bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature effect on compression property of multiaxial warp-knitted composites
Authors: Yang Xiaori , Wang Cong , Gao Xiaoping , Zhu Lvtao , Li Yonggui
Published: November 2019

The wind turbine blades are exposed to various environments all the year round, especially temperature variations during the four seasons. To study the influences of temperatures on the mechanical properties of composite materials, the compression property in the 0°, 45°, and 90° directions of the multiaxial (triaxial and quadaxial) glass fiber warp-knitted composites at −30°C, 0°C, 20°C, and 40°C was analyzed, respectively. The stress–strain curves, strength, modulus, failure strain, and the relationship between strength and temperature were obtained. The results indicated that the compression performance decreased with the increase of temperature, and the effect of temperature on quadaxial composite was more significant than that of the triaxial composite. In addition, the failure mechanisms were also analyzed according to the fracture modes and scanning electron microscopic morphologies of composites.
Spinal cord syndromes in patients with systemic lupus erythematosus: differentiating lupus myelitis, neuromyelitis optica, and multiple sclerosis
Authors: Williams J N , Speyer C B , Kreps D J , Kimbrough D J , Costenbader K , Bhattacharyya S
Published: November 2019

Objective

Non-infectious myelitis in systemic lupus erythematosus (SLE) may be due to SLE myelitis, comorbid multiple sclerosis (MS), or neuromyelitis optica (NMO). We compared characteristics of these three conditions in SLE patients at a large academic institution.

Methods

We searched for neurologic diagnoses of SLE myelitis, NMO myelitis, and MS myelitis among 2297 patients with at least four 1997 American College of Rheumatology revised criteria for SLE between 2000 and 2015. Each subject was reviewed by a neurologist to confirm the underlying neurologic diagnosis. Demographic, clinical, laboratory, and radiographic data were extracted and compared using Fisher's exact test, analysis of variance, and Wilcoxon rank-sum test.

Results

Fifteen of the 2297 subjects with SLE (0.7%) met criteria for a spinal cord syndrome: seven had SLE myelitis, three had AQP4 seropositive NMO, and five had MS. The median SLE Disease Activity Index 2000 score at time of neurologic syndrome presentation was higher in SLE myelitis subjects (8, interquartile range (IQR) 7–16) compared with subjects with NMO (6, IQR 0–14) or MS (2, IQR 0–4), p = 0.02. Subjects with SLE myelitis were also more likely to have elevated anti-dsDNA antibodies at presentation (86%) compared with subjects with NMO (33%) or MS (0%), p = 0.03.

Conclusion

Myelitis occurs rarely among patients with SLE. Compared with subjects with SLE + NMO and subjects with SLE + MS, subjects with SLE myelitis had higher SLE disease activity at presentation.
A Review of State-Level Procedural Guidance for Implementing Multitiered Systems of Support for Behavior (MTSS-B)
Authors: Briesch Amy M. , Chafouleas Sandra M. , Nissen Kristin , Long Stephanie
Published: November 2019

Given the authority of state government over public education, one means of narrowing the best-practice to actual-practice gap in education is by putting forth clear state guidance and recommendations to schools. To date, however, little is known about the national landscape of procedural guidance that is readily available to practitioners looking to implement multitiered systems of support for behavior (MTSS-B). The purpose of the current study was to conduct a systematic review of state department of education websites to understand what guidance is afforded to local education agencies regarding MTSS-B. Results supported that roughly half of the states provided some form of procedural guidance for MTSS-B; however, both the type (e.g., what interventions to use, how often to progress monitor) and level of guidance varied widely. When states did provide behavior-specific guidance, documents were most likely to include specification of what types of interventions and measures to utilize; information less typically focused on assessment such as indications as to how often data should be collected and reviewed or what decision rule(s) should be used to determine student responsiveness. Implications for local implementation and strengthening future state-level guidance for MTSS-B are discussed.
A Data-Driven Approach to Predicting Septic Shock in the Intensive Care Unit
Authors: Yee Christopher R , Narain Niven R , Akmaev Viatcheslav R , Vemulapalli Vijetha
Published: November 2019

Early diagnosis of sepsis and septic shock has been unambiguously linked to lower mortality and better patient outcomes. Despite this, there is a strong unmet need for a reliable clinical tool that can be used for large-scale automated screening to identify high-risk patients. We addressed the following questions: Can a novel algorithm to identify patients at high risk of septic shock 24 hours before diagnosis be discovered using available clinical data? What are performance characteristics of this predictive algorithm? Can current metrics for evaluation of sepsis be improved using novel algorithm? Publicly available data from the intensive care unit setting was used to build septic shock and control patient cohorts. Using Bayesian networks, causal relationships between diagnosis groups, procedure groups, laboratory results, and demographic data were inferred. Predictive model for septic shock 24 hours prior to digital diagnosis was built based on inferred causal networks. Sepsis risk scores were augmented by de novo inferred model and performance was evaluated. A novel predictive model to identify high-risk patients 24 hours ahead of time, with area under curve of 0.81, negative predictive value of 0.87, and a positive predictive value as high as 0.65 was built. The specificity of quick sequential organ failure assessment, systemic inflammatory response syndrome, and modified early warning score was improved when augmented with the novel model, whereas no improvements were made to the sequential organ failure assessment score. We used a data-driven, expert knowledge agnostic method to build a screening algorithm for early detection of septic shock. The model demonstrates strong performance in the data set used and provides a basis for expanding this work toward building an algorithm that is used to screen patients based on electronic medical record data in real time.
Neurofilament light levels are associated with long-term outcomes in multiple sclerosis
Authors: Kuhle Jens , Plavina Tatiana , Barro Christian , Disanto Giulio , Sangurdekar Dipen , Singh Carol M , de Moor Carl , Engle Bob , Kieseier Bernd C , Fisher Elizabeth , Kappos Ludwig , Rudick Richard A , Goyal Jaya
Published: November 2019

Background:

Neurofilament light chain (NfL) is a promising marker of disease activity/treatment response in multiple sclerosis (MS), although its predictive value for long-term clinical outcomes remains unclear.

Objective:

We measured NfL from a phase 3 trial in relapsing-remitting MS and investigated its association with outcomes after 8 and 15 years.

Methods:

NfL concentrations were measured by single molecule array assay in cerebrospinal fluid (CSF) from MS patients ( n = 235) in a 2-year randomized clinical trial (RCT) of intramuscular interferon β-1a, and in serum ( n = 164) from the extension study.

Results:

Year 2 CSF and Year 3 serum NfL were associated with brain parenchymal fraction (BPF) change over 8 years ( p < 0.0001, r = −0.46; p < 0.05. r = −0.36, respectively) and were predictive of reaching Expanded Disability Status Scale (EDSS) ⩾ 6.0 at Year 8 (odds ratio (OR) (upper vs lower tertile) = 3.4; 95% confidence interval (CI) = 1.2–9.9, p < 0.05; OR = 11.0, 95% CI = 2.0–114.6; p < 0.01, respectively). Serum NfL concentration (Year 4) was predictive of reaching EDSS score ⩾6.0 at 15 years (OR (upper vs lower tertile) = 4.9; 95% CI = 1.4–20.4; p < 0.05). NfL concentrations were complementary to 2-year BPF change in predicting long-term outcomes.

Conclusion:

Serum and CSF NfL concentrations were associated with long-term clinical outcomes in MS patients and are promising biomarkers for disease severity stratification supporting treatment decisions.
From headliners to hangovers: Digital media communication in the British rock music festival experience
Authors: Brown Alyssa E , Donne Keith , Fallon Paul , Sharpley Richard
Published: November 2019

Extant tourist experience literature focuses on ‘live’ space and time activity, while pre- and post-components are often neglected despite the opportunities offered by increasing use of digital media communication (DMC). Focusing especially on the pre-festival experience but also addressing peri- and post-phases, this study examines the role of DMC in tourists’ experiences at British rock music festivals. Interviews with festivalgoers revealed three core and inter-related themes: information, emotional response and communitas. Initial engagement with DMC enabled planning, generated feelings of anticipatory excitement and created a sense of communitas. Online activity reduced peri-festival but continued to enhance the live event experience, while the virtual communitas was extended at the post-festival phase.
Factors Affecting Caregivers’ Acceptance of the Use of Wearable Devices by Patients With Dementia: An Extension of the Unified Theory of Acceptance and Use of Technology Model
Authors: Dai Baozhen , Larnyo Ebenezer , Tetteh Ebenezer Ababio , Aboagye Abigail Konadu , Musah Abdul-Aziz Ibn
Published: November 2019

Purpose:

This study aims to examine the factors affecting caregivers’ acceptance of the use of wearable devices by patients with dementia by extending the Unified Theory of Acceptance and Use of Technology (UTAUT) model with 2 additional constructs: resistance to change (RC) and technology anxiety (TA).

Methods:

A structured online questionnaire was developed and distributed to caregivers who have either dealt previously with or were currently taking care of patients with dementia in sub-Saharan Africa. The selection of countries for the study was purely based on the availability of caregivers of patients with dementia and their readiness to take part in the survey. Questionnaire data from 350 respondents were analyzed and the hypothesis tested using partial least squares based on structural equation modeling.

Result:

The results of the extended model show that social influence, effort expectancy, facilitating conditions, and behavioral intention (BI) all had P < .05, thus were statistically significant in explaining the perceived BI and actual use of health-care wearable devices among patients with dementia as reported by caregivers. However, P value for RC and TA was greater than .05, hence were insignificant.
Robust and automatic modeling of tunnel structures based on terrestrial laser scanning measurement
Authors: Xu Xiangyang , Yang Hao , Kargoll Boris
Published: November 2019

The terrestrial laser scanning technology is increasingly applied in the deformation monitoring of tunnel structures. However, outliers and data gaps in the terrestrial laser scanning point cloud data have a deteriorating effect on the model reconstruction. A traditional remedy is to delete the outliers in advance of the approximation, which could be time- and labor-consuming for large-scale structures. This research focuses on an outlier-resistant and intelligent method for B-spline approximation with a rank (R)-based estimator, and applies to tunnel measurements. The control points of the B-spline model are estimated specifically by means of the R-estimator based on Wilcoxon scores. A comparative study is carried out on rank-based and ordinary least squares methods, where the Hausdorff distance is adopted to analyze quantitatively for the different settings of control point number of B-spline approximation. It is concluded that the proposed method for tunnel profile modeling is robust against outliers and data gaps, computationally convenient, and it does not need to determine extra tuning constants.
Introduction: A Literary Studies/Games Studies Conversation
Authors: Hutton Margaret-Anne , Barr Matthew
Published: November 2019

In this special issue of Games and Culture, we present papers originally delivered at the “Literature and Video Games: Beyond Stereotypes” event co-organized by colleagues from the University of St Andrews, the University of Glasgow, and Abertay University. Instead of gesturing toward a summary and synthesis of the published articles, we invite readers to consider these in light of the issues raised in this Introduction, which is itself a very condensed version of many exchanges between the coeditors.
Long-term (>10-year) clinical follow-up after young embolic stroke/TIA of undetermined source
Authors: Nassif M , Annink ME , Yang H , Rettig TCD , Roos YBWEM , van den Brink RBA , Tijssen JGP , Mulder BJM , de Winter RJ , Bouma BJ
Published: November 2019

Background

To date, the pathophysiology of first-ever and recurrent stroke/TIA still remains unclear in young patients with embolic stroke/TIA of undetermined source (ESUS). Clinical studies with long-term follow-up in young ESUS patients are necessary to investigate the underlying pathophysiology of first-ever and recurrent stroke/TIA in this patient population, in particular the role of new-onset atrial fibrillation.

Aims

Our aim was to study the long-term (>10-year) clinical outcome of young patients (<50 years) with ESUS.

Methods

This cohort study included all patients aged ≤ 50 years who underwent transoesophageal echocardiography for diagnostic work-up of ESUS during 1996–2008 from one tertiary center. All patients were contacted by telephone between September–November 2018 to update clinical information from medical records. The clinical outcomes of this study were incidence rates of all-cause and cardiovascular mortality, recurrent stroke/TIA, new-onset clinical AF, and ischemic vascular events.

Results

In total, 108 patients (57% female, mean age 40 ± 7.2 years [range 19–50 years], n = 72 stroke) were included. Across clinical follow-up (median 13[IQR 10–16] years), 24 patients died ( n = 14 cardiovascular). The 15-year incidence rate of recurrent stroke/TIA was 15% (incidence rate = 1.09[95%CI 0.54–1.65]/100 patient-years) and a 5.5% incidence of new-onset clinical AF (incidence rate = 0.44[95%CI 0.09–0.79]/100 patient-years) following ESUS.

Conclusions

The incidence of recurrent stroke/TIA is relatively high during long-term clinical follow-up of young patients with ESUS. In contrast, new-onset clinical AF is relatively low and therefore may not play an important part in the pathophysiology of first-ever and recurrent stroke/TIA of these patients.
Does the public’s confidence in the scientific community affect its willingness to participate in social science research? A test examining the demeanor of survey respondents
Authors: Scheitle Christopher P
Published: November 2019

Research examining the consequences of the public’s confidence in the scientific community has primarily focused on the natural or medical sciences. It is not clear whether the public’s confidence in the scientific community has implications for research and practice in the social sciences. To begin examining this question, this study assesses whether survey respondents’ confidence in the scientific community is associated with their demeanor during the survey interview. This is consequential because respondent demeanor itself has been associated with survey refusal and nonresponse to items within surveys. Analysis of the 2004–2016 General Social Survey finds that individuals expressing more confidence in the scientific community are rated as having more positive demeanors by interviewers. Respondents’ confidence in other types of institutions does not show the same association, suggesting that confidence in the scientific community is uniquely associated with respondents’ demeanor during the interview. These findings suggest that the public’s confidence in science could have implications for at least survey-based social science research.
Koryakite, NaKMg2Al2(SO4)6, a new NASICON-related anhydrous sulfate mineral from Tolbachik volcano, Kamchatka, Russia
Authors: Siidra Oleg I. , Nazarchuk Evgeny V. , Zaitsev Anatoly N. , Vlasenko Natalia S.
Published: November 2019

Exhalative mineral assemblages from fumaroles of Tolbachik volcano are very rich in anhydrous sulfate minerals of alkali and transition metals. Koryakite, ideally NaKMg2Al2(SO4)6, was found in the Yadovitaya fumarole of the Second scoria cone of the North Breach of the Great Tolbachik Fissure Eruption (1975–1976), Tolbachik volcano, Kamchatka Peninsula, Russia. Koryakite occurs as a product of fumarolic activity and closely associates with euchlorine and langbeinite. Koryakite is trigonal, R$\bar{3}$, a = 8.1124(11), c = 22.704(7) Å and V = 1294.0(5) Å3. The chemical composition determined by electron-microprobe analysis is (wt.%): Na2O 4.27, K2O 5.85, ZnO 0.31, СaO 0.31, CuO 0.76, MgO 10.15, Al2O3 11.47, Fe2O3 2.73, SO3 64.33 and SiO2 0.13, total 100.31. The empirical formula calculated on the basis of 24 O apfu is Na1.03K0.93(Mg1.89Cu0.07Ca0.04Zn0.03)Σ2.03(Al1.68Fe3+0.26)Σ1.94(S6.02Si0.02)Σ6.04O24. No natural or synthetic chemical analogues of koryakite are known to date. The topology of the [M2+2M3+2(SO4)6]2– heteropolyhedral framework in koryakite is very similar to the one in millosevichite, Al2(SO4)3 and mikasaite, Fe3+2(SO4)3. Replacement of part of the trivalent cations in the [M3+2(SO4)3]0 framework by divalent cations gives the framework a negative charge for koryakite and allows the incorporation of the alkali species in the channels. This structural mechanism is reminiscent of the concept of stuffed derivative structures. Koryakite is also structurally related to synthetic NaMgFe3+(SO4)3 and to the broader family of NASICON-related phases.
An immunoevasive strategy through clinically-relevant pan-cancer genomic and transcriptomic alterations of JAK-STAT signaling components
Authors: Chang Wai Hoong , Lai Alvina G.
Published: November 2019

Background

Since its discovery almost three decades ago, the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway has paved the road for understanding inflammatory and immunity processes related to a wide range of human pathologies including cancer. Several studies have demonstrated the importance of JAK-STAT pathway components in regulating tumor initiation and metastatic progression, yet, the extent of how genetic alterations influence patient outcome is far from being understood.

Methods

Focusing on 133 genes involved in JAK-STAT signaling, we investigated genomic, transcriptomic and clinical profiles of over 18,000 patients representing 21 diverse cancer types. We identified a core set of 28 putative gain- or loss-of-function JAK-STAT genes that correlated with survival outcomes using Cox proportional hazards regression and Kaplan-Meier analyses. Differential expression analyses between high- and low-expressing patient groups were performed to evaluate the consequences of JAK-STAT misexpression.

Results

We found that copy number alterations underpinning transcriptional dysregulation of JAK-STAT pathway genes differ within and between cancer types. Integrated analyses uniting genomic and transcriptomic datasets revealed a core set of JAK-STAT pathway genes that correlated with survival outcomes in brain, renal, lung and endometrial cancers. High JAK-STAT scores were associated with increased mortality rates in brain and renal cancers, but not in lung and endometrial cancers where hyperactive JAK-STAT signaling is a positive prognostic factor. Patients with aberrant JAK-STAT signaling demonstrated pan-cancer molecular features associated with misexpression of genes in other oncogenic pathways (Wnt, MAPK, TGF-β, PPAR and VEGF). Brain and renal tumors with hyperactive JAK-STAT signaling had increased regulatory T cell gene (Treg) expression. A combined model uniting JAK-STAT and Tregs allowed further delineation of risk groups where patients with high JAK-STAT and Treg scores consistently performed the worst.

Conclusion

Providing a pan-cancer perspective of clinically-relevant JAK-STAT alterations, this study could serve as a framework for future research investigating anti-tumor immunity using combination therapy involving JAK-STAT and immune checkpoint inhibitors.
A Tunable Dual-Band and Polarization-Insensitive Coherent Perfect Absorber Based on Double-Layers Graphene Hybrid Waveguide
Authors: Luo Xin , Cheng Zi-Qiang , Zhai Xiang , Liu Zhi-Min , Li Si-Qi , Liu Jian-Ping , Wang Ling-Ling , Lin Qi , Zhou Yan-Hong
Published: November 2019

A suspended monolayer graphene has only about 2.3% absorption rate in visible and infrared band, which limits its optoelectronic applications. To significantly increase graphene’s absorption efficiency, a tunable dual-band and polarization-insensitive coherent perfect absorber (CPA) is proposed in the mid-infrared regime, which contains the silicon array coupled in double-layers graphene waveguide. Based on the FDTD methods, dual-band perfect absorption peaks are achieved in 9611 nm and 9924 nm, respectively. Moreover, due to its center symmetric feature, the proposed absorber also demonstrates polarization-insensitive. Meanwhile, the coherent absorption peaks can be all-optically modulated by altering the relative phase between two reverse incident lights. Furthermore, by manipulating the Fermi energies of two graphene layers, two coherent absorption peaks can move over a wide spectrum range, and our designed CPA can also be changed from dual-band CPA to narrowband CPA. Thus, our results can find some potential applications in the field of developing nanophotonic devices with excellent performance working at the mid-infrared regime.
A binning tool to reconstruct viral haplotypes from assembled contigs
Authors: Chen Jiao , Shang Jiayu , Wang Jianrong , Sun Yanni
Published: November 2019

Background

Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed.

Results

We developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction.

Conclusions

In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. It competes favorably with other tools on viral contig binning. The source codes are available at:https://github.com/chjiao/VirBin.
Predictive modelling using pathway scores: robustness and significance of pathway collections
Authors: Segura-Lepe Marcelo P. , Keun Hector C. , Ebbels Timothy M. D.
Published: November 2019

Background

Transcriptomic data is often used to build statistical models which are predictive of a given phenotype, such as disease status. Genes work together in pathways and it is widely thought that pathway representations will be more robust to noise in the gene expression levels. We aimed to test this hypothesis by constructing models based on either genes alone, or based on sample specific scores for each pathway, thus transforming the data to a ‘pathway space’. We progressively degraded the raw data by addition of noise and examined the ability of the models to maintain predictivity.

Results

Models in the pathway space indeed had higher predictive robustness than models in the gene space. This result was independent of the workflow, parameters, classifier and data set used. Surprisingly, randomised pathway mappings produced models of similar accuracy and robustness to true mappings, suggesting that the success of pathway space models is not conferred by the specific definitions of the pathway. Instead, predictive models built on the true pathway mappings led to prediction rules with fewer influential pathways than those built on randomised pathways. The extent of this effect was used to differentiate pathway collections coming from a variety of widely used pathway databases.

Conclusions

Prediction models based on pathway scores are more robust to degradation of gene expression information than the equivalent models based on ungrouped genes. While models based on true pathway scores are not more robust or accurate than those based on randomised pathways, true pathways produced simpler prediction rules, emphasizing a smaller number of pathways.
ProTstab – predictor for cellular protein stability
Authors: Yang Yang , Ding Xuesong , Zhu Guanchen , Niroula Abhishek , Lv Qiang , Vihinen Mauno
Published: November 2019

Background

Stability is one of the most fundamental intrinsic characteristics of proteins and can be determined with various methods. Characterization of protein properties does not keep pace with increase in new sequence data and therefore even basic properties are not known for far majority of identified proteins. There have been some attempts to develop predictors for protein stabilities; however, they have suffered from small numbers of known examples.

Results

We took benefit of results from a recently developed cellular stability method, which is based on limited proteolysis and mass spectrometry, and developed a machine learning method using gradient boosting of regression trees. ProTstab method has high performance and is well suited for large scale prediction of protein stabilities.

Conclusions

The Pearson’s correlation coefficient was 0.793 in 10-fold cross validation and 0.763 in independent blind test. The corresponding values for mean absolute error are 0.024 and 0.036, respectively. Comparison with a previously published method indicated ProTstab to have superior performance. We used the method to predict stabilities of all the remaining proteins in the entire human proteome and then correlated the predicted stabilities to protein chain lengths of isoforms and to localizations of proteins.
Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection
Authors: Ma Xuelian , Zhao Xiaomin , Wang Kaili , Tang Xiaoyi , Guo Jianxiong , Mi Mi , Qi Yanping , Chang Lingling , Huang Yong , Tong Dewen
Published: November 2019

Background

Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown.

Results

In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML).

Conclusions

The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.
Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation
Authors: Fonseca-García Citlali , Zayas Alejandra E. , Montiel Jesús , Nava Noreide , Sánchez Federico , Quinto Carmen
Published: November 2019

Background

Reactive oxygen species (ROS) are generated by NADPH oxidases known as respiratory burst oxidase homologs (RBOHs) in plants. ROS regulate various cellular processes, including the mutualistic interactions between legumes and nitrogen-fixing bacteria or arbuscular mycorrhizal (AM) fungi.Rbohis a multigene family comprising nine members (RbohA–I) in common bean (Phaseolus vulgaris).The RNA interference-mediated silencing ofRbohB(PvRbohB-RNAi) in this species diminished its ROS production and greatly impaired nodulation. By contrast, thePvRbohB-RNAi transgenic roots showed early hyphal root colonization with enlarged fungal hypopodia; therefore, we proposed thatPvRbohBpositively regulates rhizobial infection (Rhizobium tropici) and inhibits AM colonization byRhizophagus irregularisinP. vulgaris.

Results

To corroborate this hypothesis, an RNA-Seq transcriptomic analysis was performed to identify the differentially expressed genes in thePvRbohB-RNAi roots inoculated withRhizobium tropiciorRhizophagus irregularis. We found that, in the early stages, root nodule symbioses generated larger changes of the transcriptome than did AM symbioses inP. vulgaris. Genes related to ROS homeostasis and cell wall flexibility were markedly upregulated in the early stages of rhizobial colonization, but not during AM colonization. Compared with AM colonization, the rhizobia induced the expression of a greater number of genes encoding enzymes involved in the metabolism of auxins, cytokinins, and ethylene, which were typically repressed in thePvRbohB-RNAi roots.

Conclusions

Our research provides substantial insights into the genetic interaction networks in the early stages of rhizobia and AM symbioses withP. vulgaris, as well as the differential roles thatRbohBplays in processes related to ROS scavenging, cell wall remodeling, and phytohormone homeostasis during nodulation and mycorrhization in this legume.
The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination
Authors: Qu Chunpu , Zhao Hancheng , Chen Jinyuan , Zuo Zhuang , Sun Xue , Huang Jiahuan , Yang Chengjun , Zhang Xiuli , Zhang Peng , Quan Xiankui , Xu Zhiru , Liu Guanjun
Published: November 2019

Background

Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear.

Results

In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events.

Conclusions

Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans
Authors: Wallner Adrian , King Eoghan , Ngonkeu Eddy L. M. , Moulin Lionel , Béna Gilles
Published: November 2019

Background

Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential.

Results

We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence.

Conclusion

Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.
Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record
Authors: Hughey Jacob J. , Rhoades Seth D. , Fu Darwin Y. , Bastarache Lisa , Denny Joshua C. , Chen Qingxia
Published: November 2019

Background

The growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinical data are generally longitudinal, standard approaches for detecting genotype-phenotype associations in such linked data, notably logistic regression, do not naturally account for variation in the period of follow-up or the time at which an event occurs. Here we explored the advantages of quantifying associations using Cox proportional hazards regression, which can account for the age at which a patient first visited the healthcare system (left truncation) and the age at which a patient either last visited the healthcare system or acquired a particular phenotype (right censoring).

Results

In comprehensive simulations, we found that, compared to logistic regression, Cox regression had greater power at equivalent Type I error. We then scanned for genotype-phenotype associations using logistic regression and Cox regression on 50 phenotypes derived from the EHRs of 49,792 genotyped individuals. Consistent with the findings from our simulations, Cox regression had approximately 10% greater relative sensitivity for detecting known associations from the NHGRI-EBI GWAS Catalog. In terms of effect sizes, the hazard ratios estimated by Cox regression were strongly correlated with the odds ratios estimated by logistic regression.

Conclusions

As longitudinal health-related data continue to grow, Cox regression may improve our ability to identify the genetic basis for a wide range of human phenotypes.
Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas
Authors: Chen Mao-Sheng , Zhao Mei-Li , Wang Gui-Juan , He Hui-Ying , Bai Xue , Pan Bang-Zhen , Fu Qian-Tang , Tao Yan-Bin , Tang Ming-Yong , Martínez-Herrera Jorge , Xu Zeng-Fu
Published: November 2019

Background

In higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture inJatropha curcasL., a perennial woody plant belonging to Euphorbiaceae.

Results

Two inflorescence branching mutants were identified in germplasm collection ofJatropha.Theduo xiao hua(dxh) mutant has a seven-order branch inflorescence, and thegynoecy(g) mutant has a three-order branch inflorescence, while WTJatrophahas predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them,Jatropha ADENOSINE KINASE 2(JcADK2),ADENINE PHOSPHORIBOSYL TRANSFERASE 1(JcAPT1),CYTOKININ OXIDASE 3(JcCKX3),ISOPENTENYLTRANSFERASE 5(JcIPT5),LONELY GUY 3(JcLOG3) andJcLOG5may participate in cytokinin metabolic pathway inJatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching inJatropha. In addition, comparative transcriptome analysis showed thatArabidopsishomologous genesJatropha AGAMOUS-LIKE 6(JcAGL6),JcAGL24,FRUITFUL(JcFUL),LEAFY(JcLFY),SEPALLATAs(JcSEPs),TERMINAL FLOWER 1(JcTFL1), andWUSCHEL-RELATED HOMEOBOX 3(JcWOX3), were differentially expressed in inflorescence buds betweendxhandgmutants and WT plants, indicating that they may participate in inflorescence development inJatropha. The expression ofJcTFL1was downregulated, while the expression ofJcLFYandJcAP1were upregulated in inflorescences in low-branchgmutant.

Conclusions

Cytokinin is an important regulator in controlling inflorescence branching inJatropha.The regulation of inflorescence architecture by the genes involved in floral development, includingTFL1,LFYandAP1, may be conservative inJatrophaandArabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture inJatropha.
Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process
Authors: Yuan Huwei , Chen Juanjuan , Yang Ying , Shen Chenjia , Xu Dongbin , Wang Junfeng , Yan Daoliang , He Yi , Zheng Bingsong
Published: November 2019

Background

Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level.

Results

A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process.

Conclusions

Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.
Associations between health-related quality of life, physical function and pain in older women with osteoporosis and vertebral fracture
Authors: Stanghelle Brita , Bentzen Hege , Giangregorio Lora , Pripp Are Hugo , Bergland Astrid
Published: November 2019

Background

Osteoporosis and vertebral fractures represent a major health burden worldwide, and the prevalence of osteoporosis is expected to increase as the world’s population ages. Suffering from vertebral fracture has a substantial impact on the individual’s health-related quality of life (HRQoL), physical function and pain. Complex health challenges experienced by older people with osteoporosis and vertebral fractures call for identification of factors that may influence HRQoL, as some of these factors may be modifiable. The objective is to examine the independent associations between HRQoL, physical function and pain in older women with osteoporosis and vertebral fracture.

Methods

This study has a cross-sectional design, using data from 149 home-dwelling Norwegian women with osteoporosis and vertebral fracture, aged 65+. Data on HRQoL (Short Form 36 (SF-36), Quality of Life Questionnaire of the European Foundation for Osteoporosis (QUALEFFO-41)), physical function (walking speed, balance and strength), pain, as well as sociodemographic information were collected. Simple linear regression analyses were conducted and multivariable regression models were fitted to investigate the associations.

Results

Lower levels of HRQoL were significantly associated with lower levels of physical function, measured by walking speed, and higher levels of pain. Pain was significantly associated with all of the subscales in SF-36, with the exception of Mental Health and Mental Component Score, and all the subscales of QUALEFFO-41. Walking speed was significantly associated with 5 of 8 subscales of SF-36 (except Bodily Pain, Vitality, Mental Health and Mental Component Score), and with 4 of 6 subscales of QUALEFFO-41 (except Score Pain and Mood).

Conclusion

This study shows that pain and walking speed were, independently of one another, associated with HRQoL in older women with osteoporosis and vertebral fracture. These findings can inform clinicians and health managers about the importance of pain management and exercise interventions in health care for this group. Future research should address interventions targeting both physical function and pain with HRQoL as an outcome.

Registration

ClincialTrials.gov Identifier: NCT02781974. Registered 18.05.16. Retrospectively registered.
Co-occurrence of human papillomavirus (HPV) in newborns and their parents
Authors: Skoczyński Mariusz , Goździcka-Józefiak Anna , Kwaśniewska Anna
Published: November 2019

Background

The potential HPV transmission route includes horizontal transmission “in utero” and vertical transmission from parents. Less is known about the role of child’s father as a potential source of HPV infection and involved in the pathogen’s epidemic chain. A possible consequence of perinatal infection includes HPV-related childhood diseases and carrying the risk of cervical cancer development in female offspring. In view of the evidence, studies of HPV co-occurrence in one or both parents and their offspring seem vital for the implementation of respective preventive measures. Consequently, the aim of this study was to determine the incidence of common HPV 16/18 infections in newborns and their parents, and to assess its role of the periconceptional transmission.

Methods

To determine the incidence of common HPV infections in newborns from single pregnancies and their parents. The study included 146 pregnant women, as well as their partners, and newborns. They were tested for the presence of HPV 16/18 DNA using the PCR method. HPV types 16 and/or 18 were identified using type-specific PCR primers. The quality of the extracted DNA was evaluated by PCR using PC03/PC04 β-globin-specific primers. The relationship between the presence of neonatal and parental HPV infection was analyzed using a multivariable regression model. Calculations were carried out with the Statistica 10.

Results

The presence of HPV DNA was detected in 19 (13,01%) newborns, 28 (19,18%) mothers, and 20 (13,7%) fathers. The viral DNA was detected in 14 newborns delivered by HPV-positive mothers (OR = 26,08; CI: 8,07-84,31, p < 0.001), 12 descendants of HPV-positive fathers (OR = 22,13; CI: 6,97-70,27, p < 0.001), and 10 children originating from two infected parents (OR = 24,20; CI: 6,84–85,57 p < 0.001). Those findings points to a increase risk of an acquired infection in newborns with HPV-positive parents.

Conclusion

Our findings suggest the possible role of the periconceptional transmission in the mode of acquired HPV 16/18 infections.