bluuebunny/crossref_metadata_2025 huggingface dataset:
Community Managed Protected Areas Conserve Aboveground Carbon Stocks: Implications for REDD+
Authors: Alejo Camilo , Walker Wayne S. , Gorelik Seth R. , Potvin Catherine
Published: March 2022

Protected Areas (PAs) represent a broad spectrum of outcomes and governance systems. Among PAs, Community Managed PAs have emerged from communities that are not exclusively indigenous and have developed social organizations to acquire land rights, participate in forest governance, and in some cases, engage in REDD+. However, regardless of the scale or counterfactual, there is no clear consensus about Community Managed PAs’ effectiveness in forest conservation and climate change mitigation. Furthermore, previous studies have been devoted to estimating PAs’ effects on deforestation before REDD+ projects began to operate. Based on Community Concessions in Petén (Guatemala) and Extractive Reserves in Acre (Brazil), we analyzed Community Managed PAs’ temporal and spatial effects on carbon stocks and avoided emissions relative to unprotected lands, other Sustainable Use PAs (IUCN V-VI), and Strict PAs (I-IV). We used carbon density maps, matching methods, geographic discontinuity designs, and sensitivity analysis between 2003 and 2015. After controlling for the influence of market access and agriculture suitability, our analysis shows that Community Managed PAs were more effective than Other Lands (i.e., unprotected) and Sustainable Use PAs, and at least as effective as Strict PAs, in preserving carbon stocks and avoiding emissions. For instance, relative to Other Lands between 2011 and 2015, Community Managed PAs resulted in net avoided emissions of 4.6 tCO2-eq/ha in Petén (Guatemala) and 2.15 tCO2-eq/ha in Acre (Brazil). While these net avoided emissions were lower than in previous years, they seem to be driven by a reduction in carbon emissions outside Community Managed PAs. Spatially, the boundaries of Community Managed PAs varied across jurisdictions. For example, the boundaries of Acre’s Community Managed PAs’ have become less effective in avoiding emissions, which translates into reduced effects on conserving carbon stocks. Our results highlight the need to assess temporal effects to exhibit jurisdiction-wide land-use dynamics and spatial effects to identify local land-use pressures emerging inside or around the boundaries of PAs. Our analysis also shows that decentralized governance in Community Managed PAs may contribute to climate change mitigation through REDD+ and forest conservation targets.
Genome-Wide Analysis for the Regulation of Gene Alternative Splicing by DNA Methylation Level in Glioma and its Prognostic Implications
Authors: Yang Zeyuan , He Yijie , Wang Yongheng , Huang Lin , Tang Yaqin , He Yue , Chen Yihan , Han Zhijie
Published: March 2022

Glioma is a primary high malignant intracranial tumor with poorly understood molecular mechanisms. Previous studies found that both DNA methylation modification and gene alternative splicing (AS) play a key role in tumorigenesis of glioma, and there is an obvious regulatory relationship between them. However, to date, no comprehensive study has been performed to analyze the influence of DNA methylation level on gene AS in glioma on a genome-wide scale. Here, we performed this study by integrating DNA methylation, gene expression, AS, disease risk methylation at position, and clinical data from 537 low-grade glioma (LGG) and glioblastoma (GBM) individuals. We first conducted a differential analysis of AS events and DNA methylation positions between LGG and GBM subjects, respectively. Then, we evaluated the influence of differential methylation positions on differential AS events. Further, Fisher’s exact test was used to verify our findings and identify potential key genes in glioma. Finally, we performed a series of analyses to investigate influence of these genes on the clinical prognosis of glioma. In total, we identified 130 glioma-related genes whose AS significantly affected by DNA methylation level. Eleven of them play an important role in glioma prognosis. In short, these results will help to better understand the pathogenesis of glioma.
Rora Regulates Neutrophil Migration and Activation in Zebrafish
Authors: Hsu Alan Y. , Wang Tianqi , Syahirah Ramizah , Liu Sheng , Li Kailing , Zhang Weiwei , Wang Jiao , Cao Ziming , Tian Simon , Matosevic Sandro , Staiger Christopher J. , Wan Jun , Deng Qing
Published: March 2022

Neutrophil migration and activation are essential for defense against pathogens. However, this process may also lead to collateral tissue injury. We used microRNA overexpression as a platform and discovered protein-coding genes that regulate neutrophil migration. Here we show that miR-99 decreased the chemotaxis of zebrafish neutrophils and human neutrophil-like cells. In zebrafish neutrophils, miR-99 directly targets the transcriptional factor RAR-related orphan receptor alpha (roraa). Inhibiting RORα, but not the closely related RORγ, reduced chemotaxis of zebrafish and primary human neutrophils without causing cell death, and increased susceptibility of zebrafish to bacterial infection. Expressing a dominant-negative form of Rorα or disrupting the roraa locus specifically in zebrafish neutrophils reduced cell migration. At the transcriptional level, RORα regulates transmembrane signaling receptor activity and protein phosphorylation pathways. Our results, therefore, reveal previously unknown functions of miR-99 and RORα in regulating neutrophil migration and anti-microbial defense.
Insights From Early Clinical Trials Assessing Response to mRNA SARS-CoV-2 Vaccination in Immunocompromised Patients
Authors: Baron Frédéric , Canti Lorenzo , Ariën Kevin K. , Kemlin Delphine , Desombere Isabelle , Gerbaux Margaux , Pannus Pieter , Beguin Yves , Marchant Arnaud , Humblet-Baron Stéphanie
Published: March 2022

It is critical to protect immunocompromised patients against COVID-19 with effective SARS-CoV-2 vaccination as they have an increased risk of developing severe disease. This is challenging, however, since effective mRNA vaccination requires the successful cooperation of several components of the innate and adaptive immune systems, both of which can be severely affected/deficient in immunocompromised people. In this article, we first review current knowledge on the immunobiology of SARS-COV-2 mRNA vaccination in animal models and in healthy humans. Next, we summarize data from early trials of SARS-COV-2 mRNA vaccination in patients with secondary or primary immunodeficiency. These early clinical trials identified common predictors of lower response to the vaccine such as anti-CD19, anti-CD20 or anti-CD38 therapies, low (naive) CD4+ T-cell counts, genetic or therapeutic Bruton tyrosine kinase deficiency, treatment with antimetabolites, CTLA4 agonists or JAK inhibitors, and vaccination with BNT162b2 versus mRNA1273 vaccine. Finally, we review the first data on third dose mRNA vaccine administration in immunocompromised patients and discuss recent strategies of temporarily holding/pausing immunosuppressive medication during vaccination.
Development of Novel Dengue NS1 Multiplex Lateral Flow Immunoassay to Differentiate Serotypes in Serum of Acute Phase Patients and Infected Mosquitoes
Authors: Lai Szu-Chia , Huang Yu-Yine , Wey Jiunn-Jye , Tsai Meng-Hung , Chen Yi-Ling , Shu Pei-Yun , Chang Shu-Fen , Hung Yi-Jen , Hou Jiu-Nan , Lin Chang-Chi
Published: March 2022

Dengue is among the most rapidly spreading arboviral disease in the world. A low-cost, easy to use point-of-care diagnostic tool for the detection and differentiation of dengue virus serotypes could improve clinical management, disease prevention, epidemiological surveillance, and outbreak monitoring, particularly in regions where multiple serotypes co-circulate. Despite widespread deployment, no commercial dengue antigen diagnostic test has proven effective in differentiating among dengue virus serotypes. In the current study, we first established mAb pairs and developed a multiplex lateral flow immunoassay for the simultaneous detection of the dengue viral NS1 antigen and identification of serotype. The proposed system, called Dengue serotype NS1 Multiplex LFIA, provides high sensitivity and specificity. In testing for JEV, ZIKV, YFV, WNV, and CHIKV, the multiplex LFIA gave no indication of cross- reactivity with cell culture supernatants of other flaviviruses or chikungunya virus. In analyzing 187 samples from patients suspected of dengue infection, the detection sensitivity for serotype D1 to D4 was 90.0%, 88.24%, 82.61%, and 83.33% and serotype specificity was 98.74%, 96.13%, 99.39%, and 97.04%, respectively. Our multiplex LFIA can also identify mono- and co-infection of different serotype of dengue viruses in mosquitoes. The proposed Multiplex LFIA provides a simple tool for the rapid detection of dengue serotypes and in the differential diagnosis of fever patients in regions where medical resources are limited and/or multiple DENVs co-circulate.
A New Flexible Graphite Composite Electrical Grounding Material
Authors: Huang Tao , Hu Yuanchao , Xie Hongping , Du Changqing , An Yunzhu , Shen Wentao , Liu Zhixiang , Cheng Meng
Published: March 2022

Corrosion is an inevitable problem of metallic grounding grids. To propose an effective method avoiding the above corrosion, a new type of non-metallic grounding material was made in this paper. It is called flexible graphite composite grounding material, namely flexible graphite composite grounding material for short. It is made by high-purity flake graphite with a stranded wire hierarchical structure. And a series of experiments have been carried out to verify its feasibility as electrical grounding material, including material resistivity and its contact resistance measurement, temperature tolerance test, mechanical performance test, and scaled electrical grounding test of several typical electrical grounding grids. These experimental results all indicate that characteristics of the new flexible graphite composite grounding material can well meet practical electrical engineering requirements.
pH-Responsive Allicin-Based Coatings With Antibacterial and Antifouling Effects in Marine Environments
Authors: Hao Xiangping , Yan Weilu , Sun Ziqing , Yang Jingzhi , Bai Yun , Qian Hongchang , Chowwanonthapunya Thee , Zhang Dawei
Published: March 2022

In this work, we report the design of pH-controlled releasing behaviors of polydopamine/tannic acid-allicin@chitosan (PDA/TA-ALL@CS) multilayer coatings to realize antibacterial and antifouling effects. The pH-responsive ALL@CS capsules were prepared using the microemulsion method with about 262–452 nm diameter. The bacteriostasis of ALL@CS microcapsules against E. coli, S. aureus, and P. aeruginosa all exceeded 94% as evaluated using the colony counting method. Because of the protonation in acid environments and deprotonation in alkaline environments for the amino groups of CS, ALL as biocides can be released from the nanocapsules and exert outstanding antibacterial properties. Confirmed by the plate colony counts, the ALL@CS capsules possessed an outstanding antibacterial effect for E. coli in acid solutions but were less effective in alkaline solutions. The PDA/TA-ALL@CS-7 coatings showed durable pH-responsive antibacterial activities with an efficiency of ∼87% after immersion in pH 8 solutions for seven days. The PDA/TA-ALL@CS coating with controlled release performance and antibacterial properties may provide a new solution for developing antifouling coating applications in the marine environment.
Mortality and Pulmonary Embolism in Acute Respiratory Distress Syndrome From COVID-19 vs. Non-COVID-19
Authors: Kutsogiannis Demetrios J. , Alharthy Abdulrahman , Balhamar Abdullah , Faqihi Fahad , Papanikolaou John , Alqahtani Saleh A. , Memish Ziad A. , Brindley Peter G. , Brochard Laurent , Karakitsos Dimitrios
Published: March 2022

Purpose

There may be a difference in respiratory mechanics, inflammatory markers, and pulmonary emboli in COVID-19 associated ARDS vs. ARDS from other etiologies. Our purpose was to determine differences in respiratory mechanics, inflammatory markers, and incidence of pulmonary embolism in patients with and without COVID-19 associated ARDS admitted in the same period and treated with a similar ventilation strategy.

Methods

A cohort study of COVID-19 associated ARDS and non COVID-19 patients in a Saudi Arabian center between June 1 and 15, 2020. We measured respiratory mechanics (ventilatory ratio (VR), recruitability index (RI), markers of inflammation, and computed tomography pulmonary angiograms.

Results

Forty-two patients with COVID-19 and 43 non-COVID patients with ARDS comprised the cohort. The incidence of “recruitable” patients using the recruitment/inflation ratio was slightly lower in COVID-19 patients (62 vs. 86%; p = 0.01). Fifteen COVID-19 ARDS patients (35.7%) developed a pulmonary embolism as compared to 4 (9.3%) in other ARDS patients (p = 0.003). In COVID-19 patients, a D-Dimer ≥ 5.0 mcg/ml had a 73% (95% CI 45–92%) sensitivity and 89% (95% CI 71–98%) specificity for predicting pulmonary embolism. Crude 60-day mortality was higher in COVID-19 patients (35 vs. 15%; p = 0.039) but three multivariate analysis showed that independent predictors of 60-day mortality included the ventilatory ratio (OR 3.67, 95% CI 1.61–8.35), PaO2/FIO2 ratio (OR 0.93; 95% CI 0.87–0.99), IL-6 (OR 1.02, 95% CI 1.00–1.03), and D-dimer (OR 7.26, 95% CI 1.11–47.30) but not COVID-19 infection.

Conclusion

COVID-19 patients were slightly less recruitable and had a higher incidence of pulmonary embolism than those with ARDS from other etiologies. A high D-dimer was predictive of pulmonary embolism in COVID-19 patients. COVID-19 infection was not an independent predictor of 60-day mortality in the presence of ARDS.
Research on the Histological Features and Pathological Types of Gastric Adenocarcinoma With Mucinous Differentiation
Authors: Meng Nian-Long , Wang Yang-kun , Wang Hai-Li , Zhou Jun-Ling , Wang Su-nan
Published: March 2022

Objective

To discuss the histological features, pathological types, and prognosis of gastric adenocarcinoma with mucinous differentiation.

Methods

Specimens of 189 cases of gastric adenocarcinoma with mucinous differentiation were collected for detailed histomorphology, immunohistochemistry, fluorescence in situ hybridization, and follow-up.

Results

In accordance with the morphological and histological structural features of the cancer cells as well as the area ratio of the mucus, gastric adenocarcinoma with mucinous differentiation was divided into four types, namely pure mucinous carcinoma, intraductal papillary mucinous carcinoma, signet ring cell type mucinous carcinoma, and mixed cell type mucinous carcinoma. Based on the macroscopic types according to Bormann's classification, pure mucinous carcinoma was mostly Type I, intraductal papillary mucinous carcinoma was mostly Type II, signet ring cell type mucinous carcinoma was mostly Type IV, and mixed cell type mucinous carcinoma was mostly Type III. The 5-year survival rate was 69.2, 64.2, 0, and 31.5%, respectively. There was a statistical difference in the lymph node metastasis rate and survival rate of the four carcinoma types. The invasion features of pure mucinous carcinoma entailed penetrating corrosively in a push-in form, without blood vessel or lymphatic metastasis and with few lymphocytes and lymphatic nodules in the marginal area. Thus, there was little lymph node metastasis and invasion of nerves. The HER2 protein expression rate was 40.2% (76/189), the HER2 gene amplification detected by FISH technology was 16.9% (32/189).

Conclusion

The independent histological type, four subtypes, and histopathological classification of gastric mucinous adenocarcinoma are important for the prognosis evaluation and precise treatment of this disease.
Comparison of Neutrophil Function in Granulocyte Concentrates From Prednisone- and G-CSF-Treated Donors: Effect of Stimulant, Leukapheresis and Storage
Authors: Murru Andréa , Allard Marie-Ève , Paré Guillaume , Vaillancourt Myriam , Boyer Lucie , Cayer Marie-Pierre , Vitry Julien , Landry Patricia , Labrecque Marie-Michèle , Robitaille Nancy , Branch Donald R. , Girard Mélissa , Fernandes Maria J.
Published: March 2022

Transfusion of granulocyte concentrates (GC) is an alternative therapy for neutropenic patients with life-threatening infections. While neutrophils are the main source of antimicrobial activity, only neutrophil numbers are used to certify GCs. The objective of this study was thus to functionally characterize neutrophils in GCs prepared by leukapheresis from G-CSF-stimulated donors and compare to the less characterized prednisone GCs. GCs prepared from healthy donors stimulated with prednisone and then G-CSF after a 6-month washout period were analyzed prior to and after leukapheresis, and after storage. Leukocyte composition, neutrophil viability, calcium mobilization, chemotaxis, phagocytosis, reactive oxygen species, cytokine production and metabolites were determined. G-CSF GCs contained significantly more neutrophils than prednisone GCs of which 40% were immature. In comparison to non-stimulated healthy donor neutrophils, prednisone GC neutrophils exhibited enhanced phagocytosis and G-CSF GC neutrophils showed decreased chemotaxis but increased IL-8 production. Leukapheresis altered prednisone GC neutrophil responses. Storage had a significant, negative impact on G-CSF GC neutrophils compared to prednisone GC neutrophils. G-CSF and prednisone GC neutrophils thus differ in maturity and function, and G-CSF GC neutrophils are more sensitive to storage. Functional testing of GC neutrophils and better storage conditions would improve the quality of this blood product.
Associations Between the Macular Microvasculatures and Subclinical Atherosclerosis in Patients With Type 2 Diabetes: An Optical Coherence Tomography Angiography Study
Authors: Yoon Jooyoung , Kang Hyo Joo , Lee Joo Yong , Kim June-Gone , Yoon Young Hee , Jung Chang Hee , Kim Yoon Jeon
Published: March 2022

Objective

To investigate the associations between the macular microvasculature assessed by optical coherence tomography angiography (OCTA) and subclinical atherosclerosis in patients with type 2 diabetes.

Methods

We included patients with type 2 diabetes who received comprehensive medical and ophthalmic evaluations, such as carotid ultrasonography and OCTA at a hospital-based diabetic clinic in a consecutive manner. Among them, 254 eyes with neither diabetic macular edema (DME) nor history of ophthalmic treatment from 254 patients were included. The presence of increased carotid intima-media thickness (IMT) (>1.0 mm) or carotid plaque was defined as subclinical atherosclerosis. OCTA characteristics focused on foveal avascular zone (FAZ) related parameters and parafoveal vessel density (VD) were compared in terms of subclinical atherosclerosis, and risk factors for subclinical atherosclerosis were identified using a multivariate logistic regression analysis.

Results

Subclinical atherosclerosis was observed in 148 patients (58.3%). The subclinical atherosclerosis group were older (p < 0.001), had a greater portion of patients who were men (p = 0.001) and who had hypertension (p = 0.042), had longer diabetes duration (p = 0.014), and lower VD around FAZ (p = 0.010), and parafoveal VD (all p < 0.05). In the multivariate logistic regression analysis, older age (p ≤ 0.001), male sex (p ≤ 0.001), lower VD around FAZ (p = 0.043), lower parafoveal VD of both superficial capillary plexus (SCP) (p = 0.011), and deep capillary plexus (DCP) (p = 0.046) were significant factors for subclinical atherosclerosis.

Conclusion

The decrease in VD around FAZ, and the VD loss in parafoveal area of both SCP and DCP were significantly associated with subclinical atherosclerosis in patients with type 2 diabetes, suggesting that common pathogenic mechanisms might predispose to diabetic micro- and macrovascular complications.
Crucial Roles of miR-625 in Human Cancer
Authors: Zhang Menggang , Xiong Fei , Zhang Shuijun , Guo Wenzhi , He Yuting
Published: March 2022

Genetic and epigenetic characteristics are core factors of cancer. MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression at the post-transcriptional level via binding to corresponding mRNAs. Recently, increasing evidence has proven that miRNAs regulate the occurrence and development of human cancer. Here, we mainly review the abnormal expression of miR-625 in a variety of cancers. In summarizing the role and potential molecular mechanisms of miR-625 in various tumors in detail, we reveal that miR-625 is involved in a variety of biological processes, such as cell proliferation, invasion, migration, apoptosis, cell cycle regulation, and drug resistance. In addition, we discuss the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks and briefly explain the specific mechanisms of competing endogenous RNAs. In conclusion, we reveal the potential value of miR-625 in cancer diagnosis, treatment, and prognosis and hope to provide new ideas for the clinical application of miR-625.
Biological Features of the Outcome-Based Intrinsic Capacity Composite Scores From a Population-Based Cohort Study: Pas de Deux of Biological and Functional Aging
Authors: Meng Lin-Chieh , Huang Shih-Tsung , Peng Li-Ning , Chen Liang-Kung , Hsiao Fei-Yuan
Published: March 2022

Introduction

This study aims to develop and validate an integrative intrinsic capacity (IC) scoring system, to investigate its associations with a wide spectrum of biomarkers and to explore the predictive value of the integrative IC score on 4-year mortality among community dwelling people aged 50 years and older.

Methods

We included 839 adults aged ≥50 years from the Social Environment and Biomarkers of Aging Study (SEBAS) and randomly divided them into derivation and validation cohorts to develop the IC scoring system. The multivariate logistic regression model was used to weight each subdomain (locomotion, sensory, vitality, psychological, and cognition) of IC according to its association with impairments in instrumental activities of daily living (IADL) and to construct the integrative IC score. Age-related biomarkers and genetic markers were compared between IC groups by ordinal logistic regression. A Cox proportional hazard model was used to examine the association between IC and mortality, and subgroup analysis was used to assess the robustness of the results among participants aged 60 years and older.

Results

A 12-score IC scoring system (AUROC = 0.83; Hosmer–Lemeshow goodness-of-fit test p = 0.17) was developed, and higher scores indicated better intrinsic capacity. High interleukin (IL)-6, high E-selectin, low serum albumin and low folate were significantly associated with low IC in the whole sample. However, high IL-6, low serum albumin, low folate, high allostatic load, and APOE ε4 genotype were significantly associated with low IC in those aged 60 years old and older. Compared to the high IC group, the low IC group was significantly associated with all-cause mortality (HR: 2.50, 95% CI: 1.22–5.11, p = 0.01 for all participants; HR 2.19, 95% CI 1.03–4.64, p = 0.04 for participants aged 60 years and older).

Conclusions

The conceptually proposed IC can be easily transformed into a scoring system considering different weights of individual subdomains, which not only predicts mortality but also suggests different pathophysiologies across the life course of aging (inflammation, nutrition, stress, and ApoE4 genotype). An intervention study is needed using the composite IC score to promote healthy aging and determine the underlying pathophysiology.
Prediction of Endometrial Carcinoma Using the Combination of Electronic Health Records and an Ensemble Machine Learning Method
Authors: Wang Wenwen , Xu Yang , Yuan Suzhen , Li Zhiying , Zhu Xin , Zhou Qin , Shen Wenfeng , Wang Shixuan
Published: March 2022

Endometrial carcinoma (EC) is a common cause of cancer death in women, and having an early accurate prediction model to identify this disease is crucial. The aim of this study was to develop a new machine learning (ML) model-based diagnostic prediction model for EC. We collected data from consecutive patients between November 2012 and January 2021 at tertiary hospitals in central China. Inclusion criteria included women undergoing endometrial biopsy, dilation and curettage, or hysterectomy. A total of 9 features, including patient demographics, vital signs, and laboratory and ultrasound results, were selected in the final analysis. This new model was combined with three top optimal ML methods, namely, logistic regression, gradient-boosted decision tree, and random forest. A total of 1,922 patients were eligible for final analysis and modeling. The ensemble model, called TJHPEC, was validated in an internal validation cohort and two external validation cohorts. The results showed that the AUC values were 0.9346, 0.8341, and 0.8649 for the prediction of total EC and 0.9347, 0.8073, and 0.871 for prediction of stage I EC. Nine clinical features were confirmed to be highly related to the prediction of EC in TJHPEC. In conclusion, our new model may be accurate for identifying EC, especially in the early stage, in the general population of central China.
Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia
Authors: Xiao Tingting , Guo Qian , Zhou Yanzi , Shen Ping , Wang Yuan , Fang Qiang , Li Mo , Zhang Shuntian , Guo Lihua , Yu Xiao , Liao Yulin , Wang Chunhui , Chi Xiaohui , Kong Xiaoyang , Zhou Kai , Zheng Beiwen , Luo Qixia , Chen Yunbo , Zhu Huaiqiu , Xiao Yonghong
Published: March 2022

Background

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. If the judgment is wrong, it may aggravate the abuse of antibiotics and further accelerate the evolution of drug resistance. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota.

Methods

A prospective study was conducted on patients with mechanical ventilation from July 2018 to December 2019 in a tertiary hospital. Multi-genomics studies (16S rRNA amplicon, metagenomics, and whole-genome sequencing [WGS]) of endotracheal deep aspirate (ETA) were performed.

Results

Fifty-two ICU patients were enrolled, including 24 with CRAB VAP (CRAB-I), 22 with CRAB colonization (CRAB-C), and six CRAB-negative patients (infection-free) (CRAB-N). Diversity of pulmonary microbiota was significantly lower in CRAB-I than in CRAB-C or CRAB-N (mean Shannon index, 1.79 vs. 2.73 vs. 4.81, P < 0.05). Abundances of 11 key genera differed between the groups. Acinetobacter was most abundant in CRAB-I (76.19%), moderately abundant in CRAB-C (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn. Metagenomics and WGS analysis showed that virulence genes were more abundant in CRAB-I than in CRAB-C. Multi-locus sequence typing (MLST) of 46 CRAB isolates revealed that the main types were ST208 (30.43%) and ST938 (15.22%), with no difference between CRAB-I and CRAB-C.

Conclusion

Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.
Production of Different Biochemicals by Paenibacillus polymyxa DSM 742 From Pretreated Brewers’ Spent Grains
Authors: Didak Ljubas Blanka , Novak Mario , Trontel Antonija , Rajković Ana , Kelemen Zora , Marđetko Nenad , Grubišić Marina , Pavlečić Mladen , Tominac Vlatka Petravić , Šantek Božidar
Published: March 2022

Brewers’ spent grains (BSG) are a by-product of the brewing industry that is mainly used as feedstock; otherwise, it has to be disposed according to regulations. Due to the high content of glucose and xylose, after pretreatment and hydrolysis, it can be used as a main carbohydrate source for cultivation of microorganisms for production of biofuels or biochemicals like 2,3-butanediol or lactate. 2,3-Butanediol has applications in the pharmaceutical or chemical industry as a precursor for varnishes and paints or in the food industry as an aroma compound. So far, Klebsiella pneumoniae, Serratia marcescens, Clostridium sp., and Enterobacter aerogenes are being used and investigated in different bioprocesses aimed at the production of 2,3-butanediol. The main drawback is bacterial pathogenicity which complicates all production steps in laboratory, pilot, and industrial scales. In our study, a gram-positive GRAS bacterium Paenibacillus polymyxa DSM 742 was used for the production of 2,3-butanediol. Since this strain is very poorly described in literature, bacterium cultivation was performed in media with different glucose and/or xylose concentration ranges. The highest 2,3-butanediol concentration of 18.61 g l–1 was achieved in medium with 70 g l–1 of glucose during 40 h of fermentation. In contrast, during bacterium cultivation in xylose containing medium there was no significant 2,3-butanediol production. In the next stage, BSG hydrolysates were used for bacterial cultivation. P. polymyxa DSM 742 cultivated in the liquid phase of pretreated BSG produced very low 2,3-butanediol and ethanol concentrations. Therefore, this BSG hydrolysate has to be detoxified in order to remove bacterial growth inhibitors. After detoxification, bacterium cultivation resulted in 30 g l–1 of lactate, while production of 2,3-butanediol was negligible. The solid phase of pretreated BSG was also used for bacterium cultivation after its hydrolysis by commercial enzymes. In these cultivations, P. polymyxa DSM 742 produced 9.8 g l–1 of 2,3-butanediol and 3.93 g l–1 of ethanol. On the basis of the obtained results, it can be concluded that different experimental setups give the possibility of directing the metabolism of P. polymyxa DSM 742 toward the production of either 2,3-butanediol and ethanol or lactate.
Portulaca oleracea Polysaccharides Modulate Intestinal Microflora in Aged Rats in vitro
Authors: Fu Qiang , Zhou Siyi , Yu Mengting , Lu Yang , He Genhe , Huang Xiaoliu , Huang Yushan
Published: March 2022

To explore the effect of Portulaca oleracea polysaccharides (POP) in regulating intestinal microflora in aged rats in vitro, its intestinal microbial composition was analyzed by 16 S rDNA high-throughput sequencing, and the level of short-chain fatty acids in fermentation broth was determined by LC-MS. POP significantly upregulated the relative abundance of Lactobacillus, Eggerthella, and Paraprevotella and significantly downregulated Escherichia_Shigella, Bacteroides, and Eubacterium nodatum groups. The pH value and ammonia nitrogen level decreased significantly in the POP-treated group, resulting in a more short-chain fatty acid consumption which changed the acid–base environment of the fermentation broth. In conclusion, POP is beneficial to aged rats because it can regulate intestinal flora, promote the growth of probiotics, and inhibit the reproduction of pathogenic bacteria.
Quantitative Imaging of Bacteriophage Amplification for Rapid Detection of Bacteria in Model Foods
Authors: Wisuthiphaet Nicharee , Yang Xu , Young Glenn M. , Nitin Nitin
Published: March 2022

Rapid detection of bacteria in water and food samples is a critical need. The current molecular methods like real-time PCR can provide rapid detection after initial enrichment. However, these methods require significant preparation steps, specialized facilities to reduce contamination, and relatively expensive reagents. This study evaluates a novel approach for detecting bacteria based on imaging of bacteriophage amplification upon infection of the target host bacteria to mitigate some of these constraints and improve the specificity of discriminating live vs. dead bacteria. Thus, this research leverages the natural ability of lytic bacteriophages to rapidly amplify their genetic material and generate progeny phages upon infecting the host bacterium. This study uses a nucleic acid staining dye, a conventional fluorescence microscope, and quantitative image analysis for imaging the amplification of bacteriophages. The sensitivity and assay time for imaging-based quantification of phage amplification for detecting Escherichia coli were compared with RT-PCR and the standard plaque-forming assay for detection phage amplification in model systems, including coconut water and spinach wash water. The results demonstrate that the imaging approach matches both the sensitivity and speed for detecting E. coli using the RT-PCR method without requiring isolation of nucleic acids, expensive reagents, and specialized facilities. The quantitative imaging results demonstrate the detection of 10 CFU/ml of E. coli in coconut water and simulated spinach wash water with a chemical oxygen demand (COD) of 3,000 ppm within 8 h, including initial enrichment of the bacteria. In summary, the results of this study illustrate a novel phage amplification-based approach for detecting target bacteria in complex food and water samples using simple sample preparation methods and low-cost reagents.
MiR-103a-3p Promotes Zika Virus Replication by Targeting OTU Deubiquitinase 4 to Activate p38 Mitogen-Activated Protein Kinase Signaling Pathway
Authors: Ye Haiyan , Kang Lan , Yan Xipeng , Li Shilin , Huang Yike , Mu Rongrong , Duan Xiaoqiong , Chen Limin
Published: March 2022

Background

MicroRNAs (miRNAs) play critical roles in regulating virus infection and replication. However, the mechanism by which miRNA regulates Zika virus (ZIKV) replication remains elusive. We aim to explore how the differentially expressed miR-103a-3p regulates ZIKV replication and to clarify the underlying molecular mechanism.

Methods

Small RNA sequencing (RNA-Seq) was performed to identify differentially expressed miRNAs in A549 cells with or without ZIKV infection and some of the dysregulated miRNAs were validated by quantitative real time PCR (qRT-PCR). The effect of miR-103a-3p on ZIKV replication was examined by transfecting miR-103a-3p mimic or negative control (NC) into A549 cells with or without p38 mitogen-activated protein kinase (MAPK) inhibitor SB203580 and expression levels of ZIKV NS5 mRNA and NS1 protein were detected by qRT-PCR and Western blot, respectively. The potential target genes for miR-103a-3p were predicted by four algorithms and further validated by mutation analysis through luciferase reporter assay. The predicated target gene OTU deubiquitinase (DUB) 4 (OTUD4) was over-expressed by plasmid transfection or silenced by siRNA transfection into cells prior to ZIKV infection. Activation status of p38 MAPK signaling pathway was revealed by looking at the phosphorylation levels of p38 (p-p38) and HSP27 (p-HSP27) by Western blot.

Results

Thirty-five differentially expressed miRNAs in ZIKV-infected A549 cells were identified by RNA-Seq analysis. Five upregulated and five downregulated miRNAs were further validated by qRT-PCR. One of the validated upregulated miRNAs, miR-103a-3p significantly stimulated ZIKV replication both at mRNA (NS5) and protein (NS1) levels. We found p38 MAPK signaling was activated following ZIKV infection, as demonstrated by the increased expression of the phosphorylation of p38 MAPK and HSP27. Blocking p38 MAPK signaling pathway using SB203580 inhibited ZIKV replication and attenuated the stimulating effect of miR-103a-3p on ZIKV replication. We further identified OTUD4 as a direct target gene of miR-103a-3p. MiR-103a-3p over-expression or OTUD4 silencing activated p38 MAPK signaling and enhanced ZIKV replication. In contrast, OTUD4 over-expression inhibited p38 MAPK activation and decreased ZIKV replication. In addition, OTUD4 over-expression attenuated the stimulating effect of miR-103a-3p on ZIKV replication and activation of p38 MAPK signaling.

Conclusion

Zika virus infection induced the expression of miR-103a-3p, which subsequently activated p38 MAPK signaling pathway by targeting OTUD4 to facilitate ZIKV replication.
Derivation and Validation of the Cognitive Impairment Prediction Model in Older Adults: A National Cohort Study
Authors: Hu Mingyue , Gao Yinyan , Kwok Timothy C. Y. , Shao Zhanfang , Xiao Lily Dongxia , Feng Hui
Published: March 2022

Objective

This prediction model quantifies the risk of cognitive impairment. This aim of this study was to develop and validate a prediction model to calculate the 6-year risk of cognitive impairment.

Methods

Participants from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) 2008–2014 and 2011–2018 surveys were included for developing the cognitive impairment prediction model. The least absolute shrinkage and selection operator, clinical knowledge, and previous experience were performed to select predictors. The Cox proportional hazard model and Fine-Gray analysis adjusting for death were conducted to construct the model. The discriminative ability was measured using C-statistics. The model was evaluated externally using the temporal validation method via the CLHLS 2002–2008 survey. A nomogram was conducted to enhance the practical use. The population attributable fraction was calculated.

Results

A total of 10,053 older adults were included for model development. During a median of 5.68 years, 1,750 (17.4%) participants experienced cognitive impairment. Eight easy-to-obtain predictors were used to develop the model. The overall proportion of death was 43.3%. The effect of age on cognitive impairment reduced after adjusting the competing risk of death. The Cox and Fine–Gray models showed a similar discriminative ability, with average C-statistics of 0.71 and 0.69 in development and external validation datasets, respectively. The model performed better in younger older adults (65–74 years). The proportion of 6-year cognitive impairment due to modifiable risk factors was 47.7%.

Conclusion

This model could be used to identify older adults aged 65 years and above at high risk of cognitive impairment and initiate timely interventions on modifiable factors to prevent nearly half of dementia.
Semi-Automated Training of Rat Ultrasonic Vocalizations
Authors: Johnson Aaron M. , Lenell Charles , Severa Elizabeth , Rudisch Denis Michael , Morrison Robert A. , Shembel Adrianna C.
Published: March 2022

Rats produce ultrasonic vocalizations (USVs) for conspecific communication. These USVs are valuable biomarkers for studying behavioral and mechanistic changes in a variety of diseases and disorders. Previous work has demonstrated operant conditioning can progressively increase the number of USVs produced by rats over multiple weeks. This operant conditioning paradigm is a useful model for investigating the effects of increased laryngeal muscle use on USV acoustic characteristics and underlying central and peripheral laryngeal sensorimotor mechanisms. Previous USV operant conditioning studies relied on manual training to elicit USV productions, which is both time and labor intensive and can introduce human variability. This manuscript introduces a semi-automated method for training rats to increase their rate of USV production by pairing commercially available operant conditioning equipment with an ultrasonic detection system. USV training requires three basic components: elicitation cue, detection of the behavior, and a reward to reinforce the desired behavior. With the semi-automated training paradigm, indirect exposure to the opposite sex or an olfactory cue can be used to elicit USV production. The elicited USV is then automatically detected by the ultrasonic acoustic system, which consequently triggers the release of a sucrose pellet reward. Our results demonstrate this semi-automated procedure produces a similar increase in USV production as the manual training method. Through automation of USV detection and reward administration, staffing requirements, human error, and subject behavioral variability may be minimized while scalability and reproducibility are increased. This automation may also result in greater experimental flexibility, allowing USV training paradigms to become more customizable for a wider array of applications. This semi-automated USV behavioral training paradigm improves upon manual training techniques by increasing the ease, speed, and quality of data collection.
Leptin Protects Against the Development and Expression of Cocaine Addiction-Like Behavior in Heterogeneous Stock Rats
Authors: Carrette Lieselot L. G. , Corral Cristina , Boomhower Brent , Brennan Molly , Crook Caitlin , Ortez Clara , Shankar Kokila , Simpson Sierra , Maturin Lisa , Solberg Woods Leah C. , Palmer Abraham A. , de Guglielmo Giordano , George Olivier
Published: March 2022

Cocaine affects food intake, metabolism and bodyweight. It has been hypothesized that feeding hormones like leptin play a role in this process. Preclinical studies have shown a mutually inhibitory relationship between leptin and cocaine, with leptin also decreasing the rewarding effects of cocaine intake. But prior studies have used relatively small sample sizes and did not investigate individual differences in genetically heterogeneous populations. Here, we examined whether the role of individual differences in bodyweight and blood leptin level are associated with high or low vulnerability to addiction-like behaviors using data from 306 heterogeneous stock rats given extended access to intravenous self-administration of cocaine and 120 blood samples from 60 of these animals, that were stored in the Cocaine Biobank. Finally, we tested a separate cohort to evaluate the causal effect of exogenous leptin administration on cocaine seeking. Bodyweight was reduced due to cocaine self-administration in males during withdrawal and abstinence, but was increased in females during abstinence. However, bodyweight was not correlated with addiction-like behavior vulnerability. Blood leptin levels after ∼6 weeks of cocaine self-administration did not correlate with addiction-like behaviors, however, baseline blood leptin levels before any access to cocaine negatively predicted addiction-like behaviors 6 weeks later. Finally, leptin administration in a separate cohort of 59 animals reduced cocaine seeking in acute withdrawal and after 7 weeks of protracted abstinence. These results demonstrate that high blood leptin level before access to cocaine may be a protective factor against the development of cocaine addiction-like behavior and that exogenous leptin reduces the motivation to take and seek cocaine. On the other hand, these results also show that blood leptin level and bodyweight changes in current users are not relevant biomarkers for addiction-like behaviors.
Spike-Timing-Dependent Plasticity Mediated by Dopamine and its Role in Parkinson’s Disease Pathophysiology
Authors: Madadi Asl Mojtaba , Vahabie Abdol-Hossein , Valizadeh Alireza , Tass Peter A.
Published: March 2022

Parkinson’s disease (PD) is a multi-systemic neurodegenerative brain disorder. Motor symptoms of PD are linked to the significant dopamine (DA) loss in substantia nigra pars compacta (SNc) followed by basal ganglia (BG) circuit dysfunction. Increasing experimental and computational evidence indicates that (synaptic) plasticity plays a key role in the emergence of PD-related pathological changes following DA loss. Spike-timing-dependent plasticity (STDP) mediated by DA provides a mechanistic model for synaptic plasticity to modify synaptic connections within the BG according to the neuronal activity. To shed light on how DA-mediated STDP can shape neuronal activity and synaptic connectivity in the PD condition, we reviewed experimental and computational findings addressing the modulatory effect of DA on STDP as well as other plasticity mechanisms and discussed their potential role in PD pathophysiology and related network dynamics and connectivity. In particular, reshaping of STDP profiles together with other plasticity-mediated processes following DA loss may abnormally modify synaptic connections in competing pathways of the BG. The cascade of plasticity-induced maladaptive or compensatory changes can impair the excitation-inhibition balance towards the BG output nuclei, leading to the emergence of pathological activity-connectivity patterns in PD. Pre-clinical, clinical as well as computational studies reviewed here provide an understanding of the impact of synaptic plasticity and other plasticity mechanisms on PD pathophysiology, especially PD-related network activity and connectivity, after DA loss. This review may provide further insights into the abnormal structure-function relationship within the BG contributing to the emergence of pathological states in PD. Specifically, this review is intended to provide detailed information for the development of computational network models for PD, serving as testbeds for the development and optimization of invasive and non-invasive brain stimulation techniques. Computationally derived hypotheses may accelerate the development of therapeutic stimulation techniques and potentially reduce the number of related animal experiments.
Comorbidities and Antithrombotic Treatment Pattern in Patients With Atrial Fibrillation
Authors: Bang Oh Young , Kim Siin , On Young Keun , Lee Myung-Yong , Jang Sung-Won , Han Seongwook , Ryu Jaeyun , Kang Seongsik , Suh Hae Sun , Kim Young-Hoon
Published: March 2022

Objective

Non-vitamin K antagonist oral anticoagulants (NOACs) are proven alternatives to warfarin for preventing stroke in patients with non-valvular atrial fibrillation. We aimed to examine the treatment patterns and patient factors associated with the use of antiplatelet agents, warfarin, and NOACs in clinical practice.

Methods

We conducted a retrospective cohort study using the Korean Health Insurance Review & Assessment Service database. Patients receiving antithrombotics were identified before and after the introduction of NOACs (from August 1, 2013 to December 30, 2014 and July 1, 2015 to November 30, 2016, respectively). Patients were included if they were aged ≥18 years, had an atrial fibrillation diagnosis, and had a CHA2DS2-VASc score ≥2. Treatment pattern was assessed by classifying patients into NOAC, warfarin, or antiplatelet users based on the first date of antithrombotic prescription. Clinical factors associated with the type of antithrombotics chosen were examined using logistic regression analyses.

Results

We identified 129,465 and 196,243 patients before and after the introduction of NOACs, respectively. The proportion of antiplatelet users was 60.7 and 53.0% before and after the introduction of NOACs, respectively. The proportion of warfarin users was higher in patients with low HAS-BLED score, high CHA2DS2-VASc score, or stroke before the NOAC era. A similar trend was observed for NOAC and warfarin users after the introduction of NOAC. Compared with antiplatelets, warfarin and NOAC uses were significantly associated with CHA2DS2-VASc score and stroke, whereas presence of myocardial infarction (MI) and peripheral arterial disease were significantly associated with antiplatelets prescription. For comparisons between NOAC and warfarin, HAS-BLED and CHA2DS2-VASc scores showed significant associations with NOAC use, whereas comorbidities including MI were significantly associated with warfarin use.

Conclusions

The treatment pattern of antithrombotics did not change with the introduction of NOACs. However, comorbidities served as an important factor in choosing treatment regardless of NOAC entry.