bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies
Authors: Han Tianyu , Li Mimi , Li Jiawei , Lv Han , Ren Bingru , Chen Jian , Li Weilin 
Published: October 2019

AbstractBackgroundSomeGynuraspecies have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genusGynuraand the relationship of the genusGynurawith other genera in the tribe Senecioneae need further research.ResultsThe chloroplast genomes of 4Gynuraspecies were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, theGynurachloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the generaGynura,DendrosenecioandLigularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Sevenndhgenes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldestArtemisiapollen fossil, the divergence time was estimated.ConclusionsSequencing the chloroplast genomes of 4Gynuraspecies helps us to solve many problems. The phylogenetic relationships and divergence time among 4Gynuraand 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the generaGynuraandLigulariawas different from that observed previous work. In a previous phylogenetic tree, the genusLigulariabelonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.
Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches
Authors: Lampert Niclas , Mikaelyan Aram , Brune Andreas 
Published: October 2019

AbstractBackgroundDiet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter.ResultsThe physicochemical conditions determined with microsensors in the guts ofErgaula capucina,Pycnoscelus surinamensis, andByrsotria rothiwere similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop ofB. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites.ConclusionOur results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.
Mild water stress-induced priming enhance tolerance to Rosellinia necatrix in susceptible avocado rootstocks
Authors: Martínez-Ferri E. , Moreno-Ortega G. , van den Berg N. , Pliego C. 
Published: October 2019

Abstract

Background
White root rot (WRR) disease caused by Rosellinia necatrix is one of the most important threats affecting avocado orchards in temperate regions. The eradication of WRR is a difficult task and environmentally friendly control methods are needed to lessen its impact. Priming plants with a stressor (biotic or abiotic) can be a strategy to enhance plant defense/tolerance against future stress episodes but, despite the known underlying common mechanisms, few studies use abiotic-priming for improving tolerance to forthcoming biotic-stress and vice versa (‘cross-factor priming’). To assess whether cross-factor priming can be a potential method for enhancing avocado tolerance to WRR disease, ‘Dusa’ avocado rootstocks, susceptible to R. necatrix, were subjected to two levels of water stress (mild-WS and severe-WS) and, after drought-recovery, inoculated with R. necatrix. Physiological response and expression of plant defense related genes after drought-priming as well as the disease progression were evaluated.

Results
Water-stressed avocado plants showed lower water potential and stomatal limitations of photosynthesis compared to control plants. In addition, NPQ and qN values increased, indicating the activation of energy dissipating mechanisms closely related to the relief of oxidative stress. This response was proportional to the severity of the water stress and was accompanied by the deregulation of pathogen defense-related genes in the roots. After re-watering, leaf photosynthesis and plant water status recovered rapidly in both treatments, but roots of mild-WS primed plants showed a higher number of overexpressed genes related with plant defense than severe-WS primed plants. Disease progression after inoculating primed plants with R. necatrix was significantly delayed in mild-WS primed plants.

Conclusions
These findings demonstrate that mild-WS can induce a primed state in the WRR susceptible avocado rootstock ‘Dusa’ and reveal that ‘cross-factor priming’ with water stress (abiotic stressor) is effective for increasing avocado tolerance against R. necatrix (biotic stressor), underpinning that plant responses against biotic and abiotic stress rely on common mechanisms. Potential applications of these results may involve an enhancement of WRR tolerance of current avocado groves and optimization of water use via low frequency deficit irrigation strategies.
A lil3 chlp double mutant with exclusive accumulation of geranylgeranyl chlorophyll displays a lethal phenotype in rice
Authors: Li Chunmei , Liu Xin , Pan Jihong , Guo Jia , Wang Qian , Chen Congping , Li Na , Zhang Kuan , Yang Bin , Sun Changhui , Deng Xiaojian , Wang Pingrong 
Published: October 2019

AbstractBackgroundPhytyl residues are the common side chains of chlorophyll (Chl) and tocopherols. Geranylgeranyl reductase (GGR), which is encoded byCHLPgene, is responsible for phytyl biosynthesis. The light-harvesting like protein LIL3 was suggested to be required for stability of GGR and protochlorophyllide oxidoreductase in Arabidopsis.ResultsIn this study, we isolated a yellow-green leaf mutant,637ys, in rice (Oryza sativa). The mutant accumulated majority of Chls with unsaturated geranylgeraniol side chains and displayed a yellow-green leaf phenotype through the whole growth period. The development of chloroplasts was suppressed, and the major agronomic traits, especially No. of productive panicles per plant and of spikelets per panicle, dramatically decreased in637ys. Besides, the mutant exhibited to be sensitive to light intensity and deficiency of tocopherols without obvious alteration in tocotrienols in leaves and grains. Map-based cloning and complementation experiment demonstrated that a point mutation on theOsLIL3gene accounted for the mutant phenotype of637ys.OsLIL3is mainly expressed in green tissues, and its encoded protein is targeted to the chloroplast. Furthermore, the637ys 502ys(lil3 chlp) double mutant exclusively accumulated geranylgeranyl Chl and exhibited lethality at the three-leaf stage.ConclusionsWe identified theOsLIL3gene through a map-based cloning approach. Meanwhile, we demonstrated that OsLIL3 is of extreme importance to the function of OsGGR, and that the complete replacement of phytyl side chain of chlorophyll by geranylgeranyl chain could be fatal to plant survival in rice.
The long non-coding RNA lncRNA973 is involved in cotton response to salt stress
Authors: Zhang Xiaopei , Dong Jie , Deng Fenni , Wang Wei , Cheng Yingying , Song Lirong , Hu Mengjiao , Shen Jian , Xu Qingjiang , Shen Fafu 
Published: October 2019

Abstract

Background
Long non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973.

Results
In this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress.

Conclusions
LncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.
Prevalence and associated anthropometric and lifestyle predictors of hypertension among adults in Kombolcha town and suburbs, Northeast Ethiopia: a community-based cross-sectional study
Authors: Hassen Biniem , Mamo Hassen 
Published: October 2019

Abstract

Background
Hypertension (HTN) is major public health challenge. Data on HTN prevalence and associated risk factors is necessary to better control it. This study aimed at estimating the prevalence of HTN and associated anthropometric and lifestyle predictors in Kombolcha and suburbs, northeast Ethiopia.

Methods
The study followed a community-based cross-sectional sampling design. Adult (≥18) residents of Kombolcha and suburbs in 11 kebeles (villages) formed the target population. Of these kebeles, 5(3 urban and 2 suburban) were selected randomly. Households (HHs) within the selected kebeles and individuals within HHs were similarly recruited in December 2016–May 2017. Anthropometric and blood pressure measurements were done. World Health Organization (WHO) STEPWISE TOOL was used to capture socio-demographic, physical activity, dietary habit, and nutritional status data.

Results
Totally 318 adults participated in the study. However, only 312 (169(54.2%) males and 143(45.8%) females) were with complete information for statistical analysis. The lowest age was 18 years, the highest 65 and the mean 38.29 ± 10.88. The prevalence of HTN was 30.8% (96/312) (95% confidence interval (CI): 25.9–36.1%), 16.4% male and 14.4% female. While 45 and older age (odds ratio (OR) 7.385, 95% CI 3.563–15.306, p < 0.0001), obesity (OR 126.286, 95% CI 34.481–462.514, p < 0.0001) and overweightness (OR 16.105, 95% CI 7.024–36.927, p < 0.0001), ‘substantially high risk’ (> 102 cm in men and > 88 cm in female) waist circumference (OR 1.788, 95% CI 1.008–3.173, p = 047), light occupational physical activity (OR 12.427, 95% CI 2.891–53.410, p = 0.001), walking or riding a bicycle for lower than 5 days/week (OR 13.000, 95% CI 5.140–32.882, p < 0.0001) and lack of sport activity (OR 18.322, 95% CI 2.430–138.169, p = 005), smoking (OR 2.283, 95% CI 1.284–4.060, p = 0.005), khat (OR 17.390, 95% CI 6.167–49.037, p < 0.0001), alcohol (OR 4.005, 95% CI 2.357–6.803, p < 0.0001), HH size of two (OR 2.474, 95% CI 1.250–4.895, p = 0.009) and ≥ 3 (OR 6.889, 95% CI 2.610–18.186, p < 0.0001); and HTN in family history (OR 19.417, 95% CI 10.251–36.778, p < 0.0001) were significant predictors of HTN in the binary logistic regression analysis; none of these were so in the multivariable model.

Conclusion
Although there was a high prevalence of HTN in the study area, its independent significant predictors were not identified.
Fall-related efficacy is a useful and independent index to detect fall risk in Japanese community-dwelling older people: a 1-year longitudinal study
Authors: Kamide Naoto , Shiba Yoshitaka , Sakamoto Miki , Sato Haruhiko , Kawamura Akie 
Published: October 2019

AbstractBackgroundFall-related efficacy has been found to be associated with both falls and fall risk factors such as physical performance. The aim of the present study was to clarify whether fall-related efficacy is, independent of physical performance and other potential risk factors, associated with future falls in community-dwelling older people.MethodsThe study participants were 237 Japanese older people aged 65 years and over who were living independently in their community. Fall-related efficacy and physical performance were assessed at baseline using the short version of the Falls Efficacy Scale-International (short FES-I) and 5-m walking time, the Timed Up and Go Test, the 5 Times Sit to Stand Test, and grip strength. Physical performance was then again assessed at 1-year follow-up. The number of falls was obtained every 6 months for 1 year after the baseline survey. Instrumental activities of daily living (IADL), depression, fall history, current medications, medical history, and pain were also investigated as potential confounding factors that have possible associations with falls. The associations between the short FES-I, physical performance, and number of falls were analyzed using Poisson regression analysis adjusted for physical performance and potential confounding factors.ResultsThe mean age of the participants (75.9% women) was 71.1 ± 4.6 years, and 92.8% could perform IADL independently. The total numbers of falls and fallers during the 1-year follow-up period were 70 and 42, respectively. On Poisson regression analysis adjusted for walking time and potential confounding factors, independent of physical performance, the short FES-I was found to be significantly associated with number of falls (relative risk = 1.09,p < 0.05). On the other hand, physical performance was not significantly associated with the number of falls.ConclusionsThe findings of the present study suggest that the short FES-I, independent of physical performance and other potential risk factors, is a useful index to detect fall risk in community-dwelling older people, and that fall-related efficacy is an important factor in terms of fall prevention.
More than a “touch of the flu”: a response to Mayrhuber et al’s ““with fever it’s the real flu I would say”: laypersons’ perception of common cold and influenza and their differences - a qualitative study in Austria, Belgium and Croatia”
Authors: Jutel Annemarie 
Published: October 2019

Abstract
This short reply contests two assumptions made by the authors of Mayrhuber et al’s. “With fever it’s the real flu I would say.” The first is that there is influenza can be reliably defined by a medical case definition. The second is that this small qualitative study can be generalisable. However, it does underline the important point that technical diagnostic terms may be used on different registers by a variety of actors in the medical setting.
Two cases of fungal cyst infection in ADPKD: is this really a rare complication?
Authors: Onuchic Laura , Sato Victor Augusto Hamamoto , de Menezes Neves Precil Diego Miranda , Balbo Bruno Eduardo Pedroso , Portela-Neto Antônio Abel , Ferreira Fernanda Trani , Watanabe Elieser Hitoshi , Watanabe Andreia , de Almeida Maria Cláudia Stockler , de Abreu Testagrossa Leonardo , Chocair Pedro Renato , Onuchic Luiz Fernando 
Published: October 2019

Abstract

Background
Cyst infection is a prevalent complication in autosomal dominant polycystic kidney disease (ADPKD) patients, however therapeutic and diagnostic approaches towards this condition remain unclear. The confirmation of a likely episode of cyst infection by isolating the pathogenic microorganism in a clinical scenario is possible only in the minority of cases. The available antimicrobial treatment guidelines, therefore, might not be appropriate to some patients.

Case presentation
We describe two unique cases of kidney cyst infection by Candida albicans, a condition that has not been previously described in literature. Both cases presented clear risk factors for Candida spp. infection. However, since there was no initial indication of cyst aspiration and culture, antifungal therapy was not immediately started and empirical treatment was initiated as recommended by the current guidelines. Antifungal treatment was instituted in both cases along the clinical course, according to their specificities.

Conclusion
Our report highlights the possibility of Candida spp. cyst infection. Failure of clinical improvement with antibiotics should raise the suspicion of a fungal infection. Identification of infected cysts should be pursued in such cases, particularly with PET-CT, and when technically possible followed by cyst aspiration and culture to guide treatment. Risk factors for this condition, such as Candida spp. colonization, previous antimicrobial therapy, hemodialysis, necrotizing pancreatitis, gastrointestinal/hepatobiliary surgical procedure, central venous catheter, total parenteral nutrition, diabetes mellitus and immunodeficiency (neutropenia < 500 neutrophils/mL, hematologic malignancy, chemotherapy, immunosuppressant drugs), should be also considered accepted criteria for empirical antifungal therapy.
Accumulate evidence for IP-10 in diagnosing pulmonary tuberculosis
Authors: Qiu Xia , Xiong Tao , Su Xiaojuan , Qu Yi , Ge Long , Yue Yan , Zeng Yan , Li Wenxing , Hu Peng , Mu Dezhi 
Published: October 2019

Abstract

Backgrounds
Pulmonary tuberculosis (PTB) is a major health and economic burden. Accurate PTB detection is an important step to eliminating TB globally. Interferon gamma-induced protein 10 (IP-10) has been reported as a potential diagnostic marker for PTB since 2007. In this study, a meta-analysis approach was used to assess diagnostic value of IP-10 for PTB.

Methods
Web of Science, PubMed, the Cochrane Library, and Embase databases were searched for studies published in English up to February 2019. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), the area under the curve (AUC) and hierarchical summary receiver operating characteristic (HSROC) curve were estimated by the HSROC model and random effect model.

Results
Eighteen studies including 2836 total participants met our inclusion criteria. The pooled sensitivity, specificity, PLR, and NLR of IP-10 for PTB detection were 86, 88%, 7.00, and 0.16, respectively. The pooled DOR was 43.01, indicating a very powerful discriminatory ability of IP-10. The AUC was 0.93 (95% CI: 0.91–0.95), showed the accuracy of IP-10 was good. Meta-regression showed that there was no heterogeneity with respect to TB burden, study design type, age, IP-10 assay method, IP-10 condition and HIV-infection status.

Conclusions
Our results showed that IP-10 is a promising marker for differentiating PTB from non-TB.
Inflammatory responses to a pathogenic West Nile virus strain
Authors: Huang Bixing , West Nic , Vider Jelena , Zhang Ping , Griffiths Rebecca E. , Wolvetang Ernst , Burtonclay Peter , Warrilow David 
Published: October 2019

Abstract

Background
West Nile virus (WNV) circulates across Australia and was referred to historically as Kunjin virus (WNVKUN). WNVKUN has been considered more benign than other WNV strains circulating globally. In 2011, a more virulent form of the virus emerged during an outbreak of equine arboviral disease in Australia.

Methods
To better understand the emergence of this virulent phenotype and the mechanism by which pathogenicity is manifested in its host, cells were infected with either the virulent strain (NSW2012), or less pathogenic historical isolates, and their innate immune responses compared by digital immune gene expression profiling. Two different cell systems were used: a neuroblastoma cell line (SK-N-SH cells) and neuronal cells derived from induced pluripotent stem cells (iPSCs).

Results
Significant innate immune gene induction was observed in both systems. The NSW2012 isolate induced higher gene expression of two genes (IL-8 and CCL2) when compared with cells infected with less pathogenic isolates. Pathway analysis of induced inflammation-associated genes also indicated generally higher activation in infected NSW2012 cells. However, this differential response was not paralleled in the neuronal cultures.

Conclusion
NSW2012 may have unique genetic characteristics which contributed to the outbreak. The data herein is consistent with the possibility that the virulence of NSW2012 is underpinned by increased induction of inflammatory genes.
Vibrio cholerae non-O1 - the first reported case of keratitis in a healthy patient
Authors: Chen Wei-Dar , Lai Li-Ju , Hsu Wei-Hsiu , Huang Tsung-Yu 
Published: October 2019

AbstractBackgroundVibrio choleraenon-O1 is a virulent pathogen that causes significant morbidity and mortality in humans. Herein, we report a case of corneal ulcer caused by this pathogen.Case presentationA 59-year-old fisherman with no systemic history was struck in the right eye by a marine shrimp and developed keratitis. Corneal scrapping culture revealed the presence of theV. choleraenon-O1, and its identification was confirmed by Analytical Profile Index 20E system and polymerase chain reaction. He was successfully treated with topical levofloxacin (0.3%) and fortified amikacin (12.5 mg/mL) for 2 weeks. The visual acuity recovered to 20/25 after treatment without complications.ConclusionsThis is the first case report of keratitis caused byV. choleraenon-O1 strain. Ocular injury by marine creatures and contaminated seawater can contribute to severe corneal ulcer. Early diagnosis can be achieved by meticulous history taking and a comprehensive laboratory workup. Simultaneously, an effective antibiotic therapy can lead to a positive outcome.