, while 111 and 87 OTUs were unique, respectively, as well as a clear distinction in OTUs was observed by unifrac binary analysis between them. Linear discriminant analysis effect size analysis found that anaerobes, such as Bifidobacterium and Pantoea at the genus level and enterobacteria including Enterobacteriaceae at the family level, were predominant in the colostrum, while the predominant bacteria on the NS were Bacteroides, Staphylococcus, and Parabacteroides at the genus level. BM is colonized by bacteria prior to baby suckling, and the diversity of the colostrum microbiota differs from that of the NS. The predominant microbiota taxa in BM indicated that they were likely to be transferred to the breast through the intestinal tract. Our study provides direct evidence for the revolutionary active migration hypothesis. Additionally, factors like intrapartum antibiotic exposure did not significantly affect the diversity of the microbiota in the BM. Therefore, it is suggested that mothers continue to provide BM for their newborns during separation.
Interaction between autophagy and the NLRP3 inflammasome in Alzheimer’s and Parkinson’s disease
Authors: Lu Ranran , Zhang Lijie , Yang Xinling
Published: October 2022

Autophagy degrades phagocytosed damaged organelles, misfolded proteins, and various pathogens through lysosomes as an essential way to maintain cellular homeostasis. Autophagy is a tightly regulated cellular self-degradation process that plays a crucial role in maintaining normal cellular function and homeostasis in the body. The NLRP3 inflammasome in neuroinflammation is a vital recognition receptor in innate cellular immunity, sensing external invading pathogens and endogenous stimuli and further triggering inflammatory responses. The NLRP3 inflammasome forms an inflammatory complex by recognizing DAMPS or PAMPS, and its activation triggers caspase-1-mediated cleavage of pro-IL-1β and pro-IL-18 to promote the inflammatory response. In recent years, it has been reported that there is a complex interaction between autophagy and neuroinflammation. Strengthening autophagy can regulate the expression of NLRP3 inflammasome to reduce neuroinflammation in neurodegenerative disease and protect neurons. However, the related mechanism is not entirely clear. The formation of protein aggregates is one of the standard features of Neurodegenerative diseases. A large number of toxic protein aggregates can induce inflammation. In theory, activation of the autophagy pathway can remove the potential toxicity of protein aggregates and delay the progression of the disease. This article aims to review recent research on the interaction of autophagy, NLRP3 inflammasome, and protein aggregates in Alzheimer’s disease (AD) and Parkinson’s disease (PD), analyze the mechanism and provide theoretical references for further research in the future.
Learning generalizable behaviors from demonstration
Authors: Rivera Corban , Popek Katie M. , Ashcraft Chace , Staley Edward W. , Katyal Kapil D. , Paulhamus Bart L.
Published: October 2022

Generalizing prior experiences to complete new tasks is a challenging and unsolved problem in robotics. In this work, we explore a novel framework for control of complex systems called Primitive Imitation for Control (PICO). The approach combines ideas from imitation learning, task decomposition, and novel task sequencing to generalize from demonstrations to new behaviors. Demonstrations are automatically decomposed into existing or missing sub-behaviors which allows the framework to identify novel behaviors while not duplicating existing behaviors. Generalization to new tasks is achieved through dynamic blending of behavior primitives. We evaluated the approach using demonstrations from two different robotic platforms. The experimental results show that PICO is able to detect the presence of a novel behavior primitive and build the missing control policy.