bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-Genome-Wide Analysis of Pantoea Ananatis Identified Genes Linked to Pathogenicity in Onion
Authors: Agarwal Gaurav , Choudhary Divya , Stice Shaun , Myers Brendon , Gitaitis Ronald , Venter Stephanus , Kvitko Brian , Dutta Bhabesh 
Published: August 2020

Abstract
Background: Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion-virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. Results: We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51) - vs. non-pathogenic (n = 30)-strains phenotypically. Pan-GWAS revealed a large core genome of 3,153 genes and a flexible accessory genome of ≤5,065 genes. Phylogenomic analysis using pan-GWAS and presence and absence variants (PAVs) distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. The pan-GWAS also predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, TraR/DksA family transcriptional regulator, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Conclusions: This is the first report of using pan-GWAS on P. ananatis for the prediction of novel genes contributing to pathogenicity in onion, which will be utilized for further functional analyses. Pan-genomic differences (using PAVs) differentiated onion pathogenic from non-pathogenic strains of P. ananatis, which has been difficult to achieve using single or multiple gene-based phylogenetic analyses. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the ‘alt’ cluster that aid in P. ananatis colonization in onion bulbs. We concluded that HiVir/PASVIL genes are associated with pathogenic P. ananatis strains and the alt gene cluster alone is not responsible for pathogenicity on onion. The pan-genome also provides clear evidence of constantly evolving accessory genes in P. ananatis that may contribute to host-range expansion and niche-adaptation.
Detailed observation of axis ring fractures using computed tomography: a retrospective analysis of 202 cases
Authors: Li Guangzhou , He Siyu , Wang Qing , Tan Mingsheng , Hu Yong , Tian Jiwei , Liu Peng , Wu Chao , Han Yujian 
Published: August 2020

Abstract
Background: There is a dearth of research observing the precise anatomical location, pattern, and frequency of the fracture lines in axis ring fractures based on large size sample database and deducing the possible injury mechanism for such fractures. The study aimed to observe the anatomical features of axis ring fractures and evaluate the probable mechanism of injury.Methods: 202 patients with axis ring fractures were identified. According to the involvement of anatomical structures, the axis ring injuries were classified into facet joint injury and pure bony injury. The axis ring was also divided into: anterior, middle, and posterior elements. The anatomical structures involvement and fracture patterns of such fractures were observed using CT. Result: 501 anatomical structures of the axis ring were involved in 202 patients, including 288 facet joints injuries and 213 bony injuries. For facet joints injuries, the most common injuries were superior articular facet injuries, and for pure bony injuries, the most common injuries were pediculoisthmic component fractures. In regard to different element of the axis ring, the injuries of anterior element were more common than that of middle or posterior element. Most of (76.2%) axis ring fractures were asymmetrical, with different elements of the axis ring damaged on different side. Conclusion: In axis ring fractures, fracture lines could occur in any part of the ring. Facet joints injuries were more common than pure bony injuries, and the injuries of anterior element were more common than that of middle or posterior element. The probable mechanism of such injuries might be hyperextension and axial load, with an additional rotational load.
Psychometric Properties of the 37-item Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog) scale in Cancer Patients.
Authors: Hajj Aline , Salameh Pascale , Khoury Rita , Hachem Roula , Sacre Hala , Chahine Georges , Kattan Joseph , Khabbaz Lydia 
Published: August 2020

Abstract
Background: The Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog) scale is a self-assessment scale validated in routine clinical practice to assess cognitive function in cancer patients. This study aimed to validate the 37-item version of FACT-Cog exploring particularly the psychometric properties of four items related to multitasking that were not previously included in the scoring algorithm and assess its correlates in Lebanese cancer patients.Methods: A cross-sectional study was carried out including 261 patients with breast, colorectal and lung cancers undergoing chemotherapy (Ethics: CEHDF1016). Validity was confirmed using a factor analyses using the principal component analysis technique with a varimax rotation. Analyses of internal consistency, “test-retest" reliability, and convergent validity were also performed. Finally, a multiple linear regression was conducted, using the total cognition scale as a dependent variable.Results: The scale had an appropriate construct validity, and items loaded on subscales with adequate sample adequacy to factor analyses outcomes. The test-retest reliability was appropriate for the total cognition score/all sub-scores except for the FACT-Cog QOL. Moreover, a weak but significant and inverse correlation between the FACT-Cog scores and patient’s pain, fatigue, anxiety and depression. Finally, better cognition functioning was noted with age and in working patients, whereas lower functioning was observed in previous smokers and in patients with ovary/brain metastasis. Conclusions: The 37-item tool is valid and reliable. Questions related to multitasking could be included in the scoring system.
Tailored Liposomal Nanotraps for the Treatment of Streptococcal Infections
Authors: Besançon Hervé , Babiychuk Viktoriia , Larpin Yu , Köffel René , Schittny Dominik , Brockhus Lara , Hathaway Lucy J. , Sendi Parham , Draeger Annette , Babiychuk Eduard 
Published: August 2020

Abstract
Background: Streptococcal infections are associated with life-threatening pneumonia and sepsis. The rise in antibiotic resistance calls for novel approaches to treat bacterial diseases. Anti-virulence strategies promote a natural way of pathogen clearance by eliminating the advantage provided to bacteria by their virulence factors. In contrast to antibiotics, anti-virulence agents are less likely to exert selective evolutionary pressure, which is a prerequisite for the development of drug resistance. As part of their virulence mechanism, many bacterial pathogens secrete cytolytic exotoxins that destroy the host cell by destabilizing their plasma membrane. Liposomal nanotraps, mimicking plasmalemmal structures of host cells that are specifically targeted by bacterial toxins are being developed in order to neutralize - by competitive sequestration - numerous exotoxins. Results: In this study, the liposomal nanotrap technology is further developed to simultaneously neutralize the whole palette of cytolysins produced by Streptococcus pneumoniae, Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis - pathogens that can cause life-threatening streptococcal toxic shock syndrome. We show that the mixture of liposomes containing high amounts of cholesterol and liposomes composed exclusively of choline-containing phospholipids is fully protective against the combined action of exotoxins secreted by these pathogens. Conclusions: Unravelling the universal mechanisms that define targeting of host cells by streptococcal cytolysins paves the way for a broad-spectrum anti-toxin therapy that can be applied without a diagnostic delay for the treatment of bacterial infections including those caused by antibiotic-resistant pathogens.
Artificial Pneumothorax Improves Radiofrequency Ablation of Pulmonary Metastases close to Mediastinum
Authors: Zuo Taiyang , Lin Wenli , Liu Fengyong , Xu Jinshun 
Published: August 2020

Abstract
Background

To investigate the feasibility, safety and efficacy of percutaneous radiofrequency ablation (RFA) of pulmonary metastases from hepatocellular carcinoma (HCC) contiguous with the mediastinum using the artificial pneumothorax technique.
Method:

A total of 40 lesions in 32 patients with pulmonary metastases from HCC contiguous with the mediastinum accepted RFA treatment from August 2014 to May 2018 via the artificial pneumothorax technique. After ablation, clinical outcomes were followed up by contrast enhanced CT. Technical success, local tumor progression (LTP), intrapulmonary distant recurrence (IDR), and adverse events were evaluated. Overall survival (OS) and local tumor progression free survival (LTPFS) were recorded for each patient.
Results

The tumor size was 1.4 ± 0.6 cm in diameter. RFA procedures were all successfully performed without intra-ablative complications. Technical success was noted in 100% of the patients. 5 cases of LTP and 8 cases of IDR occurred following the secondary RFA for treatment. Slight pain was reported in all patients. No major complications were observed. The 1, 2, and 3-year LTPFS rates were 90.6%, 81.2%, and 71.8%, and the 1, 2, and 3-year OS rates were 100%, 100% and 87.5%, respectively.
Conclusion

Artificial pneumothorax adjuvant RFA is a feasible, safe, and efficient method for treatment of pulmonary metastases from HCC contiguous with the mediastinum.
Tumor LAG-3 and NY-ESO-1 expression predict durable clinical benefits of immune checkpoint inhibitors in advanced non-small cell lung cancer
Authors: Jung Eun Hee , Jang Hee Ryung , Kim Se Hyun , Suh Koung Jin , Kim Yu Jung , Lee Ju-Hyun , Chung Jin-Haeng , Kim Miso , Keam Bhumsuk , Kim Tae Min , Kim Dong-Wan , Heo Dae Seog , Lee Jong Seok 
Published: August 2020

Abstract
Background

Immune checkpoint inhibitors (ICIs) are an established treatment for non-small cell lung cancer (NSCLC) that have demonstrated durable clinical benefits (DCBs). Previous studies have suggested that NY-ESO-1 and LAG-3 could be surrogate markers of ICI responses in NSCLC; therefore, we explored the predictive value of NY-ESO-1 and LAG-3 expression in NSCLC.
Methods

We retrospectively reviewed the records of 38 patients with advanced NSCLC treated with anti-PD-1 monoclonal antibodies from 2013 to 2016 at Seoul National University Hospital and Seoul National University Bundang Hospital after failed platinum-based chemotherapy. Tumor tissues from each patient were subjected to immunohistochemical analysis to determine NY-ESO-1, LAG-3, and PD-L1 expression, whose ability to predict progression-free survival (PFS) and overall survival (OS) was then analyzed alongside their positive (PPV) and negative (NPV) predictive values.
Results

NY-ESO-1 or LAG-3 expression was detected in all tumor samples from patients with high PD-L1 expression and was significantly associated with favorable patient outcomes, unlike PD-L1 expression. Patients whose tumors expressed both NY-ESO-1 and LAG-3 had a high DCB rate and those with triple-positive PD-L1, LAG-3, and NY-ESO expression had a superior median OS and PFS compared to those in patients with triple-negative expression. Furthermore, LAG-3 and NY-ESO-1 co-expression was an independent predictor of both PFS and OS, while LAG-3 displayed a good NPV.
Conclusion

Therefore, patients with NSCLC who co-express NY-ESO-1 or LAG-3 with PD-L1 exhibit greater DCBs and improved long-term survival following anti-PD-1 therapy. Moreover, NY-ESO-1 and LAG-3 could be novel predictive biomarkers of survival and should be considered in the future use of ICIs.
Comparison of bispectral index and patient state index during sevoflurane anesthesia in children: a prospective observational study
Authors: Ji Sang-Hwan , Jang Young-Eun , Kim Eun-Hee , Lee Ji-Hyun , Kim Jin-Tae , Kim Hee-Soo 
Published: August 2020

Abstract
Background: Cortical electroencephalography (EEG)-based devices are used to monitor the depth of anesthesia. In this study, we compared the values of bispectral index (BIS) and patient state index (PSI) during sevoflurane anesthesia in children. The ability/accuracy of BIS and PSI to predict the steady and recovery state of anesthesia was evaluated based on prediction probability (Pk) values and the secondary outcomes were agreement and correlation of two monitors. Methods: Fifty children (3-12 years old) were enrolled and the patients received sevoflurane anesthesia with remifentanil. Before the induction of anesthesia, BIS and PSI sensors were simultaneously placed on the forehead, and data were collected until the end of anesthesia. Steady state was defined as the period following intubation until the cessation of sevoflurane, while recovery state was defined as the period following the cessation of sevoflurane until awake. The prediction probability (Pk), agreement or correlation of BIS and PSI in different anesthesia state were calculated. Results: Anesthesia reduced mean BIS and PSI values. Pk of BIS (95% confidential interval (CI) [0.78-0.91])) and PSI (95% CI [0.82-0.91]) for anesthesia were 0.85 and 0.87, respectively. Agreement was 0.79 for recovery state and 0.73 for steady state. Conclusions: Pk values were comparable for BIS and PSI. Agreement between BIS and PSI measurements in the same state was relatively good. Therefore, these monitors are appropriate for monitoring for different state of anesthesia in pediatric population. Trial Registry Number: Clinical Trials.gov NCT03792334.
Construction of a High-Density Genetic Map via Genome Resequencing and QTL Detection for Key Fiber Traits in Asiatic Cotton
Authors: Li Yaohua , Mo Tong , Ran Lingfang , Zeng Jianyan , Wang Chuannan , Zhong Ziman , Liang Aimin , Xiao Yuehua 
Published: August 2020

Abstract
Background: Asiatic cotton (Gossypium arboreum, genome A2) is one of diploid cotton species producing spinnable fibers. However, few studies on the genetic mechanism of key fiber traits of Asiatic cotton have been reported. Sequencing technology advancement and the release of Asiatic cotton genome made it possible to construct a high-density SNP genetic map and further untapped QTL detection.Results: The Asiatic cotton cultivars SXY No.1 and CSLZ were crossed to develop a recombinant inbred line (RIL) population with 189 lines. Whole genome resequencing technology was employed to construct a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. Based on fiber quality and yield component trait data from three environments, a total of 177 QTL were identified for 8 key fiber traits explaining 5.0-37.4% of the phenotypic variance. Besides, 48 stable QTL, including 15 for upper quartile length (UQL), 18 for fiber fineness (FF), 1 for immature fiber content (IFC), 4 for fiber neps count (FNC), 3 for lint percentage (LP), 7 for seed index (SI), were detected in more than one environment.Conclusions: Using a RIL population and whole genome resequencing strategy, this study presented a high-density genetic map of G. arboreum and identified 48 stable QTL for 6 key fiber traits (UQL, FF, IFC, FNC, LP, SI). Our work laid solid foundation for subsequent fine mapping of QTL for key fiber traits and cloning of controlling genes.
Gut microbiome, a potential indicator for differential diagnosis of major depressive disorder and general anxiety disorder
Authors: Dong Zaiquan , Shen Xiaoling , Hao Yanni , Li Jin , Li Haoran , Xu Haizheng , Kuang Weihong 
Published: August 2020

Abstract
Background Major depressive disorder (MDD) and general anxiety disorder (GAD) share many common features, leading to many challenges in their differential diagnosis. Given the importance of the microbiota-gut-brain axis, we aimed to investigate the differences in gut microbiota between representative cases of these two diseases and sought to develop a microbiome-based approach for their differential diagnosis.Methods We enrolled 23 patients with MDD, 21 patients with GAD, and 10 healthy subjects (health control, HC) in the present study. We used 16S rRNA gene sequencing analysis to determine the microbial compositions of gut microbiome based on Illumina Miseq according to Illumina’s standard protocol.Results We found that patients with MDD or GAD exhibited significant differences in the relative abundance of gut microbiota. We identified the microbial signatures of subjects with MDD and GAD relative to HC and found differences in levels of Faecalibacterium and LachnospiraceaeND3007group. Moreover, we also found correlations between the bacteria and neuroendocrine and clinical symptoms, namely, a significant negative correlation between Fusicatenibacter and free thyroxine(FT4) in MDD, significant negative correlation between Fusicatenibacter and cortisol (PTC) in GAD, positive correlation between LachnospiraceaeND3007group and sleep disturbance factor of Hamilton Depression Rating Scale, and negative correlation between LachnospiraceaeND3007group and PTC (all P<0.05).Conclusions The present study elucidated a unique gut microbiome signature associated with MDD and GAD that could facilitate differential diagnosis and targeted therapy.
Plasmodium vivax infection compromises reticulocyte stability.
Authors: Clark Martha , Kanjee Usheer , Rangel Gabriel , Chery Laura , Mascarenhas Anjali , Gomes Edwin , Rathod Pradipsinh , Brugnara Carlo , Ferreira Marcello , Duraisingh Manoj 
Published: August 2020

Abstract
The structural integrity of the host red blood cell (RBC) must be maintained for propagation of Plasmodium spp. during the disease causing blood-stage of malaria infection. Plasmodium vivax infection is restricted to reticulocytes. To assess the impact of P. vivax infection on reticulocyte stability, we developed a flow cytometry-based assay capable of measuring osmotic stability within heterogeneous RBC populations. We found that P. vivax preferred young reticulocytes are more osmotically stable than older reticulocytes and normocytes, and P. vivax infection decreased reticulocyte stability to levels observed for RBC disorders that cause hemolytic anemia. Moreover, P. vivax reticulocyte destabilization was more significant than P. falciparum normocyte destabilization. Finally, we found that P. vivax new permeability pathways contribute to the decreased osmotic stability of infected-reticulocytes. These results reveal a key vulnerability of P. vivax that could be manipulated to yield both in vitro culture and novel therapeutics.
Machine Learning Identifies the miR-196b and miR-34c-5p as the Chemotherapy Response Biomarkers of Lung Adenocarcinoma
Authors: Lan Yuanmin , Xue Jiqing , Chen Liang , Wu Dongwei , Wang Wei , Shen Kezhen , Chen Piji 
Published: August 2020

Abstract
BackgrooundLung adenocarcinoma is one of the most common malignant lung cancers. Although platinum-based chemotherapy is the first-line adjuvant treatment for middle and late stage lung adenocarcinoma, the response of chemotherapy varies between patients. Moreover, there are no effective biomarkers that could predict chemotherapy response in clinical practice. MiRNAs that are stable in all types of body fluid have demonstrated their diagnostic and prognostic capacity in variety of cancers. Here, we utilized three different machine learning algorithms to identify miRNA signatures specific to chemotherapy response in lung cancer. MethodsThrough a public dataset, a panel of miRNAs for response to chemotherapy was identified by Machine Learning. The predictive capacity was determined by the receiver operation curve. A cohort involving 30 patients with lung adenocarcinoma was utilized for validate the miRNA panel. ResultsMachine Learnings identified five chemotherapy response featured miRNAs (miR-196b, miR-34c-5p, miR-181b, miR-27b and miR-26a). The putative targets of these miRNA signatures are enriched in the biosynthesis. Two of these miRNA signatures (miR-196b and miR-34c-5p) were validated for their chemotherapy response prediction in our 30 serum samples of lung adenocarcinoma with the accuracy of 0.90 and 0.93, respectively. ConclusionsOur study demonstrates circulating miRNA could potentially be predictive biomarker for chemotherapy response in lung adenocarcinoma.
Tumor infiltrated macrophage-the fighter defends against recurrence of stage Ⅱcolorectal cancer
Authors: Yang Wen-Jing , Wang Xiao-Min , Zhang Gan-Lin , Yu Ming-Wei , Cao Ke-Xin , Tan Si-Yu , Yang Guo-Wang 
Published: August 2020

Abstract
BackgroundBiomarkers which can robustly predict the recurrence of stage II colorectal cancer (CRC) have been urgent needed. Immune cells highly related to the recurrence and prognosis of CRC. However, whether the immune cells take part in the recurrence of stage II CRC has not known.MethodsExplored the roles and possible mechanism of immune cells in the recurrence of stage II CRC by public databases.ResultsTumor Immune Estimation Resource (TIMER) analysis indicated the macrophage infiltration level in stage II CRC: Significantly higher in the nonrecurrence group than that in the recurrence group; Significantly negative correlated with the recurrence-related hub gene transferrin (TF); Significantly positive correlated with the improved disease-free survival (DFS) and overall survival (OS). And macrophage infiltration related-gene recurrent model (GRM) (area under the curve (AUC) = 0.906) provide a better performance than the GRM established previously (AUC = 0.882) to predict the recurrence of stage II CRC. Gene Set Enrichment Analysis (GSEA) analysis indicated macrophage (M1) infiltrated in the tumor microenvironment (TME) defending against recurrence as a dynamic process: M1 was activated by receiving the stimulus signals (LPS/IFN- γ) which released by CRC cells, then infiltrating and recognizing the tumor to secrete IL-6 to directly or indirectly act on TF or create anti-tumor TME to kill tumor cells.ConclusionsThis study maybe provides a novel immunological perspective to explore the mechanism of recurrence and improve clinical practice performance in stage II CRC.