bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-Step Ahead Prediction of Reheat Steam Temperature of a 660 MW Coal-Fired Utility Boiler Using Long Short-Term Memory
Authors: Tan Peng , Zhu Hengyi , He Ziqian , Jin Zhiyuan , Zhang Cheng , Fang Qingyan , Chen Gang
Published: March 2022

With increases in the penetration of renewables in grids, there is an increasing demand for coal-fired power plants to operate flexibly. Regulation of reheat steam temperature is of great importance for the safe and efficient operation of coal-fired power plants. However, the difficulty of reheat steam temperature regulation increases largely during flexible operation due to the large delay and nonlinear properties, especially those units designed to shoulder base load and with limited regulating strategy. A multistep prediction model on the reheat steam temperature of a 660-MW coal-fired utility boiler was developed based on long short-term memory. The results show that the multistep prediction model performs well. The average root mean square error and mean absolute percentage error values of the five-step prediction results are less than 0.52°C and 0.07%, respectively. The correlation coefficients of the five-step predictions are all greater than 0.95. With a sample interval of 30 s, the model provides an accurate prediction of reheat steam temperature within 2.5 min, which could supply an important reference for the reheat steam temperature regulation.
Reduced Nitrous Oxide Emissions From Drained Temperate Agricultural Peatland After Coverage With Mineral Soil
Authors: Wang Yuqiao , Paul Sonja M. , Jocher Markus , Alewell Christine , Leifeld Jens
Published: March 2022

Peatlands drained for agriculture emit large amounts of nitrous oxide (N2O) and thereby contribute to global warming. In order to counteract soil subsidence and sustain agricultural productivity, mineral soil coverage of drained organic soil is an increasingly used practice. This management option may also influence soil-borne N2O emissions. Understanding the effect of mineral soil coverage on N2O emissions from agricultural peatland is necessary to implement peatland management strategies which not only sustain agricultural productivity but also reduce N2O emissions. In this study, we aimed to quantify the N2O emissions from an agriculturally managed peatland in Switzerland and to evaluate the effect of mineral soil coverage on these emissions. The study was conducted over two years on a grassland on drained nutrient-rich fen in the Swiss Rhine Valley which was divided into two parts, both with identical management. One site was not covered with mineral soil (reference “Ref”), and the other site had a ∼40 cm thick mineral soil cover (coverage “Cov”). The grassland was intensively managed, cut 5–6 times per year, and received c. 230 kg N ha−1 yr−1 of nitrogen fertilizer. N2O emissions were continuously monitored using an automatic time integrating chamber (ATIC) system. During the experimental period, site Ref released 20.5 ± 2.7 kg N ha−1 yr−1 N2O-N, whereas the N2O emission from site Cov was only 2.3 ± 0.4 kg N ha−1 yr−1. Peak N2O emissions were mostly detected following fertilizer application and lasted for 2–3 weeks before returning to the background N2O emissions. At both sites, N2O peaks related to fertilization events contributed more than half of the overall N2O emissions. However, not only the fertilization induced N2O peaks but also background N2O emissions were lower with mineral soil coverage. Our data suggest a strong and continued reduction in N2O emissions with mineral soil cover from the investigated organic soil. Mineral soil coverage, therefore, seems to be a promising N2O mitigation option for intensively used drained organic soils when a sustained use of the drained peatland for intensive agricultural production is foreseen, and potential rewetting and restoration of the peatland are not possible.
Age of First Territory Settlement of Golden Eagles Aquila chrysaetos in a Variable Competitive Landscape
Authors: Whitfield D. Philip , Fielding Alan H. , Anderson David , Benn Stuart , Dennis Roy , Grant Justin , Weston Ewan D.
Published: March 2022

With life-history traits involving high survival, low reproductive output, years of natal dispersal and deferred maturity, the population ecology and behaviour of large raptors which occur at low densities can be difficult to study. The age at which large raptors first settle on a prospective breeding territory receives relatively little attention, but is a key metric in population modelling including, for example, projections of reintroduction projects. It can also be a barometer of the “health” of populations and the availability of breeding opportunities. The advancement of GPS-telemetry has proved invaluable in gaining insights into several aspects of large raptor ecology and behaviour. Age of first territory settlement (AFTS) is one such aspect. AFTS is important in modelling population trajectories and considering individuals’ lifetime reproductive success. We used an algorithm based on GPS-records from dispersing Golden Eagles tagged as nestlings in Scotland to estimate AFTS. While the lifespan of GPS-tags can bias against settlement dates of older birds, they can also potentially reveal settlement ages difficult or impossible to discern from other methods. We found a range of ages for AFTS, including those in their second calendar year; much younger than previously documented by other methods. Ground-truthing – when possible and if inevitably slightly delayed – confirmed territory occupation on field-based survey criteria. We found that eagles settled younger in vacant territories and when older in occupied existing territories. Birds’ sex had no effect on AFTS. Birds which dispersed earlier from their natal territory (indicative of “quality” from some previous research) had no association with AFTS. Our results indicate that within technological temporal limits GPS-data can provide for accurate and precise estimations of AFTS including early settlement not consistently or precisely recorded by other methods. Within our study’s variable competitive landscape we found that AFTS was associated with the availability of territorial opportunities but not with the timing of dispersal. These findings have consequences for studying and understanding large raptor population dynamics.
The Diversity Decline in Wild and Managed Honey Bee Populations Urges for an Integrated Conservation Approach
Authors: Panziera Delphine , Requier Fabrice , Chantawannakul Panuwan , Pirk Christian W. W. , Blacquière Tjeerd
Published: March 2022

Many parts of the globe experience severe losses and fragmentation of habitats, affecting the self-sustainability of pollinator populations. A number of bee species coexist as wild and managed populations. Using honey bees as an example, we argue that several management practices in beekeeping threaten genetic diversity in both wild and managed populations, and drive population decline. Large-scale movement of hive stocks, introductions into new areas, breeding programs and trading of queens contribute to reducing genetic diversity, as recent research demonstrated for wild and managed honey bees within a few decades. Examples of the effects of domestication in other organisms show losses of both genetic diversity and fitness functions. Cases of natural selection and feralization resulted in maintenance of a higher genetic diversity, including in a Varroa destructor surviving population of honey bees. To protect the genetic diversity of honey bee populations, exchange between regions should be avoided. The proposed solution to selectively breed all local subspecies for a use in beekeeping would reduce the genetic diversity of each, and not address the value of the genetic diversity present in hybridized populations. The protection of Apis mellifera’s, Apis cerana’s and Apis koschevnikovi’s genetic diversities could be based on natural selection. In beekeeping, it implies to not selectively breed but to leave the choice of the next generation of queens to the colonies, as in nature. Wild populations surrounded by beekeeping activity could be preserved by allowing Darwinian beekeeping in a buffer zone between the wild and regular beekeeping area.
Parasite-Mediated Mate Preferences in a Cooperatively Breeding Rodent
Authors: Lutermann Heike , Butler Kemba B. , Bennett Nigel C.
Published: March 2022

Females of many species discriminate among males when choosing a mate and this can bear indirect and direct benefits including the avoidance of parasite transmission from infested males. In rodents, this may be mediated by androgen hormones that affect the expression of urinary odors. Female choosiness may also vary with a female’s infestation status, with infested females being less choosy. In the current study we tested the preference of cooperatively breeding highveld mole-rat (Cryptomys hottentotus hottentotus) females for male urinary odors from healthy males and those naturally infested with a cestode (Mathevotaenia sp.). Thirty females (15 healthy, 15 infested) were allowed to explore a Y-maze with urine samples from healthy and infested males and the frequency of entering choice arms and chambers as well as the duration spend with each odor sample was recorded. Infestation status did neither affect male body mass, urinary testosterone, nor cortisol levels or the body condition of females. Although overall female activity was not affected by infestation status, infested females entered choice arms and chambers significantly less frequently than healthy females. Surprisingly, healthy females preferred odors from infested males while the opposite was true for infested females, independent of male hormone levels. As the study species lives in groups that tend to share the same infestation status, we suggest that highveld mole-rat females may exhibit a preference for unfamiliar odors, possibly as an indicator of genetic diversity, rather than discriminate between infestation status of males. Similar mechanisms may also play a role in other social species.
Examining k-Nearest Neighbor Small Area Estimation Across Scales Using National Forest Inventory Data
Authors: Bell David M. , Wilson Barry T. , Werstak Charles E. , Oswalt Christopher M. , Perry Charles H.
Published: March 2022

National forest inventories (NFI), such as the one conducted by the United States Forest Service Forest Inventory and Analysis (FIA) program, provide valuable information regarding the status of forests at regional to national scales. However, forest managers often need information at stand to landscape scales. Given various small area estimation (SAE) approaches, including design-based and model-based estimation, it may not be clear which is most appropriate for the user’s application. In this study, our objective was to assess the uncertainty in tree aboveground live carbon (ALC) estimates for differing modes of SAE across multiple scales to provide guidance for appropriate scales of application. We calculated means and variances for ALC with design-based (Horvitz-Thompson), model-assisted (generalized regression), and model-based (k-nearest neighbor synthetic) estimators for estimation units over a range of sizes for 30 subregions in California, United States. For larger areas (10,000–64,800 ha), relative efficiencies greater than one indicated that the generalized regression estimator (GREG) generated estimates with less error than the Horvitz-Thompson estimator (HT), while the bias-adjusted synthetic estimator relative efficiency compared to either the Horvitz-Thompson or model-assisted estimators exceeded one for areas 25,000 ha and smaller. Variance estimates from the unadjusted synthetic estimator underestimated the total error, because the estimator ignores bias and thus only addresses model variance. Across scales (250–64,800 ha, 0–27 plots per area of interest), 93% of the variation in the synthetic estimator’s relative standard error was explained by forest area, forest dominance, and regional variation in forest landscapes. Our results support model-assisted estimation use except for small areas where few plots (<10 in the current study) are available for generating estimates in spite of biases in estimates. However, users should exercise caution when interpreting model-based estimates of error as they may not account for model mis-specification, and thus induced bias. This research explored multiple scales of application for SAE procedures applied to NFI data regarding carbon pools, potentially supporting a multi-scale approach to forest monitoring. Our results guides users in developing defensible estimates of carbon pools, particularly as it relates to the limits of inference at a variety of spatial scales.
Identification of Novel Mutations in Chinese Infants With Citrullinemia
Authors: Cheng Zhi , He Xiwen , Zou Fa , Xu Zhen-E , Li Chun , Liu Hao , Miao Jingkun
Published: March 2022

Citrullinemia is a rare autosomal recessive disorder characterized by elevated concentrations of citrulline in the blood resulting from malfunction of the urea cycle. It is categorized into two types, types I and II, which are caused by argininosuccinate synthase 1 (ASS1), and citrin (SLC25A13) gene mutations, respectively. In this study, we performed genetic analysis on nine Chinese infants with citrullinemia using next-generation sequencing, which identified a novel mutation (p.Leu313Met) and a rare mutation (p.Thr323Ile, rs1250895424) of ASS1. We also found a novel splicing mutation of SLC25A13: c.1311 + 4_+7del. Functional analysis of the ASS1 missense mutations showed that both significantly impaired the enzyme activity of ASS1, with the p. Thr323Ile mutation clearly affecting the interaction between ASS1 and protein arginine methyltransferase 7 (PRMT7). These findings expand the mutational spectrum of ASS1 and SLC25A13, and further our understanding of the molecular genetic mechanism of citrullinemia in the Chinese population.
Transcriptome Sequencing-Based Mining of Genes Associated With Pubertal Initiation in Dolang Sheep
Authors: Zhang Zhishuai , Sui Zhiyuan , Zhang Jihu , Li Qingjin , Zhang Yongjie , Xing Feng
Published: March 2022

Improving the fertility of sheep is an important goal in sheep breeding as it greatly increases the productivity. Dolang sheep is a typical representative breed of lamb in Xinjiang and is the main local sheep breed and meat source in the region. To explore the genes associated with the initiation of puberty in Dolang sheep, the hypothalamic tissues of Dolang sheep prepubertal, pubertal, and postpubertal periods were collected for RNA-seq analysis on the Illumina platform, generating 64.08 Gb clean reads. A total of 575, 166, and 648 differentially expressed genes (DEGs) were detected in prepuberty_vs._puberty, postpuberty_vs._prepuberty, and postpuberty_vs._puberty analyses, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, the related genes involved in the initiation of puberty in Dolang sheep were mined. Ten genes that have direct or indirect functions in the initiation of puberty in Dolang sheep were screened using the GO and KEGG results. Additionally, quantitative real-time PCR was used to verify the reliability of the RNA-Seq data. This study provided a new approach for revealing the mechanism of puberty initiation in sheep and provided a theoretical basis and candidate genes for the breeding of early-pubertal sheep by molecular techniques, and at the same time, it is also beneficial for the protection, development, and utilization of the fine genetic resources of Xinjiang local sheep.
Whole Transcriptome Mapping Identifies an Immune- and Metabolism-Related Non-coding RNA Landscape Remodeled by Mechanical Stress in IL-1β-Induced Rat OA-like Chondrocytes
Authors: Zhang Jiaming , Hao Xiaoxia , Chi Ruimin , Liu Jiawei , Shang Xingru , Deng Xiaofeng , Qi Jun , Xu Tao
Published: March 2022

Background: Osteoarthritis (OA) is a common degenerative joint disease. The aims of this study are to explore the effects of mechanical stress on whole transcriptome landscape and to identify a non-coding transcriptome signature of mechanical stress.

Methods: Next-generation RNA sequencing (RNA-seq) was performed on IL-1β-induced OA-like chondrocytes stimulated by mechanical stress. Integrated bioinformatics analysis was performed and further verified by experimental validations.

Results: A total of 5,022 differentially expressed mRNAs (DEMs), 88 differentially expressed miRNAs (DEMIs), 1,259 differentially expressed lncRNAs (DELs), and 393 differentially expressed circRNAs (DECs) were identified as the transcriptome response to mechanical stress. The functional annotation of the DEMs revealed the effects of mechanical stress on chondrocyte biology, ranging from cell fate, metabolism, and motility to endocrine, immune response, and signaling transduction. Among the DELs, ∼92.6% were identified as the novel lncRNAs. According to the co-expressing DEMs potentially regulated by the responsive DELs, we found that these DELs were involved in the modification of immune and metabolism. Moreover, immune- and metabolism-relevant DELs exhibited a notable involvement in the competing endogenous RNA (ceRNA) regulation networks. Silencing lncRNA TCONS_00029778 attenuated cellular senescence induced by mechanical stress. Moreover, the expression of Cd80 was elevated by mechanical stress, which was rescued by silencing TCONS_00029778.

Conclusion: The transcriptome landscape of IL-1β-induced OA-like chondrocytes was remarkably remodeled by mechanical stress. This study identified an immune- and metabolism-related ncRNA transcriptome signature responsive to mechanical stress and provides an insight of ncRNAs into chondrocyte biology and OA.
Conventional Therapies Deplete Brain-Infiltrating Adaptive Immune Cells in a Mouse Model of Group 3 Medulloblastoma Implicating Myeloid Cells as Favorable Immunotherapy Targets
Authors: Abbas Zahra , George Courtney , Ancliffe Mathew , Howlett Meegan , Jones Anya C. , Kuchibhotla Mani , Wechsler-Reya Robert J. , Gottardo Nicholas G. , Endersby Raelene
Published: March 2022

Medulloblastoma is the most common childhood brain cancer. Mainstay treatments of radiation and chemotherapy have not changed in decades and new treatment approaches are crucial for the improvement of clinical outcomes. To date, immunotherapies for medulloblastoma have been unsuccessful, and studies investigating the immune microenvironment of the disease and the impact of current therapies are limited. Preclinical models that recapitulate both the disease and immune environment are essential for understanding immune-tumor interactions and to aid the identification of new and effective immunotherapies. Using an immune-competent mouse model of aggressive Myc-driven medulloblastoma, we characterized the brain immune microenvironment and changes induced in response to craniospinal irradiation, or the medulloblastoma chemotherapies cyclophosphamide or gemcitabine. The role of adaptive immunity in disease progression and treatment response was delineated by comparing survival outcomes in wildtype C57Bl/6J and in mice deficient in Rag1 that lack mature T and B cells. We found medulloblastomas in wildtype and Rag1-deficient mice grew equally fast, and that craniospinal irradiation and chemotherapies extended survival equally in wildtype and Rag1-deficient mice, suggesting that tumor growth and treatment response is independent of T and B cells. Medulloblastomas were myeloid dominant, and in wildtype mice, craniospinal irradiation and cyclophosphamide depleted T and B cells in the brain. Gemcitabine treatment was found to minimally alter the immune populations in the brain, resulting only in a depletion of neutrophils. Intratumorally, we observed an abundance of Iba1+ macrophages, and we show that CD45high cells comprise the majority of immune cells within these medulloblastomas but found that existing markers are insufficient to clearly delineate resident microglia from infiltrating macrophages. Ultimately, brain resident and peripheral macrophages dominate the brain and tumor microenvironment and are not depleted by standard-of-care medulloblastoma therapies. These populations therefore present a favorable target for immunotherapy in combination with front-line treatments.
Capturing 3D Chromatin Maps of Human Primary Monocytes: Insights From High-Resolution Hi-C
Authors: Xia Yu , Liu Xiaowen , Mu Wenli , Ma Chunyan , Wang Laicheng , Jiao Yulian , Cui Bin , Hu Shengnan , Gao Ying , Liu Tao , Sun Huanxin , Zong Shuai , Liu Xin , Zhao Yueran
Published: March 2022

Although the variation in chromatin architecture during adaptive immune responses has been thoroughly investigated, the 3D landscape of innate immunity is still unknown. Herein, chromatin regulation and heterogeneity among human primary monocytes were investigated. Peripheral blood was collected from two healthy persons and two patients with systemic lupus erythematosus (SLE), and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq analyses. Raw data from the THP1 cell line Hi-C library were used for comparison. For each sample, we constructed three Hi-C libraries and obtained approximately 3 billion paired-end reads in total. Resolution analysis showed that more than 80% of bins presented depths greater than 1000 at a 5 kb resolution. The constructed high-resolution chromatin interaction maps presented similar landscapes in the four individuals, which showed significant divergence from the THP1 cell line chromatin structure. The variability in chromatin interactions around HLA-D genes in the HLA complex region was notable within individuals. We further found that the CD16-encoding gene (FCGR3A) is located at a variable topologically associating domain (TAD) boundary and that chromatin loop dynamics might modulate CD16 expression. Our results indicate both the stability and variability of high-resolution chromatin interaction maps among human primary monocytes. This work sheds light on the potential mechanisms by which the complex interplay of epigenetics and spatial 3D architecture regulates chromatin in innate immunity.
Landscape of Infiltrated Immune Cell Characterization in Uveal Melanoma to Improve Immune Checkpoint Blockade Therapy
Authors: Lv Xiaohui , Ding Min , Liu Yan
Published: March 2022

Background

Numerous studies indicated that tumor-infiltrated immune cells (TIC) in the microenvironment are substantially linked to immunotherapy response and cancer prognosis. However, systematic studies of infiltrated immune cell characterization in uveal melanoma (UM) for prognosis and immune checkpoint blockade therapy are lacking.

Methods

UM datasets were extracted from open access resources (TCGA and GEO databases). The tumor-infiltrated immune cells in the microenvironment were decoded by using the CIBERSORT algorithm, which was further applied to classify UM patients into subgroups using an unsupervised clustering method. The Boruta algorithm and principal component analysis were used to calculate the TIC scores for UM patients. Kaplan–Meier curves were plotted to prove the prognostic value of TIC scores. Besides, the correlations of the TIC score with clinical features, mutated characteristics, and the immune therapeutic response were subsequently investigated.

Results

As a result, we defined three subtypes among 171 UM patients according to the TIC profiles and then calculated the TIC score to characterize the immune patterns for all patients. We discovered that high-TIC score patients with low BAP1 and high EIF1AX mutations have a better prognosis than low-TIC score patients. Activation of immune inflammatory response and increase in immune checkpoint-related genes in high-TIC score patients may account for good prognosis and immunotherapy response. Three melanoma cohorts received immunotherapy, proving that high-TIC score patients have substantial clinical and immune therapeutic improvements. Besides, several potential therapeutic agents were identified in the low-TIC score group.

Conclusion

Our study afforded a comprehensive view of infiltrated immune cell characterization to elucidate different immune patterns of UM. We also established a robust TIC-score signature, which may work as a prognostic biomarker and immune therapeutic predictor.
Fisheries Surveys Are Essential Ocean Observing Programs in a Time of Global Change: A Synthesis of Oceanographic and Ecological Data From U.S. West Coast Fisheries Surveys
Authors: Gallo Natalya D. , Bowlin Noelle M. , Thompson Andrew R. , Satterthwaite Erin V. , Brady Briana , Semmens Brice X.
Published: March 2022

As climate change and other anthropogenic impacts on marine ecosystems accelerate in the 21st century, there is an increasing need for sustained ocean time series. A robust and collaborative network of regional monitoring programs can detect early signs of unanticipated changes, provide a more holistic understanding of ecosystem responses, and prompt faster management actions. Fisheries-related surveys that collect fisheries-independent data (hereafter referred to as “fisheries surveys”) are a key pillar of sustainable fisheries management and are ubiquitous in the United States and other countries. From the perspective of ocean observing, fisheries surveys offer three key strengths: (1) they are sustained due to largely consistent funding support from federal and state public sector fisheries agencies, (2) they collect paired physical, chemical, and biological data, and (3) they have large and frequently overlapping spatial footprints that extend into the offshore region. Despite this, information about fisheries survey data collection can remain poorly known to the broader academic and ocean observing communities. During the 2019 CalCOFI Symposium, marking the 70th anniversary of the California Cooperative Oceanic Fisheries Investigations (CalCOFI), representatives from 21 ocean monitoring programs on the North American West Coast came together to share the status of their monitoring programs and examine opportunities to leverage efforts to support regional ecosystem management needs. To increase awareness about collected ocean observing data, we catalog these ongoing ocean time series programs and detail the activities of the nine major federal or state fisheries surveys on the U.S. West Coast. We then present three case studies showing how fisheries survey data contribute to the understanding of emergent ecosystem management challenges: marine heatwaves, ocean acidification, and contaminant spills. Moving forward, increased cross-survey analyses and cooperation can improve regional capacity to address emerging challenges. Fisheries surveys represent a foundational blueprint for ecosystem monitoring. As the international community moves toward a global strategy for ocean observing needs, fisheries survey programs should be included as data contributors.
Impact of Mesoscale Circulation on the Structure of River Plumes During Large Rainfall Events Inshore of the East Australian Current
Authors: Li Junde , Roughan Moninya , Kerry Colette , Rao Shivanesh
Published: March 2022

Estuarine outflow can have a significant impact on physical and ecological systems in the coastal ocean. Along southeastern Australia, inshore of the East Australian Current, the shelf is narrow, the coastal circulation is advection dominated, and river estuarine outflow tends to be low, hence river plumes have largely been ignored. For these reasons, we lack an understanding of the spatial and temporal evolution of river plumes during large rainfall events (which are projected to increase in frequency and intensity), and the interaction of the mesoscale circulation with the estuarine outflow remains to be explored. Using a high-resolution (750 m) hydrodynamic model, we simulate idealized plumes from 4 estuaries during three different mesoscale circulation scenarios and investigate the spatial and temporal evolution of the estuarine outflow under two contrasting rainfall events (normal and large). We explore the plume from the largest of the 4 rivers, the Hawkesbury River, to understand the impact of the mesoscale circulation. During the first EAC mode, the plume spreads both northward and southeastward. The offshore spread of the plume is the largest in this scenario (~12.5 km east of the river mouth) in the wet event. In the second EAC mode, this plume dispersal is toward the north and east, driven by the proximity of a cyclonic eddy on the shelf, with an eastward extension of 11 km. In the third EAC mode, most of this river plume spreads southward with some to the north, again dictated by the position of the cyclonic eddy. The cross-shelf dispersal is a minimum of 9.5 km from the river mouth. It takes around 6 days for the freshwater spatial extent of the plume in the wet event to return to the base case. These results show the importance of mesoscale EAC circulation on the shelf circulation when considering river plumes dispersal. Knowledge of the ultimate fate of riverborne material, dilution and cumulative effects will enable better environmental management of this dynamic region for the local government.
Clinical Analysis of Renal Failure Caused by Malakoplakia: A Case Report and Literature Review
Authors: Wang Zhenting , Ren Jiannan
Published: March 2022

Background

A 52-year-old middle-aged woman developed fatigue, poor appetite and elevated CRE levels 6 months ago without known causes of these symptoms. After repeated anti-infective and renal function improvement treatment, her symptoms did not significantly improve and local progress. Pathological examination confirmed soft spot disease of left kidney and bladder.

Tests

Plain computed tomography (CT) scan of the lungs and urinary system; CT enhancement of the abdomen and pelvis, magnetic resonance (MR) enhancement of the abdomen and pelvis; positron emission tomography (PET)-CT; ultrasonography of the urinary system; cystoscopy, biopsy; and laboratory examination including urine routine and culture, urine protein quantification, cytology and culture of drainage fluid smear, routine blood test, and assessment of C-reactive protein, sedimentation, procalcitonin, liver function, renal function, electrolytes, thyroid function, parathyroid function, and cardiac enzymes.

Diagnosis

Left-sided renal and bladder malakoplakia, chronic renal insufficiency (CKD stage 4), renal anemia, complicated urinary tract infection (Escherichia coli + smooth bacilli), chronic urinary retention, abscess of the left psoas major and iliac fossa, type II diabetes mellitus, grade III hypertension (very high risk), and post cholecystectomy.

Treatment

Hospitalized urinary catheterization, anti-infective treatment, diagnostic anti-tuberculosis treatment, gastrointestinal dialysis, correction of anemia treatment, nutritional support, left lumbar enlargement, iliac fossa abscess puncture drainage, left nephrectomy.
An Integrated Proteomics and Metabolomics Strategy for the Mechanism of Calcium Oxalate Crystal-Induced Kidney Injury
Authors: Gao Songyan , Chao Yufan , Li Na , Li Henghui , Zhao Hongxia , Liu Xinru , Chen Wei , Dong Xin
Published: March 2022

Renal fibrosis is the pathological repair reaction of the kidney to chronic injury, which is an important process of chronic kidney disease (CKD) progressing to end-stage renal failure. Nephrolithiasis is one of the most common renal diseases, with waist and abdomen pain, hematuria, urinary tract infection, and other clinical symptoms, which can increase the risk of renal fibrosis. Oxalate crystal-induced kidney injury is an early stage of nephrolithiasis; it is of great significance to explore the mechanism for the prevention and treatment of nephrolithiasis. A rodent model of calcium oxalate (CaOx) crystal-induced kidney injury was used in the present study, and a network analysis method combining proteomics and metabolomics was conducted to reveal the mechanism of crystal kidney injury and to provide potential targets for the intervention of nephrolithiasis. Using the metabolomics method based on the UHPLC-Q/TOF-MS platform and the iTRAQ quantitative proteomics method, we screened a total of 244 metabolites and 886 proteins from the kidney tissues that had significant changes in the Crystal group compared with that in the Control group. Then, the ingenuity pathway analysis (IPA) was applied to construct a protein-to-metabolic regulatory network by correlating and integrating differential metabolites and proteins. The results showed that CaOx crystals could induce inflammatory reactions and oxidative stress through Akt, ERK1/2, and P38 MAPK pathways and affect amino acid metabolism and fatty acid β-oxidation to result in kidney injury, thus providing an important direction for the early prevention and treatment of nephrolithiasis.
Modulated Gut Microbiota for Potential COVID-19 Prevention and Treatment
Authors: Zhao Shuai , Feng Pengya , Meng Wenbo , Jin Weilin , Li Xun , Li Xiangkai
Published: March 2022

COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gained global attention. SARS-CoV-2 identifies and invades human cells via angiotensin-converting enzyme 2 receptors, which is highly expressed both in lung tissues and intestinal epithelial cells. The existence of the gut-lung axis in disease could be profoundly important for both disease etiology and treatment. Furthermore, several studies reported that infected patients suffer from gastrointestinal symptoms. The gut microbiota has a noteworthy effect on the intestinal barrier and affects many aspects of human health, including immunity, metabolism, and the prevention of several diseases. This review highlights the function of the gut microbiota in the host's immune response, providing a novel potential strategy through the use of probiotics, gut microbiota metabolites, and dietary products to enhance the gut microbiota as a target for COVID-19 prevention and treatment.
Risk of Colorectal Cancer in Patients With Irritable Bowel Syndrome: A Meta-Analysis of Population-Based Observational Studies
Authors: Wu Xinhui , Wang Jingxi , Ye Zhen , Wang Jin , Liao Xibei , Liv Mengsi , Svn Zhen
Published: March 2022

Background and Aims

Evidence on the association between irritable bowel syndrome (IBS) and colorectal cancer (CRC) risk is inconsistent. Therefore, we aimed to examine whether IBS leads to an increased risk for CRC using a systematic review and meta-analysis approach.

Methods

PubMed, Embase, and Web of Science were systematically searched to identify all relevant literature published through July 30, 2021. The pooled risk ratios (RRs) and corresponding 95% confidence intervals (CIs) for CRC after diagnosis of IBS were computed using random-and fixed-effects models and stratified by age, follow-up time, gender, and study design. The quality of included studies was assessed by the Newcastle-Ottawa scale.

Results

We included six studies consisting of 1,085,024 participants. Overall, the risk of detecting CRC after the initial IBS diagnosis was significantly higher than non-IBS controls (RR = 1.52, 95% CI: 1.04–2.22, P = 0.032). The peak of elevated risk occurred within the first year of IBS diagnosis (RR = 6.84, 95% CI: 3.70–12.65, P < 0.001), and after 1 year, the risk of CRC was similar to that of the general population (RR = 1.02, 95% CI: 0.88–1.18, P = 0.813). Notably, we found that the RR of CRC was more significant in IBS patients younger than 50 years compared to those older than 50 years (RR = 2.03, 95% CI: 1.17-3.53, P = 0.012 vs. 1.28, 95%CI: 0.94-1.75, P = 0.118, respectively). Gender and study design did not affect the results.

Conclusion

The risk of CRC within one year of the initial IBS diagnosis was increased approximately six-fold, whereas the long-term risk was not increased. However, current evidence does not support that IBS leads to an increased incidence of CRC, and the early excess risk is more likely attributable to misclassification resulting from overlapping symptoms rather than causation. Clinicians must remain vigilant for the CRC risk in patients younger than 50 years with IBS-like symptoms to avoid delaying necessary screening.
Dramatic Effect of Botulinum Toxin Type A on Hypertrophic Scar: A Promising Therapeutic Drug and Its Mechanism Through the SP-NK1R Pathway in Cutaneous Neurogenic Inflammation
Authors: Zhang Shunuo , Li Ke , Yu Zhixi , Chai Jun , Zhang Zheng , Zhang Yixin , Min Peiru
Published: March 2022

Background

Hypertrophic scar formation may be related to cutaneous neurogenic inflammation (CNI) through the substance P-neurokinin 1 receptor (SP-NK1R) signaling pathway. As a widely used drug in aesthetic clinical work, botulinum toxin type A (BTX-A) has a therapeutic effect on scars, but the actual mechanism remains unclear. This study aimed to clarify the potential mechanism by which BTX-A inhibits CNI in hypertrophic scars both in vitro and in vivo.

Methods

Tissue samples were obtained from surgical excisions. Immunohistological analysis was used to locate SP in human hypertrophic scars and normal skin. RT-PCR and western blot analysis were used to evaluate the expression of collagens after SP/BTX-A treatment. A rabbit ear scar model was used to explore the in vivo effect of BTX-A on scar treatment.

Results

SP and NK-1R were overexpressed in hypertrophic scars compared to normal skin tissues. Collagen secretion of hypertrophic scar-derived fibroblasts increased with increasing doses of SP. However, BTX-A may downregulate collagen expression through SP-NK1R pathway with or without the presence of SP inducing agent capsaicin. Meanwhile, SP inhibited the expression of NK-1R, and this inhibition was blocked by pretreatment with BTX-A. In vivo, intralesional BTX-A injection can also reduce the volume of scars and inhibit collagen secretion. Capsaicin may cause more severe scar manifestations, while the therapeutic effect of BTX-A remains.

Conclusion

Our research confirms that CNI stimulates fibroblasts during scar formation, while BTX-A can reduce collagen secretion by inhibiting the SP-NK1R signaling pathway, thus identifying a novel therapeutic target for this benign solid skin tumor.
Endotoxin Translocation and Gut Barrier Dysfunction Are Related to Variceal Bleeding in Patients With Liver Cirrhosis
Authors: Triantos Christos , Kalafateli Maria , Assimakopoulos Stelios F. , Karaivazoglou Katerina , Mantaka Aikaterini , Aggeletopoulou Ioanna , Spantidea Panagiota I. , Tsiaoussis Georgios , Rodi Maria , Kranidioti Hariklia , Goukos Dimitrios , Manolakopoulos Spilios , Gogos Charalambos , Samonakis Dimitrios N. , Daikos Georgios L. , Mouzaki Athanasia , Thomopoulos Konstantinos
Published: March 2022

Background

Bacterial infections are associated with the risk of variceal bleeding through complex pathophysiologic pathways.

Objectives

The primary objective of the present case-control study was to investigate the role of bacterial translocation and intestinal barrier dysfunction in the pathogenesis of variceal bleeding. A secondary objective was to determine independent predictors of key outcomes in variceal bleeding, including bleeding-related mortality.

Methods

Eighty-four (n = 84) consecutive patients participated in the study, 41 patients with acute variceal bleeding and 43 patients with stable cirrhosis, and were followed up for 6 weeks. Peripheral blood samples were collected at patient admission and before any therapeutic intervention.

Results

Child-Pugh (CP) score (OR: 1.868; p = 0.044), IgM anti-endotoxin antibody levels (OR: 0.954; p = 0.016) and TGF-β levels (OR: 0.377; p = 0.026) were found to be significant predictors of variceal bleeding. Regression analysis revealed that albumin (OR: 0.0311; p = 0.023), CRP (OR: 3.234; p = 0.034) and FABP2 levels (OR:1.000, p = 0.040), CP score (OR: 2.504; p = 0.016), CP creatinine score (OR: 2.366; p = 0.008), end-stage liver disease model (MELD), Na (OR: 1.283; p = 0.033), portal vein thrombosis (OR: 0.075; p = 0.008), hepatocellular carcinoma (OR: 0.060; p = 0.003) and encephalopathy (OR: 0.179; p = 0.045) were significantly associated with 6-week mortality.

Conclusions

Bacterial translocation and gut barrier impairment are directly related to the risk of variceal bleeding. Microbiota-modulating interventions and anti-endotoxin agents may be promising strategies to prevent variceal bleeding.
The Transcription Factor VpxlnR Is Required for the Growth, Development, and Virulence of the Fungal Pathogen Valsa pyri
Authors: He Feng , Kange Alex-Machio , Yang Jie , Xiao Jiaxin , Wang Rongbo , Yang Lu , Jia Yifan , Fu Zheng Qing , Zhao Yancun , Liu Fengquan
Published: March 2022

Pears (Pyrus sp.) are widely cultivated in China, and their yield accounts for more than 60% of global pear production. The fungal pathogen Valsa pyri is a major causal agent of pear canker disease, which results in enormous losses of pear production in northern China. In this study, we characterized a Zn2Cys6 transcription factor that contains one GAL4 domain and a fungal-trans domain, which are present in VpxlnR. The vpxlnR gene expression was upregulated in the invasion stage of V. pyri. To investigate its functions, we constructed gene deletion mutants and complementary strains. We observed that the growth of the vpxlnR mutants was reduced on potato dextrose agar (PDA), Czapek plus glucose or sucrose compared with that of the wild-type strain. Additionally, vpxlnR mutants exhibited loss of function in fruiting body formation. Moreover, vpxlnR mutants were more susceptible to hydrogen peroxide (H2O2) and salicylic acid (SA) and were reduced in their virulence at the early infection stage. According to a previous study, VpxlnR-interacting motifs containing NRHKGNCCGM were searched in the V. pyri genome, and we obtained 354 target genes, of which 148 genes had Clusters of Orthologous Groups (COG) terms. PHI-BLAST was used to identify virulence-related genes, and we found 28 hits. Furthermore, eight genes from the 28 PHI-BLAST hits were further assessed by yeast one-hybrid (Y1H) assays, and five target genes, salicylate hydroxylase (VP1G_09520), serine/threonine-protein kinase (VP1G_03128), alpha-xylosidase (VP1G_06369), G-protein beta subunit (VP1G_02856), and acid phosphatase (VP1G_03782), could interact with VpxlnR in vivo. Their transcript levels were reduced in one or two vpxlnR mutants. Taken together, these findings imply that VpxlnR is a key regulator of growth, development, stress, and virulence through controlling genes involved in signaling pathways and extracellular enzyme activities in V. pyri. The motifs interacting with VpxlnR also provide new insights into the molecular mechanism of xlnR proteins.
Integrated Analysis of the miRNAome and Transcriptome Reveals miRNA–mRNA Regulatory Networks in Catharanthus roseus Through Cuscuta campestris-Mediated Infection With “Candidatus Liberibacter asiaticus”
Authors: Zeng Chunhua , Wu Haodi , Cao Mengji , Zhou Changyong , Wang Xuefeng , Fu Shimin
Published: March 2022

Citrus Huanglongbing (HLB) is the most devastating disease of citrus caused by the Gram-negative phloem-limited bacterium “Candidatus Liberibacter asiaticus” (CLas). It can be transmitted by the Asian citrus psyllid “Diaphorina citri,” by grafting, and by the holoparasitic dodder. In this study, the non-natural host periwinkle (Catharanthus roseus) was infected via dodder (Cuscuta campestris) from CLas-infected citrus plants, and the asymptomatic leaves (AS) were subjected to transcriptomic and small-RNA profiling. The results were analyzed together with a transcriptome dataset from the NCBI repository that included leaves for which symptoms had just occurred (S) and yellowing leaves (Y). There were 3,675 differentially expressed genes (DEGs) identified in AS, and 6,390 more DEGs in S and further 2109 DEGs in Y. These DEGs were commonly enriched in photosystem, chloroplast, membrane, oxidation-reduction process, metal/zinc ion binding on GO. A total of 14,974 DEGs and 336 DE miRNAs (30 conserved and 301 novel) were identified. Through weighted gene co-expression network and nested network analyses, two critical nested miRNA–mRNA regulatory networks were identified with four conserved miRNAs. The primary miR164-NAC1 network is potentially involved in plant defense responses against CLas from the early infection stage to symptom development. The secondary network revealed the regulation of secondary metabolism and nutrient homeostasis through miR828-MYB94/miR1134-HSF4 and miR827-ATG8 regulatory networks, respectively. The findings discovered new potential mechanisms in periwinkle–CLas interactions, and its confirmation can be done in citrus–CLas system later on. The advantages of periwinkle plants in facilitating the quick establishment and greater multiplication of CLas, and shortening latency for disease symptom development make it a great surrogate for further studies, which could expedite our understanding of CLas pathogenesis.
Application of Arbuscular Mycorrhizal Fungi in Vineyards: Water and Biotic Stress Under a Climate Change Scenario: New Challenge for Chilean Grapevine Crop
Authors: Aguilera Paula , Ortiz Nancy , Becerra Ninozhka , Turrini Alessandra , Gaínza-Cortés Felipe , Silva-Flores Patricia , Aguilar-Paredes Ana , Romero Juan Karlo , Jorquera-Fontena Emilio , Mora María de La Luz , Borie Fernando
Published: March 2022

The cropVitis vinifera(L.) is of great economic importance as Chile is one of the main wine-producing countries, reaching a vineyard area of 145,000 ha. This vine crop is usually very sensitive to local condition changes and agronomic practices; therefore, strategies to counteract the expected future decrease in water level for agricultural irrigation, temperature increase, extreme water stress (abiotic stress), as well as increase in pathogenic diseases (biotic stress) related to climate change will be of vital importance for this crop. Studies carried out in recent years have suggested that arbuscular mycorrhizal fungi (AMF) can provide key ecosystem services to host plants, such as water uptake implementation and enhanced absorption of nutrients such as P and N, which are key factors for improving the nutritional status of the vine. AMF use in viticulture will contribute also to sustainable agronomic management and bioprotection against pathogens. Here we will present (1) the current status of grapevines in Chile, (2) the main problems in grapevines related to water stress and associated with climate change, (3) the importance of AMF to face water stress and pathogens, and (4) the application of AMF as a biotechnological and sustainable tool in vineyards.
The Microbiome, an Important Factor That Is Easily Overlooked in Male Infertility
Authors: Wang Hefeng , Xu Anran , Gong Liping , Chen Zhaowen , Zhang Bin , Li Xiuyun
Published: March 2022

Humankind has been interested in reproduction for millennia. Infertility, in which male factors contribute to approximately 50%, is estimated to concern over 72 million people worldwide. Despite advances in the diagnosis, medical treatment, and psychosocial management of male infertility over the past few decades, approximately 30% of male infertility is still thought to be idiopathic. Despite emerging advances in the microbiome associated with male infertility have indicated that the microbiome may be a key factor to the management of male infertility, roles, and mechanisms of the microbiome remain ambiguous. Here, we mainly discussed the association between microbial infection in the genital tract and male infertility, effect of antimicrobial therapy on male reproduction, association between microbial dysbiosis and male infertility, and effect of probiotic intervention on male reproduction. This review made progress toward establishing a relationship between the microbiome and male infertility, and explored the role of the microbiome in male infertility. We call for more high-quality studies to focus on the relationship between microbes and male infertility, and strongly suggest increasing awareness among sterile males with microbial infection and/or microbial dysbiosis when they seek fertility help.