bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrum of ctxB genotypes, antibiogram profiles and virulence genes of Vibrio cholerae serogroups isolated from environmental water sources from Odisha, India
Authors: Pal Bibhuti Bhusan , Samal Debasish , Nayak Smruti Ranjan , Pany Swatishree 
Published: March 2023

Abstract
Background
The present study reports on the comprehensive analysis of Vibrio cholerae O1 and non-O1/non-O139 serogroups isolated from environmental water sources during cholera outbreaks, epidemics and surveillance studies between years 2007 to 2019 from different districts of Odisha, India.

Methods
A total of 85 stocked cultures of V. cholerae O1 and non-O1/non-O139 strains were analyzed for different ctxB genotypes, toxic genes, antibiogram profiles through PCR assays and pulsotyped by pulsed-field gel electrophoresis (PFGE).

Results
From all V. cholerae strains tested, 51 isolates were O1 Ogawa and the rest 34 strains were non-O1/non-O139. All the V. cholerae O1 strains were altered El Tor variants carrying ctxB1, ctxB3 and ctxB7 genotypes. However, only ctxB1 genotypes were present in V. cholerae non-O1/non-O139. Though non-O1/non-O139 strains were negative by O1 antisera, 20% strains were positive for rfbO1 gene by PCR assay. All the V. cholerae isolates possessed a variety of virulence genes including ace, ctxAB, toxR, zot, hlyA which were in higher percentage in the case of V. cholerae O1. The Vibrio cholerae O1 and non-O1-/non-O139 strains showed multiple antibiotic resistances in 2007 and 2012. The PCR detection of four resistance associated genes (strB, dfrA1, sulll, SXT) confirmed higher prevalence in V. cholerae non-O1/non-O139 strains. The PFGE analysis revealed 3 pulsotypes having 93% similarity among V. cholerae O1 strains.

Conclusion
This study indicates the changing epidemiology, antibiogram patterns and continuous genetic variation in environmental V. cholerae strains of Odisha over the years. So continuous surveillance is necessary to understand the changing patterns of V. cholerae different serogroups isolated from stool and water samples from Odisha.
Evaluation of the mTORC activity in the presence of Toxoplasma gondii and azathioprine in human monocyte cell line
Authors: Nemati Sara , Mohammad Rahimi Hanieh , Meyfour Anna , Pazoki Hossein , Asadzadeh Aghdaei Hamid , Shahrokh Shabnam , Mirjalali Hamed 
Published: March 2023

Abstract
Background
Autophagy is an important part of pathogenesis of IBD. Thiopurines such as azathioprine (AZA) are approved drugs for clinical practices in IBD patients. Besides, as an escape strategy, Toxoplasma gondii can use the mTORC1 complex to inactivate autophagy.

Methods
In this study, we investigated whether T. gondii tachyzoites may modulate autophagy and interfere the effects of azathioprine in IBD treatment. PMA-activated human monocyte cell line (THP-1) was infected with fresh T. gondii RH tachyzoites. After 5 h of infection, the cells were treated with AZA for 6 h. The expression of atg5, atg7, atg12, lc3b, and β-actin (BACT) genes was evaluated using quantitative real-time PCR. To analyze the phosphorylation of ribosomal protein S6 (rpS6), western blot using specific primary antibodies was performed.

Results
The results of real-time PCR revealed that AZA, T. gondii tachyzoites, and a combination of AZA and T. gondii tachyzoites upregulated atg5 gene for 4.297-fold (P-value = 0.014), 2.49-fold (P-value = 0.006), and 4.76-fold (P-value = 0.001), respectively. The atg7 gene showed significant upregulation (2.272-fold; P-value = 0.014) and (1.51-fold; P-value = 0.020) in AZA and AZA / T. gondii, respectively. The expression of atg12 gene was significantly downregulated in AZA and T. gondii tachyzoites for (8.85-fold; P-value = 0.004) and (2.005-fold; P-value = 0.038), respectively, but upregulated in T. gondii/AZA (1.52-fold; P-value = 0.037). In addition, the lc3b gene was only significantly changed in AZA / T. gondii (3.028-fold; P-value = 0.001). Western blot analysis showed that T. gondii tachyzoites significantly phosphorylated rpS6, and tachyzoites did not interfere the effects of AZA to phosphorylate the rpS6.

Conclusion
Taken together, although AZA and T. gondii similarly affects the expression levels of atg5, atg7, and atg12, but T. gondii does not seem to modulate the effects of AZA via mTORC functions.
Genome-wide identification and expression analysis of wall-associated kinase (WAK) and WAK-like kinase gene family in response to tomato yellow leaf curl virus infection in Nicotiana benthamiana
Authors: Zhong Xueting , Li Jiapeng , Yang Lianlian , Wu Xiaoyin , Xu Hong , Hu Tao , Wang Yajun , Wang Yaqin , Wang Zhanqi 
Published: March 2023

Abstract
Background
Tomato yellow leaf curl virus (TYLCV) is a major monopartite virus in the family Geminiviridae and has caused severe yield losses in tomato and tobacco planting areas worldwide. Wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) are a subfamily of the receptor-like kinase family implicated in cell wall signaling and transmitting extracellular signals to the cytoplasm, thereby regulating plant growth and development and resistance to abiotic and biotic stresses. Recently, many studies on WAK/WAKL family genes have been performed in various plants under different stresses; however, identification and functional survey of the WAK/WAKL gene family of Nicotiana benthamiana have not yet been performed, even though its genome has been sequenced for several years. Therefore, in this study, we aimed to identify the WAK/WAKL gene family in N. benthamiana and explore their possible functions in response to TYLCV infection.

Results
Thirty-eight putative WAK/WAKL genes were identified and named according to their locations in N. benthamiana. Phylogenetic analysis showed that NbWAK/WAKLs are clustered into five groups. The protein motifs and gene structure compositions of NbWAK/WAKLs appear to be highly conserved among the phylogenetic groups. Numerous cis-acting elements involved in phytohormone and/or stress responses were detected in the promoter regions of NbWAK/WAKLs. Moreover, gene expression analysis revealed that most of the NbWAK/WAKLs are expressed in at least one of the examined tissues, suggesting their possible roles in regulating the growth and development of plants. Virus-induced gene silencing and quantitative PCR analyses demonstrated that NbWAK/WAKLs are implicated in regulating the response of N. benthamiana to TYLCV, ten of which were dramatically upregulated in locally or systemically infected leaves of N. benthamiana following TYLCV infection.

Conclusions
Our study lays an essential base for the further exploration of the potential functions of NbWAK/WAKLs in plant growth and development and response to viral infections in N. benthamiana.
Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis
Authors: Bhushan Shashi , Singh Amit Kumar , Thakur Yogendra , Baskar Ramamurthy 
Published: March 2023

AbstractIn the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BSR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation (e.g. BSR (F1 38 = 0.9, F2 38 = 1.14, F3 38 = 1.02, F4 38 = 0.5, F5 38 = 0.76)). On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates (BSR (F1 38 = 0.9, F1 43 = 0.53, F1 48 = 0.79, F1 53 = 0.83 and F2 38 = 1.14, F2 43 = 0.57, F2 48 = 0.64, F2 53 = 0.94). We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.
AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis
Authors: Sun Miao , Xu Qin-Yi , Zhu Zhi-Peng , Liu Pei-Zhuo , Yu Jian-Xiang , Guo Yao-Xian , Tang Shu , Yu Zhi-Fang , Xiong Ai-Sheng 
Published: March 2023

Abstract
Background
Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

Results
Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. ‘Jinnanshiqin’. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H2O2 and MDA, and the inhibition of O2− generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

Conclusions
The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.
Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis
Authors: Cao Yunpeng , Fan Tingting , Wang Lihu , Zhang Lin , Li Yanli 
Published: March 2023

Abstract
Background
MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes.

Results
Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content.

Conclusion
Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.
Physiological, transcriptome and co-expression network analysis of chlorophyll-deficient mutants in flue-cured tobacco
Authors: Feng Yuqing , Li Yujing , Zhao Yuanyuan , Shi Hongzhi 
Published: March 2023

Abstract
Background
Photosynthetic pigments in higher plants, including chlorophyll (Chl) and carotenoids, are crucial for photosynthesis and photoprotection. Chl-deficient tobacco seedlings generally have a lower photosynthesis rate and higher nitrate-nitrogen (NO3-N) content, which causes a profound influence on tobacco yield and quality. In this study, a stable albino leaf mutant (Al) and slight-green leaf mutant (SG) obtained from the common flue-cured tobacco (Nicotiana tabacum L.) cultivar ‘Zhongyan 100’ (ZY100) by mutagenesis with ethyl methanesulfonate (EMS) were used as materials. The differences between the Chl-deficient mutants and the wild-type (WT) were analyzed in terms of biomass, photosynthetic fluorescence parameters, and carbon- and nitrogen-related physiological parameters. RNA sequencing (RNA-seq) and weighted gene co-expression network analysis (WGCNA) were used to explore the key pathways and candidate genes regulating differentiated chlorophyll and nitrate content.

Results
The results showed that, when compared to the WT, the Chl content and biomass of mutant plants were considerably lower while the NO3-N content was substantially elevated. The net photosynthetic rate, photosynthetic fluorescence parameters, carbohydrate, soluble protein, and carbon- and nitrogen-related enzyme activities all decreased in leaves of mutants and the development of chloroplasts was abnormal. Applying more nitrogen improved the growth and development of mutants, whereas NO3-N content distinctively increased compared with that of the WT. Through transcriptome sequencing, the downregulated genes in mutants were enriched in plant hormone signal transduction and nitrogen metabolism, which are involved in pigment biosynthesis and the carbon fixation pathway. In addition, two hub genes and seven transcription factors identified from the blue module through WGCNA were likely to be key candidate factors involved in chlorophyll synthesis and nitrate accumulation.

Conclusion
Our results demonstrated that differences in chlorophyll and nitrate content were caused by the combined effects of chloroplast development, photosynthesis, as well as related biological activity. In addition, transcriptome results provide a bioinformatics resource for further functional identification of key pathways and genes responsible for differences in chlorophyll and nitrate content in tobacco plants.
Involvement of KCa3.1 channel activity in immediate perioperative cognitive and neuroinflammatory outcomes
Authors: Saxena Sarah , Nuyens Vincent , Rodts Christopher , Jamar Kristina , Albert Adelin , Seidel Laurence , Cherkaoui-Malki Mustapha , Boogaerts Jean G. , Wulff Heike , Maze Mervyn , Kruys Véronique , Vamecq Joseph 
Published: March 2023

Abstract
Background
Potassium channels (KCa3.1; Kv1.3; Kir2.1) are necessary for microglial activation, a pivotal requirement for the development of Perioperative Neurocognitive Disorders (PNDs). We previously reported on the role of microglial Kv1.3 for PNDs; the present study sought to determine whether inhibiting KCa3.1 channel activity affects neuroinflammation and prevents development of PND.

Methods
Mice (wild-type [WT] and KCa3.1−/−) underwent aseptic tibial fracture trauma under isoflurane anesthesia or received anesthesia alone. WT mice received either TRAM34 (a specific KCa3.1 channel inhibitor) dissolved in its vehicle (miglyol) or miglyol alone. Spatial memory was assessed in the Y-maze paradigm 6 h post-surgery/anesthesia. Circulating interleukin-6 (IL-6) and high mobility group box-1 protein (HMGB1) were assessed by ELISA, and microglial activitation Iba-1 staining.

Results
In WT mice surgery induced significant cognitive decline in the Y-maze test, p = 0.019), microgliosis (p = 0.001), and increases in plasma IL-6 (p = 0.002) and HMGB1 (p = 0.001) when compared to anesthesia alone. TRAM34 administration attenuated the surgery-induced changes in cognition, microglial activation, and HMGB1 but not circulating IL-6 levels. In KCa3.1−/− mice surgery neither affected cognition nor microgliosis, although circulating IL-6 levels did increase (p < 0.001).

Conclusion
Similar to our earlier report with Kv1.3, perioperative microglial KCa3.1 blockade decreases immediate perioperative cognitive changes, microgliosis as well as the peripheral trauma marker HMGB1 although surgery-induced IL-6 elevation was unchanged. Future research should address whether a synergistic interaction exists between blockade of Kv1.3 and KCa3.1 for preventing PNDs.
Does prolonged prone position affect intracranial pressure? prospective observational study employing Optic nerve sheath diameter measurements
Authors: Demir Ufuk , Taşkın Öztürk , Yılmaz Ayşe , Soylu Veysel G. , Doğanay Zahide 
Published: March 2023

Abstract
Background
Our aim in this observational prospective study is to determine whether the prone position has an effect on intracranial pressure, by performing ultrasound-guided ONSD (Optic Nerve Sheath Diameter) measurements in patients with acute respiratory distress syndrome (ARDS) ventilated in the prone position.

Methods
Patients hospitalized in the intensive care unit with a diagnosis of ARDS who were placed in the prone position for 24 h during their treatment were included in the study. Standardized sedation and neuromuscular blockade were applied to all patients in the prone position. Mechanical ventilation settings were standardized. Demographic data and patients’ pCO2, pO2, PaO2/FiO2, SpO2, right and left ONSD data, and complications were recorded at certain times over 24 h.

Results
The evaluation of 24-hour prone-position data of patients with ARDS showed no significant increase in ONSD. There was no significant difference in pCO2 values either. PaO2/FiO2 and pO2 values demonstrated significant cumulative increases at all times. Post-prone SPO2 values at the 8th hour and later were significantly higher when compared to baseline (p < 0.001).

Conclusion
As a result of this study, it appears that the prone position does not increase intracranial pressure during the first 24 h and can be safely utilized, given the administration of appropriate sedation, neuromuscular blockade, and mechanical ventilation strategy. ONSD measurements may increase the safety of monitoring in patients ventilated in the prone position.
Myocardial tissue changes detected by cardiac MRI in a patient with suspected systemic sarcoidosis
Authors: Vanchin Byambasuren , Ka Mame Madjiguène , Arendt Christophe T. , Escher Felicitas , Nagel Eike , Puntmann Valentina O. 
Published: March 2023

Abstract
Background
The role of cardiac magnetic resonance imaging in the early management of chronic cardiac inflammatory conditions is growing. Our case enlightens the benefit of quantitative mapping in the monitoring and treatment guidance in systemic sarcoidosis.

Case presentation
We report about a 29-year-old man with an ongoing dyspnea and bihilar lymphadenopathy, suggesting sarcoidosis. Cardiac magnetic resonance showed high mapping values, but no scarring. In follow-ups, cardiac remodeling was noted; cardioprotective treatment normalized cardiac function and mapping markers. Definitive diagnosis was achieved in extracardiac lymphatic tissue during a relapse.

Conclusion
This case shows the role that mapping markers can play in the detection and treatment at early stage of systemic sarcoidosis.
Trends in antiplatelet strategies 12-months following coronary stent placement in anticoagulated patients
Authors: Gamvroulas Eleni M. , Jones Aubrey E. , Saunders John A. , Jones Tara L. , Witt Daniel M. 
Published: March 2023

Abstract
Background
Antithrombotic guidelines for patients undergoing percutaneous coronary interventions (PCIs) and also requiring anticoagulant medications are evolving. This study describes changes to antithrombotic therapy and associated outcomes 12-months following PCI in patients requiring ongoing anticoagulation therapy.

Methods
Records of patients identified from queries of electronic medical records were manually reviewed to verify changes to antithrombotic therapy from discharge to 12-months and at 12-months following PCI, and episodes of major bleeding, clinically relevant non-major bleeding (CRNMB), major adverse cardiovascular or neurological events (MACNE), and all-cause mortality outcomes during an additional 6-months follow-up.

Results
Patients (n = 120) receiving anticoagulation therapy at 12-months post PCI were classified into the following groups according to antiplatelet therapy status: no antiplatelet therapy (n = 16), single antiplatelet therapy (SAPT) (n = 85), and dual antiplatelet therapy (DAPT) (n = 19). Between 12- and 18-months following PCI there were 2 major bleeds, 7 CRNMB, 6 MACNE, 2 venous thromboembolisms, and 5 deaths. All but one bleeding episode occurred in the SAPT group. The odds of remaining on DAPT at 12-months were higher in patients who had PCI for acute coronary syndrome (odds ratio [OR] 2.91, 95% confidence interval [CI] 0.96, 8.77), and in those experiencing MACNE in the 12-months following PCI (OR 1.95, 95% CI 0.67, 5.66), but these associations were not statistically significant.

Conclusion
Most anticoagulated patients were continued on antiplatelet therapy 12-months post PCI. Bleeding was numerically more common in anticoagulated patients continuing SAPT therapy beyond 12 months. There was significant variability in antithrombotic prescribing patterns 12-months post PCI suggesting a potential opportunity for standardizing care in this patient population.
Spatiotemporal reproduction number with Bayesian model selection for evaluation of emerging infectious disease transmissibility: an application to COVID-19 national surveillance data
Authors: Rotejanaprasert Chawarat , Lawson Andrew B. , Maude Richard J. 
Published: March 2023

AbstractBackgroundTo control emerging diseases, governments often have to make decisions based on limited evidence. The effective or temporal reproductive number is used to estimate the expected number of new cases caused by an infectious person in a partially susceptible population. While the temporal dynamic is captured in the temporal reproduction number, the dominant approach is currently based on modeling that implicitly treats people within a population as geographically well mixed.MethodsIn this study we aimed to develop a generic and robust methodology for estimating spatiotemporal dynamic measures that can be instantaneously computed for each location and time within a Bayesian model selection and averaging framework. A simulation study was conducted to demonstrate robustness of the method. A case study was provided of a real-world application to COVID-19 national surveillance data in Thailand.ResultsOverall, the proposed method allowed for estimation of different scenarios of reproduction numbers in the simulation study. The model selection chose the true serial interval when included in our study whereas model averaging yielded the weighted outcome which could be less accurate than model selection. In the case study of COVID-19 in Thailand, the best model based on model selection and averaging criteria had a similar trend to real data and was consistent with previously published findings in the country.ConclusionsThe method yielded robust estimation in several simulated scenarios of force of transmission with computing flexibility and practical benefits. Thus, this development can be suitable and practically useful for surveillance applications especially for newly emerging diseases. As new outbreak waves continue to develop and the risk changes on both local and global scales, our work can facilitate policymaking for timely disease control.