bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometric Complexity and the Information-Theoretic Comparison of Functional-Response Models
Authors: Novak Mark , Stouffer Daniel B.
Published: November 2021

The assessment of relative model performance using information criteria like AIC and BIC has become routine among functional-response studies, reflecting trends in the broader ecological literature. Such information criteria allow comparison across diverse models because they penalize each model's fit by its parametric complexity—in terms of their number of free parameters—which allows simpler models to outperform similarly fitting models of higher parametric complexity. However, criteria like AIC and BIC do not consider an additional form of model complexity, referred to as geometric complexity, which relates specifically to the mathematical form of the model. Models of equivalent parametric complexity can differ in their geometric complexity and thereby in their ability to flexibly fit data. Here we use the Fisher Information Approximation to compare, explain, and contextualize how geometric complexity varies across a large compilation of single-prey functional-response models—including prey-, ratio-, and predator-dependent formulations—reflecting varying apparent degrees and forms of non-linearity. Because a model's geometric complexity varies with the data's underlying experimental design, we also sought to determine which designs are best at leveling the playing field among functional-response models. Our analyses illustrate (1) the large differences in geometric complexity that exist among functional-response models, (2) there is no experimental design that can minimize these differences across all models, and (3) even the qualitative nature by which some models are more or less flexible than others is reversed by changes in experimental design. Failure to appreciate model flexibility in the empirical evaluation of functional-response models may therefore lead to biased inferences for predator–prey ecology, particularly at low experimental sample sizes where its impact is strongest. We conclude by discussing the statistical and epistemological challenges that model flexibility poses for the study of functional responses as it relates to the attainment of biological truth and predictive ability.
Being the Winner Is Being the Loser When Playing a Parental Tug-of-War – A New Framework on Stability of Biparental Care
Authors: Wojczulanis-Jakubas Katarzyna
Published: November 2021

Because there are basic sexual differences in reproductive potential, and the cost of parental care is assumed to be high, biparental care is viewed as a constant tug-of-war between the partners. This raises the question of the system’s evolutionary stability. Several models have been proposed to resolve this problem but none has received unequivocal support. Here, I propose a framework that not only integrates the earlier theoretical ideas (sealed bids, negotiation) but also considers the importance of the environment (frequently neglected in previous models) and views the cost of parental care from a different perspective (costly in terms of parent’s survival only when performed close to the boundary of parental capacity). The framework suggests that sexual conflict may not be such a significant factor mediating parental care as commonly assumed, and that a parent trying to shift the parental burden onto the partner – assumed to be the winner in the tug-of-war interplay – is actually more likely to be a loser, as doing so may put the success of the current breeding attempt in jeopardy, thereby reducing overall fitness of the parent. Once it is realized that the importance of sexual conflict is actually much less than it seems, it becomes clear that the stability of the biparental care system no longer seems to be such a puzzling issue.
Individual Variation in Dietary Wariness Is Predicted by Head Color in a Specialist Feeder, the Gouldian Finch
Authors: Eccles Georgina R. , Bethell Emily J. , Greggor Alison L. , Mettke-Hofmann Claudia
Published: November 2021

Shifts in resource availability due to environmental change are increasingly confronting animals with unfamiliar food types. Species that can rapidly accept new food types may be better adapted to ecological change. Intuitively, dietary generalists are expected to accept new food types when resources change, while dietary specialists would be more averse to adopting novel food. However, most studies investigating changes in dietary breadth focus on generalist species and do not delve into potential individual predictors of dietary wariness and the social factors modulating these responses. We investigated dietary wariness in the Gouldian finch, a dietary specialist, that is expected to avoid novel food. This species occurs in two main head colors (red, black), which signal personality in other contexts. We measured their initial neophobic responses (approach attempts before first feed and latency to first feed) and willingness to incorporate novel food into their diet (frequency of feeding on novel food after first feed). Birds were tested in same-sex pairs in same and different head color pairings balanced across experiments 1 and 2. Familiar and novel food (familiar food dyed) were presented simultaneously across 5 days for 3 h, each. Gouldian finches fed on the familiar food first demonstrating food neophobia, and these latencies were repeatable. Birds made more approach attempts before feeding on novel than familiar food, particularly red-headed birds in experiment 1 and when partnered with a black-headed bird. Individuals consistently differed in their rate of incorporation of novel food, with clear differences between head colors; red-headed birds increased their feeding visits to novel food across experimentation equaling their familiar food intake by day five, while black-headed birds continually favored familiar food. Results suggest consistent among individual differences in response to novel food with red-headed birds being adventurous consumers and black-headed birds dietary conservatives. The differences in food acceptance aligned with responses to novel environments on the individual level (found in an earlier study) providing individuals with an adaptive combination of novelty responses across contexts in line with potential differences in movement patterns. Taken together, these novelty responses could aid in population persistence when faced with environmental changes.
Shifting Perspectives in Polar Research: Global Lessons on the Barriers and Drivers for Securing Academic Careers in Natural Sciences
Authors: Figuerola Blanca , Valiente Nicolas , Barbosa Andres , Brasier Madeleine J. , Colominas-Ciuró Roger , Convey Peter , Liggett Daniela , Fernández-Martínez Miguel Angel , Gonzalez Sergi , Griffiths Huw J. , Jawak Shridhar D. , Merican Faradina , Noll Daly , Prudencio Janire , Quaglio Fernanda , Pertierra Luis R.
Published: November 2021

The polar regions provide valuable insights into the functioning of the Earth’s regulating systems. Conducting field research in such harsh and remote environments requires strong international cooperation, extended planning horizons, sizable budgets and long-term investment. Consequently, polar research is particularly vulnerable to societal and economic pressures during periods of austerity. The global financial crisis of 2008, and the ensuing decade of economic slowdown, have already adversely affected polar research, and the current COVID-19 pandemic has added further pressure. In this article we present the outcomes of a community survey that aimed to assess the main barriers and success factors identified by academic researchers at all career stages in response to these global crises. The survey results indicate that the primary barriers faced by polar early and mid-career researchers (EMCRs) act at institutional level, while mitigating factors are developed at individual and group levels. Later career scientists report pressure toward taking early retirement as a means of institutions saving money, reducing both academic leadership and the often unrecognized but vital mentor roles that many play. Gender and social inequalities are also perceived as important barriers. Reorganization of institutional operations and more effective strategies for long-term capacity building and retaining of talent, along with reduction in non-research duties shouldered by EMCRs, would make important contributions toward ensuring continued vitality and innovation in the polar research community.
Converging Effects of Three Different Endocrine Disrupters on Sox and Pou Gene Expression in Developing Rat Hippocampus: Possible Role of microRNA in Sex Differences
Authors: Lichtensteiger Walter , Bassetti-Gaille Catherine , Rehrauer Hubert , Georgijevic Jelena Kühn , Tresguerres Jesus A.F. , Schlumpf Margret
Published: November 2021

Endocrine disrupting chemicals (EDCs) can impair hippocampus-dependent behaviors in rat offspring and in children. In search for key processes underlying this effect, we compared the transcriptomes of rat hippocampus on postnatal day 6 after gestational and lactational exposure to three different EDCs at doses known to impair development of learning and memory. Aroclor 1254, a commercial PCB mixture (5 mg/kg or 0.5 mg/kg), or bisphenol A (5 mg/kg or 0.5 mg/kg) were administered in chow, chlorpyrifos (3 mg/kg or 1 mg/kg) was injected subcutaneously. Male hippocampus exhibited a common effect of all three chemicals on genes involved in cell-autonomous processes, Sox6, Sox11, Pou2f2/Oct2, and Pou3f2/Brn2, all upregulated at the high dose. Additional genes of the Sox and Pou families were affected by only one or two of the chemicals. Real time RT PCR showed a comparable expression change for bisphenol A also at the lower dose. Female hippocampus exhibited much fewer genes with expression changes (almost none with false discovery rate <0.05), and none of the genes of the Sox and Pou families was affected. Since gene network analyses in male hippocampus suggested a link between Sox6 and miR-24, known to be repressed by activation of ER-alpha and to repress Sox6 in other tissues, this microRNA was measured. miR-24 was downregulated by all chemicals at the high dose in males. Values of Sox6 mRNA and miR-24 were inversely correlated in individual male hippocampus samples, supporting the hypothesis that the change in Sox6 expression resulted from an action of miR-24. In contrast, miR-24 levels remained unchanged in hippocampus of females. A sexually dimorphic response of miR-24 may thus be at the basis of the sex difference in Sox6 expression changes following exposure to the three chemicals. ER-alpha expression was also sex-dependent, but the expression changes did not parallel those of potential downstream genes such as Sox6. Sox6 is known to suppress differentiation of Parvalbumin (Pvalb)-expressing interneurons. Individual Sox6 levels (FPKM) were inversely correlated with levels of Pvalb, but not with markers of Sox6-independent interneuron subpopulations, Nos1 and 5HT3aR. Effects on interneuron development are further suggested, in males, by expression changes of Nrg1 and its receptor Erbb4, controlling interneuron migration. Our study disclosed new types of EDC-responsive morphogenetic genes, and illustrated the potential relevance of microRNAs in sexually dimorphic EDC actions.
Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics
Authors: Ding Yanjun , Cui Mintian , Qian Jun , Wang Chao , Shen Qi , Ren Hongbiao , Li Liangshuang , Zhang Fengmin , Zhang Ruijie
Published: November 2021

Autoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different ADs. However, the theoretical research about similarity between ADs is still limited. In this work, we first computed the genetic similarity between 26 ADs based on three measurements: network similarity (NetSim), functional similarity (FunSim), and semantic similarity (SemSim), and systematically identified three significant pairs of similar ADs: rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), myasthenia gravis (MG) and autoimmune thyroiditis (AIT), and autoimmune polyendocrinopathies (AP) and uveomeningoencephalitic syndrome (Vogt-Koyanagi-Harada syndrome, VKH). Then we investigated the gene ontology terms and pathways enriched by the three significant AD pairs through functional analysis. By the cluster analysis on the similarity matrix of 26 ADs, we embedded the three significant AD pairs in three different disease clusters respectively, and the ADs of each disease cluster might have high genetic similarity. We also detected the risk genes in common among the ADs which belonged to the same disease cluster. Overall, our findings will provide significant insight in the commonalities of different ADs in genetics, and contribute to the discovery of novel biomarkers and the development of new therapeutic methods for ADs.
Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India
Authors: Nimavat Jay , Mootapally Chandrashekar , Nathani Neelam M. , Dave Devyani , Kher Mukesh N. , Mahajan Mayur S. , Joshi Chaitanya G. , Bhatt Vaibhav D.
Published: November 2021

Humankind has suffered many pandemics in history including measles, SARS, MERS, Ebola, and recently the novel Coronavirus disease caused by SARS-CoV-2. As of September 2021, it has affected over 200 million people and caused over 4 million deaths. India is the second most affected country in the world. Up to this date, more than 38 Lakh viral genomes have been submitted to public repositories like GISAID and NCBI to analyze the virus phylogeny and mutations. Here, we analyzed 2349 genome sequences of SARS-CoV-2 submitted in GISAID by a single institute pertaining to infections from the Gujarat state to know their variants and phylogenetic distributions with a major focus on the spike protein. More than 93% of the genomes had one or more mutations in the spike glycoprotein. The D614G variant in spike protein is reported to have a very high frequency of >95% globally followed by the L452R and P681R, thus getting significant attention. The antigenic propensity of a small peptide of 29 residues from 597 to 625 of the spike protein variants having D614 and G614 showed that G614 has a little higher antigenic propensity. Thus, the D614G is the cause for higher viral antigenicity, however, it has not been reported to be effective to be causing more deaths.
LBX2-AS1 Activates FSTL3 by Binding to Transcription Factor RARα to Foster Proliferation, Migration, and Invasion of Thyroid Cancer
Authors: Li Jia , Shen Jie , Qin Lan , Lu Dongyan , Ding Enci
Published: November 2021

Background: Thyroid cancer is a frequent endocrine tumor in women. It is of great significance to investigate the molecular mechanism of progression of thyroid cancer.

Methods: Gene expression data set and clinical data were downloaded from The Cancer Genome Atlas database for differential expression analysis. The triplet of downstream transcription factors (TFs) and modulatory genes of target lncRNA in thyroid cancer was predicted by the lncMAP database. mRNA and protein expression of lncRNA LBX2-AS1, RARα, and FSTL3 were detected by qRT-PCR and western blot. The localization of lncRNA LBX2-AS1 in cells was tested by Fluorescence in situ hybridization assay. The RNA immunoprecipitation assay was applied to verify the binding relationship between lncRNA LBX2-AS1 and FSTL3. ChIP and dual-luciferase assays were used to prove the binding relationship between RARα and FSTL3. Cell function experiments were used to test cell proliferation, migration and invasion in each treatment group. The role of lncRNA LBX2-AS1 in thyroid cancer progression was also confirmed in nude mice.

Results: Bioinformatics analysis indicated that lncRNA LBX2-AS1, RARα, FSTL3 were remarkably fostered in thyroid cancer tissue, and LBX2-AS1 was evidently correlated with clinical features. The LncMAP triplet prediction showed that LBX2-AS1 recruited TF RARα to modulate FSTL3. RIP assay confirmed that LBX2-AS1 was prominently enriched on RARα. ChIP and dual-luciferase report assays unveiled that RARα bound to the promoter region of FSTL3 and functioned as a TF. Cell function experiments uncovered that LBX2-AS1 boosted the progression of thyroid cancer. The rescue experiments showed that LBX2-AS1 recruited the TF RARα to hasten the transcription activity of FSTL3 and thus promoted the development of thyroid cancer.

Conclusion: The integrative results demonstrated that LBX2-AS1 activated FSTL3 by binding to TF RARα to hasten proliferation, migration and invasion of thyroid cancer.
Overt Acute Hepatitis B Deteriorates in Females: Destructive Immunity With an Exaggerated Interleukin-17 Pathway
Authors: Chang Ming-Ling , Yeh Chau-Ting , Chien Rong-Nan , Liaw Yun-Fan
Published: November 2021

Background and Aims

We previously showed that overt acute hepatitis B (AHB) was more severe in female patients. Using the same cohort and AHB mouse model, we examined the underlying mechanism.

Methods

Baseline biochemistry, virological and cytokine assays, and T helper (Th)1 and Th2 immune markers of 118 consecutive patients were analyzed. The decompensated livers of AHB and chronic hepatitis B (CHB) patients who underwent liver transplantation were analyzed immunohistochemically. B6 mice were hydrodynamically injected with pHBV1.3 plasmids.

Results

Decompensated AHB patients (n=41) were older, more often female, and had higher alanine aminotransferase (ALT), soluble programmed cell death protein 1 (sPD-1) levels, and neutrophil-lymphocyte ratios but lower rates of HBeAg positivity and quantitative HBsAg, interferon (IFN)-γ-inducible protein 10 (IP-10), IFN-γ, and interleukin-4 (IL-4) levels than the compensated patients. Female sex (95% CI OR=1.07~54.9), age (1.06~1.40), and ALT levels (1.001~1.004) were associated with hepatic decompensation. Higher sPD-1 but lower IFN-γ and IL-4 levels were observed in female patients. Compared to CHB, decompensated AHB livers had more IL-17-positive cells but fewer HBsAg-positive cells and lower CD4/CD8 ratios. Higher serum IL-17 levels were noted in the female AHB mice than those in the males.

Conclusions

Females predominated in decompensated AHB, in which downregulated IFN-γ and IL-4 with augmented hepatic IL-17-positive cell development indicated accelerating destructive immunity to enhance viral clearance. The early surge of serum IL-17 was confirmed in the female AHB mice. Targeting the pathway involving IFN-γ, IL-4, and IL-17 might prevent liver transplantation or fatality in decompensated AHB.
Real-Life Indications of Interleukin-1 Blocking Agents in Hereditary Recurrent Fevers: Data From the JIRcohort and a Literature Review
Authors: Vinit Caroline , Georgin-Lavialle Sophie , Theodoropoulou Aikaterini , Barbier Catherine , Belot Alexandre , Mejbri Manel , Pillet Pascal , Pachlopnik Jana , Poignant Sylvaine , Rebelle Charlotte , Woerner Andreas , Koné-Paut Isabelle , Hentgen Véronique
Published: November 2021

Background

Interleukin (IL)-1 inhibitors represent the main treatment in patients with colchicine-resistant/intolerant familial Mediterranean fever (crFMF), mevalonate kinase deficiency (MKD), and tumor necrosis factor receptor-associated periodic syndrome (TRAPS). However, the reasons for the use of IL-1 inhibitors in these diseases are still not completely clarified.

Objective

Identify real-life situations that led to initiating anakinra or canakinumab treatment in hereditary recurrent fevers (HRFs), combining data from an international registry and an up-to-date literature review.

Patients and Methods

Data were extracted from the JIRcohort, in which clinical information (demographic data, treatment, disease activity, and quality of life) on patients with FMF, MKD, and TRAPS was retrospectively collected. A literature search was conducted using Medline, EMBASE, and Cochrane databases.

Results

Complete data of 93 patients with HRF (53.8% FMF, 31.2% MKD, and 15.1% TRAPS) were analyzed. Data from both the registry and the literature review confirmed that the main reasons for use of IL-1 blockers were the following: failure of previous treatment (n = 57, 61.3% and n = 964, 75.3%, respectively), persistence of disease activity with frequent attacks (n = 44, 47.3% and n = 1,023, 79.9%) and/or uncontrolled inflammatory syndrome (n = 46, 49.5% and n = 398, 31.1%), severe disease complication or associated comorbidities (n = 38, 40.9% and n = 390, 30.4%), and worsening of patients’ quality of life (n = 36, 38.7% and n = 100, 7,8%). No reasons were specified for 12 (16.4%) JIRcohort patients and 154 (12%) patients in the literature.

Conclusion

In the absence of standardized indications for IL-1 inhibitors in crFMF, MKD, and TRAPS, these results could serve as a basis for developing a treat-to-target strategy that would help clinicians codify the therapeutic escalation with IL-1 inhibitors.
Anti-Drug Antibodies in Pigtailed Macaques Receiving HIV Broadly Neutralising Antibody PGT121
Authors: Lee Wen Shi , Reynaldi Arnold , Amarasena Thakshila , Davenport Miles P. , Parsons Matthew S. , Kent Stephen J.
Published: November 2021

Broadly neutralising antibodies (bNAbs) may play an important role in future strategies for HIV control. The development of anti-drug antibody (ADA) responses can reduce the efficacy of passively transferred bNAbs but the impact of ADA is imperfectly understood. We previously showed that therapeutic administration of the anti-HIV bNAb PGT121 (either WT or LALA version) controlled viraemia in pigtailed macaques with ongoing SHIV infection. We now report on 23 macaques that had multiple treatments with PGT121. We found that an increasing number of intravenous doses of PGT121 or human IgG1 isotype control antibodies (2-4 doses) results in anti-PGT121 ADA induction and low plasma concentrations of PGT121. ADA was associated with poor or absent suppression of SHIV viremia. Notably, ADA within macaque plasma recognised another human bNAb 10E8 but did not bind to the variable domains of PGT121, suggesting that ADA were primarily directed against the constant regions of the human antibodies. These findings have implications for the development of preclinical studies examining multiple infusions of human bNAbs.
The Versatile Gasdermin Family: Their Function and Roles in Diseases
Authors: Zou Ju , Zheng Yixiang , Huang Yan , Tang Daolin , Kang Rui , Chen Ruochan
Published: November 2021

The gasdermin (GSDM) family, a novel group of structure-related proteins, consists of GSDMA, GSDMB, GSDMC, GSDMD, GSDME/DNFA5, and PVJK/GSDMF. GSDMs possess a C-terminal repressor domain, cytotoxic N-terminal domain, and flexible linker domain (except for GSDMF). The GSDM-NT domain can be cleaved and released to form large oligomeric pores in the membrane that facilitate pyroptosis. The emerging roles of GSDMs include the regulation of various physiological and pathological processes, such as cell differentiation, coagulation, inflammation, and tumorigenesis. Here, we introduce the basic structure, activation, and expression patterns of GSDMs, summarize their biological and pathological functions, and explore their regulatory mechanisms in health and disease. This review provides a reference for the development of GSDM-targeted drugs to treat various inflammatory and tissue damage-related conditions.
Innate Lymphoid Cells and Myocardial Infarction
Authors: Yang Wenling , Lin Jibin , Zhou Jin , Zheng Yuqi , Jiang Shijiu , He Shaolin , Li Dazhu
Published: November 2021

Myocardial infarction results from obstruction of a coronary artery that causes insufficient blood supply to the myocardium and leads to ischemic necrosis. It is one of the most common diseases threatening human health and is characterized by high morbidity and mortality. Atherosclerosis is the pathological basis of myocardial infarction, and its pathogenesis has not been fully elucidated. Innate lymphoid cells (ILCs) are an important part of the human immune system and participate in many processes, including inflammation, metabolism and tissue remodeling, and play an important role in atherosclerosis. However, their specific roles in myocardial infarction are unclear. This review describes the current understanding of the relationship between innate lymphoid cells and myocardial infarction during the acute phase of myocardial infarction, myocardial ischemia-reperfusion injury, and heart repair and regeneration following myocardial infarction. We suggest that this review may provide new potential intervention targets and ideas for treatment and prevention of myocardial infarction.
Combination of HLA-DR on Mycobacterium tuberculosis-Specific Cells and Tuberculosis Antigen/Phytohemagglutinin Ratio for Discriminating Active Tuberculosis From Latent Tuberculosis Infection
Authors: Luo Ying , Xue Ying , Tang Guoxing , Lin Qun , Song Huijuan , Liu Wei , Yin Botao , Huang Jin , Wei Wei , Mao Liyan , Wang Feng , Sun Ziyong
Published: November 2021

Background

Novel approaches for tuberculosis (TB) diagnosis, especially for distinguishing active TB (ATB) from latent TB infection (LTBI), are urgently warranted. The present study aims to determine whether the combination of HLA-DR on Mycobacterium tuberculosis (MTB)-specific cells and TB antigen/phytohemagglutinin (TBAg/PHA) ratio could facilitate MTB infection status discrimination.

Methods

Between June 2020 and June 2021, participants with ATB and LTBI were recruited from Tongji Hospital (Qiaokou cohort) and Sino-French New City Hospital (Caidian cohort), respectively. The detection of HLA-DR on MTB-specific cells upon TB antigen stimulation and T-SPOT assay were simultaneously performed on all subjects.

Results

A total of 116 (54 ATB and 62 LTBI) and another 84 (43 ATB and 41 LTBI) cases were respectively enrolled from Qiaokou cohort and Caidian cohort. Both HLA-DR on IFN-γ+TNF-α+ cells and TBAg/PHA ratio showed discriminatory value in distinguishing between ATB and LTBI. Receiver operator characteristic (ROC) curve analysis showed that HLA-DR on IFN-γ+TNF-α+ cells produced an area under the ROC curve (AUC) of 0.886. Besides, TBAg/PHA ratio yield an AUC of 0.736. Furthermore, the combination of these two indicators resulted in the accurate discrimination with an AUC of 0.937. When the threshold was set as 0.36, the diagnostic model could differentiate ATB from LTBI with a sensitivity of 92.00% and a specificity of 81.82%. The performance obtained in Qiaokou cohort was further validated in Caidian cohort.

Conclusions

The combination of HLA-DR on MTB-specific cells and TBAg/PHA ratio could serve as a robust tool to determine TB disease states.
Interaction Between Commensal Bacteria, Immune Response and the Intestinal Barrier in Inflammatory Bowel Disease
Authors: Chen Yongyan , Cui Wenwen , Li Xiao , Yang Huan
Published: November 2021

In inflammatory bowel disease (IBD), intestinal mucosa cell and intestinal epithelial cell are severely damaged, and then their susceptibility to bacteria increases, so many commensal bacteria become pathogenic. The pathogenic commensal bacteria can stimulate a series of compensatory immune responses in the intestine. However, the immune response prevents the intestinal tract from restoring homeostasis, which in turn produces an indispensable inflammatory response. On the contrary, in IBD, the fierce inflammatory response contributes to the development of IBD. However, the effect of commensal bacteria on inflammation in IBD has not been clearly studied. Therefore, we further summarize the changes brought about by the changes of commensal bacteria to the inflammation of the intestines and their mutual influence. This article reviews the protective mechanism of commensal bacteria in healthy people and the mechanism of commensal bacteria and immune response to the destruction of the intestinal barrier when IBD occurs. The treatment and prevention of IBD are also briefly summarized.
Parkinson’s Disease Is Associated With Dysregulation of Circulatory Levels of lncRNAs
Authors: Honarmand Tamizkar Kasra , Gorji Pooneh , Gholipour Mahdi , Hussen Bashdar Mahmud , Mazdeh Mehrdokht , Eslami Solat , Taheri Mohammad , Ghafouri-Fard Soudeh
Published: November 2021

Long non-coding RNAs (lncRNAs) have been recently reported to be involved in the pathoetiology of Parkinson’s disease (PD). Circulatory levels of lncRNAs might be used as markers for PD. In the present work, we measured expression levels of HULC, PVT1, MEG3, SPRY4-IT1, LINC-ROR and DSCAM-AS1 lncRNAs in the circulation of patients with PD versus healthy controls. Expression of HULC was lower in total patients compared with total controls (Expression ratio (ER)=0.19, adjusted P value<0.0001) as well as in female patients compared with female controls (ER=0.071, adjusted P value=0.0004). Expression of PVT1 was lower in total patients compared with total controls (ER=0.55, adjusted P value=0.0124). Expression of DSCAM-AS1 was higher in total patients compared with total controls (ER=5.67, P value=0.0029) and in male patients compared with male controls (ER=9.526, adjusted P value=0.0024). Expression of SPRY4-IT was higher in total patients compared with total controls (ER=2.64, adjusted P value<0.02) and in male patients compared with male controls (ER=3.43, P value<0.03). Expression of LINC-ROR was higher in total patients compared with total controls (ER=10.36, adjusted P value<0.0001) and in both male and female patients compared with sex-matched controls (ER=4.57, adjusted P value=0.03 and ER=23.47, adjusted P value=0.0019, respectively). Finally, expression of MEG3 was higher in total patients compared with total controls (ER=13.94, adjusted P value<0.0001) and in both male and female patients compared with sex-matched controls (ER=8.60, adjusted P value<0.004 and ER=22.58, adjusted P value<0.0085, respectively). ROC curve analysis revealed that MEG3 and LINC-ROR have diagnostic power of 0.77 and 0.73, respectively. Other lncRNAs had AUC values less than 0.7. Expression of none of lncRNAs was correlated with age of patients, disease duration, disease stage, MMSE or UPDRS. The current study provides further evidence for dysregulation of lncRNAs in the circulation of PD patients.
Clostridium butyricum Alleviates Enterotoxigenic Escherichia coli K88-Induced Oxidative Damage Through Regulating the p62-Keap1-Nrf2 Signaling Pathway and Remodeling the Cecal Microbial Community
Authors: Li Haihua , Shang Zhiyuan , Liu Xuejiao , Qiao Yingying , Wang Kewei , Qiao Jiayun
Published: November 2021

Clostridium butyricum (CB) can enhance antioxidant capacity and alleviate oxidative damage, but the molecular mechanism by which this occurs remains unclear. This study used enterotoxigenic Escherichia coli (ETEC) K88 as a pathogenic model, and the p62-Keap1-Nrf2 signaling pathway and intestinal microbiota as the starting point to explore the mechanism through which CB alleviates oxidative damage. After pretreatment with CB for 15 d, mice were challenged with ETEC K88 for 24 h. The results suggest that CB pretreatment can dramatically reduce crypt depth (CD) and significantly increase villus height (VH) and VH/CD in the jejunum of ETEC K88-infected mice and relieve morphological lesions of the liver and jejunum. Additionally, compared with ETEC-infected group, pretreatment with 4.4×106 CFU/mL CB can significantly reduce malondialdehyde (MDA) level and dramatically increase superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) levels in the serum. This pretreatment can also greatly increase the mRNA expression levels of tight junction proteins and genes related to the p62-Keap1-Nrf2 signaling pathway in the liver and jejunum in ETEC K88-infected mice. Meanwhile, 16S rDNA amplicon sequencing revealed that Clostridium disporicum was significantly enriched after ETEC K88 challenge relative to the control group, while Lactobacillus was significantly enriched after 4.4×106 CFU/mL CB treatment. Furthermore, 4.4×106 CFU/mL CB pretreatment increased the short-chain fatty acid (SCFA) contents in the cecum of ETEC K88-infected mice. Moreover, we found that Lachnoclostridium, Roseburia, Lactobacillus, Terrisporobacter, Akkermansia, and Bacteroides are closely related to SCFA contents and oxidative indicators. Taken together, 4.4×106 CFU/mL CB pretreatment can alleviate ETEC K88-induced oxidative damage through activating the p62-Keap1-Nrf2 signaling pathway and remodeling the cecal microbiota community in mice.
Are HIV-1-Specific Antibody Levels Potentially Useful Laboratory Markers to Estimate HIV Reservoir Size? A Review
Authors: Zaongo Silvere D. , Sun Feng , Chen Yaokai
Published: November 2021

Despite the benefits achieved by the widespread availability of modern antiretroviral therapy (ART), HIV RNA integration into the host cell genome is responsible for the creation of latent HIV reservoirs, and represents a significant impediment to completely eliminating HIV infection in a patient via modern ART alone. Several methods to measure HIV reservoir size exist; however, simpler, cheaper, and faster tools are required in the quest for total HIV cure. Over the past few years, measurement of HIV-specific antibodies has evolved into a promising option for measuring HIV reservoir size, as they can be measured via simple, well-known techniques such as the western blot and enzyme-linked immunosorbent assay (ELISA). In this article, we re-visit the dynamic evolution of HIV-1-specific antibodies and the factors that may influence their levels in the circulation of HIV-positive individuals. Then, we describe the currently-known relationship between HIV-1-specific antibodies and HIV reservoir size based on study of data from contemporary literature published during the past 5 years. We conclude by highlighting current trends, and discussing the individual HIV-specific antibody that is likely to be the most reliable antibody for potential future utilization for quantification of HIV reservoir size.
A Unique Diel Pattern in Carbonate Chemistry in the Seagrass Meadows of Dongsha Island: The Enhancement of Metabolic Carbonate Dissolution in a Semienclosed Lagoon
Authors: Chou Wen-Chen , Fan Lan-Feng , Yang Chang-Chang , Chen Ying-Hsuan , Hung Chin-Chang , Huang Wei-Jen , Shih Yung-Yen , Soong Keryea , Tseng Hsiao-Chun , Gong Gwo-Ching , Chen Hung-Yu , Su Cheng-Kuan
Published: November 2021

In contrast to other seagrass meadows where seawater carbonate chemistry generally shows strong diel variations with higher pH but lower partial pressure of CO2 (pCO2) during the daytime and lower pH but higher pCO2 during nighttime due to the alternation in photosynthesis and respiration, the seagrass meadows of the inner lagoon (IL) on Dongsha Island had a unique diel pattern with extremely high pH and low pCO2 across a diel cycle. We suggest that this distinct diel pattern in pH and pCO2 could be associated with the enhancement of total alkalinity (TA) production coupled to carbonate sediment dissolution in a semienclosed lagoon. The confinement of the IL may hamper water exchange and seagrass detritus export to the adjacent open ocean, which may result in higher organic matter loading to the sediments, and longer residence time of the water in the IL, accompanied by microbial respiration (both aerobic and anaerobic) that may reduce carbonate saturation level to drive carbonate dissolution and thus TA elevation, thereby forming such a unique diel pattern in carbonate chemistry. This finding further highlights the importance of considering TA production through metabolic carbonate dissolution when evaluating the potential of coastal blue carbon ecosystems to buffer ocean acidification and to absorb atmospheric CO2, in particular in a semienclosed setting.
Characterizing the Profile of Recreational Fishers Who Share Their Catches on Social Media
Authors: Vitale Giulia , Dedeu Arnau L. , Pujol Marta , Sbragaglia Valerio
Published: November 2021

Social media may provide information for monitoring recreational fisheries, but several caveats prevent operationalization. Specifically, the fraction and profile of recreational fishers sharing their catches is not known. Our aim was to advance the monitoring capacities of recreational fishing using social media data. We collected data with onsite (face-to-face) survey and online (emails) questionnaires to characterize marine recreational fishers sharing catches on digital platforms (“sharers”) along with other demographic or fishing information. In the online survey we found that 38% of recreational fishers share their catches using digital platforms (including the private messaging platform WhatsApp), but such proportion dropped to 12% when considering only public or semi-public social media (Instagram was the most commonly used platform, followed by Facebook, YouTube, and Twitter). A similar pattern was found with the online questionnaire where sharers represented 37% of recreational fishers (including WhatsApp), while such proportion dropped to 21% when considering only public or semi-public social media. In general, sharers were more avid (24 and 35 yearly fishing trips for onsite and online survey, respectively) compared to non-sharers (18 and 31 yearly fishing trips). Sharers also spent more money on each fishing trip (on average 26 and 31 euro for onsite and online survey, respectively) than non-sharers (on average 21 and 28 euro for onsite and online survey, respectively), but they had similar chances of catching something. However, for fishers with catches, the harvest per unit effort of sharers was higher than that of non-sharers (0.4 and 0.5 kg/h with respect to 0.3 and 0.4 kg/h, for onsite and online survey, respectively). Moreover, recreational fishers that caught trophy, iconic, or emblematic species were more inclined to share their catches. This study represents an important advancement for integrating social media data into the monitoring of recreational fishing.
Diversity of Three Small Type’s Giant Clams and Their Associated Endosymbiotic Symbiodiniaceae at Hainan and Xisha Islands, South China Sea
Authors: Chao Qiqi , Gu Zhifeng , Wang Aimin , Liu Chunsheng , Yang Yi
Published: November 2021

Giant clams are found in a mutualistic association with Symbiodiniaceae dinoflagellates, however, the diversity of the giant clams, as well as the diversity and distribution of Symbiodiniaceae in different Tridacnine species remain relatively poorly studied in the South China Sea. In this study, a total of 100 giant clams belonging to small type’s giant clams, Tridacna maxima, T. crocea, and T. noae, were collected from Hainan and Xisha Islands. Based on mtDNA cytochrome c oxidase subunit 1 gene (COI) and 16S rRNA fragments, T. maxima and T. crocea showed a closer phylogenetic relationship than T. noae. All the three species of giant clams hosted Symbiodiniaceae including genera Symbiodinium (formerly Clade A) and Cladocopium (formerly Clade C). Geographically, symbionts in Cladocopium are restricted to Xisha Islands, probably because Cladocopium prefers to inhabit in waters with higher mean temperatures. The endosymbiont specificity among the three giant clam species was also detected. T. noae and T. crocea are found to harbor Symbiodinium preferentially, compared with Cladocopium. These results could provide important information to understand various endosymbionts occurring in giant clams in the South China Sea.
Agricultural and Aquaculture Wastes as Concrete Components: A Review
Authors: Wang Wei , Wei Wuyou , Gao Shan , Chen Guiming , Yuan Jian , Li Yu
Published: November 2021

The application of agricultural and aquaculture waste in concrete greatly reduces the pressure on the ecological environment brought by traditional concrete production. The use of agricultural and aquaculture wastes as cement replacement, aggregate replacement and fiber reinforcement has showed great potential. Making full use of these wastes can help the development of sustainable concrete. This paper provides an objective evaluation and summary of agricultural waste and aquaculture waste in green concrete. Agricultural waste is divided into natural plant fiber, agricultural waste ash and multi-application waste according to useful function and alternative methods, such as sisal fiber, olive waste ash, and bamboo. Aquaculture waste mainly refers to some shells such as oyster shell. This paper analyzes the advantages and disadvantages of agricultural and aquaculture waste concrete applications that have been reported and shows how different agricultural and aquaculture wastes are made in concrete. The selection of appropriate treatment methods and usage scenarios is extremely important for agricultural and aquaculture waste concrete, which can determine whether the concrete has reliable performance. This paper will lay a foundation for the progress of waste concrete and provide reliable help for the development of environmental protection concrete.
Association Between Platelet Levels on Admission and 90-day Mortality in Patients With Exertional Heatstroke, a 10 Years Cohort Study
Authors: Zhong Li , Wu Ming , Ji Jingjing , Wang Conglin , Liu Zhifeng
Published: November 2021

Background: Heatstroke is a common clinical symptom in summer with high mortality requiring identification of appropriate and rapid methods of assessment.

Method: This is a retrospective study that included the recent 10 years clinical data of heatstroke patients. A total of n = 186 patients were included in this study and grouped based on platelet (PLT) abnormality observed on admission.

Results: In the study group, n = 120 patients (64.5%) patients had normal PLT and n = 66 patients (35.5%) had abnormal PLT. Compared with PLT-normal group, PLT-abnormal group had higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores [median 15.0 (IQR 11.5–21.5) vs. 9.0 (IQR 7.0–12.5)] and SOFA scores [median 6.0 (IQR 4.0–10.0) vs. 2.0 (IQR 2.0–4.0)], lower Sequential Organ Failure Assessment (GCS)[median 8.0 (IQR 5.0–12.0) vs. 13.0 (IQR 9.0–14.0)]. The PLT-abnormal group had severe organ damage, including damage to the coagulation system, liver, and kidney (all p < 0.05). Significant differences were noted in 90-day survival between the two groups even after correction for Age, GCS, White blood cell count (WBC), Neutrophil, International normalized ratio (INR), Activated partial thromboplastin time (APTT), Procalcitonin (PCT), Alanine aminotransferase (ALT), Creatine (CR), D-Dime (D-D) (Before correction P < 0.001; After correction P = 0.009).The area under the ROC curve for the prediction of mortality based on PLT was 80.7% (95% CI 0.726–0.888, P < 0.001), the optimal cutoff value was 94, the sensitivity was 77.3%, and the specificity was 82.6%.

Conclusion: Patients with heatstroke with platelet abnormalities during admission have more severe organ impairment and a lower 90-day survival rate even when adjusted for other factors.
The COVID-19 Pandemic and the Incidence of the Non-COVID-19 Pneumonia in Adults
Authors: Huang Chienhsiu
Published: November 2021

Introduction: The coronavirus disease 2019 (COVID-19) lockdown strategies were associated with a significant decrease in the common respiratory viral diseases and decreased the need for hospitalization among children in the COVID-19 outbreak. However, the trend of non-COVID-19 pneumonia in adult people remains uncertain. Our aim is to assess the impact of the COVID-19 pandemic on the incidence of the non-COVID-19 pneumonia in adult people and understand whether the substantial decrease in pneumonia cases is the same as the decline in the incidence of respiratory viral disease activity.

Methods: We conducted a retrospective analysis of adult patients presenting with pneumonia from January 2019 to December 2020. Details on all the demographics of the patient of pneumonia, hospital course details, prior admission history within 3 months, respiratory culture, and antibiotics sensitivity test were also obtained.

Results: The number of adult patients with community-acquired pneumonia in 2020 was lower than that in 2019, which decreased by 74 patients in 2020. The decreasing number of patients with community-acquired pneumonia between 2019 and 2020 was from −13.9% in January to March 2020 to −39.7% in October to December 2020. The decreasing number of patients with community-acquired pneumonia between 2019 and 2020 was from −14.8% in the youngest cohort to −28.7% in those aged ≥85 years. The number of reduced patients with community-acquired pneumonia is greater in late seasons and older age, respectively. The number of adult patients with hospital-acquired pneumonia in 2020 was lower than that in 2019, which decreased by 23 patients in 2020. The decreasing number of patients with hospital-acquired pneumonia between 2019 and 2020 was from −20.0% in January to March 2020 to −52.4% in October to December 2020. The decreasing number of patients with hospital-acquired pneumonia between 2019 and 2020 was from 0% in the youngest cohort to −45.6% in those aged ≥ 85 years. The number of reduced patients with hospital-acquired pneumonia is greater in late seasons and older age, respectively.

Conclusion: Interventions applied to control the COVID-19 pandemic were effective not only in substantial changes in the seasonal influenza activity, but also in decreasing adult pneumonia cases.
Case Report: Anti-neutrophil Cytoplasmic Antibody-Associated Vasculitis With Acute Renal Failure and Pulmonary Hemorrhage May Occur After COVID-19 Vaccination
Authors: Chen Chien-Chou , Chen Hsin-Yang , Lu Chun-Chi , Lin Shih-Hua
Published: November 2021

The rare and severe adverse effects associated with coronavirus disease of 2019 (COVID-19) vaccination have been under-appreciated, resulting in many instances of inappropriate management. We describe the case of an elderly woman who developed anti-neutrophil cytoplasmic antibody-associated vasculitis with pulmonary renal syndrome approximately 3 weeks after the first dose of COVID-19 mRNA vaccination (Moderna). Her nasopharyngeal polymerase chain reaction test for the COVID-19 RNA virus was negative. Gross hematuria, heavy proteinuria, acute renal failure (serum creatinine up to 6.5 mg/dL), and hemoptysis coupled with a marked increase in serum anti-myeloperoxidase-O antibody were observed. Renal biopsy showed severe vasculitis with pauci-immune crescent glomerulonephritis. The pulmonary hemorrhage was resolved and renal function improved following combined plasma exchange and the administration of systemic steroids and anti-CD20 therapy. The early examination of urinalysis and renal function may be crucial for identifying glomerulonephritis and acute renal failure in susceptible patients after COVID-19 vaccination.