bluuebunny/crossref_metadata_2025 huggingface dataset:
Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation
Authors: Chen Fanghui , Sheng Le , Xu Chenjie , Li Jun , Ali Ilyas , Li Honglin , Cai Yafei
Published: July 2021

The dairy cattle suffer from severe liver dysfunction during the pathogenesis of ketosis. The Ufm1 conjugation system is crucial for liver development and homeostasis. Ufm1 binding protein (Ufbp1) is a putative Ufm1 target and an integral component, but its role in ketosis-induced liver injury is unclear so far. The purpose of this study is to explore the key role of Ufbp1 in liver fibrosis caused by ketosis in vivo and in vitro. Liver tissues were collected from ketotic cows and Ufbp1 conditional knockout (CKO) mice in vivo. However, Ufbp1–/– mouse embryonic fibroblast cells and Hela cells were used for in vitro validation. Subsequently, various assays were performed to reveal the underlying molecular mechanisms of the Ufbp1 protective effect. In this study, hepatic fibrosis, endoplasmic reticulum (ER) stress, and apoptosis were reported in the liver of ketotic cows, fibrotic markers (alpha-smooth muscle actin, Collagen1) and ER stress markers (glucose-regulated protein 78, CEBP homologous protein) were upregulated remarkably, and the apoptosis-related genes (Bcl2, Bax) were in line with expectations. Interestingly, Ufbp1 expression was almost disappeared, and Smad2/Smad3 protein was largely phosphorylated in the liver of ketotic cows, but Ufbp1 deletion caused Smad3 phosphorylation apparently, rather than Smad2, and elevated ER stress was observed in the CKO mice model. At the cellular level, Ufbp1 deficiency led to serious fibrotic and ER stress response, Smad3 was activated by phosphorylation significantly and then was translocated into the nucleus, whereas p-Smad2 was largely unaffected in embryonic fibroblast cells. Ufbp1 overexpression obviously suppressed Smad3 phosphorylation in Hela cells. Ufbp1 was found to be in full combination with Smad3 using endogenous immunoprecipitation. Taken together, our findings suggest that downregulation or ablation of Ufbp1 leads to Smad3 activation, elevated ER stress, and hepatocyte apoptosis, which in turn causes liver fibrosis. Ufbp1 plays a protective role in ketosis-induced liver injury.
Luteolin Orchestrates Porcine Oocyte Meiotic Progression by Maintaining Organelle Dynamics Under Oxidative Stress
Authors: Park Soo-Hyun , Jeong Pil-Soo , Joo Ye Eun , Kang Hyo-Gu , Kim Min Ju , Lee Sanghoon , Song Bong-Seok , Kim Sun-Uk , Cho Seong-Keun , Sim Bo-Woong
Published: July 2021

Increasing evidence has demonstrated that oxidative stress impairs oocyte maturation, but the underlying mechanisms remain largely unknown. Here, for the first time, we examined the antioxidant role of luteolin in meiotic progression and the underlying mechanisms. Supplementation of 5 μM luteolin increased the rates of first polar body extrusion and blastocyst formation after parthenogenetic activation, and the expression levels of oocyte competence (BMP15 and GDF9)-, mitogen-activated protein kinase (MOS)-, and maturation promoting factor (CDK1 and Cyclin B)-related genes were also improved. Luteolin supplementation decreased intracellular reactive oxygen species levels and increased the expression levels of oxidative stress-related genes (SOD1, SOD2, and CAT). Interestingly, luteolin alleviated defects in cell organelles, including actin filaments, the spindle, mitochondria, the endoplasmic reticulum, and cortical granules, caused by H2O2 exposure. Moreover, luteolin significantly improved the developmental competence of in vitro-fertilized embryos in terms of the cleavage rate, blastocyst formation rate, cell number, cellular survival rate, and gene expression and markedly restored the competencies decreased by H2O2 treatment. These findings revealed that luteolin supplementation during in vitro maturation improves porcine meiotic progression and subsequent embryonic development by protecting various organelle dynamics against oxidative stress, potentially increasing our understanding of the underlying mechanisms governing the relationship between oxidative stress and the meiotic events required for successful oocyte maturation.
Identification of Novel Serum Metabolic Biomarkers as Indicators in the Progression of Intravenous Leiomyomatosis: A High Performance Liquid Chromatography-Tandem Mass Spectrometry-Based Study
Authors: Ge Zhitong , Feng Penghui , Zhang Zijuan , Li Jianchu , Yu Qi
Published: July 2021

Background

Intravenous leiomyomatosis (IVL) is a rare estrogen-dependent neoplasm. However, identifiable and reliable biomarkers are still not available for clinical application, especially for the diagnosis and prognosis of the disease.

Methods

In the present study, 30 patients with IVL and 30 healthy controls were recruited. Serum samples were isolated from these participants for further high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis to study metabolomics alterations and identify differentially expressed metabolites based on orthogonal partial least-squares discriminant analysis (OPLS-DA). Subsequently, lasso regression analysis and a generalized linear regression model were applied to screen out hub metabolites associated with the progression of IVL.

Results

First, 16 metabolites in the positive ion mode were determined from the 240 identifiable metabolites at the superclass level, with ten metabolites upregulated in the IVL group and the remaining six metabolites downregulated. Our data further proved that four metabolites [hypoxanthine, acetylcarnitine, glycerophosphocholine, and hydrocortisone (cortisol)] were closely related to the oncogenesis of IVL. Hypoxanthine and glycerophosphocholine might function as protective factors in the development of IVL (OR = 0.19 or 0.02, respectively). Nevertheless, acetylcarnitine and hydrocortisone (cortisol), especially the former, might serve as risk indicators for the disease to promote the development or recurrence of IVL (OR = 18.16 or 2.10, respectively). The predictive accuracy of these hub metabolites was further validated by the multi-class receiver operator characteristic curve analysis (ROC) with the Scikit-learn algorithms.

Conclusion

Four hub metabolites were finally determined via comprehensive bioinformatics analysis, and these substances could potentially serve as novel biomarkers in predicting the prognosis or progression of IVL.
Cellular and Molecular Insights Into the Etiology of Subfertility/Infertility in Crossbred Bulls (Bos taurus × Bos indicus): A Review
Authors: Kumaresan Arumugam , Elango Kamaraj , Datta Tirtha Kumar , Morrell Jane M.
Published: July 2021

Crossbreeding of indigenous cattle (Bos indicus) with improved (Bos taurus) breeds gained momentum and economic relevance in several countries to increase milk production. While production performance of the crossbred offspring is high due to hybrid vigor, they suffer from a high incidence of reproductive problems. Specifically, the crossbred males suffer from serious forms of subfertility/infertility, which can have a significant effect because semen from a single male is used to breed several thousand females. During the last two decades, attempts have been made to understand the probable reasons for infertility in crossbred bulls. Published evidence indicates that testicular cytology indices, hormonal concentrations, sperm phenotypic characteristics and seminal plasma composition were altered in crossbred compared to purebred males. A few recent studies compared crossbred bull semen with purebred bull semen using genomics, transcriptomics, proteomics and metabolomics; molecules potentially associated with subfertility/infertility in crossbred bulls were identified. Nevertheless, the precise reason behind the poor quality of semen and high incidence of sub-fertility/infertility in crossbred bulls are not yet well defined. To identify the underlying etiology for infertility in crossbred bulls, a thorough understanding of the magnitude of the problem and an overview of the prior art is needed; however, such systematically reviewed information is not available. Therefore, the primary focus of this review is to compile and analyze earlier findings on crossbred bull fertility/infertility. In addition, the differences between purebred and crossbred males in terms of testicular composition, sperm phenotypic characteristics, molecular composition, environmental influence and other details are described; future prospects for research on crossbred males are also outlined.
Long Non-coding RNA Signature for Liver Metastasis of Colorectal Cancers
Authors: Liu Fang , Song Zhen-Mei , Wang Xiao-Di , Du Shi-Yu , Peng Na , Zhou Jing-Rui , Zhang Ming-Gang
Published: July 2021

Colorectal cancer ranks within the top three cancers both in terms of incidence as well as deaths. Metastasis is often the major cause of mortality and liver is the primary and most common site to which colorectal cancers metastasize. We tested the prognostic ability of a long non-coding RNA (lncRNA) signature in liver metastatic colorectal cancers. We first evaluated expression levels of several lncRNAs in eight excised liver metastases from primary colorectal cancers and found significantly upregulated lncRNAs HOTAIR and MALAT1 along with significantly downregulated LOC285194. We further compared the expression levels of HOTAIR, MALAT1 and LOC285194 in primary colorectal tumors at the time of initial diagnosis and correlated them with disease progression and liver metastasis. HOTAIR and MALAT1 were significantly upregulated and LOC285194 was significantly downregulated in twelve patients who were diagnosed with liver metastasis within 5 years of initial diagnosis, compared to the five patients with no metastasis. A positive signature comprising of high HOTAIR/MALAT1 and low LOC285194 also correlated with progression to higher grade tumors. Thus, the lncRNA signature comprising of high HOTAIR/MALAT1 and low LOC285194 could be a prognostic signature for liver metastasis as well as overall poor survival.
Decreased m6A Modification of CD34/CD276(B7-H3) Leads to Immune Escape in Colon Cancer
Authors: Zhou Yiran , Zhou Haodong , Shi Jianlin , Guan Aoran , Zhu Yankun , Hou Zongliu , Li Ruhong
Published: July 2021

Previous studies have reported that m6a modification promotes tumor immune escape by affecting tumor microenvironment (TME). Due to the complexity of TME, a single biomarker is insufficient to describe the complex biological characteristics of tumor and its microenvironment. Therefore, it is more meaningful to explore a group of effective biomarkers reflecting different characteristics of cancer to evaluate the biological characteristics of solid tumors. Here, the immune gene CD34/CD276 with different m6A peak was obtained by m6A sequencing (MeRIP-seq) of colon cancer (CRC)clinical samples and combined with MsIgDB database, which was used to perform cluster analysis on TCGA-COAD level 3 data. The CD34/CD276 as a molecular marker for CRC prognosis was confirmed by survival analysis and immunohistochemical assay. Further bioinformatics analysis was carried out to analyze the molecular mechanism of CD34/CD276 affecting the TME through m6a-dependent down-regulation and ultimately promoting immune escape of CRC.
A Lytic Yersina pestis Bacteriophage Obtained From the Bone Marrow of Marmota himalayana in a Plague-Focus Area in China
Authors: Liang Junrong , Qin Shuai , Duan Ran , Zhang Haoran , Wu Weiwei , Li Xu , Tang Deming , Fu Guoming , Lu Xinmin , Lv Dongyue , He Zhaokai , Mu Hui , Xiao Meng , Yang Jinchuan , Jing Huaiqi , Wang Xin
Published: July 2021

A lytic Yersinia pestis phage vB_YpP-YepMm (also named YepMm for briefly) was first isolated from the bone marrow of a Marmota himalayana who died of natural causes on the Qinghai-Tibet plateau in China. Based on its morphologic (isometric hexagonal head and short non-contractile conical tail) and genomic features, we classified it as belonging to the Podoviridae family. At the MOI of 10, YepMm reached maximum titers; and the one-step growth curve showed that the incubation period of the phage was about 10 min, the rise phase was about 80 min, and the lysis amount of the phage during the lysis period of 80 min was about 187 PFU/cell. The genome of the bacteriophage YepMm had nucleotide-sequence similarity of 99.99% to that of the Y. pestis bacteriophage Yep-phi characterized previously. Analyses of the biological characters showed that YepMm has a short latent period, strong lysis, and a broader lysis spectrum. It could infect Y. pestis, highly pathogenic bioserotype 1B/O:8 Y. enterocolitica, as well as serotype O:1b Y. pseudotuberculosis—the ancestor of Y. pestis. It could be further developed as an important biocontrol agent in pathogenic Yersinia spp. infection.
New Developments in Exosomal lncRNAs in Cardiovascular Diseases
Authors: Yuan Zhu , Huang Weiqiang
Published: July 2021

Long non-coding RNAs (lncRNAs) are non-coding RNAs with lengths >200 nt and are involved in the occurrence and development of cardiovascular diseases (CVDs). Exosomes are secreted and produced by various cell types. Exosome contents include various ncRNAs, proteins and lipids. Exosomes are also important mediators of intercellular communication. The proportion of lncRNAs in exosomes is low, but increasing evidence suggests that exosomal lncRNAs play important roles in CVDs. We focused on research progress in exosomal lncRNAs in atherosclerosis, myocardial infarction, myocardial ischemia-reperfusion injury, cardiac angiogenesis, cardiac aging, rheumatic heart disease, and chronic kidney disease combined with CVD. The potential diagnostic and therapeutic effects of exosomal lncRNAs in CVDs are summarized based on preclinical studies involving animal and cell models and circulating exosomes in clinical patients. Finally, the challenges and possible prospects of exosomes and exosomal lncRNAs in clinical applications related to CVD are discussed.
A Benchmark for Data Imputation Methods
Authors: Jäger Sebastian , Allhorn Arndt , Bießmann Felix
Published: July 2021

With the increasing importance and complexity of data pipelines, data quality became one of the key challenges in modern software applications. The importance of data quality has been recognized beyond the field of data engineering and database management systems (DBMSs). Also, for machine learning (ML) applications, high data quality standards are crucial to ensure robust predictive performance and responsible usage of automated decision making. One of the most frequent data quality problems is missing values. Incomplete datasets can break data pipelines and can have a devastating impact on downstream ML applications when not detected. While statisticians and, more recently, ML researchers have introduced a variety of approaches to impute missing values, comprehensive benchmarks comparing classical and modern imputation approaches under fair and realistic conditions are underrepresented. Here, we aim to fill this gap. We conduct a comprehensive suite of experiments on a large number of datasets with heterogeneous data and realistic missingness conditions, comparing both novel deep learning approaches and classical ML imputation methods when either only test or train and test data are affected by missing data. Each imputation method is evaluated regarding the imputation quality and the impact imputation has on a downstream ML task. Our results provide valuable insights into the performance of a variety of imputation methods under realistic conditions. We hope that our results help researchers and engineers to guide their data preprocessing method selection for automated data quality improvement.
Behavior Change Techniques and the Effects Associated With Digital Behavior Change Interventions in Sedentary Behavior in the Clinical Population: A Systematic Review
Authors: Martín-Martín Jaime , Roldán-Jiménez Cristina , De-Torres Irene , Muro-Culebras Antonio , Escriche-Escuder Adrian , Gonzalez-Sanchez Manuel , Ruiz-Muñoz María , Mayoral-Cleries Fermin , Biró Attila , Tang Wen , Nikolova Borjanka , Salvatore Alfredo , Cuesta-Vargas Antonio I.
Published: July 2021

Background: Sedentary behavior (SB) negatively impact health and is highly prevalent in the population. Digital behavior change interventions (DBCIs) have been developed to modify behaviors such as SB by technologies. However, it is unknown which behavior change techniques (BCTs) are most frequently employed in SB as well as the effect associated with DBCIs in this field. The aim of this systematic review was: (a) to evaluate the BCT most frequently employed in digital health including all technologies available and interventions aimed at increasing physical activity (PA), reducing sedentary time, and improving adherence to exercise in the clinical population, and (b) to review the effect associated with DBCIs in this field.

Methods: The database used was Medline, as well as Scopus, Scielo, and Google Scholar. For the search strategy, we considered versions of behavior/behavioral, mHealth/eHealth/telemedicine/serious game/gamification. The terms related to PA and SB were included, the criteria for inclusion were randomized clinical trials (RCTs), adults, intervention based on digital media, and outcome variable lifestyle modification; a last 5 years filter was included. Michie's Taxonomy was used to identify BCTs. The study was registered under the number PROSPERO CRD42019138681.

Results: Eighteen RCTs were included in the present systematic review, 5 of them healthy adults, and 13 of them with some illness. Studies included 2298 sedentary individuals who were followed up for 5 weeks−3 years. The most used BCTs were goal setting, problem solving, review outcomes/goals, feedback on behavior and outcomes of behavior, self-monitoring of behavior, social support, information about health consequences, and behavior practice/rehearsal. The effect associated with DBCIs showed improvements, among several related to PA and physiologic self-reported and anthropometric outcomes.

Conclusion: The BCTs most used in digital health to change outcomes related to SB were goals and planning, feedback and monitoring, social support, natural consequences, repetition, and substitution. Besides these findings, DBCIs are influenced by several factors like the type of intervention, patients' preferences and values, or the number of BCTs employed. More research is needed to determine with precision which DBCIs or BCTs are the most effective to reduce SB in the clinical population.
Anthropogenic Influences on Dissolved Organic Matter in Three Coastal Bays, North China
Authors: Li Penghui , Zhao Chen , Liu Ke , Xiao Xiaotong , Wang Yujue , Wang Yuntao , He Ding
Published: July 2021

Coastal bays bear anthropogenic influence strongly, and thus dissolved organic matter (DOM) in coastal bays, which is an important component of global carbon cycling, could be heavily affected by anthropogenic inputs. Utilizing absorbance, fluorescence spectroscopy, and stable carbon isotope (δ13C), this study analyzed the characteristics and distribution of DOM in three coastal bays (Jiaozhou Bay, Sishili Bay, and Taozi Bay), located in North China. The results showed that there was always a high concentration of DOM near the river mouth in all three bays and the DOM concentration decreased along the salinity gradient in Jiaozhou Bay, indicating the riverine inputs are the main factor that causes the variation of DOM in these coastal bays. The effects of inflowing rivers on DOM in coastal bays differed with their watershed characteristics (i.e., agricultural/urban). In addition, humic-like DOM components were found to be positively correlated with the apparent oxygen utilization, suggesting microbial activities could contribute to the DOM in this region. There was generally a higher averaged concentration of fluorescent DOM in surface water than that in bottom water in Jiaozhou Bay. In contrast, higher humic-like DOM was found in bottom water than that in surface water in Sishili Bay and Taozi Bay, which could be attributed to aquaculture activities and biological production. Moreover, photodegradation/photobleaching, dumping, and sewage discharge had their effects on DOM in coastal bays. This study demonstrates that DOM in coastal bays is regulated by multiple sources (rivers, aquaculture, dumping, and sewage) and processes (biological production and photodegradation), and anthropogenic activities have their influences on optical and isotopic characteristics of DOM in coastal bays.
“I can Just Get all the Bits That I Need”: Practitioners’ Use of Open-Access Sport Science Podcasts
Authors: Shaw Matthew P. , McNamara Scott W. T.
Published: July 2021

The aim of the current investigation was to explore practitioners’ attitudes toward and reasons for listening to open-access podcasts. It is well accepted within the literature that sport and exercise practitioners, such as coaches and sport scientists, perceive several barriers to access of scientific and academic research. Open-access podcasts may provide an alternative platform for developing esoteric knowledge. Nine sport and exercise practitioners (including gym owners, nutritionists, and sport coaches) participated in the investigation. A single-semi structured interview was conducted, and data were analyzed using a thematic network analysis approach. Three themes were constructed from the data—flexibility of podcast listening, convenience of podcast listening, practitioners’ need for authentic and novel information.
How to Promote Diversity and Inclusion in Educational Settings: Behavior Change, Climate Surveys, and Effective Pro-Diversity Initiatives
Authors: Moreu Gil , Isenberg Naomi , Brauer Markus
Published: July 2021

We review recent developments in the literature on diversity and inclusion in higher education settings. Diversity interventions increasingly focus on changing behaviors rather than mental constructs such as bias or attitudes. Additionally, there is now a greater emphasis on the evaluation of initiatives aimed at creating an inclusive climate. When trying to design an intervention to change behavior, it is advised to focus on a segment of the population (the “target audience”), to try to get people to adopt a small number of specific new behaviors (the “target behaviors”), and to address in the intervention the factors that affect the likelihood that members of the target audience will engage in the new target behaviors (the “barriers and benefits”). We report our recent work developing a climate survey that allows researchers and practitioners to identify these elements in a particular department or college. We then describe recent inclusion initiatives that have been shown to be effective in rigorous empirical studies. Taken together this paper shows that by implementing techniques based on research in the behavioral sciences it is possible to increase the sense of belonging, the success, and the graduation rate of minority students in STEM.
Biocomputational Architecture Based on Particle Physics
Authors: Heidari Farahbod , Mahdavinejad Mohammadjavad , Werner Liss C. , Roohabadi Maryam , Sarmadi Hanieh
Published: July 2021

Domestic greywater produced via household chores has a major contribution to environmental pollution and is also the best-untapped energy source. Since the past decade, in the different fields, enormous efforts have been made to reach the bio-energy from bio-waste. These efforts consist of a wide range of thermochemical, bio-chemical, and microbial fuel cells; etc. however, all these efforts are in their infancy. They have high cost and are efficient on a large-scale; furthermore, these efforts used a non-intelligent process that has led to lack of development in this type of review. This ongoing research presents the smart design process that leads to hybrid energy via the intersection of computation, wastewater, and microorganisms and aims to introduce the novel bio-computational machine based on particle Physics. Therefore, we will investigate the mixture of the microbial fuel cells, specifically “Spirulina” micro-algae, and household chores greywater. In the computational framework, we propose high-precise fluid simulation with the advantage of particle position and dynamic physics for the conversion of the mixture of “Spirulina medium,” and household chore greywater makes energy control possible through flow, and management of the type of solution mix, by transferring data from the modules to the digital environment. Finally, these datasets simulate behavior based on the physical properties of each particle. The procedure works in a parametric computer-aided design (CAD) environment and through Grasshopper within Rhinoceros Software by syncing bio-computational machine to the digital environment. The solenoid valve and fluid flow controller applied between the nutritious tank and energy conversion tank measure nutritional consumption and sends it to the digital environment numerically with an Arduino-Uno board kit. These batch numerical signals are stored in our local database then are combined with the particle physics engine and simulate the material behavior; also, they provide the ability to control our bio-computational machine digitally.
Numerical Analysis on the Performance of High Concentration Photovoltaic Systems Under the Nonuniform Energy Flow Density
Authors: Chen Haifei , Wang Yunjie , Ding Yuwei , Cai Baorui , Yang Jie
Published: July 2021

Photovoltaic panels can directly convert solar energy into electricity, but temperature will have a certain impact on the efficiency of photovoltaic cells. Especially under the condition of nonuniform energy flow density of high-power concentration, it is of great significance to maintain the temperature uniformity of cells. Therefore, based on the radiation under nonuniform heat flux density, four heat exchangers were proposed: single-channel serpentine flow, multi-channel flat plate, full jet, and single-jet nozzle. Taking into account the uniformity of the cell temperature, the single-jet nozzle and single-channel serpentine flow can better maintain the uniformity of the temperature field compared with other heat exchangers. Especially under high-concentration energy flow density, considering the quality of heat and electricity, the performance of the four-jet nozzles is the best from the perspective of exergy efficiency. Under the condition of four-jet nozzles, the electrical efficiency and thermal efficiency of the cell can be maintained at about 29 and 62.5%, respectively, and the exergy efficiency of the system can reach 31%.
Cross-Ecosystem Linkages: Transfer of Polyunsaturated Fatty Acids From Streams to Riparian Spiders via Emergent Insects
Authors: Kowarik Carmen , Martin-Creuzburg Dominik , Robinson Christopher T.
Published: July 2021

Polyunsaturated fatty acids (PUFAs) are essential resources unequally distributed throughout landscapes. Certain PUFAs, such as eicosapentaenoic acid (EPA), are common in aquatic but scarce in terrestrial ecosystems. In environments with low PUFA availability, meeting nutritional needs requires either adaptations in metabolism to PUFA-poor resources or selective foraging for PUFA-rich resources. Amphibiotic organisms that emerge from aquatic ecosystems represent important resources that can be exploited by predators in adjacent terrestrial habitats. Here, we traced PUFA transfer from streams to terrestrial ecosystems, considering benthic algae as the initial PUFA source, through emergent aquatic insects to riparian spiders. We combined carbon stable isotope and fatty acid analyses to follow food web linkages across the ecosystem boundary and investigated the influence of spider lifestyle (web building vs. ground dwelling), season, and ecosystem degradation on PUFA relations. Our data revealed that riparian spiders consumed considerable amounts of aquatic-derived resources. EPA represented on average 15 % of the total fatty acids in riparian spiders. Season had a strong influence on spider PUFA profiles, with highest EPA contents in spring. Isotope data revealed that web-building spiders contain more aquatic-derived carbon than ground dwelling spiders in spring, although both spider types had similarly high EPA levels. Comparing a natural with an anthropogenically degraded fluvial system revealed higher stearidonic acid (SDA) contents and Σω3/Σω6 ratios in spiders collected along the more natural river in spring but no difference in spider EPA content between systems. PUFA profiles of riparian spiders where distinct from other terrestrial organism and more closely resembled that of emergent aquatic insects (higher Σω3/Σω6 ratio). We show here that the extent to which riparian spiders draw on aquatic PUFA subsidies can vary seasonally and depends on the spider’s lifestyle, highlighting the complexity of aquatic-terrestrial linkages.
P2RY14 Is a Potential Biomarker of Tumor Microenvironment Immunomodulation and Favorable Prognosis in Patients With Head and Neck Cancer
Authors: Li Qingxiang , Xu Le , Li Yuke , Yang Rong , Qiao Qiao , Wang Yifei , Wang Lin , Guo Yuxing , Guo Chuanbin
Published: July 2021

The tumor microenvironment (TME) has a crucial role in tumor development, progression, and treatment response. Yet, the exact interaction between cancer biology and the TME is not fully understood. The following study analyzed the correlation between immune/stromal/estimate scores and survival prognosis in head and neck squamous cell carcinoma (HNSC) using a bioinformatic method. As a result, a predictive biomarker, UDP-glucose-specific G(i) protein-coupled P2Y receptor (P2RY14), was discovered. The potential role of P2RY14-driven signaling pathways in the immune-remodeling of TME was then investigated. Briefly, low immune scores were associated with unfavorable prognosis and clinical-stage, larger tumor size, and the down-regulation of P2RY14 in HNSC patients. In addition, the survival analysis showed that HNSC patients with high expression had longer survival than patients with low expression from both TCGA databases and our own patients. We further discovered that P2RY14 is involved in the immune activity in the TME of HNSC; a downregulation of P2RY14 resulted in being an indicator for the conversion of TME status (from immune-dominant to metabolic-dominant status). The intersection analysis of genes co-expressed with P2RY14 indicated that the T-cell receptor signaling pathway and PD-L1 expression and PD-1 checkpoint pathway were candidate signaling pathways driven by the P2RY14 gene in HNSC. Further investigation of immune-associated signaling pathways regulated by P2RY14 may help HNSC patients gain higher immunotherapy benefits.
Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
Authors: Scobeyeva Victoria A. , Artyushin Ilya V. , Krinitsina Anastasiya A. , Nikitin Pavel A. , Antipin Maxim I. , Kuptsov Sergei V. , Belenikin Maxim S. , Omelchenko Denis O. , Logacheva Maria D. , Konorov Evgenii A. , Samoilov Andrey E. , Speranskaya Anna S.
Published: July 2021

Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus—Allium—is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes’ annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the “normal” or “pseudo” state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
The Spike of SARS-CoV-2: Uniqueness and Applications
Authors: Kumavath Ranjith , Barh Debmalya , Andrade Bruno Silva , Imchen Madangchanok , Aburjaile Flavia Figueira , Ch Athira , Rodrigues Diego Lucas Neres , Tiwari Sandeep , Alzahrani Khalid J. , Góes-Neto Aristóteles , Weener Marianna E. , Ghosh Preetam , Azevedo Vasco
Published: July 2021

The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point‐of‐care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.
Serglycin-Deficiency Causes Reduced Weight Gain and Changed Intestinal Cytokine Responses in Mice Infected With Giardia intestinalis
Authors: Li Zhiqiang , Peirasmaki Dimitra , Svärd Staffan , Åbrink Magnus
Published: July 2021

The proteoglycan serglycin (SG) is expressed by different innate and adaptive immune cells, e.g. mast cells, macrophages, neutrophils, and cytotoxic T lymphocytes, where SG contributes to correct granule storage and extracellular activity of inflammatory mediators. Here the serglycin-deficient (SG−/−) mouse strain was used to investigate the impact of SG on intestinal immune responses during infection with the non-invasive protozoan parasite Giardia intestinalis. Young (≈11 weeks old) oral gavage-infected congenic SG−/− mice showed reduced weight gain as compared with the infected SG+/+ littermate mice and the PBS-challenged SG−/− and SG+/+ littermate mice. The infection caused no major morphological changes in the small intestine. However, a SG-independent increased goblet cell and granulocyte cell count was observed, which did not correlate with an increased myeloperoxidase or neutrophil elastase activity. Furthermore, infected mice showed increased serum IL-6 levels, with significantly reduced serum IL-6 levels in infected SG-deficient mice and decreased intestinal expression levels of IL-6 in the infected SG-deficient mice. In infected mice the qPCR analysis of alarmins, chemokines, cytokines, and nitric oxide synthases (NOS), showed that the SG-deficiency caused reduced intestinal expression levels of TNF-α and CXCL2, and increased IFN-γ, CXCL1, and NOS1 levels as compared with SG-competent mice. This study shows that SG plays a regulatory role in intestinal immune responses, reflected by changes in chemokine and cytokine expression levels and a delayed weight gain in young SG−/− mice infected with G. intestinalis.
Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Ichthyophthirius multifiliis Through Co-Expression and Machine Learning
Authors: Roh HyeongJin , Kim Nameun , Lee Yoonhang , Park Jiyeon , Kim Bo Seong , Lee Mu Kun , Park Chan-Il , Kim Do-Hyung
Published: July 2021

Ichthyophthirius multifiliisis a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transcriptomic responses in the liver and head kidney and hemato-serological indexes were profiled underI. multifiliisinfection and recovery to investigate systemic immuno-physiological characteristics. Several strategies for massive transcriptomic interpretation, such as differentially expressed genes (DEGs), Poisson linear discriminant (PLDA), and weighted gene co-expression network analysis (WGCNA) models were used to investigate the featured genes/pathways while minimizing the disadvantages of individual methods. During the course of infection, 6,097 and 2,931 DEGs were identified in the head kidney and liver, respectively. Markers of protein processing in the endoplasmic reticulum, oxidative phosphorylation, and the proteasome were highly expressed. Likewise, simultaneous ferroptosis and cellular reconstruction was observed, which is strongly linked to multiple organ dysfunction. In contrast, pathways relevant to cellular replication were up-regulated in only the head kidney, while endocytosis- and phagosome-related pathways were notably expressed in the liver. Moreover, interestingly, most immune-relevant pathways (e.g., leukocyte trans-endothelial migration, Fc gamma R-mediated phagocytosis) were highly activated in the liver, but the same pathways in the head kidney were down-regulated. These conflicting results from different organs suggest that interpretation of co-expression among organs is crucial for profiling of systemic responses during infection. The dual-organ transcriptomics approaches presented in this study will greatly contribute to our understanding of multi-organ interactions underI. multifiliisinfection from a broader perspective.
Potential Role of CD47-Directed Bispecific Antibodies in Cancer Immunotherapy
Authors: Yang Yan , Yang Zheng , Yang Yun
Published: July 2021

The prosperity of immunological therapy for cancer has aroused enormous passion for exploiting the novel targets of cancer immunotherapy. After the approval of blinatumomab, a bispecific antibody (bsAb) targeting on CD19 for acute lymphoblastic leukemia, a few of CD47-targeted bsAbs for cancer immunotherapy, are currently in clinical research. In our review of CD47-targeted bsAbs, we described the fundamental of bsAbs. Then, we summarized the information of four undergoing phase I researches, reviewed the main toxicities relevant to CD47-targeted bsAb immunological therapy of on-target cytotoxicity to healthy cells and a remarkable antigen-sink. Finally, we described possible mechanisms of resistance to CD47-targeted bsAb therapy. More clinical researches are supposed to adequately confirm its security and efficacy in clinical practice.
NLRP3 Inflammasome in Metabolic-Associated Kidney Diseases: An Update
Authors: Xiong Wei , Meng Xian-Fang , Zhang Chun
Published: July 2021

Metabolic syndrome (MS) is a group of complex metabolic disorders syndrome, which refers to the pathological state of metabolism disorder of protein, fat, carbohydrate and other substances in human body. The kidney is an important organ of metabolism, and various metabolic disorders can lead to the abnormalities in the structure and function of the kidney. The recognition of pathogenesis and treatment measures of renal damage in MS is a very important part for the renal function preserve. Inflammatory response caused by various metabolic factors is a protective mechanism of the body, but persistent inflammation will become a harmful factor and aggravate kidney damage. Inflammasomes are sensors of the innate immune system that play crucial roles in initiating inflammation in response to acute infections and chronic diseases. They are multiprotein complex composed of cytoplasmic sensors (mainly NLR family members), apoptosis-associated speck-like protein (ASC or PYCARD) and pro-caspase-1. After receiving exogenous and endogenous stimuli, the sensors begin to assemble inflammasome and then promote the release of inflammatory cytokines IL-1β and IL-18, resulting in a special way of cell death named pyroptosis. In the kidney, NLRP3 inflammasome can be activated by a variety of pathways, which eventually leads to inflammatory infiltration, renal intrinsic cell damage and renal function decline. This paper reviews the function and specific regulatory mechanism of inflammasome in kidney damage caused by various metabolic disorders, which will provide a new therapeutic perspective and targets for kidney diseases.
Use of an INLA Latent Gaussian Modeling Approach to Assess Bird Population Changes Due to the Development of Offshore Wind Farms
Authors: Vilela Raul , Burger Claudia , Diederichs Ansgar , Bachl Fabian E. , Szostek Lesley , Freund Anika , Braasch Alexander , Bellebaum Jochen , Beckers Brian , Piper Werner , Nehls Georg
Published: July 2021

The utilization of marine renewable energies such as offshore wind farming leads to globally expanding human activities in marine habitats. While knowledge on the responses to offshore wind farms and associated shipping traffic is accumulating now at a fast pace, it becomes important to assess the population impacts on species affected by those activities. In the North Sea, the protected diver species Red-throated Diver (Gavia stellata) and Black-throated Diver (Gavia arctica) widely avoid offshore wind farms. We used an explicit spatio-temporal Bayesian model to get a robust estimate of the diver population during the spring season between 2001 and 2018, based on a set of aerial surveys from long-term monitoring programs within the German North Sea. Despite the erection of 20 offshore wind farms in the study area and marked responses of divers to wind farms, model results indicated that there was no population decline, and overall numbers fluctuated around 16,600 individuals, with average annual 95% CI ranging between 13,400 and 21,360 individuals. Although, avoidance behavior due to wind farm development led to a more narrowly focused spatial distribution of the birds centered in the persistent high concentration zone in the Eastern German Bight Special Protection Area, the results provide no indication of negative fitness consequences on these long-lived species. However, more research is needed on habitat use and food availability in this regard.
Efficacy and Safety of Peroral Endoscopic Myotomy for Sigmoid-Type Achalasia: A Systematic Review and Meta-Analysis
Authors: Xu Jin , Zhong Chunyu , Huang Shu , Zeng Xinyi , Tan Shali , Shi Lei , Peng Yan , Lü Muhan , Ma Lianjun , Tang Xiaowei
Published: July 2021

Background: The efficacy and safety of peroral endoscopic myotomy (POEM) in the treatment of sigmoid-type achalasia is unknown. This meta-analysis aims to explore the clinical outcomes of POEM for sigmoid-type achalasia.

Method: We searched all relevant studies published up to September 2020 in PubMed, Embase, and Cochrane library databases. Meta-analyses for clinical success, Eckardt score, angle of esophageal tortuosity, diameter of esophagus, lower esophageal sphincter (LES) pressure, integrated relaxation pressure (IRP), adverse events, and gastroesophageal reflux diseases were performed based on random or fixed-effects models as needed.

Results: We found a total of eight studies that provided data on 248 patients. Overall, the pooled clinical success was achieved in 211 sigmoid-type achalasia patients [90.4%; 95% confidence interval (CI), 85.5%−93.8%]. The pre- and post-POEM Eckardt scores, angle of esophageal tortuosity, diameter of esophageal, LES pressure, and IRP were significantly improved (All p < 0.05). The pooled adverse events rate was 13.0% (95% CI, 3.6%−37.4%). The pooled objective confirmation of reflux rate was 41.5% (95% CI, 26.5%−58.3%), and symptomatic reflux rate was 12.5% (95% CI, 8.3%−18.4%).

Conclusions: Our current evidence indicated that POEM is an effective and safe therapeutic modality for the treatment of sigmoid-type achalasia.
Features of Bacterial Microbiota in the Wild Habitat of Pulsatilla tongkangensis, the Endangered “Long-Sepal Donggang Pasque-Flower Plant,” Endemic to Karst Topography of Korea
Authors: Dutta Swarnalee , Na Chae Sun , Lee Yong Hoon
Published: July 2021

Microbes associated with plants significantly influence the development and health of the plants. The diversity and function of microbiomes associated with the long-sepal Donggang pasque-flower (DPF) plant, an endemic and endangered species in karst ecosystems, remain unexplored. In this study, we investigated the features of bacterial communities associated with the rhizosphere and roots of DPF plants and their functions in plant growth promotion. The DPF plants were collected from natural and cultivated habitats, and their 16S rDNA was sequenced to assess the bacterial community structures. The bacterial microbiota was more diverse in wild than in cultivated plants. The core bacterial microbiota commonly functioned as endophytes in both wild and cultivated DPF plants, although there were some differences. The identified bacterial strains benefited plants through nitrogen fixation, phosphate solubilization, or phytohormone production, inducing measurable growth differences inArabidopsis thaliana. To the best of our knowledge, this study is the first to report the bacterial community structures associated with the rhizosphere soil and roots of DPF plants in karst ecosystems. The bacterial strains isolated in this study could be used to aid sustainable growth and restoration of rare plants in karst ecosystems. Our systematic research on the microbiomes associated with these endangered plants will contribute to their conservation as well as development of better cultivation.
Prioritizing Disease-Related Microbes Based on the Topological Properties of a Comprehensive Network
Authors: Yang Haixiu , Tong Fan , Qi Changlu , Wang Ping , Li Jiangyu , Cheng Liang
Published: July 2021

Many microbes are parasitic within the human body, engaging in various physiological processes and playing an important role in human diseases. The discovery of new microbe–disease associations aids our understanding of disease pathogenesis. Computational methods can be applied in such investigations, thereby avoiding the time-consuming and laborious nature of experimental methods. In this study, we constructed a comprehensive microbe–disease network by integrating known microbe–disease associations from three large-scale databases (Peryton, Disbiome, and gutMDisorder), and extended the random walk with restart to the network for prioritizing unknown microbe–disease associations. The area under the curve values of the leave-one-out cross-validation and the fivefold cross-validation exceeded 0.9370 and 0.9366, respectively, indicating the high performance of this method. Despite being widely studied diseases, in case studies of inflammatory bowel disease, asthma, and obesity, some prioritized disease-related microbes were validated by recent literature. This suggested that our method is effective at prioritizing novel disease-related microbes and may offer further insight into disease pathogenesis.