bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual-Use Quickscan: A Web-Based Tool to Assess the Dual-Use Potential of Life Science Research
Authors: Vennis Iris M. , Schaap Mirjam M. , Hogervorst Petra A. M. , de Bruin Arnout , Schulpen Sjors , Boot Marijke A. , van Passel Mark W. J. , Rutjes Saskia A. , Bleijs Diederik A.
Published: December 2021

Research on pathogenic organisms is crucial for medical, biological and agricultural developments. However, biological agents as well as associated knowledge and techniques, can also be misused, for example for the development of biological weapons. Potential malicious use of well-intended research, referred to as “dual-use research”, poses a threat to public health and the environment. There are various international resources providing frameworks to assess dual-use potential of the research concerned. However, concrete instructions for researchers on how to perform a dual-use risk assessment is largely lacking. The international need for practical dual-use monitoring and risk assessment instructions, in addition to the need to raise awareness among scientists about potential dual-use aspects of their research has been identified over the last years by the Netherlands Biosecurity Office, through consulting national and international biorisk stakeholders. We identified that Biorisk Management Advisors and researchers need a practical tool to facilitate a dual-use assessment on their specific research. Therefore, the Netherlands Biosecurity Office developed a web-based Dual-Use Quickscan (www.dualusequickscan.com), that can be used periodically by researchers working with microorganisms to assess potential dual-use risks of their research by answering a set of fifteen yes/no questions. The questions for the tool were extracted from existing international open resources, and categorized into three themes: characteristics of the biological agent, knowledge and technology about the biological agent, and consequences of misuse. The results of the Quickscan provide the researcher with an indication of the dual-use potential of the research and can be used as a basis for further discussions with a Biorisk Management Advisor. The Dual-Use Quickscan can be embedded in a broader system of biosafety and biosecurity that includes dual-use monitoring and awareness within organizations. Increased international attention to examine pathogens with pandemic potential has been enhanced by the current COVID-19 pandemic, hence monitoring of dual-use potential urgently needs to be encouraged.
Programmed Cell Death Recruits Macrophages Into the Developing Mouse Cochlea
Authors: Borse Vikrant , Kaur Tejbeer , Hinton Ashley , Ohlemiller Kevin , Warchol Mark E.
Published: December 2021

Programmed cell death (PCD) plays a critical role in the development and maturation of the cochlea. Significant remodeling occurs among cells of the greater epithelial ridge (GER) of Kölliker’s organ, leading to tissue regression and formation of the inner sulcus. In mice, this event normally occurs between postnatal days 5–15 (P5-15) and is regulated by thyroid hormone (T3). During this developmental time period, the cochlea also contains a large population of macrophages. Macrophages are frequently involved in the phagocytic clearance of dead cells, both during development and after injury, but the role of macrophages in the developing cochlea is unknown. This study examined the link between developmental cell death in the GER and the recruitment of macrophages into this region. Cell death in the basal GER begins at P5 and enhanced numbers of macrophages were observed at P7. This pattern of macrophage recruitment was unchanged in mice that were genetically deficient for CX3CR1, the receptor for fractalkine (a known macrophage chemoattractant). We found that injection of T3 at P0 and P1 caused GER cell death to begin at P3, and this premature PCD was accompanied by earlier recruitment of macrophages. We further found that depletion of macrophages from the developing cochlea (using CX3CR1DTR/+ mice and treatment with the CSF1R antagonist BLZ945) had no effect on the pattern of GER regression. Together, these findings suggest that macrophages are recruited into the GER region after initiation of developmental PCD, but that they are not essential for GER regression during cochlear remodeling.
Single-Cell RNA Sequencing Revealed the Heterogeneity of Gonadal Primordial Germ Cells in Zebra Finch (Taeniopygia guttata)
Authors: Jung Kyung Min , Seo Minseok , Kim Young Min , Kim Jin Lee , Han Jae Yong
Published: December 2021

Primordial germ cells (PGCs) are undifferentiated gametes with heterogeneity, an evolutionarily conserved characteristic across various organisms. Although dynamic selection at the level of early germ cell populations is an important biological feature linked to fertility, the heterogeneity of PGCs in avian species has not been characterized. In this study, we sought to evaluate PGC heterogeneity in zebra finch using a single-cell RNA sequencing (scRNA-seq) approach. Using scRNA-seq of embryonic gonadal cells from male and female zebra finches at Hamburger and Hamilton (HH) stage 28, we annotated nine cell types from 20 cell clusters. We found that PGCs previously considered a single population can be separated into three subtypes showing differences in apoptosis, proliferation, and other biological processes. The three PGC subtypes were specifically enriched for genes showing expression patterns related to germness or pluripotency, suggesting functional differences in PGCs according to the three subtypes. Additionally, we discovered a novel biomarker, SMC1B, for gonadal PGCs in zebra finch. The results provide the first evidence of substantial heterogeneity in PGCs previously considered a single population in birds. This discovery expands our understanding of PGCs to avian species, and provides a basis for further research.
Location-Dependent DNA Methylation Signatures in a Clonal Invasive Crayfish
Authors: Tönges Sina , Venkatesh Geetha , Andriantsoa Ranja , Hanna Katharina , Gatzmann Fanny , Raddatz Günter , Carneiro Vitor Coutinho , Lyko Frank
Published: December 2021

DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental parameters have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of context-dependent DNA methylation signatures in a clonal animal.
Merozoite Proteins Discovered by qRT-PCR-Based Transcriptome Screening of Plasmodium falciparum
Authors: Hou Nan , Li Shanshan , Jiang Ning , Piao Xianyu , Ma Yu , Liu Shuai , Chen Qijun
Published: December 2021

The development of malaria vaccines and medicines depends on the discovery of novel malaria protein targets, but the functions of more than 40% of P. falciparum genes remain unknown. Asexual parasites are the critical stage that leads to serious clinical symptoms and that can be modulated by malaria treatments and vaccines. To identify critical genes involved in the development of Plasmodium parasites within erythrocytes, the expression profile of more than 5,000 genes distributed across the 14 chromosomes of the PF3D7 strain during its six critical developmental stages (merozoite, early-ring, late-ring, early trophozoite, late-trophozoite, and middle-schizont) was evaluated. Hence, a qRT-PCR-based transcriptome of the erythrocytic developmental process of P. falciparum was revealed. Weighted gene coexpression network analyses revealed that a large number of genes are upregulated during the merozoite release process. Further gene ontology analysis revealed that a cluster of genes is associated with merozoite and may be apical complex components. Among these genes, 135 were comprised within chromosome 14, and 80% of them were previously unknown in functions. Western blot and immunofluorescence assays using newly developed corresponding antibodies showed that some of these newly discovered proteins are highly expressed in merozoites. Further invasion inhibition assays revealed that specific antibodies against several novel merozoite proteins can interfere with parasite invasion. Taken together, our study provides a developmental transcriptome of the asexual parasites of P. falciparum and identifies a group of previously unknown merozoite proteins that may play important roles in the process of merozoite invasion.
Alterations of the Oral Microbiota Profiles in Chinese Patient With Oral Cancer
Authors: Li Zixuan , Chen Gang , Wang Panpan , Sun Minglei , Zhao Junfang , Li Ang , Sun Qiang
Published: December 2021

Oral cancer is the most common malignant tumor in the oral and maxillofacial region, of which more than 90% is squamous cell carcinoma. The incidence of oral cancer is on the rise worldwide. An imbalance between the microorganism composition and its host may lead to the occurrence of oral malignant tumors. Accumulating evidence suggests that the oral microbiota plays an important role in oral cancer; however, the association between oral microbiota and oral cancer has not yet been comprehensively studied. In this study, metagenomic sequencing was used to compare the microbial composition of three groups of samples from Chinese patients with oral cancer, patients with precancerous lesion, and normal individuals. In terms of microbiota richness, the oral microbiota of patients with precancerous lesions was richer than that of oral cancer patients and healthy controls, whereas in terms of microbiota diversity, there was little difference between the three groups. The three groups of samples exhibited statistically significant differences in microbiota composition and metabolic function at the family, genus, and species levels (P < 0.05). The differentially enriched phylum in oral cancer samples was Bacteroidetes (P < 0.05). At the genus level, the main differentially enriched taxa were Prevotella, Peptostreptococcus, Carnobacterium, and Diastella (P < 0.05). The species level was differentially enriched in Prevotella intermedia and Peptostreptococcus stomatis (p < 0.05). The prediction of microbiota function shows that oral cancer is mainly associated with coenzyme A biosynthesis, phosphopantothenic acid biosynthesis, inosine 5’-phosphate degradation, and riboflavin biosynthesis. Furthermore, the increase in C-reactive protein level in oral cancer patients was found to be closely related to P. intermedia. Overall, oral bacterial profiles showed significant differences between the oral cancer group and normal group. Hence, microbes can be employed as diagnostic markers and treatment targets for oral cancer.
Usage-Based Individual Differences in the Probabilistic Processing of Multi-Word Sequences
Authors: McConnell Kyla , Blumenthal-Dramé Alice
Published: December 2021

While it is widely acknowledged that both predictive expectations and retrodictive integration influence language processing, the individual differences that affect these two processes and the best metrics for observing them have yet to be fully described. The present study aims to contribute to the debate by investigating the extent to which experienced-based variables modulate the processing of word pairs (bigrams). Specifically, we investigate how age and reading experience correlate with lexical anticipation and integration, and how this effect can be captured by the metrics of forward and backward transition probability (TP). Participants read more and less strongly associated bigrams, paired to control for known lexical covariates such as bigram frequency and meaning (i.e., absolute control, total control, absolute silence, total silence) in a self-paced reading (SPR) task. They additionally completed assessments of exposure to print text (Author Recognition Test, Shipley vocabulary assessment, Words that Go Together task) and provided their age. Results show that both older age and lesser reading experience individually correlate with stronger TP effects. Moreover, TP effects differ across the spillover region (the two words following the noun in the bigram).
CT Angiography Manual Multiplanar Vessel Diameter Measurement vs. Semiautomated Perpendicular Area Minimal Caliber Computation of Internal Carotid Artery Stenosis
Authors: Siepmann Timo , Barlinn Kristian , Floegel Thomas , Barlinn Jessica , Pallesen Lars-Peder , Puetz Volker , Kitzler Hagen H.
Published: December 2021

Objective: To determine the diagnostic agreement of CT angiography (CTA) manual multiplanar reformatting (MPR) stenosis diameter measurement and semiautomated perpendicular stenosis area minimal caliber computation of extracranial internal carotid artery (ICA) stenosis.

Methods: We analyzed acute cerebral ischemia CTA at our tertiary stroke center in a 12-month period. Prospective NASCET-type stenosis grading for each ICA was independently performed using (1) MPR to manually determine diameters and (2) perpendicular stenosis area with minimal caliber semiautomated computation to grade luminal constriction. Corresponding to clinically relevant NASCET strata, results were grouped into severity ranges: normal, 1–49%, 50–69%, and 70–99%, and occlusion.

Results: We included 647 ICA pairs from 330 patients (median age of 74 [66–80, IQR]; 38–92 years; 58% men; median NIHSS 4 [1–9, IQR]). MPR diameter and semiautomated caliber measurements resulted in stenosis grades of 0–49% in 143 vs. 93, 50–69% in 29 vs. 27, 70–99% in 6 vs. 14, and occlusion in 34 vs. 34 ICAs (p = 0.003), respectively. We found excellent reliability between repeated manual CTA assessments of one expert reader (ICC = 0.997; 95% CI, 0.993–0.999) and assessments of two expert readers (ICC = 0.972; 95% CI, 0.936–0.988). For the semiautomated vessel analysis software, both intrarater reliability and interrater reliability were similarly strong (ICC = 0.981; 95% CI, 0.952–0.992 and ICC = 0.745; 95% CI, 0.486–0.883, respectively). However, Bland–Altman analysis revealed a mean difference of 1.6% between the methods within disease range with wide 95% limits of agreement (−16.7–19.8%). This interval even increased with exclusively considered vessel pairs of stenosis ≥1% (mean 5.3%; −24.1–34.7%) or symptomatic stenosis ≥50% (mean 0.1%; −25.7–26.0%).

Conclusion: Our findings suggest that MPR-based diameter measurement and the semiautomated perpendicular area minimal caliber computation methods cannot be used interchangeably for the quantification of ICA steno-occlusive disease.
Mitochondrial Metabolism in Myocardial Remodeling and Mechanical Unloading: Implications for Ischemic Heart Disease
Authors: Jiang Min , Xie Xiaoye , Cao Feng , Wang Yabin
Published: December 2021

Ischemic heart disease refers to myocardial degeneration, necrosis, and fibrosis caused by coronary artery disease. It can lead to severe left ventricular dysfunction (LVEF ≤ 35–40%) and is a major cause of heart failure (HF). In each contraction, myocardium is subjected to a variety of mechanical forces, such as stretch, afterload, and shear stress, and these mechanical stresses are clinically associated with myocardial remodeling and, eventually, cardiac outcomes. Mitochondria produce 90% of ATP in the heart and participate in metabolic pathways that regulate the balance of glucose and fatty acid oxidative phosphorylation. However, altered energetics and metabolic reprogramming are proved to aggravate HF development and progression by disturbing substrate utilization. This review briefly summarizes the current insights into the adaptations of cardiomyocytes to mechanical stimuli and underlying mechanisms in ischemic heart disease, with focusing on mitochondrial metabolism. We also discuss how mechanical circulatory support (MCS) alters myocardial energy metabolism and affects the detrimental metabolic adaptations of the dysfunctional myocardium.
Device-Based Sympathetic Nerve Regulation for Cardiovascular Diseases
Authors: Li Le , Hu Zhao , Xiong Yulong , Yao Yan
Published: December 2021

Sympathetic overactivation plays an important role in promoting a variety of pathophysiological processes in cardiovascular diseases (CVDs), including ventricular remodeling, vascular endothelial injury and atherosclerotic plaque progression. Device-based sympathetic nerve (SN) regulation offers a new therapeutic option for some CVDs. Renal denervation (RDN) is the most well-documented method of device-based SN regulation in clinical studies, and several large-scale randomized controlled trials have confirmed its value in patients with resistant hypertension, and some studies have also found RDN to be effective in the control of heart failure and arrhythmias. Pulmonary artery denervation (PADN) has been clinically shown to be effective in controlling pulmonary hypertension. Hepatic artery denervation (HADN) and splenic artery denervation (SADN) are relatively novel approaches that hold promise for a role in cardiovascular metabolic and inflammatory-immune related diseases, and their first-in-man studies are ongoing. In addition, baroreflex activation, spinal cord stimulation and other device-based therapies also show favorable outcomes. This review summarizes the pathophysiological rationale and the latest clinical evidence for device-based therapies for some CVDs.
Developing Self-Efficacy and Behavioral Intentions Among Underrepresented Students in STEM: The Role of Active Learning
Authors: Kuchynka Sophie , Reifsteck Tina V. , Gates Alexander E. , Rivera Luis M.
Published: December 2021

Increasing academic participation among students from ethnic-racial underrepresented groups in STEM yields societal benefits including ameliorating economic ramifications of the labor shortages in STEM, improving scientific innovation, and providing opportunity, access, and participation in high-status STEM fields. Two longitudinal studies with students from underrepresented groups investigated the role of active learning interventions in the development of STEM self-efficacy and intentions to pursue STEM in the future. Study 1 longitudinally tracked high school students participating in a 4-week geoscience program that applied active learning techniques ranging from hands on experiments to peer discussion. High school student participants displayed increases in self-efficacy and STEM intentions from the start to completion of the program, an effect that was observed exclusively among those who reported strong program quality. Study 2 examined the role of mentorship effectiveness with a sample of community college STEM students interested in transferring to a 4-year college. Students’ relatively strong self-efficacy and STEM intentions at the start of the semester remained stable through the end of the semester. Altogether, the present research highlights the role of positive, inclusive educational climates in promoting STEM success among students from underrepresented group members.
A Novel Nomogram for Predicting Gestational Diabetes Mellitus During Early Pregnancy
Authors: Kang Mei , Zhang Hui , Zhang Jia , Huang Kaifeng , Zhao Jinyan , Hu Jie , Lu Cong , Shao Jiashen , Weng Jianrong , Yang Yuemin , Zhuang Yan , Xu Xianming
Published: December 2021

Objective

Gestational diabetes mellitus (GDM) is a serious threat to maternal and child health. However, there isn’t a standard predictive model for the disorder in early pregnancy. This study is to investigate the association of blood indexes with GDM and establishes a practical predictive model in early pregnancy for GDM.

Methods

This is a prospective cohort study enrolling 413 pregnant women in the department of Obstetrics and Gynecology in Shanghai General Hospital from July 2020 to April 2021.A total of 116pregnantwomen were diagnosed with GDM during the follow-up. Blood samples were collected at early trimester (gestational weeks 12-16) and second trimester(gestational weeks 24-26 weeks). A predictive nomogram was established based on results of the multivariate logistic model and 5-fold cross validation. We evaluate the nomogram by the area under the receiver operating characteristic curve (AUC), calibration curves and decision curve analysis (DCAs).

Results

Significant differences were observed between the GDM and normal controls among age, pre-pregnancy BMI, whether the pregnant women with complications, the percentage of B lymphocytes, fasting plasma glucose (FPG), HbA1c, triglyceride and the level of progesterone in early trimester. Risk factors used in nomogram included age, pre-pregnancy BMI, FPG, HbA1c, the level of IgA, the level of triglyceride, the percentage of B lymphocytes, the level of progesterone and TPOAb in early pregnancy. The AUC value was 0.772, 95%CI (0.602,0.942). The calibration curves for the probability of GDM demonstrated acceptable agreement between the predicted outcomes by the nomogram and the observed values. DCA curves showed good positive net benefits in the predictive model.

Conclusions

A novel predictive nomogram was developed for GDM in our study, which could do help to patient counseling and management during early pregnancy in clinical practice.
Lipidomics Reveals Serum Specific Lipid Alterations in Diabetic Nephropathy
Authors: Xu Tingting , Xu Xiaoyan , Zhang Lu , Zhang Ke , Wei Qiong , Zhu Lin , Yu Ying , Xiao Liangxiang , Lin Lili , Qian Wenjuan , Wang Jue , Ke Mengying , An Xiaofei , Liu Shijia
Published: December 2021

In diabetes mellitus (DM), disorders of glucose and lipid metabolism are significant causes of the onset and progression of diabetic nephropathy (DN). However, the exact roles of specific lipid molecules in the pathogenesis of DN remain unclear. This study recruited 577 participants, including healthy controls (HCs), type-2 DM (2-DM) patients, and DN patients, from the clinic. Serum samples were collected under fasting conditions. Liquid chromatography-mass spectrometry-based lipidomics methods were used to explore the lipid changes in the serum and identify potential lipid biomarkers for the diagnosis of DN. Lipidomics revealed that the combination of lysophosphatidylethanolamine (LPE) (16:0) and triacylglycerol (TAG) 54:2-FA18:1 was a biomarker panel for predicting DN. The receiver operating characteristic analysis showed that the panel had a sensitivity of 89.1% and 73.4% with a specificity of 88.1% and 76.7% for discriminating patients with DN from HCs and 2-DM patients. Then, we divided the DN patients in the validation cohort into microalbuminuria (diabetic nephropathy at an early stage, DNE) and macroalbuminuria (diabetic nephropathy at an advanced stage, DNA) groups and found that LPE(16:0), phosphatidylethanolamine (PE) (16:0/20:2), and TAG54:2-FA18:1 were tightly associated with the stages of DN. The sensitivity of the biomarker panel to distinguish between patients with DNE and 2-DM, DNA, and DNE patients was 65.6% and 85.9%, and the specificity was 76.7% and 75.0%, respectively. Our experiment showed that the combination of LPE(16:0), PE(16:0/20:2), and TAG54:2-FA18:1 exhibits excellent performance in the diagnosis of DN.
Role of FGF Receptors and Their Pathways in Adrenocortical Tumors and Possible Therapeutic Implications
Authors: Sbiera Iuliu , Kircher Stefan , Altieri Barbara , Lenz Kerstin , Hantel Constanze , Fassnacht Martin , Sbiera Silviu , Kroiss Matthias
Published: December 2021

Adrenocortical carcinoma (ACC) is a rare endocrine malignancy and treatment of advanced disease is challenging. Clinical trials with multi-tyrosine kinase inhibitors in the past have yielded disappointing results. Here, we investigated fibroblast growth factor (FGF) receptors and their pathways in adrenocortical tumors as potential treatment targets. We performed real-time RT-PCR of 93 FGF pathway related genes in a cohort of 39 fresh frozen benign and malignant adrenocortical, 9 non-adrenal tissues and 4 cell lines. The expression of FGF receptors was validated in 166 formalin-fixed paraffin embedded (FFPE) tissues using RNA in situ hybridization (RNAscope) and correlated with clinical data. In malignant compared to benign adrenal tumors, we found significant differences in the expression of 16/94 FGF receptor pathway related genes. Genes involved in tissue differentiation and metastatic spread through epithelial to mesechymal transition were most strongly altered. The therapeutically targetable FGF receptors 1 and 4 were upregulated 4.6- and 6-fold, respectively, in malignant compared to benign adrenocortical tumors, which was confirmed by RNAscope in FFPE samples. High expression of FGFR1 and 4 was significantly associated with worse patient prognosis in univariate analysis. After multivariate adjustment for the known prognostic factors Ki-67 and ENSAT tumor stage, FGFR1 remained significantly associated with recurrence-free survival (HR=6.10, 95%CI: 1.78 – 20.86, p=0.004) and FGFR4 with overall survival (HR=3.23, 95%CI: 1.52 – 6.88, p=0.002). Collectively, our study supports a role of FGF pathways in malignant adrenocortical tumors. Quantification of FGF receptors may enable a stratification of ACC for the use of FGFR inhibitors in future clinical trials.
The Interannual Variability of the Fall Size of Young-of-The-Year Chub (Squalius cephalus): Influence of Phenology, Growth Patterns and Abiotic Factors
Authors: Logez Maxime , Bounket Bernadette , Gibert Pierre , Carrel Georges , Diouloufet Virginie , Colombet Xavier , Morat Fabien
Published: December 2021

Long-term surveys confirm the rapidity of environmental and biological changes undergone by endangered species but that also concerned relatively “tolerant” species, especially common rheophilic species such as European chub (Squalius cephalus, Linnaeus 1758). As many organisms, fish are highly vulnerable during their first life stages. Body size is a determinant factor for ecosystem functioning and for fish to survive to predators or to winter conditions. While numerous studies has already demonstrated the large variability of autumnal size of fish hatched during the year, few have focused on the factors explaining these interannual variations and on the growth patterns underlying these distributions. Using otoliths of young-of-the-year (YOY), we studied how the interannual variability in fall sizes of chub might be related to varying phenology, temperature, hydrology and growth patterns. YOY were sampled in three sections of the same reach of the Rhône River with contrasted hydrological regime: an artificial deep lotic channel (the tailrace of Bollène), a bypassed section with both lotic and lentic areas (former river channel before dam construction) and a reservoir with lentic deep waters. Sampling was performed on each sector during two thermally distinct years. Temperature had an important effect on both phenology and growth rate but it was not expressed similarly among river sections. Fish hatched earlier in the warmer year. Fish sizes were positively correlated with growing degree-days, but with distinct relationships between years and sections. The growth was faster in the warmer year, and in the warmer section, but differences in growth patterns varied between sections. In the bypassed section, the difference was slight, almost not significant, even if temperatures were very different between the 2 years considered. Autumnal variations in size could be explained either by an earlier phenology or by a faster growth due to higher temperatures occurring during the final part of the growing period. Our results were in accordance with general theory’s predictions relating individual growth to temperature, but they also showed that other factors might mitigate the influence of temperature on fish early life stages.
Shifting Goalposts: Setting Restoration Targets for Waterbirds in the Murray-Darling Basin Under Climate Change
Authors: Bino Gilad , Brandis Kate , Kingsford Richard T. , Porter John
Published: December 2021

The Murray-Darling Basin (the Basin) is the largest river system in Australia, supplying about 40% of the country’s irrigated agricultural output. Associated water resource development has come with a heavy price for the Basin’s freshwater ecosystems degrading them over decades. Australian governments are attempting to achieve environmental sustainability by returning water to the environment through buy-back of irrigation licences and improved water efficiencies. To determine effectiveness, basin-wide management objectives were established for key indicators, including waterbird populations and life histories which can effectively indicate ecosystem function and condition, driven by flow and flooding regimes. Ongoing monitoring of waterbird numbers indicates continued declines. We evaluated the feasibility of meeting established waterbird objectives under existing and predicted climates. We modelled long-term waterbird numbers using one of the world’s largest ongoing waterbird surveys (1983–2020), covering about 13.5% of the area of the entire Basin. Our findings suggest that under near future climate change projections, waterbird numbers will likely continue to decline, and remain below restoration targets set for the Basin. We discuss the current policy settings for using environmental water to support waterbird populations, recommending adjustments to restore the Basin’s waterbird populations and their wetlands in order to meet Australia’s conservation targets in relation to the ongoing global crisis of biodiversity loss.
Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies
Authors: Marczyk Michal , Macioszek Agnieszka , Tobiasz Joanna , Polanska Joanna , Zyla Joanna
Published: December 2021

A typical genome-wide association study (GWAS) analyzes millions of single-nucleotide polymorphisms (SNPs), several of which are in a region of the same gene. To conduct gene set analysis (GSA), information from SNPs needs to be unified at the gene level. A widely used practice is to use only the most relevant SNP per gene; however, there are other methods of integration that could be applied here. Also, the problem of nonrandom association of alleles at two or more loci is often neglected. Here, we tested the impact of incorporation of different integrations and linkage disequilibrium (LD) correction on the performance of several GSA methods. Matched normal and breast cancer samples from The Cancer Genome Atlas database were used to evaluate the performance of six GSA algorithms: Coincident Extreme Ranks in Numerical Observations (CERNO), Gene Set Enrichment Analysis (GSEA), GSEA-SNP, improved GSEA for GWAS (i-GSEA4GWAS), Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), and Over-Representation Analysis (ORA). Association of SNPs to phenotype was calculated using modified McNemar’s test. Results for SNPs mapped to the same gene were integrated using Fisher and Stouffer methods and compared with the minimum p-value method. Four common measures were used to quantify the performance of all combinations of methods. Results of GSA analysis on GWAS were compared to the one performed on gene expression data. Comparing all evaluation metrics across different GSA algorithms, integrations, and LD correction, we highlighted CERNO, and MAGENTA with Stouffer as the most efficient. Applying LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. When Fisher or Stouffer were used with LD, sensitivity and reproducibility were also better. Using any integration method was beneficial in comparison with a minimum p-value method in specific combinations. The correlation between GSA results from genomic and transcriptomic level was the highest when Stouffer integration was combined with LD correction. We thoroughly evaluated different approaches to GSA in GWAS in terms of performance to guide others to select the most effective combinations. We showed that LD correction and Stouffer integration could increase the performance of enrichment analysis and encourage the usage of these techniques.
Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis
Authors: Dong Yani , Lyu Likang , Wen Haishen , Shi Bao
Published: December 2021

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.
A Stabilized, Monomeric, Receptor Binding Domain Elicits High-Titer Neutralizing Antibodies Against All SARS-CoV-2 Variants of Concern
Authors: Ahmed Shahbaz , Khan Mohammad Suhail , Gayathri Savitha , Singh Randhir , Kumar Sahil , Patel Unnatiben Rajeshbhai , Malladi Sameer Kumar , Rajmani Raju S. , van Vuren Petrus Jansen , Riddell Shane , Goldie Sarah , Girish Nidhi , Reddy Poorvi , Upadhyaya Aditya , Pandey Suman , Siddiqui Samreen , Tyagi Akansha , Jha Sujeet , Pandey Rajesh , Khatun Oyahida , Narayan Rohan , Tripathi Shashank , McAuley Alexander J. , Singanallur Nagendrakumar Balasubramanian , Vasan Seshadri S. , Ringe Rajesh P. , Varadarajan Raghavan
Published: December 2021

Saturation suppressor mutagenesis was used to generate thermostable mutants of the SARS-CoV-2 spike receptor-binding domain (RBD). A triple mutant with an increase in thermal melting temperature of ~7°C with respect to the wild-type B.1 RBD and was expressed in high yield in both mammalian cells and the microbial host, Pichia pastoris, was downselected for immunogenicity studies. An additional derivative with three additional mutations from the B.1.351 (beta) isolate was also introduced into this background. Lyophilized proteins were resistant to high-temperature exposure and could be stored for over a month at 37°C. In mice and hamsters, squalene-in-water emulsion (SWE) adjuvanted formulations of the B.1-stabilized RBD were considerably more immunogenic than RBD lacking the stabilizing mutations and elicited antibodies that neutralized all four current variants of concern with similar neutralization titers. However, sera from mice immunized with the stabilized B.1.351 derivative showed significantly decreased neutralization titers exclusively against the B.1.617.2 (delta) VOC. A cocktail comprising stabilized B.1 and B.1.351 RBDs elicited antibodies with qualitatively improved neutralization titers and breadth relative to those immunized solely with either immunogen. Immunized hamsters were protected from high-dose viral challenge. Such vaccine formulations can be rapidly and cheaply produced, lack extraneous tags or additional components, and can be stored at room temperature. They are a useful modality to combat COVID-19, especially in remote and low-resource settings.
Next-Generation Sequencing and Proteomics of Cerebrospinal Fluid From COVID-19 Patients With Neurological Manifestations
Authors: Wang Haijun , Zhang Zili , Zhou Junfen , Han Shuqing , Kang Zhenyu , Chuang Haoyu , Fan Heng , Zhao Hongyang , Wang Lin , Ning Yunjia , Sarapultsev Alexey , Li Willis X. , Li Jinghong , Lin Zhicheng , Luo Shanshan , Xiong Nian , Hu Desheng
Published: December 2021

The SARS-CoV-2 and its variants are still hitting the world. Ever since the outbreak, neurological involvements as headache, ageusia, and anosmia in COVID-19 patients have been emphasized and reported. But the pathogenesis of these new-onset neurological manifestations in COVID-19 patients is still obscure and controversial. As difficulty always lay in the diagnosis of neurological infection, current reports to validate the presence of SARS-CoV-2 in cerebrospinal fluid (CSF) almost relied on the basic methods and warranted improvement. Here we reported a case series of 8 patients with prominent new-onset neurological manifestations, who were screened out from a patch of 304 COVID-19 confirmed patients. Next-generation sequencing (NGS) and proteomics were conducted in the simultaneously obtained CSF and serum samples of the selected patients, with three non-COVID-19 patients with matched demographic features used as the controls for proteomic analysis. SARS-CoV-2 RNA was detected in the CSF of four COVID-19 patients and was suspicious in the rest four remaining patients by NGS, but was negative in all serum samples. Proteomic analysis revealed that 185 and 59 proteins were differentially expressed in CSF and serum samples, respectively, and that only 20 proteins were shared, indicating that the proteomic changes in CSF were highly specific. Further proteomic annotation highlighted the involvement of complement system, PI3K-Akt signaling pathway, enhanced cellular interaction, and macrophages in the CSF proteomic alterations. This study, equipped with NGS and proteomics, reported a high detection rate of SARS-CoV-2 in the CSF of COVID-19 patients and the proteomic alteration of CSF, which would provide insights into understanding the pathological mechanism of SARS-CoV-2 CNS infection.
Extracellular Vesicle Associated miRNAs Regulate Signaling Pathways Involved in COVID-19 Pneumonia and the Progression to Severe Acute Respiratory Corona Virus-2 Syndrome
Authors: Meidert Agnes S. , Hermann Stefanie , Brandes Florian , Kirchner Benedikt , Buschmann Dominik , Billaud Jean-Noël , Klein Matthias , Lindemann Anja , Aue Elisa , Schelling Gustav , Pfaffl Michael W. , Reithmair Marlene
Published: December 2021

Background

Extracellular vesicles (EVs) are mediators of cell-to-cell communication in inflammatory lung diseases. They function as carriers for miRNAs which regulate mRNA transcripts and signaling pathways after uptake into recipient cells. We investigated whether miRNAs associated with circulating EVs regulate immunologic processes in COVID-19.

Methods

We prospectively studied 20 symptomatic patients with COVID-19 pneumonia, 20 mechanically ventilated patients with severe COVID-19 (severe acute respiratory corona virus-2 syndrome, ARDS) and 20 healthy controls. EVs were isolated by precipitation, total RNA was extracted, profiled by small RNA sequencing and evaluated by differential gene expression analysis (DGE). Differentially regulated miRNAs between groups were bioinformatically analyzed, mRNA target transcripts identified and signaling networks constructed, thereby comparing COVID-19 pneumonia to the healthy state and pneumonia to severe COVID-19 ARDS.

Results

DGE revealed 43 significantly and differentially expressed miRNAs (25 downregulated) in COVID-19 pneumonia when compared to controls, and 20 miRNAs (15 downregulated) in COVID-19 ARDS patients in comparison to those with COVID-19 pneumonia. Network analysis for comparison of COVID-19 pneumonia to healthy controls showed upregulated miR-3168 (log2FC=2.28, padjusted<0.001), among others, targeting interleukin-6 (IL6) (25.1, 15.2 - 88.2 pg/ml in COVID-19 pneumonia) and OR52N2, an olfactory smell receptor in the nasal epithelium. In contrast, miR-3168 was significantly downregulated in COVID-19 ARDS (log2FC=-2.13, padjusted=0.003) and targeted interleukin-8 (CXCL8) in a completely activated network. Toll-like receptor 4 (TLR4) was inhibited in COVID-19 pneumonia by miR-146a-5p and upregulated in ARDS by let-7e-5p.

Conclusion

EV-derived miRNAs might have important regulative functions in the pathophysiology of COVID-19: CXCL8 regulates neutrophil recruitment into the lung causing epithelial damage whereas activated TLR4, to which SARS-CoV-2 spike protein binds strongly, increases cell surface ACE2 expression and destroys type II alveolar cells that secrete pulmonary surfactants; both resulting in pulmonary-capillary leakage and ARDS. These miRNAs may serve as biomarkers or as possible therapeutic targets.
Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together
Authors: Zhang Lin , Poorbaugh Josh , Dougan Michael , Chen Peter , Gottlieb Robert L. , Huhn Gregory , Beasley Stephanie , Daniels Montanea , Ngoc Vy Trinh Thi , Crisp Melissa , Freitas Joshua Joaquin , Vaillancourt Peter , Patel Dipak R. , Nirula Ajay , Kallewaard Nicole L. , Higgs Richard E. , Benschop Robert J.
Published: December 2021

Background

Neutralizing monoclonal antibodies (mAbs) to SARS-CoV-2 are clinically efficacious when administered early, decreasing hospitalization and mortality in patients with mild or moderate COVID-19. We investigated the effects of receiving mAbs (bamlanivimab alone and bamlanivimab and etesevimab together) after SARS-CoV-2 infection on the endogenous immune response.

Methods

Longitudinal serum samples were collected from patients with mild or moderate COVID-19 in the BLAZE-1 trial who received placebo (n=153), bamlanivimab alone [700 mg (n=100), 2800 mg (n=106), or 7000 mg (n=98)], or bamlanivimab (2800 mg) and etesevimab (2800 mg) together (n=111). A multiplex Luminex serology assay measured antibody titers against SARS-CoV-2 antigens, including SARS-CoV-2 protein variants that evade bamlanivimab or etesevimab binding, and SARS-CoV-2 pseudovirus neutralization assays were performed.

Results

The antibody response in patients who received placebo or mAbs had a broad specificity. Titer change from baseline against a receptor-binding domain mutant (Spike-RBD E484Q), as well as N-terminal domain (Spike-NTD) and nucleocapsid protein (NCP) epitopes were 1.4 to 4.1 fold lower at day 15-85 in mAb recipients compared with placebo. Neutralizing activity of day 29 sera from bamlanivimab monotherapy cohorts against both spike E484Q and beta variant (B.1.351) were slightly reduced compared with placebo (by a factor of 3.1, p=0.001, and 2.9, p=0.002, respectively). Early viral load correlated with the subsequent antibody titers of the native, unmodified humoral response (p<0.0001 at Day 15, 29, 60 and 85 for full-length spike).

Conclusions

Patients with mild or moderate COVID-19 treated with mAbs develop a wide breadth of antigenic responses to SARS-CoV-2. Small reductions in titers and neutralizing activity, potentially due to a decrease in viral load following mAb treatment, suggest minimal impact of mAb treatment on the endogenous immune response.
Overlapping but Disparate Inflammatory and Immunosuppressive Responses to SARS-CoV-2 and Bacterial Sepsis: An Immunological Time Course Analysis
Authors: Loftus Tyler J. , Ungaro Ricardo , Dirain Marvin , Efron Philip A. , Mazer Monty B. , Remy Kenneth E. , Hotchkiss Richard S. , Zhong Luer , Bacher Rhonda , Starostik Petr , Moldawer Lyle L. , Brakenridge Scott C.
Published: December 2021

Both severe SARS-CoV-2 infections and bacterial sepsis exhibit an immunological dyscrasia and propensity for secondary infections. The nature of the immunological dyscrasias for these differing etiologies and their time course remain unclear. In this study, thirty hospitalized patients with SARS-CoV-2 infection were compared with ten critically ill patients with bacterial sepsis over 21 days, as well as ten healthy control subjects. Blood was sampled between days 1 and 21 after admission for targeted plasma biomarker analysis, cellular phenotyping, and leukocyte functional analysis via enzyme-linked immunospot assay. We found that circulating inflammatory markers were significantly higher early after bacterial sepsis compared with SARS-CoV-2. Both cohorts exhibited profound immune suppression through 21 days (suppressed HLA-DR expression, reduced mononuclear cell IFN-gamma production), and expanded numbers of myeloid-derived suppressor cells (MDSCs). In addition, MDSC expansion and ex vivo production of IFN-gamma and TNF-alpha were resolving over time in bacterial sepsis, whereas in SARS-CoV-2, immunosuppression and inflammation were accelerating. Despite less severe initial physiologic derangement, SARS-CoV-2 patients had similar incidence of secondary infections (23% vs 30%) as bacterial sepsis patients. Finally, COVID patients who developed secondary bacterial infections exhibited profound immunosuppression evident by elevated sPD-L1 and depressed HLA-DR. Although both bacterial sepsis and SARS-CoV-2 are associated with inflammation and immune suppression, their immune dyscrasia temporal patterns and clinical outcomes are different. SARS-CoV-2 patients had less severe early inflammation and organ dysfunction but had persistent inflammation and immunosuppression and suffered worse clinical outcomes, especially when SARS-CoV-2 infection was followed by secondary bacterial infection.
SARS-CoV-2 Antibodies Are Persisting in Saliva for More Than 15 Months After Infection and Become Strongly Boosted After Vaccination
Authors: Pinilla Yudi T. , Heinzel Constanze , Caminada Lena-Fabienne , Consolaro Douglas , Esen Meral , Kremsner Peter G. , Held Jana , Kreidenweiss Andrea , Fendel Rolf
Published: December 2021

SARS-CoV-2 antibodies in saliva serve as first line of defense against the virus. They are present in the mucosa, more precisely in saliva, after a recovered infection and also following vaccination. We report here the antibody persistence in plasma and in saliva up to 15 months after mild COVID-19. The IgG antibody response was measured every two months in 72 participants using an established and validated in-house ELISA assay. In addition, the virus inhibitory activity of plasma antibodies was assessed in a surrogate virus neutralization test before and after vaccination. SARS-CoV-2-specific antibody concentrations remained stable in plasma and saliva and the response was strongly boosted after one dose COVID-19 vaccination.