bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leishmania infection induces a limited differential gene expression in the sand fly midgut
Authors: Coutinho-Abreu Iliano V. , Serafim Tiago D. , Meneses Claudio , Kamhawi Shaden , Oliveira Fabiano , Valenzuela Jesus G. 
Published: August 2020

Abstract
Background: Sand flies are the vectors of Leishmania parasites. To develop in the sand fly midgut, Leishmania multiplies and undergoes various stage differentiations giving rise to the infective form, the metacyclic promastigotes. To determine the changes in sand fly midgut gene expression caused by the presence of Leishmania, we performed RNA-Seq of uninfected and Leishmania infantum-infected Lutzomyia longipalpis midguts from seven different libraries corresponding to time points which cover the various Leishmania developmental stages. Results: The combined transcriptomes resulted in the de novo assembly of 13,841 sand fly midgut transcripts. Importantly, only 113 sand fly transcripts, about 1%, were differentially expressed in the presence of Leishmania parasites. Further, we observed distinct differentially expressed sand fly midgut transcripts corresponding to the presence of each of the various Leishmania stages suggesting that each parasite stage influences midgut gene expression in a specific manner. Two main patterns of sand fly gene expression modulation were noted. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> 32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 2 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by Leishmania infection with small fold changes (< 32 fold). The molecular functions of these genes have been associated with the metabolism of lipids and detoxification of xenobiotics. Conclusion: Overall, our data suggest that the presence of Leishmania produces a limited change in the midgut transcript expression profile in sand flies. Further, Leishmania modulates sand fly gene expression early on in the developmental cycle in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points where a massive number of parasites in the anterior midgut results only in modest changes in midgut gene expression.
Multi-tissue transcriptome analysis using hybrid-sequencing reveals potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (Azadirachta indica)&nbsp;
Authors: Wang Huiyan , Wang Ning , Huo Yixin 
Published: August 2020

Abstract
Background: Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which is not an eco-friendly and sustainable process. The low yield and discontinuous supply of azadirachtin A impedes further applications. The biosynthetic pathway of azadirachtin A is still unknown and is the focus of our study. Results: We attempted to explore azadirachtin A biosynthetic pathway and identified the key genes involved by analyzing transcriptome data from five neem tissues through the hybrid-sequencing (Illumina HiSeq and Pacific Biosciences Single Molecule Real-Time (SMRT)) approach. Candidates were first screened by comparing the expression levels between the five tissues. After phylogenetic analysis, domain prediction, and molecular docking studies, 22 candidates encoding 2,3-oxidosqualene cyclase (OSC), alcohol dehydrogenase, cytochrome P450 (CYP450), acyltransferase, and esterase were proposed to be potential genes involved in azadirachtin A biosynthesis. Among them, two unigenes encoding homologs of MaOSC1 and MaCYP71CD2 were identified. A unigene encoding the complete homolog of MaCYP71BQ5 was reported. Accuracy of the assembly was verified by quantitative real-time PCR (qRT-PCR) and full-length PCR cloning. Conclusions: By integrating and analyzing transcriptome data from hybrid-seq technology, 22 differentially expressed genes (DEGs) were finally selected as candidates involved in azadirachtin A pathway. The obtained reliable and accurate sequencing data provided important novel information for understanding neem genome. Our data shed new light on understanding the biosynthesis of other triterpenoids in neem trees and provides a reference for exploring other valuable natural product biosynthesis in plants.
Defining pain and interference recovery trajectories after acute non-catastrophic musculoskeletal trauma through Growth Mixture Modeling&nbsp;
Authors: Lee Joshua , Walton David M. , Tremblay Paul , May Curtis , Millard Wanda , Elliott James M. , MacDermid Joy C. 
Published: August 2020

Abstract
BackgroundRecovery trajectories support early identification of delayed recovery and can inform personalized management or phenotyping of risk profiles in patients. The objective of this study was to investigate the trajectories in pain severity and functional interference following non-catastrophic musculoskeletal (MSK) trauma in an international, mixed injury sample. MethodsA prospective longitudinal cohort (n= 241) was formed from patients identified within four weeks of trauma, from attendance at emergency or urgent care centres located in London, ON, Canada, or Chicago, IL, USA. Pain interference was measured via the Brief Pain Inventory (London cohort) or the Neck Disability Index (Chicago cohort). Pain severity was captured in both cohorts using the numeric pain rating scale. Growth mixture modeling and RM repeated measures ANOVA approaches identified distinct trajectories of recovery within pain interference and pain severity data. ResultsFor pain interference, the three trajectories were labeled accordingly: Class 1 = Rapid recovery (lowest intercept, full or near full recovery by 3 months, 32.0% of the sample); Class 2 = Delayed recovery (higher intercept, recovery by 12 months, 26.7% of the sample); Class 3 = Minimal or no recovery (higher intercept, persistently high interference scores at 12 months, 41.3% of the sample). For pain severity, the two trajectories were labeled: Class 1 = Rapid recovery (lower intercept, recovery by 3 months, 81.3% of the sample); and Class 2 = Minimal or no recovery (higher intercept, flat curve, 18.7% of the sample). The “Minimal or No Recovery” trajectory could be predicted by female sex and axial (vs. peripheral) region of trauma with 74.3% accuracy across the 3 classes for the % Interference outcome. For the Pain Severity outcome, only region (axial trauma, 81.3% accuracy) predicted the “Minimal or No Recovery” trajectory. ConclusionsThese results suggest that three meaningful recovery trajectories can be identified in an international, mixed-injury sample when pain interference is the outcome, and two recovery trajectories emerge when pain severity is the outcome. Females in the sample or people who suffered axial injuries (head, neck, or low back) were more likely to be classed in poor outcome trajectories. Trial registrationNational Institutes of Health - clinicaltrials.gov (NCT02711085; Retrospectively registered Mar 17, 2016)
Aortic stiffness and central hemodynamics in treatment naïve HIV infection: A cross-sectional study.
Authors: Martínez-Ayala Pedro , Alanis-Sánchez Guillermo Adrian , Gonzalez-Hernández Luz Alicia , Álvarez-Zavala Monserrat , Cabrera-Silva Rodolfo Ismael , Andrade-Villanueva Jaime Federico , Sánchez-Reyes Karina , Ramos-Solano Moisés , Castañeda-Zaragoza Diego Alberto , Cardona-Müller David , Tostuka-Sutto Sylvia , Cardona-Muñoz Ernesto , Ramos-Becerra Carlos Gerardo 
Published: August 2020

Abstract
Background: Human immunodeficiency virus (HIV) infection is associated with a greater risk of cardiovascular disease (CVD). HIV infection causes a chronic inflammatory state and increases oxidative stress which can cause endothelial dysfunction and arterial stiffness. Aortic stiffness measured by carotid femoral-pulse wave velocity (cfPWV) and central hemodynamics are independent cardiovascular risk factors and have the prognostic ability for CVD. We assessed cfPWV and central hemodynamics in young individuals with recent HIV infection diagnosis and without antiretroviral therapy. We hypothesized that individuals living with HIV would present greater cfPWV and central hemodynamics (central systolic blood pressure and pulse pressure) compared to uninfected controls.Methods. We recruited 51 treatment-naïve individuals living with HIV (HIV(+)) without previous CVD and 51 age- and sex-matched controls (HIV negative (-)). We evaluated traditional CVD risk factors including metabolic profile, blood pressure (BP), smoking, HIV viral load, and CD4+ T-cells count. Arterial stiffness and central hemodynamics were evaluated by cfPWV, central systolic BP, and central pulse pressure (cPP) via applanation tonometry.Results. HIV(+) individuals presented a greater prevalence of smoking, reduced high-density lipoprotein cholesterol, and body mass index. 65.9% of HIV(+) individuals exhibited lymphocyte CD4+ T-cells count <500 cells/µL. There was no difference in brachial or central BP between groups; however, HIV(+) individuals showed significantly lower cPP. We observed a greater cfPWV (mean difference= 0.5 m/s; p<0.01) in HIV(+) compared to controls, even after adjusting for heart rate, mean arterial pressure and smoking.Conclusion: In the early stages of infection, non-treated HIV individuals present a greater prevalence of traditional CVD risk factors, arterial stiffness, and normal or in some cases central hemodynamics.
Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori&nbsp;BmN4 cell line
Authors: Levin Michal , Scheibe Marion , Butter Falk 
Published: August 2020

Abstract
BackgroundThe process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-Seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. ResultsCombining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6,200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. ConclusionsWe show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.
Point prevalence mapping reveals hotspot for onchocerciasis transmission in the Ndikinimeki Health District (Centre Region, Cameroon)
Authors: Aza’ah Afor René , Sumo Laurentine , Ntonifor Ngum Helen , Bopda Jean , Heumou Rolph Bamou , Djeunga Hugues Nana 
Published: August 2020

Abstract
Background

Ivermectin-based preventive chemotherapy (PC) is distributed annually to all at-risk individuals to control and/or eliminate onchocerciasis. Information on the impact of mass ivermectin administration on onchocerciasis transmission are scanty, and it is tricky to appreciate the progress towards elimination and engage corrective measures. To fill that gap in the Centre Region in Cameroon, the current onchocerciasis endemicity level in the Ndikinimeki Health District after about two decades of mass treatments was assessed.

Methods

A cluster-based cross-sectional survey was carried out in the Ndikinimeki Health District and all volunteers aged ≥5 years were (i) interviewed on their compliance to ivermectin over the past five years and (ii) underwent clinical (nodule palpation and visual search for onchocercal lesions) and parasitological examinations (skin snip) for onchocerciasis.

Results

The overall Onchocerca volvulus prevalence was 7.0% (95% CI: 5.2-9.3). The prevalence of the disease was significantly higher in the communities Kiboum 1 and Kiboum 2 compared to the other communities (highest prevalence in Makénéné Town Water: 8.5%; 95% CI: 2.3-20.4) (χ2 = 51.314, df = 11, P = 0.0001). The proportion of systematic non-compliers to ivermectin was 23.3% (95% CI: 19.9-27.1) among individuals interviewed. In the sentinel sites (Kiboum communities), onchocerciasis prevalence decreased from 95.2% (95% CI: 88.3-98.1) to 23.7% (95% CI: 14.7-36.0).

Conclusions

This study has revealed that the Ndikinimeki Health District is hypo-endemic for onchocerciasis after about two decades of preventive chemotherapy. However, transmission is ongoing, with a potential hotspot in the Kiboum 1 and Kiboum 2 communities, which are known as first-line communities (closest to the breeding sites of the vector). Alternative or complementary strategies to annual ivermectin appear compulsory to accelerate the momentum towards onchocerciasis elimination.
Validation of Coronal Mass Ejection Arrival-Time Forecasts by Magnetohydrodynamic Simulations based on Interplanetary Scintillation Observations
Authors: Iwai Kazumasa , Shiota Daikou , Tokumaru Munetoshi , Fujiki Ken'ichi , Den Mitsue , Kubo Yûki 
Published: August 2020

Abstract
Coronal mass ejections (CMEs) cause various disturbances of the space environment; therefore, forecasting their arrival time is very important. However, forecasting accuracy is hindered by limited CME observations in interplanetary space. This study investigates the accuracy of CME arrival times at the Earth forecasted by three-dimensional (3D) magnetohydrodynamic (MHD) simulations based on interplanetary scintillation (IPS) observations. In this system, CMEs are approximated as spheromaks with various initial speeds. Ten MHD simulations with different CME initial speed are tested, and the density distributions derived from each simulation run are compared with IPS data observed by the Institute for Space-Earth Environmental Research (ISEE), Nagoya University. The CME arrival time of the simulation run that most closely agrees with the IPS data is selected as the forecasted time. We then validate the accuracy of this forecast using 12 halo CME events. The average absolute arrival-time error of the IPS-based MHD forecast is approximately 5.0 h, which is one of the most accurate predictions that ever been validated, whereas that of MHD simulations without IPS data, in which the initial CME speed is derived from white-light coronagraph images, is approximately 6.7 h. This suggests that the assimilation of IPS data into MHD simulations can improve the accuracy of CME arrival-time forecasts. The average predicted arrival times are earlier than the actual arrival times. These early predictions may be due to overestimation of the magnetic field included in the spheromak and/or underestimation of the drag force from the background solar wind, the latter of which could be related to underestimation of CME size or background solar wind density.
Imaging biomarkers of contrast-enhanced computed tomography predict survival in oesophageal cancer after definitive concurrent chemoradiotherapy
Authors: Zeng Chengbing , Zhai Tiantian , Chen Jianzhou , Guo Longjia , Huang Baotian , Guo Hong , Liu Guozhi , Zhuang Tingting , Liu Weitong , Luo Ting , Wu Yanxuan , Peng Guopeng , Li Derui , Chen Chuangzhen 
Published: August 2020

Abstract
Background: This study aimed to evaluate the predictive potential of contrast-enhanced computed tomography (CT)-based imaging biomarkers (IBMs) for the treatment outcomes of oesophageal squamous cell carcinoma (OSCC) patients after definitive concurrent chemoradiotherapy (CCRT). Methods: Altogether, 154 patients with OSCC who underwent definitive CCRT were included in this retrospective study. All patients were separated randomly to a training cohort (n=99) and the validation cohort (n=55). Pre-treatment contrast-enhanced CT scans were obtained for all patients and used for the extraction of IBMs. An IBM score was constructed by using the least absolute shrinkage and selection operator with Cox regression analysis in the training cohort and tested in the validation cohort. IBM nomograms were built based on IBM scores for individualized survival estimation. Finally, a decision curve analysis was performed to estimate the clinical usefulness of the nomograms. Results: Altogether, 96 IBMs were extracted from each contrast-enhanced CT scan. The IBM score constructed by 11 CT-based IBMs, using LASSO-Cox regression method in training cohort. The multivariate analysis revealed that IBM score was the independent prognostic factor correlated with overall survival (OS) and progression-free survival (PFS). In the training cohort, the C-indices of IBM scores were 0.734 (95%CI, 0.664–0.804) and 0.678 (95%CI, 0.607–0.745) for OS and PFS, respectively. In the validation cohort, C-indices were 0.672 (95%CI, 0.578–0.766) and 0.662 (95%CI, 0.573–0.751) for OS and PFS, respectively. Kaplan-Meier survival analysis showed significantly different between risk subgroups in training and validation cohort. The decision curve showed the clinical usefulness of IBM score. Conclusions: The IBM score based on pre-treatment contrast-enhanced CT could predict the OS and PFS for patients with OSCC after definitive CCRT. Further multicentre studies with larger sample sizes are warranted.
Better muscle strength can decrease the risk of arthralgia and back &amp; joint stiffness in Kurdish men; a cross-sectional study using data from RaNCD cohort study
Authors: Pasdar Yahya , Hamzeh Behrooz , Moradi Shima , Najafi Farid , Moradinazar Mehdi , Shamsi Mohammadbagher , Shakiba Ebrahim 
Published: August 2020

Abstract
Background

Musculoskeletal disorders can reduce the quality of life and work capacity. In this study, we found that better muscle strength could prevent musculoskeletal pain, including arthralgia and back & joint stiffness. The study assessed handgrip strength (HGS) in relation to low back pain and arthralgia in Kurdish men.

Methods

This cross-sectional study was conducted using data from Ravansar non-communicable diseases (RaNCD) cohort study on 2164 men aged 35-65 years. HGS was measured using a hand-held hydraulic hand grip dynamometer. Low back pain, arthralgia, and joint stiffness were evaluated by the RaNCD cohort study physician using a standard questionnaire.

Results

The results showed that 21.39% and 24.58% of studied participants had low back pain and arthralgia, respectively. Among the participants with low back pain, 14.5% had back stiffness, and among those with arthralgia, 12.8% had joint stiffness. The mean of HGS in participants with arthralgia and back & joint stiffness was significantly less than those without these disorders (P<0.001, P=0.05, and P= 0.005, respectively). Multiple-adjusted OR and 95% confidence intervals (CI) for arthralgia and back and joint stiffness across muscle strength showed the HGS increase to be associated with a lower risk of arthralgia and back &joint stiffness, but not low back pain.

Conclusions

Our results highlighted that higher HGS was associated with a lower risk of arthralgia and back & joint stiffness. However, there was no association between HGS and low back pain. Exercise and adherence to proper nutrition are suggested to enhance muscle strength in order to reduce musculoskeletal pain.
Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year
Authors: Dang Hanli , Zhang Tao , Li Guifang , Mu Yudi , Lv Xinhua , Wang Zhongke , Zhuang Li 
Published: August 2020

Abstract
Background The dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites. Results In this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1–3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1–3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2,432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium. Conclusions This study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.