bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of neutralizing antibodies produced by papaya mosaic virus nanoparticles fused to the E2EP3 peptide epitope of Chikungunya envelope
Authors: Rothan Hussin A. , Yusof Rohana 
Published: March 2020

AbstractChikungunya virus (CHIKV) infection is the cause of acute symptoms and chronic symmetrical polyarthritis associated with long-term morbidity and mortality. Currently, there is no available licensed vaccine or particularly useful drug for human use against CHIKV infection. This study was conducted to evaluate the efficacy of antibodies produced by papaya mosaic virus (PapMV) nanoparticles fused to E2EP3 peptide of CHIKV envelope as a recombinant CHIKV vaccine. PapMV, PapMV E2EP3, and E2EP3 PapMV were produced in E. coli with an approximate size of 27 to 30 kDa. ICR mice (5 to 6 weeks of age) were injected subcutaneously with 25 micrograms of vaccine construct, and ELISA measured the titer of CHIKV specific IgG antibodies. The results showed that both recombinant proteins E2EP3 PapMV and PapMV E2EP3 were able to induce IgG antibodies production in immunized mice against CHIKV while immunization with recombinant PapMV showed no IgG antibodies induction. The neutralizing activity of the antibodies generated by either E2EP3 PapMV or PapMV E2EP3 exhibited similar inhibition to CHIKV replication in Vero cells using the cells based antibody neutralizing assay and analyzed by plaque formation assay. This study showed the effectiveness of nanoparticles vaccine generated by fusing epitope peptide of CHIKV envelope to papaya mosaic virus envelope in inducing a robust immune response in mice against CHIKV. The data showed that levels of neutralizing antibodies correlate with a protective immune response CHIKV replication.
A Novel Non-hypermucoviscous ST11 Hypervirulent Carbapenem-resistantKlebsiella pneumoniaeLacking Classical Virulence Factors
Authors: Zhang Min , Zhang Jinyong , Li Jia , Xu Shuye , Hu Chunxia , Deng Qiuyang , Wu Xianglin , Xiao Lihua , Liu Zhou , Yang Xiyao , Hu Xiaoqian , Zhang Wenhui , Wang Nan , Yang Liqi , Liu Shiyi , Cui Ruiqin , Hui Zhen , Zhong Yuxin , Luo Yutian , Chen Huaisheng , Wu Weiyuan , Wu Jinsong , Lu Yuemei , Liu Xueyan , Zou Quanming , Huang Wei 
Published: March 2020

BackgroundHypervirulentKlebsiella pneumoniaelacking classical virulence factors is uncommon, and the virulence mechanisms of this organism are not understood.MethodsFollowing a retrospective study of carbapenem-resistantK. pneumoniaebased on core genome multilocus sequence typing (cgMLST), isolates that caused high mortality were investigated with a genome-wide association study (GWAS), proteome analysis and an animal model.ResultsThe sublineage of sequence type 11 (ST11)K. pneumoniae, which belongs to complex type 3176 (CT3176) and K-locus 47 (KL47), was highlighted due to the high mortality of infected patients. GWAS analysis showed thatampRwas associated with the CT3176 isolates. In a mouse model, the mortality ofampR-carrying isolates was comparable to that of the typical hypervirulent isolate GM2. Even during the first 24 hours of infection, the bacterial load and pathological changes of theampR-carrying isolates in the lungs were more severe than those of GM2. TheampRcomplement mutant was able to enhance the virulence of the KL47 isolate but not the virulence of KL1. Proteome analysis showed that the expression of WcaJ in theampR+isolates was significantly higher than that in theampR−isolates, and this result was also confirmed by transcription tests and capsule staining. It is suggested that the enhancement of the initial stage of capsule synthesis may be the cause of the high virulence of these non-hypermucoviscous ST11 carbapenem-resistantK. pneumoniaeisolates.ConclusionsNon-hypermucoviscous ST11 hypervirulent carbapenem-resistantK. pneumoniaewarrants continued surveillance and investigation.
Vicarious traumatization in the general public, members, and non-members of medical teams aiding in COVID-19 control
Authors: Li Zhenyu , Ge Jingwu , Yang Meiling , Feng Jianping , Qiao Mei , Jiang Riyue , Bi Jiangjiang , Zhan Gaofeng , Xu Xiaolin , Wang Long , Zhou Qin , Zhou Chenliang , Pan Yinbing , Liu Shijiang , Zhang Haiwei , Yang Jianjun , Zhu Bin , Hu Yimin , Hashimoto Kenji , Jia Yan , Wang Haofei , Wang Rong , Liu Cunming , Yang Chun 
Published: March 2020

AbstractSince December 2019, more than 79,000 people have been diagnosed with infection of the Corona Virus Disease 2019 (COVID-19). A large number of medical staff were dispersed for Wuhan city and Hubei province to aid COVID-19 control. Psychological stress, especially vicarious traumatization (VT) caused by the COVID-19 pandemic, should not be ignored. To address this concern, the study employed a total of 214 general public (GP) and 526 nurses to evaluate VT scores via a mobile app-based questionnaire. Results showed that the VT scores slightly increased across periods of aiding COVID-19 control, although no statistical difference was noted (P = 0.083). However, the study found lower scores for VT in nurses [median = 69; interquartile range (IQR) = 56–85] than those of the GP (median = 75.5; IQR = 62–88.3) (P = 0.017). In addition, the VT scores for front-line nurses (FLNs; median = 64; IQR = 52–75), including scores for physiological and psychological responses, were significantly lower than those of non-front-line nurses (nFLNs; median = 75.5; IQR = 63–92) (P < 0.001). Interestingly, the VT scores of the GP were significantly higher than those of the FLNs (P < 0.001). However, no statistical difference was observed compared with those of nFLNs (P > 0.05). Importantly, nFLNs are more likely to suffer from VT, which might be related to two factors, namely, gender [odds ratio (OR) = 3.1717; 95% confidence interval (CI) = 4.247–18.808; P = 0.002] and fertility [OR = 2.072; 95%CI = 0.626–24.533; P = 0.039]. Therefore, increased attention should be paid to the psychological problems of the medical staff, especially nFLNs, and GP under the situation of the spread and control of COVID-19. Early strategies that aim to prevent and treat VT in medical staff and GP are extremely necessary.
Machine learning-based CT radiomics model for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection: A multicenter study
Authors: Qi Xiaolong , Jiang Zicheng , Yu Qian , Shao Chuxiao , Zhang Hongguang , Yue Hongmei , Ma Baoyi , Wang Yuancheng , Liu Chuan , Meng Xiangpan , Huang Shan , Wang Jitao , Xu Dan , Lei Junqiang , Xie Guanghang , Huang Huihong , Yang Jie , Ji Jiansong , Pan Hongqiu , Zou Shengqiang , Ju Shenghong 
Published: March 2020

AbstractObjectivesTo develop and test machine learning-based CT radiomics models for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection.DesignCross-sectionalSettingMulticenterParticipantsA total of 52 patients with laboratory-confirmed SARS-CoV-2 infection and their initial CT images were enrolled from 5 designated hospitals in Ankang, Lishui, Zhenjiang, Lanzhou, and Linxia between January 23, 2020 and February 8, 2020. As of February 20, patients remained in hospital or with non-findings in CT were excluded. Therefore, 31 patients with 72 lesion segments were included in the final analysis.InterventionCT radiomics models based on logistic regression (LR) and random forest (RF) were developed on features extracted from pneumonia lesions in training and inter-validation datasets. The predictive performance was further evaluated in test dataset on lung lobe- and patients-level.Main outcomesShort-term hospital stay (≤10 days) and long-term hospital stay (>10 days).ResultsThe CT radiomics models based on 6 second-order features were effective in discriminating short- and long-term hospital stay in patients with pneumonia associated with SARS-CoV-2 infection, with areas under the curves of 0.97 (95%CI 0.83-1.0) and 0.92 (95%CI 0.67-1.0) by LR and RF, respectively, in the test dataset. The LR model showed a sensitivity and specificity of 1.0 and 0.89, and the RF model showed similar performance with sensitivity and specificity of 0.75 and 1.0 in test dataset.ConclusionsThe machine learning-based CT radiomics models showed feasibility and accuracy for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection.
Infected macrophages engage alveolar epithelium to metabolically reprogram myeloid cells and promote antibacterial inflammation
Authors: Liu Xin , Boyer Mark A. , Holmgren Alicia M. , Shin Sunny 
Published: March 2020

AbstractAlveolar macrophages are the primary immune cells that first detect lung infection. However, only one macrophage patrols every three alveoli. How this limited number of macrophages provides protection is unclear, as numerous pathogens block cell-intrinsic immune responses. The intracellular pathogenLegionella pneumophilainhibits host translation, thereby impairing the ability of infected macrophages to produce critical cytokines. Nevertheless, infected macrophages induce an IL-1-dependent inflammatory response by recruited myeloid cells that controls infection. Here, we show that collaboration with the alveolar epithelium is critical, in that IL-1 instructs the alveolar epithelium to produce GM-CSF. Intriguingly, GM-CSF drives maximal cytokine production in bystander myeloid cells by enhancing PRR-induced glycolysis. Our findings reveal that alveolar macrophages engage alveolar epithelial signals to metabolically reprogram myeloid cells and amplify antibacterial inflammation.One Sentence SummaryThe alveolar epithelium is a central signal relay between infected and bystander myeloid cells that orchestrates antibacterial defense.
Differential tissue stiffness of body column facilitates locomotion ofHydraon solid substrates
Authors: Naik Suyash , Unni Manu , Sinha Devanshu , Rajput Shatruhan Singh , Reddy P. Chandramouli , Kartvelishvily Elena , Solomonov Inna , Sagi Irit , Chatterji Apratim , Patil Shivprasad , Galande Sanjeev 
Published: March 2020

AbstractThe bell-shaped members of Cnidaria typically move around by swimming, whereas theHydrapolyp can perform locomotion on solid substrates in aquatic environment. To address the biomechanics of locomotion on rigid substrates, we studied the ‘somersaulting’ locomotion inHydra. We applied atomic force microscopy to measure the local mechanical properties ofHydra’sbody column and identified the existence of differential Young’s modulus between the shoulder region versus rest of the body column at 3:1 ratio. We show that somersault primarily depends on differential tissue stiffness of the body column and is explained by computational models that accurately recapitulate the mechanics involved in this process. We demonstrate that perturbation of the observed stiffness variation in the body column by modulating the extracellular matrix (ECM) polymerization impairs the ‘somersault’ movement. These results provide mechanistic basis for the evolutionary significance of differential extracellular matrix properties and tissue stiffness.
Validity of dynamical analysis to characterize heart rate and oxygen consumption during effort tests
Authors: Mongin D. , Chabert C. , Caparros A. Uribe , Collado A. , Hermand E. , Hue O. , Alvero Cruz J. R. , Courvoisier D. S. 
Published: March 2020

ABSTRACTPerformance is usually assessed by simple indices stemming from cardiac and respiratory data measured during graded exercise test. The goal of this study is to test the interest of using a dynamical analysis of these data. Therefore, two groups of 32 and 14 athletes from two different cohorts performed two different graded exercise testing before and after a period of training or deconditioning. Heart rate (HR) and oxygen consumption (VO2) were measured. The new dynamical indices were the value without effort, the characteristic time and the amplitude (gain) of the HR and VO2response to the effort. The gain of HR was moderately to strongly associated with other performance indices, while the gain for VO2increased with training and decreased with deconditioning with an effect size slightly higher than VO2max. Dynamical analysis performed on the first 2/3 of the effort tests showed similar patterns than the analysis of the entire effort tests, which could be useful to assess individuals who cannot perform full effort tests. In conclusion, the dynamical analysis of HR and VO2obtained during effort test, especially through the estimation of the gain, provides a good characterization of physical performance, robust to less stringent effort test conditions.
TipQAD: an automated tool for quantifying apical fluorescence dynamics in tip-growing cells
Authors: Tambo Asongu L. , Bhanu Bir , Luo Nan , Rong Duoyan , Wang Fei , Craddock Christian , Lavagi Irene , Yang Zhenbiao 
Published: March 2020

ABSTRACTCell polarity is a fundamental property essential for the function and development of all cellular organisms. Tip growth is an extreme form of polar growth requiring spatiotemporally dynamic but highly coordinated cellular activities. Quantification of these dynamic activities is important for the systematic study of the mechanisms controlling cell polarity, but an automated and unbiased method for analyzing and quantification of tip-growing cells has been missing. In this paper, we developed a computational model and an associated tool called TipQAD for quantifying the spatiotemporal dynamics of fluorescence protein (FP) labeled molecules or structures in tip-growing cells. This tool robustly and accurately measured the spatial distribution and temporal dynamics of FP-labeled proteins in the cytoplasm or the plasma membrane at the tip region of several types of tip-growing cells. We also demonstrated its ability to analyze data from FRAP experiments. In conclusion, this tool showed great potential for automated measurements of the spatiotemporal dynamics of fluorescent-labeled cellular molecules and structures.
Environmental DNA sampling in a terrestrial environment: methods to detect a critically endangered frog and a global pathogen
Authors: Burns Thomas J. , Clemann Nick , van Rooyen Anthony R. , Scheele Ben C. , Weeks Andrew R. , Driscoll Don A. 
Published: March 2020

AbstractEnvironmental DNA techniques have become established as a useful tool for biological monitoring and are used extensively to determine species presence in aquatic systems. However, their application in terrestrial systems has been more limited, likely in part due to difficulties in choosing where to sample and ensuring that collected DNA reflects current species presence. We developed methods to sample eDNA in the terrestrial environment and trialled them under controlled and field conditions. We targeted three species, an elusive critically endangered frog, an abundant non-threatened frog, and the globally distributed amphibian skin pathogen chytrid fungus, which has been implicated in the decline of over 500 amphibian species. We used a sandpaper-sampling surface to ‘trap’ DNA. After sampling, we washed the surface and filtered the wash water to gather material for DNA extraction and subsequent qPCR. Our controlled condition experiments demonstrated that frog and chytrid fungus DNA was detectable after as few as five contacts between a frog and the sampling surface. Furthermore, this DNA remained detectable after two weeks in cool, shaded, outdoor conditions. Our field experiments demonstrated that these techniques were transferable to natural habitats, where we detected both the common and rare amphibian target species, as well as chytrid fungus. Field sampling eDNA results were broadly consistent with those derived from conventional survey methods. Our methods have potential application in non-invasive sampling of amphibians and other species in terrestrial systems, broadening the applicability of eDNA techniques for species detection and monitoring.
Fourier shell correlation criteria for local resolution estimation
Authors: Rohou Alexis 
Published: March 2020

AbstractThe resolution of three-dimensional (3D) maps obtained by electron microscopy and reconstruction is rarely constant, owing to the flexibility or compositional variability of the macromolecules of interest. Accurately estimating the local resolution within 3D reconstruction volumes is desirable for analytical purposes, and may help improve the reconstruction process itself. One approach to estimating the local resolution is to compute Fourier shell correlations (FSC) between equivalent local regions of maps computed from half datasets: the estimated local resolution is that of the Fourier shell where the FSC drops below a pre-established threshold value. Existing thresholds can lead to significant over-estimates of the local resolution because they do not take into account the low number of independent voxels in low-resolution Fourier shells typically encountered when dealing with small sub-volumes. We derive a modified FSC threshold criterion, and a simple statistical test of whether the FSC significantly exceeds it, which aims to remedy this by taking into account the bias and variance of the FSC as an estimator of signal-to-noise ratio.
Defining Strawberry Uniformity using 3D Imaging and Genetic Mapping
Authors: Li Bo , Cockerton Helen M. , Johnson Abigail W. , Karlström Amanda , Stavridou Eleftheria , Deakin Greg , Harrison Richard J. 
Published: March 2020

AbstractStrawberry uniformity is a complex trait, influenced by multiple genetic and environmental components. To complicate matters further, the phenotypic assessment of strawberry uniformity is confounded by the difficulty of quantifying geometric parameters ‘by eye’ and variation between assessors. An in-depth genetic analysis of strawberry uniformity has not been undertaken to date, due to the lack of accurate and objective data. Nonetheless, uniformity remains one of the most important fruit quality selection criteria for the development of a new variety. In this study, a 3D-imaging approach was developed to characterise berry uniformity. We show that circularity of the maximum circumference had the closest predictive relationship with the manual uniformity score. Combining five or six automated metrics provided the best predictive model, indicating that human assessment of uniformity is highly complex. Furthermore, visual assessment of strawberry fruit quality in a multi-parental QTL mapping population has allowed the identification of genetic components controlling uniformity. A “regular shape” QTL was identified and found to be associated with three uniformity metrics. The QTL was present across a wide array of germplasm, indicating a strong candidate for marker-assisted breeding. A greater understanding of berry uniformity has been achieved through the study of the relative impact of automated metrics on human perceived uniformity. Furthermore, the comprehensive definition of strawberry uniformity using 3D imaging tools has allowed precision phenotyping, which has improved the accuracy of trait quantification. This tool has allowed us to illustrate the use of advanced image analysis towards the breeding of greater uniformity in strawberry.
Structural basis of transcription-translation coupling
Authors: Wang Chengyuan , Molodtsov Vadim , Firlar Emre , Kaelber Jason T. , Blaha Gregor , Su Min , Ebright Richard H. 
Published: March 2020

AbstractIn bacteria, transcription and translation are coupled processes, in which movement of RNA polymerase (RNAP) synthesizing mRNA is coordinated with movement of the first ribosome translating mRNA. Coupling is modulated by the transcription factors NusG--which is thought to bridge RNAP and ribosome--and NusA. Here, we report cryo-EM structures ofEscherichia colitranscription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P-site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A; previously termed “expressome”). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.One Sentence SummaryCryo-EM defines states that mediate NusG- and NusA-dependent transcription-translation coupling in bacteria
The Effect of Obesity on Pain Severity and Pain Interference
Authors: Basem Jade , White Robert S. , Chen Stephanie A. , Mauer Elizabeth , Steinkamp Michele L. , Inturrisi Charles E. , Witkin Lisa 
Published: March 2020

ABSTRACTBackground and objectivesObesity is one of the most prevalent comorbidities associated with chronic pain, the experience of which can severely interfere with activities of daily living and increase the utilization of clinical resources. Obesity is also a risk factor for increased pain severity (pain intensity) and pain interference (pain related disability). We hypothesize that a higher level of obesity, as measured by body mass index (BMI), would be associated with increased levels of pain severity and interference in a population of chronic pain clinic patients.MethodsParticipant data was pulled from a multi-site chronic pain outpatient database from 7/8/2011 to 10/17/2016. The Brief Pain Inventory (BPI), opioid prescriptions, and basic demographic information were queried and we categorized participants into three different ordinal categories based on recorded BMI levels (underweight, normal and overweight, obese). Bivariate analyses were performed to compare pain outcomes by BMI and by other demographic/clinical patient characteristics. Multivariable linear regressions were constructed to model each of four pain severity scores in addition to total pain interference score. All models examined BMI as the primary predictor, controlling for age, receipt of a pain procedure within 45 days prior to the pain clinic encounter, opioid prescription within 45 days prior to the encounter, and diagnosis. The total pain interference model additionally included pain severity (as measured by worst pain in the past 24 hours) as a covariate.Results2509 patients were included in the study. The median BMI was 27 and the median age was 59 years. 77% of patients were diagnosed with musculoskeletal pain conditions. Bivariate tests revealed significant differences between BMI groups for all pain severity scores and for total pain interference score. On multivariable modelling controlling for age, pain procedure within 45 days prior to pain clinic encounter, opioid prescription with 45 days prior, and diagnosis, obese patients had significantly higher pain severity (as measured by worst, least, average, and current pain in the past 24 hours) as well as higher pain interference (as measured by the overall pain interference score) than normal weight and overweight patients.ConclusionIn our study of pain clinic patients, obesity was found to be associated with increased pain severity and pain interference. We believe that this relationship is multifactorial and bidirectional. Pain phyisicans should consider the impact of obesity when addressing pain management for patients.