bluuebunny/crossref_metadata_2025 huggingface dataset:
Conifer Seedling Survival in Response to High Surface Temperature Events of Varying Intensity and Duration
Authors: Rank Robin , Maneta Marco , Higuera Philip , Holden Zachary , Dobrowski Solomon
Published: January 2022

Forests face accelerating threats due to increases in the severity and frequency of drought and heat stress associated with climate change. In particular, changing patterns of forest regeneration after disturbance will be important in predicting future forest distribution across the western United States, where patterns of recurring fire and regrowth are important in establishing landscape dynamics. To predict shifting landscape patterns, it will be important to identify environmental boundaries for forest regeneration using environmental variables with clear consequences for seedling survival. Here, we explore soil surface temperature as an environmental variable with direct consequences for seedling survival and forest regeneration potential. We conducted a literature search to identify five previous laboratory experiments, spanning a period of 1924 to 1986, that exposed conifer seedlings to elevated soil surface temperatures for varying durations. We then synthesized the data from these studies to explore the survival of western U.S. conifer species in response to differing surface temperature levels. We found mortality thresholds consistent with previously reported measurements in field and lab studies, but found that as surface temperatures reach these lethal thresholds the duration of exposure matters greatly to survival outcomes. This work leverages an intuitive climate metric with clear consequences for seedling survival as an indicator of forest regeneration potential.
A Tracing Model for the Evolutionary Equilibrium of Octoploids
Authors: Wang Jing , Lv Xuemin , Feng Li , Dong Ang , Liang Dan , Wu Rongling
Published: January 2022

Testing Hardy-Weinberg equilibrium (HWE) is a fundamental approach for inferring population diversity and evolution, but its application to octoploids containing eight chromosome sets has not well been justified. We derive a mathematical model to trace how genotype frequencies transmit from parental to offspring generations in the natural populations of autooctoploids. We find that octoploids, including autooctolpoids undergoing double reduction, attach asymptotic HWE (aHWE) after 15 generations of random mating, in a contrast to diploids where one generation can assure exact equilibrium and, also, different from tetraploids that use 5 generations to reach aHWE. We develop a statistical procedure for testing aHWE in octoploids and apply it to analyze a real data set from octoploid switchgrass distributed in two ecologically different regions, demonstrating the usefulness of the test procedure. Our model provides a tool for studying the population genetic diversity of octoploids, inferring their evolutionary history, and identifying the ecological relationship of octoploid-genome structure with environmental adaptation.
Identify DNA-Binding Proteins Through the Extreme Gradient Boosting Algorithm
Authors: Zhao Ziye , Yang Wen , Zhai Yixiao , Liang Yingjian , Zhao Yuming
Published: January 2022

The exploration of DNA-binding proteins (DBPs) is an important aspect of studying biological life activities. Research on life activities requires the support of scientific research results on DBPs. The decline in many life activities is closely related to DBPs. Generally, the detection method for identifying DBPs is achieved through biochemical experiments. This method is inefficient and requires considerable manpower, material resources and time. At present, several computational approaches have been developed to detect DBPs, among which machine learning (ML) algorithm-based computational techniques have shown excellent performance. In our experiments, our method uses fewer features and simpler recognition methods than other methods and simultaneously obtains satisfactory results. First, we use six feature extraction methods to extract sequence features from the same group of DBPs. Then, this feature information is spliced together, and the data are standardized. Finally, the extreme gradient boosting (XGBoost) model is used to construct an effective predictive model. Compared with other excellent methods, our proposed method has achieved better results. The accuracy achieved by our method is 78.26% for PDB2272 and 85.48% for PDB186. The accuracy of the experimental results achieved by our strategy is similar to that of previous detection methods.
PRECISION.seq: An R Package for Benchmarking Depth Normalization in microRNA Sequencing
Authors: Zou Jian , Düren Yannick , Qin Li-Xuan
Published: January 2022

We present a new R package PRECISION.seq for assessing the performance of depth normalization in microRNA sequencing data. It provides a pair of microRNA sequencing data sets for the same set of tumor samples, additional pairs of data sets simulated by re-sampling under various patterns of differential expression, and a collection of numerical and graphical tools for assessing the performance of normalization methods. Users can easily assess their chosen normalization method and compare its performance to nine methods already included in the package. PRECISION.seq enables an objective and systematic evaluation of normalization methods in microRNA sequencing using realistically distributed and robustly benchmarked data under a wide range of differential expression patterns. To our best knowledge, this is the first such tool available. The data sets and source code of the R package can be found at https://github.com/LXQin/PRECISION.seq.
Phenotypic Spectrum and Molecular Basis in a Chinese Cohort of Osteogenesis Imperfecta With Mutations in Type I Collagen
Authors: Chen Peikai , Tan Zhijia , Shek Hiu Tung , Zhang Jia-nan , Zhou Yapeng , Yin Shijie , Dong Zhongxin , Xu Jichun , Qiu Anmei , Dong Lina , Gao Bo , To Michael Kai Tsun
Published: January 2022

Osteogenesis imperfecta (OI) is a rare inherited connective tissue dysplasia characterized with skeletal fragility, recurrent fractures and bone deformity, predominantly caused by mutations in the genes COL1A1 or COL1A2 that encode the chains of type I collagen. In the present study, clinical manifestations and genetic variants were analysed from 187 Chinese OI patients, majority of whom are of southern Chinese origin. By targeted sequencing, 63 and 58 OI patients were found carrying mutations in COL1A1 and COL1A2 respectively, including 8 novel COL1A1 and 7 novel COL1A2 variants. We validated a novel splicing mutation in COL1A1. A diverse mutational and phenotypic spectrum was observed, coupling with the heterogeneity observed in the transcriptomic data derived from osteoblasts of six patients from our cohort. Missense mutations were significantly associated (χ2p = 0.0096) with a cluster of patients with more severe clinical phenotypes. Additionally, the severity of OI was more correlated with the quality of bones, rather than the bone mineral density. Bone density is most responsive to bisphosphonate treatment during the juvenile stage (10–15 years old). In contrast, height is not responsive to bisphosphonate treatment. Our findings expand the mutational spectrum of type I collagen genes and the genotype-phenotype correlation in Chinese OI patients. The observation of effective bisphosphonate treatment in an age-specific manner may help to improve OI patient management.
The Role of RAB GTPases and Its Potential in Predicting Immunotherapy Response and Prognosis in Colorectal Cancer
Authors: Jiang Xuefei , Yang Lanlan , Gao Qianling , Liu Yiting , Feng Xingzhi , Ye Shubiao , Yang Zihuan
Published: January 2022

Background: Colorectal cancer (CRC) is the third most common cancer worldwide, in which aberrant activation of the RAS signaling pathway appears frequently. RAB proteins (RABs) are the largest Ras small GTPases superfamily that regulates intracellular membrane trafficking pathways. The dysregulation of RABs have been found in various diseases including cancers. Compared with other members of Ras families, the roles of RABs in colorectal cancer are less well understood.

Methods: We analyzed the differential expression and clinicopathological association of RABs in CRC using RNA sequencing and genotyping datasets from TCGA samples. Moreover, the biological function of RAB17 and RAB34 were investigated in CRC cell lines and patient samples.

Results: Of the 62 RABs we analyzed in CRC, seven (RAB10, RAB11A, RAB15, RAB17, RAB19, RAB20, and RAB25) were significantly upregulated, while six (RAB6B, RAB9B, RAB12, RAB23, RAB31, and RAB34) were significantly downregulated in tumor tissues as compared to normal. We found that the upregulated-RABs, which were highly expressed in metabolic activated CRC subtype (CMS3), are associated with cell cycle related pathways enrichment and positively correlated with the mismatch repair (MMR) genes in CRC, implying their role in regulating cell metabolism and tumor growth. While, high expression of the downregulated-RABs were significantly associated with poor prognostic CRC mesenchymal subtypes (CMS4), immune checkpoint genes, and tumor infiltrating immune cells, indicating their role in predicting prognosis and immunotherapy efficacy. Interestingly, though RAB34 mRNA is downregulated in CRC, its high expression is significantly associated with poor prognosis. In vitro experiments showed that RAB17 overexpression can promote cell proliferation via cell cycle regulation. While, RAB34 overexpression can promote cell migration and invasion and is associated with PD-L1/PD-L2 expression increase in CRC cells.

Conclusions: Our study showed that RABs may play important roles in regulating cell cycle and immune-related pathways, therefore might be potential biomarkers in predicting prognosis and immunotherapy response in CRC.
The Basis and Promise of Programmable RNA Editing and Modification
Authors: Lo Nicholas , Xu Xin , Soares Fraser , He Housheng Hansen
Published: January 2022

One key advantage of RNA over genomic editing is its temporary effects. Aside from current use of DNA-targeting CRISPR-Cas9, the more recently discovered CRISPR-Cas13 has been explored as a means of editing due to its RNA-targeting capabilities. Specifically, there has been a recent interest in identifying and functionally characterizing biochemical RNA modifications, which has spurred a new field of research known as “epitranscriptomics”. As one of the most frequently occurring transcriptome modifications, N6-methyladenosine (m6A) has generated much interest. The presence of m6A modifications is under the tight control of a series of regulators, and the ability of fusing these proteins or demethylases to catalytically inactive CRISPR proteins have resulted in a new wave of programmable RNA methylation tools. In addition, studies have been conducted to develop different CRISPR/Cas and base editor systems capable of more efficient editing, and some have explored the effects of in vivo editing for certain diseases. As well, the application of CRISPR and base editors for screening shows promise in revealing the phenotypic outcomes from m6A modification, many of which are linked to physiological, and pathological effects. Thus, the therapeutic potential of CRISPR/Cas and base editors for not only m6A related, but other RNA and DNA related disease has also garnered insight. In this review, we summarize/discuss the recent findings on RNA editing with CRISPR, base editors and non-CRISPR related tools and offer a perspective regarding future applications for basic and clinical research.
A Comprehensive Evaluation of the Antibody-Verified Status of Eplets Listed in the HLA Epitope Registry
Authors: Bezstarosti Suzanne , Bakker Kim H. , Kramer Cynthia S. M. , de Fijter Johan W. , Reinders Marlies E. J. , Mulder Arend , Claas Frans H. J. , Heidt Sebastiaan
Published: January 2022

Matching strategies based on HLA eplets instead of HLA antigens in solid organ transplantation may not only increase the donor pool for highly sensitized patients, but also decrease the incidence of de novo donor-specific antibody formation. However, since not all eplets are equally capable of inducing an immune response, antibody verification is needed to confirm their ability to be bound by antibodies, such that only clinically relevant eplets are considered. The HLA Epitope Registry has documented all theoretically defined HLA eplets along with their antibody verification status and has been the foundation for many clinical studies investigating eplet mismatch in transplantation. The verification methods for eplets in the Registry range from polyclonal sera from multi- and uni-parous women to murine and human monoclonal antibodies (mAbs), and antibodies purified by adsorption and elution from sera of HLA immunized individuals. The classification of antibody verification based on different methods for validation is problematic, since not all approaches represent the same level of evidence. In this study, we introduce a classification system to evaluate the level of evidence for the antibody-verified status of all eplets in the HLA Epitope Registry. We demonstrate that for a considerable number of eplets, the antibody-verified status is solely based on polyclonal serum reactivity of multiparous women or on reactivity of murine mAbs. Furthermore, we noted that a substantial proportion of patient sera analyses and human mAb data presented in the HLA Epitope Registry Database has never been published in a peer-reviewed journal. Therefore, we tested several unpublished human HLA-specific mAbs by luminex single antigen beads assay to analyze their HLA reactivity for eplet antibody verification. Although the majority of analyzed mAbs indeed verified their assigned eplets, this was not the case for a number of eplets. This comprehensive overview of evidence for antibody verification of eplets in the HLA Epitope Registry is instrumental for future investigations towards eplet immunogenicity and clinical studies considering antibody-verified eplet mismatch in transplantation and warrants further standardization of antibody verification using high quality data.
Inborn Errors of Immunity and Their Phenocopies: CTLA4 and PD-1
Authors: Hao Yuwei , Cook Matthew C.
Published: January 2022

Elucidating links between genotype and phenotype in patients with rare inborn errors of immunity (IEIs) provides insights into mechanisms of immune regulation. In many autosomal dominant IEIs, however, variation in expressivity and penetrance result in complex genotype-phenotype relations, while some autosomal recessive IEIs are so rare that it is difficult to draw firm conclusions. Phenocopies arise when an environmental or non-genetic factor replicates a phenotype conferred by a specific genotype. Phenocopies can result from therapeutic antibodies or autoantibodies that target a protein to replicate aspects of the phenotype conferred by mutations in the gene encoding the same protein. Here, we consider IEIs arising from rare genetic variants in CTLA4 and PDCD1 and compare clinical and laboratory manifestations arising as drug-induced phenocopies (immune related adverse events, IRAEs) in cancer patients treated with immune checkpoint inhibitors (ICI) and identify outstanding questions regarding mechanism of disease.
The Natural Cytotoxicity Receptor NKp44 (NCR2, CD336) Is Expressed on the Majority of Porcine NK Cells Ex Vivo Without Stimulation
Authors: Mair Kerstin H. , Crossman Assiatu J. , Wagner Bettina , Babasyan Susanna , Noronha Leela , Boyd Patricia , Zarlenga Dante , Stadler Maria , van Dongen Katinka A. , Gerner Wilhelm , Saalmüller Armin , Lunney Joan K.
Published: January 2022

Natural killer (NK) cells have been studied extensively in humans and mice for their vital role in the vertebrate innate immune system. They are known to rapidly eliminate tumors or virus infected cells in an immune response utilizing their lytic properties. The natural cytotoxicity receptors (NCRs) NKp30 (NCR3), NKp44 (NCR2), and NKp46 (NCR1) are important mediators of NK-cell cytotoxicity. NKp44 expression was reported for NK cells in humans as well as in some non-human primates and found exclusively on activated NK cells. Previously, no information was available on NKp44 protein expression and its role in porcine lymphocytes due to the lack of species-specific monoclonal antibodies (mAbs). For this study, porcine-specific anti-NKp44 mAbs were generated and their reactivity was tested on blood and tissue derived NK cells in pigs of different age classes. Interestingly, NKp44 expression was detectedex vivoalready on resting NK cells; moreover, the frequency of NKp44+NK cells was higher than that of NKp46+NK cells in most animals analyzed. Uponin vitrostimulation with IL-2 or IL-15, the frequency of NKp44+NK cells, as well as the intensity of NKp44 expression at the single cell level, were increased. Since little is known about swine NK cells, the generation of a mAb (clone 54-1) against NKp44 will greatly aid in elucidating the mechanisms underlying the differentiation, functionality, and activation of porcine NK cells.
Hygiene Hypothesis Indicators and Prevalence of Antinuclear Antibodies in US Adolescents
Authors: Meier Helen C. S. , Sandler Dale P. , Wilkerson Jesse , Miller Frederick W. , Dinse Gregg E. , Parks Christine G.
Published: January 2022

Autoimmunity prevalence, as measured by antinuclear antibodies (ANA), is increasing in U.S. adolescents. Improved hygiene and cleaner environments in childhood may reduce exposure to infections and other immune challenges, resulting in improper immune responses to later-life exposures. We examined associations of hygiene hypothesis indicators, including asthma, allergies, and antibodies to infectious agents, with ANA prevalence, measured by HEp-2 immunofluorescence, in adolescents (aged 12-19 years) over a 25-year time span in the National Health and Nutrition Examination Survey (NHANES) (N=2,709), adjusting for age, sex, race/ethnicity, body mass index, education and survey cycle, overall and within individual time periods, using logistic regression. Prevalence of ANA in adolescents increased from 5.0% in 1988-1991 to 12.8% in 2011-2012. ANA were positively associated with diagnosis of asthma in early childhood (OR: 2.07, CI: 1.09–3.99) and the effect estimate for current hay fever was elevated but not statistically significant (OR: 1.55, CI: 0.85–2.84). Fewer than 2% of those with ANA in 1988-1991 had been diagnosed with asthma, compared with 18% in 1999-2000, and 27% in 2003-2004 and 2011-2012. ANA trended negatively with Helicobacter pylori antibodies (OR: 0.49, CI: 0.24–0.99). ANA may be useful as an additional indicator of inadequate immune education in adolescence, a critical period of growth and development.
Comparative Transcriptional Analysis Identified Characteristic Genes and Patterns in HIV-Infected Immunological Non-Responders
Authors: Liu Xiaosheng , Lin Ling , Lu Lianfeng , Li Xiaodi , Han Yang , Qiu Zhifeng , Li Xiaoxia , Li Yanling , Song Xiaojing , Cao Wei , Li Taisheng
Published: January 2022

Purpose

The incomplete immune reconstitution is a complex phenomenon among human immunodeficiency virus (HIV)-infected patients despite the fact that they have achieved persistent viral suppression under the combined antiretroviral therapy. This study aims to screen and verify the immunological characteristics and underlying mechanisms of immunological non-responders (INRs).

Methods

The RNA-seq and the differentially expressed genes (DEGs) analysis were used to explore potential characteristics among INRs. Gene Ontology (GO) enrichment, ingenuity pathway analysis (IPA) analysis, Gene set enrichment analysis (GSEA) analysis, and the weighted gene co-expression network analysis (WGCNA) were used to explore the potential mechanism. The transcriptional meta-analysis was used to analyze the external efficiency.

Results

The RNA-seq identified 316 DEGs among INRs. The interferon signaling pathway was enrichedviaGO and IPA analysis among DEGs. The combined GSEA and WGCNA analysis confirmed that the IFN response was more correlated with INR. Furthermore, IFI27 (IFN-α Inducible Protein 27, also known as ISG12) was chosen based on combined DEG analysis, WGCNA analysis, and the transcriptional meta-analysis conducted on other published datasets about INRs. The expression of IFI27 was significantly negatively correlated with the CD4+ T-cell counts of PLWH, and the predictive efficiency of IFI27 level in distinguishing PLWH with poor immune recovery was also with significant power (AUC = 0.848).

Conclusion

The enhanced expression of IFI27 and the IFN response pathway are among the important immunological characteristics of INRs and exhibited promising efficiency as biomarkers for CD4+T-cell recovery.
Enhanced Immunomodulatory Effect of Intravenous Immunoglobulin by Fc Galactosylation and Nonfucosylation
Authors: Mimura Yusuke , Mimura-Kimura Yuka , Saldova Radka , Rudd Pauline M. , Jefferis Roy
Published: January 2022

Intravenous immunoglobulin (IVIG) is used as an immunomodulatory agent in the treatment of various autoimmune/inflammatory diseases although its mechanism of action remains elusive. Recently, nonfucosylated IgG has been shown to be preferentially bound to Fcγ receptor IIIa (FcγRIIIa) on circulating natural killer cells; therefore, we hypothesized that nonfucosylated IVIG may modulate immune responses through FcγRIIIa blockade. Here, homogeneous fucosylated or nonfucosylated glycoforms of normal polyclonal IgG bearing sialylated, galactosylated or nongalactosylated Fc oligosaccharides were generated by chemoenzymatic glycoengineering to investigate whether the IgG glycoforms can inhibit antibody-dependent cellular cytotoxicity (ADCC). Among the six IgG glycoforms, galactosylated, nonfucosylated IgG [(G2)2] had the highest affinity to FcγRIIIa and 20 times higher potency to inhibit ADCC than native IgG. A pilot study of IVIG treatment in mice with collagen antibody-induced arthritis highlighted the low-dose (G2)2 glycoform of IVIG (0.1 g/kg) as an effective immunomodulatory agent as the 10-fold higher dose of native IVIG. These preliminary results suggest that the anti-inflammatory activity of IVIG is in part mediated via activating FcγR blockade by galactosylated, nonfucosylated IgG and that such nonfucosylated IgG glycoforms bound to FcγRs on immune cells play immunomodulatory roles in health and disease. This study provides insights into improved therapeutic strategies for autoimmune/inflammatory diseases using glycoengineered IVIG and recombinant Fc.
Case Report: A Case of Epstein-Barr Virus-Associated Acute Liver Failure Requiring Hematopoietic Cell Transplantation After Emergent Liver Transplantation
Authors: Nakajima Koji , Hiejima Eitaro , Nihira Hiroshi , Kato Kentaro , Honda Yoshitaka , Izawa Kazushi , Kawabata Naoko , Kato Itaru , Ogawa Eri , Sonoda Mari , Okamoto Tatsuya , Okajima Hideaki , Yasumi Takahiro , Takita Junko
Published: January 2022

Hepatic manifestations of Epstein-Barr virus (EBV) infection are relatively common, mild, and self-limiting. Although fulminant hepatic failure has been reported in a few cases, the contributing factors are unclear. This report discusses a pediatric case of EBV-associated acute liver failure that required urgent liver transplantation; however, liver damage continued to progress post-liver replacement. Monoclonal CD8+ T cells that preferentially infiltrated the native and transplanted liver were positive for EBV-encoded small RNA, suggesting a pathophysiology similar to that of EBV-associated hemophagocytic lymphohistiocytosis and chronic active EBV infection. Therefore, subsequent chemotherapy and hematopoietic cell transplantation was conducted, which led to cure. This is the first case of EBV-associated acute liver failure that relapsed post-liver transplant. As such, it sheds light on an under-recognized clinical entity: liver-restricted hyperinflammation caused by EBV-infected monoclonal CD8+ T cells. This phenomenon needs to be recognized and differentiated from hepatitis/hepatic failure caused by EBV-infected B cells, which has a relatively benign clinical course.
Light-Sheet Scattering Microscopy to Visualize Long-Term Interactions Between Cells and Extracellular Matrix
Authors: Zhou Xiangda , Zhao Renping , Yanamandra Archana K. , Hoth Markus , Qu Bin
Published: January 2022

Visualizing interactions between cells and the extracellular matrix (ECM) mesh is important to understand cell behavior and regulatory mechanisms by the extracellular environment. However, long term visualization of three-dimensional (3D) matrix structures remains challenging mainly due to photobleaching or blind spots perpendicular to the imaging plane. Here, we combine label-free light-sheet scattering microcopy (LSSM) and fluorescence microscopy to solve these problems. We verified that LSSM can reliably visualize structures of collagen matrices from different origin including bovine, human and rat tail. The quality and intensity of collagen structure images acquired by LSSM did not decline with time. LSSM offers abundant wavelength choice to visualize matrix structures, maximizing combination possibilities with fluorescently-labelled cells, allowing visualizing of long-term ECM-cell interactions in 3D. Interestingly, we observed ultrathin thread-like structures between cells and matrix using LSSM, which were not observed by normal fluorescence microscopy. Transient local alignment of matrix by cell-applied forces can be observed. In summary, LSSM provides a powerful and robust approach to investigate the complex interplay between cells and ECM.
Diversity of Dysregulated Long Non-Coding RNAs in HBV-Related Hepatocellular Carcinoma
Authors: Samudh Nazia , Shrilall Creanne , Arbuthnot Patrick , Bloom Kristie , Ely Abdullah
Published: January 2022

Infection with the hepatitis B virus (HBV) continues to pose a major threat to public health as approximately 292 million people worldwide are currently living with the chronic form of the disease, for which treatment is non-curative. Chronic HBV infections often progress to hepatocellular carcinoma (HCC) which is one of the world’s leading causes of cancer-related deaths. Although the process of hepatocarcinogenesis is multifaceted and has yet to be fully elucidated, several studies have implicated numerous long non-coding RNAs (lncRNAs) as contributors to the development of HCC. These host-derived lncRNAs, which are often dysregulated as a consequence of viral infection, have been shown to function as signals, decoys, guides, or scaffolds, to modulate gene expression at epigenetic, transcriptional, post-transcriptional and even post-translational levels. These lncRNAs mainly function to promote HBV replication and oncogene expression or downregulate tumor suppressors. Very few lncRNAs are known to suppress tumorigenesis and these are often downregulated in HCC. In this review, we describe the mechanisms by which lncRNA dysregulation in HBV-related HCC promotes tumorigenesis and cancer progression.
Assessing Effects of Sediment Delivery to Coral Reefs: A Caribbean Watershed Perspective
Authors: Rogers Caroline S. , Ramos-Scharrón Carlos E.
Published: January 2022

Coral reefs in the western Atlantic and Caribbean are deteriorating primarily from disease outbreaks, increasing seawater temperatures, and stress due to land-based sources of pollutants including sediments associated with land use and dredging. Sediments affect corals in numerous ways including smothering, abrasion, shading, and inhibition of coral recruitment. Sediment delivery resulting in deposition and water quality deterioration can cause degradation at the spatial scale of corals or entire reefs. We still lack rigorous long-term studies of coral cover and community composition before, during and after major sediment stress, and evidence of recovery after watershed management actions. Here we present an overview of the effects of terrestrial sediments on corals and coral reefs, with recent advances in approaches to watershed assessment relevant to the delivery of sediments to these ecosystems. We present case studies of northeastern Caribbean watersheds to illustrate challenges and possible solutions and to draw conclusions about the current state of knowledge of sediment effects on coral reefs. With a better understanding of erosion and the pathways of sediment discharge to nearshore reefs, there is the increased potential for management interventions.
Western Gull Foraging Behavior as an Ecosystem State Indicator in Coastal California
Authors: Cimino Megan A. , Shaffer Scott A. , Welch Heather , Santora Jarrod A. , Warzybok Pete , Jahncke Jaime , Schroeder Isaac , Hazen Elliott L. , Bograd Steven J.
Published: January 2022

With accelerating climate variability and change, novel approaches are needed to warn managers of changing ecosystem state and to identify appropriate management actions. One strategy is using indicator species—like seabirds as ecosystem sentinels—to monitor changes in marine environments. Here, we explore the utility of western gulls (Larus occidentalis) breeding on Southeast Farallon Island as a proxy of ecosystem state in coastal California by investigating the interannual variability in gull foraging behavior from 2013 to 2019 in relation to upwelling conditions, prey abundances, and overlap with humpback whales (Megaptera novaeangliae) as gulls frequently feed in association with whales. Western gulls have a flexible diet and forage on land and at-sea. We combined gull GPS tracking data during the incubation phase, ecosystem survey data on multiple predator and prey species, and derived oceanographic upwelling products. When foraging at sea, gulls overlapped with cool upwelled waters. During 2015–2017, 25% more gull foraging trips visited land than in other years, where land trips were on average ∼8 h longer and 40% further than sea trips, which coincided with high compression of coastally upwelled waters (habitat compression) in 2015–2016. Gull foraging behavior was related to local prey abundances, where more foraging occurred near shore or on land when prey abundances were low. However, visual surveys indicated that ∼70% of humpback whale observations co-occurred with gulls, and the year with the most foraging on land (2017) corresponded to regionally low relative whale abundances, suggesting gull movement patterns could be an indicator of whale presence. Further, both whales and gulls forage near-shore under high upwelling habitat compression and low krill abundance. Hence, the deployment of year-round tags on gulls with the capability of near real-time data accessibility could provide important fine-scale metrics for conservation and management of the threatened yet recovering eastern Pacific humpback whale population between infrequent and coarse surveys. Entanglement in fishing gear and ship strikes are major inhibitors to whale recovery and have increased concomitantly with human use of ocean resources. Moreover, as climate variability and change increase, novel indicators should be explored and implemented to inform marine spatial planning and protect species across multiple scales from new risks.
Microbiome Structuring Within a Coral Colony and Along a Sedimentation Gradient
Authors: Fifer James E. , Bui Vy , Berg Justin T. , Kriefall Nicola , Klepac Courtney , Bentlage Bastian , Davies Sarah W.
Published: January 2022

Reef-building corals form complex relationships with a wide range of microbial partners, including symbiotic algae in the family Symbiodiniaceae and various bacteria. These coral-associated communities can be shaped to varying degrees by environmental context. Sedimentation can structure a coral’s microbial community by altering light availability for symbiotic algae, triggering the coral’s stress response, or serving as a reservoir for both pathogenic and essential bacterial and algal symbionts. To examine the influence of sedimentation on a coral’s microbiome, we used 16S rDNA and ITS-2 amplicon sequencing to characterize the bacterial and algal communities associated with the massive scleractinian coral Porites lobata across pairs of sites along a naturally occurring sedimentation gradient in Fouha Bay, southern Guam. Additionally, we investigate the influence of proximity to sediment on the coral colony scale, by sampling from the edge and center of colonies as well as the nearby sediment. The P. lobata colonies associated with several different genotypes of Cladocopium C15 algal symbionts and often harbored different genotypes within a single colony. However, the different Cladocopium genotypes showed no structuring according to colony position or location along the sedimentation gradient. Bacterial communities were largely consistent across the sedimentation gradient, however, some rarer taxa were differentially abundant across sites. Planococcaceae shows higher abundance closer to the river mouth in coral colonies in both the edge and center of colonies. Peredibacter also shows high abundance near the river mouth but only in sediment and the edges of the colony. We find sediment plays a larger role structuring bacterial communities at the colony scale compared to a coral’s position along the sedimentation gradient. Edge communities look more similar to the sediment compared to the center communities and are also enriched in similar pathways such as those involved in nitrogen fixation. We also find center samples to be dominated by Endozoicomonas compared to the edge, supporting a role for this taxon in structuring bacterial communities and limiting bacterial diversity in coral colonies. Together these results show the differential impact sedimentation can have between sections of the coral colony microhabitat.
The Bonding Interface and Tribological Properties of Cu–Graphite Sandwich Composites Fabricated via Accumulative Roll-Bonding Processes
Authors: Liu Jinping , Ding Yi , Sun Ke , Zeng Longfei , Xiao Xiangpeng , Cao Wei , Guan Lijun , Ran Jingyou , Sun Zhe , Shi Shuaifei , Zhang Jianbo
Published: January 2022

Copper–graphite sandwich composites are new functional composites with excellent tribological and mechanical properties. More and more researchers prepare the sandwich composites by accumulative roll-bonding processes due to severe plasticity deformation. The microstructure and properties of copper–graphite sandwich composites prepared by continual annealing and accumulative roll-bonding processes for eight rolling cycles were investigated. The results showed that with the increase of rolling cycles, the dispersion of graphite particles between two copper layers along a rolling direction became more uniform, the pores at the interface between graphite particles and the Cu matrix gradually disappeared, and the hardness of copper–graphite composites gradually increased. After eight rolling cycles, the Vickers hardness of the composites increased by 140.8% as compared with that of annealed pure copper. During friction, the steel balls can meet some graphite particles in the composites rolled by four cycles. The friction coefficient and wear loss of copper–graphite composites gradually decreased with the increase of rolling cycles. Compared with the composites rolled by one cycle, the friction coefficient and wear loss of the composites rolled by eight cycles were reduced by 32.5 and 49.0%, respectively. The main wear mechanism gradually evolved from fatigue wear and abrasive wear to adhesive wear, and then to fatigue wear.
Hemp From Disordered Lines for New Staple Fibre Yarns and High-Performance Composite Applications
Authors: Graupner Nina , Weber David E. , Bell Erik G. , Lehmann Karl-Heinz , Hilgers Hans-Willi , Randerath Herbert , Gries Thomas , Walenta Isabel , Joulian Marc , Müssig Jörg
Published: January 2022

The use of natural fibre-reinforced plastics for higher-stressed applications is currently often limited by the high price of high-quality semi-finished products. Therefore, the present study deals with developing yarns from cost-effective hemp from a disordered separation process (total fibre line) for composite reinforcements. Composites were fabricated using a miniature pultrusion process with thermosetting matrices from the yarns. The results show that around 90% of the flexural strength and flexural modulus of identically produced flax composites could be achieved with maximum values of 282 MPa for the flexural strength and 23.4 GPa for the flexural modulus. The yarns were additionally used to manufacture quasi-unidirectional fabrics to produce composite laminates using different manufacturing processes. The highest values were obtained for a laminate with 39 vol% fibre content, produced with a resin injection process in an autoclave, achieving a tensile strength of 155 MPa, Young’s modulus of 19.4 GPa, a flexural strength of 174 MPa and bending modulus of 12.4 GPa. The characteristic values are sufficient to use the materials in applications with higher mechanical requirements.
Research on the Mechanical Integrity of Low-Density Cement Mortar
Authors: Renjun Xie , Zhiqiang Wu , Xiaowei Cheng , Xiucheng Ni
Published: January 2022

Poor mechanical integrity of cement sheaths during the production of oil and gas wells may cause air channeling and water channeling issues in the wells, leading to severe safety problems, and adversely affecting the safety and efficiency of the oil and gas resources production. This article focuses on a low-density cement slurry system with added floating beads. The compressive strength and flexural strength of cement stones, the mechanical integrity of cement rings, and triaxial mechanical properties were assessed. The optimal dosage of floating beads and the evolution of the cement stone’s mechanical properties and deformation ability were discussed. Bonding strengths of the first and the second interfaces were evaluated using the shrinkage test results of the cement mortar. Finally, the microscopic mechanism of the change in mechanical properties was analyzed by scanning electron microscopy. The results showed that the cement mortar exhibited the best compressive strength, mechanical integrity, and deformability after blending with 15% floating beads. At the same time, the volume shrinkage of the cement mortar mixed with 15% floating beads was the smallest, only 0.00667%, plausibly indicating good bonding with a casing and the formation to reduce the occurrence of gas channeling. Finally, the microscopic test of the cement mortar showed that the bonding between floating beads and cement was not tight, so internal cracks in the cement easily developed along the bonding part of cement and floating beads. The more floating beads were mixed, the more likely was cement mortar destroyed.
Case Report: Dislocation Into Vitreous Cavity and Removal of a Posterior Chamber Phakic Intraocular Lens
Authors: He Jingliang , Zhang Li , Zheng Fang , Fang Xiaoyun
Published: January 2022

Purpose:

To report a rare case of delayed dislocation of a novel posterior chamber phakic intraocular lens into the vitreous cavity, which was successfully treated by a reformed technique.

Case Presentation

A 29-year-old female received Ejinn phakic refractory lens (EPRL) implantation to correct her high myopia. Spontaneous dislocation into the vitreous cavity occurred 26-months post-operatively without traumatic history. Pars plana vitrectomy combined with cutting the EPRL into two equal pieces was performed to remove the dislocated EPRL.

Conclusion

Dislocation into the vitreous cavity of EPRL can be successfully and easily removed by our reformed technique. Concerns about zonules-related complications pre-operatively, intraoperatively, and post-operatively must be raised in the practice of EPRL implantation.
Trends and Disparities in Quality of Life Among Older Adults From 1998 to 2018 in China: A National Observational Study
Authors: Liu Jue , Wang Jun
Published: January 2022

Objective

To investigate 20-year trends and disparities in quality of life among older adults in China from 1998 to 2018.

Methods

Our study was based on eight representative nationwide health surveys among older adults conducted in China from 1998 to 2018. Quality of life data were obtained from 91,993 individuals aged 65 years or above. All surveys included identical indicators of self-reported quality of life, demographic factors, socioeconomic status, lifestyle habits, and health status. The trends in the standardized prevalence of poor quality of life from 1998 to 2018 were examined by locally weighted scatterplot smoothing regression (LOWESS) analysis. We assessed the prevalence of poor quality of life and its related factors by logistic regression models after adjusting for potential confounders.

Results

The prevalence of poor quality of life was 38.2% (95% CI: 37.9–38.5%). The trends of poor quality of life showed an inverted “U” shape, that the prevalence increased from 27.8% in 1998 to 43.6% in 2008, and then decreased from 39.2% in 2011 to 32.1% in 2018. Disparities in the prevalence of poor quality of life were exacerbating among participants with low or moderate household income per capita and participants with high household income per capita from 1998 to 2018. After controlling potential confounders, living in rural areas, aged below 80 years, unmarried, living alone, low household income, current smoker, poor dietary diversity, never participating in organized social activities, with chronic diseases, functional disability, poor self-reported health, and unhealthy psychological status were risk factors related with poor quality of life in the multivariate model (all p < 0.05).

Conclusion

During the past two decades, poor quality of life in Chinese older adults showed an inverted “U” trend from 1998 to 2018 that the prevalence of poor quality of life peaked in 2008 and declined since China's deepening health system reform in 2009. However, disparities in the poor quality of life were exacerbating among participants with different socioeconomic statuses. Strengthening the health system is of great importance in improving the quality of life. More efforts are needed to reduce the disparities in the quality of life among the population at the different socioeconomic levels.
Calpain Inhibitor Calpeptin Alleviates Ischemia/Reperfusion-Induced Acute Kidney Injury via Suppressing AIM2 Inflammasome and Upregulating Klotho Protein
Authors: Wu Yong , Yang Huan , Cheng Ming , Shi Jialin , Zhang Weichen , Liu Shaojun , Zhang Minmin
Published: January 2022

Renal ischemia/reperfusion injury is a major contributor of acute kidney injury (AKI), leading to renal cell necrosis, apoptosis, and inflammation. Calpains, a family of Ca2+-dependent cysteine proteases, play a pivotal role in the pathogenesis of renal diseases. Several studies have reported calpain inhibitors showing remarkable reno-protective effects against proteinuria and α-klotho deficiency-induced renal aging symptoms, particularly against glomerulus injury. However, little is known about the role of the calpain inhibitor calpeptin in acute kidney injury. The present study aims to investigate the potential mechanism of downregulation of Calpain 1 and 2 activity by calpeptin in the ischemia/reperfusion (IR)-induced AKI model. Firstly, we observed that the contents of Calpain 1 and 2 were significantly increased in the renal biopsy of clinical AKI patients, especially in the diseased tubules space. To investigate the impacts of calpain activity inhibition, we further pretreated with calpeptin in both the IR mouse model and in the HK-2 cells hypoxia model. We found that the calpain inhibitor calpeptin improved renal functional deterioration, attenuated pathological structure damage, and decreased tubular cell apoptosis in the IR injury-induced AKI mice model. Mechanistically, calpeptin significantly suppressed the AIM2 (absent in melanoma 2) and NLRP3 (NOD-like receptor protein 3) inflammasome signaling pathways and increased Klotho protein levels. Furthermore, immunofluorescence assays demonstrated that the application of calpeptin effectively inhibited Calpain 1 activation and gasdermin D (GSDMD) cleavage in the renal tubules of IR mice. Taken together, our both in vivo and in vitro experiments suggest that calpeptin conveyed reno-protection in AKI might be mediated by the inhibition of AIM2 inflammasome activation and upregulation of Klotho protein. As such, we provide new evidence that Calpain 1 and 2 activation may be closely associated with the pathogenesis of clinical AKI. The calpain-mediated AIM2 inflammasome signaling pathway and distinct interaction between calpain and Klotho may provide a potential novel preventative and therapeutic target for acute kidney injury.
Niches and Seasonal Changes, Rather Than Transgenic Events, Affect the Microbial Community of Populus × euramericana ‘Neva’
Authors: Huang Yali , Dong Yan , Ren Yachao , Wang Shijie , Li Yongtan , Du Kejiu , Lin Xin , Yang Minsheng
Published: January 2022

Exploring the complex spatiotemporal changes and colonization mechanism of microbial communities will enable microbial communities to be better used to serve agricultural and ecological operations. In addition, evaluating the impact of transgenic plants on endogenous microbial communities is necessary for their commercial application. In this study, microbial communities of Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-BADH genes (ECAA1 line), Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-NTHK1 genes (ECAB1 line), and non-transgenic Populus × euramericana ‘Neva’ from rhizosphere soil, roots, and phloem collected in different seasons were compared and analyzed. Our analyses indicate that the richness and diversity of bacterial communities were higher in the three Populus × euramericana ‘Neva’ habitats than in those of fungi. Bacterial and fungal genetic-distance-clustering results were similar; rhizosphere soil clustered in one category, with roots and phloem in another. The diversity and evenness values of the microbial community were: rhizosphere soil > phloem > root system. The bacterial communities in the three habitats were dominated by the Proteobacteria, and fungal communities were dominated by the Ascomycota. The community composition and abundance of each part were quite different; those of Populus × euramericana ‘Neva’ were similar among seasons, but community abundance fluctuated. Seasonal fluctuation in the bacterial community was greatest in rhizosphere soil, while that of the fungal community was greatest in phloem. The transgenic lines ECAA1 and ECAB1 had a bacterial and fungal community composition similar to that of the control samples, with no significant differences in community structure or diversity among the lines. The abundances of operational taxonomic units (OTUs) were low, and differed significantly among the lines. These differences did not affect the functioning of the whole specific community. Sampling time and location were the main driving factors of changes in the Populus × euramericana ‘Neva’ microbial community. Transgenic events did not affect the Populus × euramericana ‘Neva’ rhizosphere or endophytic microbial communities. This study provides a reference for the safety evaluation of transgenic plants and the internal colonization mechanism of microorganisms in plants.