bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes
Authors: Toju Hirokazu , Tanaka Yu 
Published: May 2018

AbstractCyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, as effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics, and agricultural practices, more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes [Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales), and Purpureocillium (Hypocreales)] co-occurred in the soybean rhizosphere at a small spatial scale. Overall, this study suggests how “consortia” of anti-nematode microbes can derive from indigenous (resident) microbiomes, thereby providing basic information for managing anti-nematode microbial communities in agroecosystems.
A quantitative framework for investigating the reliability of network construction
Authors: Cirtwill Alyssa R. , Eklöf Anna , Roslin Tomas , Wootton Kate , Gravel Dominique 
Published: May 2018

ABSTRACTDescriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances, and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. Here we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction and its implications for the estimation of network properties. We then outline a framework to quantify the uncertainty around each interaction. We illustrate this framework using the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions which we could, however, limit with informative priors. Through these efforts, we demonstrate the utility of our approach and the importance of acknowledging the uncertainty inherent in network studies. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change networks analyses and yield greater realism.
Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise
Authors: Pertea Mihaela , Shumate Alaina , Pertea Geo , Varabyou Ales , Chang Yu-Chi , Madugundu Anil K. , Pandey Akhilesh , Salzberg Steven L. 
Published: May 2018

AbstractWe assembled the sequences from 9,795 RNA sequencing experiments, collected from 31 human tissues and hundreds of subjects as part of the GTEx project, to create a new, comprehensive catalog of human genes and transcripts. The new human gene database contains 43,162 genes, of which 21,306 are protein-coding and 21,856 are noncoding, and a total of 323,824 transcripts, for an average of 7.5 transcripts per gene. Our expanded gene list includes 4,998 novel genes (1,178 coding and 3,819 noncoding) and 97,511 novel splice variants of protein-coding genes as compared to the most recent human gene catalogs. We detected over 30 million additional transcripts at more than 650,000 sites, nearly all of which are likely to be nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells.
Mental health consumer participation in undergraduate occupational therapy student assessment: No negative impact
Authors: Logan Alexandra , Yule Elisa , Taylor Michael , Imms Christine 
Published: May 2018

Background/aimAustralian accreditation standards for occupational therapy courses require consumer participation in the design, delivery and evaluation of programs. This study investigated whether a mental health consumer – as one of two assessors for an oral assessment in a mental health unit – impacted engagement, anxiety states and academic performance of undergraduate occupational therapy students.MethodsStudents (n = 131 eligible) self‐selected into two groups but were blinded to the group differences (assessor panel composition) until shortly prior to the oral assessment. Control group assessors were two occupational therapy educators, while consumer group assessors included an occupational therapy educator and a mental health consumer.ResultsPre‐ and post‐assessment data were successfully matched for 79 students (overall response rate = 73.1%). No evidence was found of significant differences between the two groups for engagement, anxiety or academic performance (all P values >0.05).ConclusionIncluding mental health consumers as assessors did not negatively impact student engagement and academic performance, nor increase student anxiety beyond that typically observed in oral assessment tasks. The findings provide support for expanding the role of mental health consumers in the education and assessment of occupational therapy students. Development of methods to determine the efficacy of consumer involvement remains an area for future research.
The Association of Proxy Care Engagement with Proxy Reports of Patient Experience and Quality of Life
Authors: Roydhouse Jessica K. , Gutman Roee , Keating Nancy L. , Mor Vincent , Wilson Ira B. 
Published: May 2018

ObjectiveTo assess the association of proxy‐specific covariates with proxy‐reported patient cancer care experience, quality rating, and quality of life.Data Sources/Study SettingSecondary analysis of data from the Cancer Care Outcomes Research and Surveillance (CanCORS) study.Study DesignCross‐sectional observational study. The respondents were proxies for patients with incident colorectal or lung cancer.Data Collection/Extraction MethodsAnalyses used linear regression models and adjusted for patient sociodemographic and clinical characteristics. Outcomes included patients’ experiences with medical care, nursing care, and care coordination, overall quality ratings, and physical and mental health, all scored on 0–100 scales (0 = worst, 100 = best). Independent variables included the proxy's relationship with the patient and engagement in patient care.Principal FindingsOf 1,011 proxies, most were the patient's spouse (50 percent) or child (36 percent). Although most proxies (66 percent) always attended medical visits, 3 percent reported never attending. After adjustment, on average children reported worse experiences and poorer quality care than spouses (4–9 points lower across outcomes). Proxies who never attended medical visits reported significantly worse medical care (−11 points, 95 percent CI = −18 to −3) and care coordination (−13 points, 95 percent CI = −20 to −6).ConclusionsCollecting data on proxy engagement in care is warranted if proxy responses are used.
Far‐Infrared Optimization of the Fragrance‐Improving Process with Temperature and Humidity Control for Green Tea
Authors: Hua Jin‐Jie , Yuan Hai‐Bo , Deng Yu‐Liang , Jiang Yong‐Wen , Wang Jin‐Jin , Dong Chun‐Wang , Li Jia 
Published: May 2018

AbstractIn this study, a Box–Behnken design was used to explore the effect of a new technology on green tea fragrance improvement and to optimize fragrance‐improving with a bilayer far‐infrared fragrance‐improving machine with temperature and humidity control. Based on the results of previous single‐factor experiments, the main biochemical composition and sensory evaluation scores of the fragrance‐improved samples were used as investigation indices. The new fragrance‐improving technology was compared with the traditional far‐infrared fragrance‐improving process, roller pot fragrance improvement, and hot air rotary fragrance improvement. The results show that the optimal parameter combination of the new technology consists of a temperature of 128.00 °C, relative humidity of 70.00 g/h, and transmission speed of 435.00 r/min. With these process parameters, the amino acids, tea polyphenols, flavonoids, soluble sugar, catechins, and caffeine in the fragrance‐improved samples reached 3.86%, 32.29%, 5.59%, 4.45%, 8.97%, and 2.75%, respectively. The quality material weight value was 11.72%. The shape, color, taste, and aroma of the fragrance‐improved samples made using these parameters were found to be best, with a sensory quality score of 87.40, which is significantly higher than that of other fragrance‐improving methods. The energy consumption was 0.19 RMB/kg, which was reduced by more than 50% compared with the other methods, and the production efficiency was more than 30% higher than the traditional methods. This new far‐infrared fragrance‐improving technology overcomes the yellowish and grayish color of fragrance‐improved tea samples that is caused by the traditional fragrance‐improving approach, and will provide technical guidance for actual green tea production.Practical ApplicationOur proposed approach innovatively integrates humidity and rotational speed as factors for fragrance improvement in Chinese tea process. The findings of this work provide new technical for fragrance improvement processes.
Microbial community analyses of produced waters from high‐temperature oil reservoirs reveal unexpected similarity between geographically distant oil reservoirs
Authors: Kim Daehyun D. , O'Farrell Corynne , Toth Courtney R. A. , Montoya Oscar , Gieg Lisa M. , Kwon Tae‐Hyuk , Yoon Sukhwan 
Published: May 2018

SummaryAs a preliminary investigation for the development of microbial‐enhanced oil recovery strategies for high‐temperature oil reservoirs (~70 to 90°C), we have investigated the indigenous microbial community compositions of produced waters from five different high‐temperature oil reservoirs near Segno, Texas, U.S. (~80 to 85°C) and Crossfield, Alberta, Canada (~75°C). The DNA extracted from these low‐biomass‐produced water samples were analysed with MiSeq amplicon sequencing of partial 16S rRNA genes. These sequences were analysed along with additional sequence data sets available from existing databases. Despite the geographical distance and difference in the physicochemical properties, the microbial compositions of the Segno and Crossfield produced waters exhibited unexpectedly high similarity, as indicated by the results of beta diversity analyses. The major operational taxonomic units included acetoclastic and hydrogenotrophic methanogens (Methanosaetaceae, Methanobacterium and Methanoculleus), as well as bacteria belonging to the families Clostridiaceae and Thermotogaceae, which have been recognized to include thermophilic, thermotolerant, and/or spore‐forming subtaxa. The sequence data retrieved from the databases exhibited different clustering patterns, as the communities from close geographical locations invariably had low beta diversity and the physicochemical properties and conditions of the reservoirs apparently did not have a substantial role in shaping of microbial communities.
Diagnostic value of microRNAs derived from exosomes in bronchoalveolar lavage fluid of early‐stage lung adenocarcinoma: A pilot study
Authors: Kim Ji Eun , Eom Jung Seop , Kim Won‐young , Jo Eun Jung , Mok Jeongha , Lee Kwangha , Kim Ki Uk , Park Hye‐kyung , Lee Min Ki , Kim Mi‐hyun 
Published: May 2018

BackgroundLow‐dose computed tomography can identify smaller nodules more often than chest radiography in lung screening. However, complications from invasive diagnostic procedures performed to detect nodules are common. Exosomes contain a diverse array of biomolecules that reflect the biological state of the cell from which they are released. The aim of this study was to investigate the diagnostic value of bronchoalveolar lavage (BAL) fluid exosomal microRNAs (miRNAs) for early‐stage lung adenocarcinoma.MethodsWe evaluated miRNAs (miR‐7, miR‐21, miR‐126, Let‐7a, miR‐17, and miR‐19) known to have diagnostic value for lung adenocarcinoma. Exosomes were isolated from the BAL fluid of control subjects (n = 15) and patients with lung adenocarcinoma (n = 13). Exosomal miRNA was analyzed using a commercial kit containing probes targeting six selected miRNAs. Results were validated via quantitative PCR.ResultsThe presence of miRNAs was confirmed in exosomes from BAL fluid of both lung adenocarcinoma patients and control subjects. miR‐126 (P < 0.001) and Let‐7a (P = 0.015) levels were significantly higher in the BAL fluid of lung adenocarcinoma patients than in control subjects. The BAL fluid miRNA signature was confirmed using an independent set of paired adenocarcinoma and normal tissue samples (n = 4). Lung adenocarcinoma tissues showed increased expression of miR‐126 (P = 0.039) compared to normal tissue samples.ConclusionWe identified a close correlation between BAL fluid exosomal miRNAs and tumor miRNAs. BAL fluid exosomal miRNAs obtained through noninvasive methods could serve as diagnostic biomarkers in early‐stage lung adenocarcinoma.
Intronic variant of EGFR is associated with GBAS expression and survival outcome of early‐stage non‐small cell lung cancer
Authors: Hong Mi Jeong , Lee Shin Yup , Choi Jin Eun , Kang Hyo‐Gyoung , Do Sook Kyung , Lee Jang Hyuck , Yoo Seung Soo , Lee Eung Bae , Seok Yangki , Cho Sukki , Jheon Sanghoon , Lee Jaehee , Cha Seung Ick , Kim Chang Ho , Park Jae Yong 
Published: May 2018

BackgroundGenome‐wide association studies have indicated that most of the currently identified disease and trait‐associated single nucleotide polymorphisms (SNPs) are intronic or intergenic. RegulomeDB is a recently developed database that provides functional annotations for regulatory features of SNPs located in non‐coding regions. We evaluated the potential regulatory SNPs in the EGFR gene region using RegulomeDB and their associations with prognosis after surgery in non‐small cell lung cancer (NSCLC) patients.MethodsA total of 698 patients with surgically resected NSCLC were enrolled and seven SNPs were selected based on the RegulomeDB database. All SNPs were genotyped using SEQUENOM MassARRAY iPLEX assay.ResultsAmong the seven SNPs evaluated, rs9642391 (EGFR ivs19+2851C>G) was significantly associated with survival outcome (adjusted hazard ratio [HR] for overall survival = 0.70, 95% confidence interval [CI] 0.56–0.87, P = 0.001; adjusted HR for disease‐free survival = 0.82, 95% CI 0.70–0.97, P = 0.02; under a codominant model). According to RegulomeDB, rs9642391C>G, which is located in intron 19 of EGFR, was predicted to influence the expression of GBAS but not EGFR. As predicted, rs9642391C>G was associated with GBAS (P = 0.024) but not EGFR messenger RNA expression in tumor tissues.ConclusionIn conclusion, our study provides evidence that rs9642391C>G in the intron of EGFR is associated with GBAS expression and survival outcomes of patients with surgically resected early‐stage NSCLC.
babette: BEAUti 2, BEAST2 and Tracer for R
Authors: Bilderbeek Richèl J. C. , Etienne Rampal S. 
Published: May 2018

AbstractIn the field of phylogenetics, BEAST2 is one of the most widely used software tools. It comes with the graphical user interfaces BEAUti 2, DensiTree and Tracer, to create BEAST2 configuration files and to interpret BEAST2's output files. However, when many different alignments or model setups are required, a workflow of graphical user interfaces is cumbersome.Here, we present a free, libre and open‐source package,babette: ‘BEAUti 2, BEAST2 and Tracer for R’, for the R programming language.babettecreates BEAST2 input files, runs BEAST2 and parses its results, all from an R function call.We describebabette's usage and the novel functionality it provides compared to the original tools and we give some examples.Asbabetteis designed to be of high quality and extendable, we conclude by describing the further development of the package.
Whole‐of‐community interventions to reduce population‐level harms arising from alcohol and other drug use: a systematic review and meta‐analysis
Authors: Stockings Emily , Bartlem Kate , Hall Alix , Hodder Rebecca , Gilligan Conor , Wiggers John , Sherker Shauna , Wolfenden Luke 
Published: May 2018

AbstractBackground and aimsWhole‐of‐community interventions aim to reduce alcohol and other drug (AOD) use and harms by mobilizing community leaders, organizations and policy‐makers to respond effectively to AOD use. The aim of this review is to estimate the effectiveness of whole‐of‐community interventions in reducing population‐level harms arising from AOD use.DesignA systematic review of electronic databases CENTRAL, Embase, Medline, Medline in Process and PsycINFO was conducted from database inception to August 2017. Eligible trials had a parallel comparison group, implemented interventions in two or more community settings, and reported data on AOD use or harms.SettingIntervention settings included schools, sporting clubs, police and law enforcement agencies, community centres, local media and retail premises.ParticipantsTwenty‐four trials from 63 publications were included (n = 249 125 participants).MeasurementsOutcomes from AOD consumption (quantity and frequency), AOD‐related crime and AOD‐related accidents, injuries and hospital admissions. Data were pooled using random‐effects inverse variance meta‐analysis in Review Manager version 5.3.FindingsRisk of bias was mostly high, due to lack of random allocation, selective reporting and significant attrition. Meta‐analyses indicated significant reductions in risky drinking [Alcohol Use Disorders Identification Scale (AUDIT) > 8; three trials (7 data points), relative risk (RR) = 0.78, 95% confidence interval (CI) = 0.62–0.99)], but found no impact on past‐month alcohol use (five trials, RR = 0.95, 95% CI = 0.89–1.02), binge drinking (five trials, RR = 0.97, 95% CI = 0.89–1.06) or 12‐month marijuana use (two trials, RR = 0.98, 95% CI = 0.86–1.11). Narrative synthesis indicated some reductions in AOD‐related assault rates and arrests, but were equivocal for quantity of alcohol consumed, 12‐month illicit drug use, assault or abuse, motor vehicle accidents and hospital admissions.ConclusionsInterventions to reduce alcohol and other drug use and harms applied to whole communities have resulted so far in small reductions in risky alcohol consumption, but have had little impact upon past month alcohol use, binge drinking or 12‐month marijuana use and the studies have been subject to high risk of bias.
Effects of chlorogenic acid (CGA) supplementation during in vitro maturation culture on the development and quality of porcine embryos with electroporation treatment after in vitro fertilization
Authors: Nguyen Thanh‐Van , Wittayarat Manita , Do Lanh Thi Kim , Nguyen Thanh Van , Nii Masahiro , Namula Zhao , Kunihara Toshiki , Tanihara Fuminori , Hirata Maki , Otoi Takeshige 
Published: May 2018

AbstractElectroporation is the technique of choice to introduce an exogenous gene into embryos for transgenic animal production. Although this technique is practical and effective, embryonic damage caused by electroporation treatment remains a major problem. This study was conducted to evaluate the optimal culture system for electroporation‐treated porcine embryos by supplementation of chlorogenic acid (CGA), a potent antioxidant, during in vitro oocyte maturation. The oocytes were treated with various concentrations of CGA (0, 10, 50, and 100 μmol/L) through the duration of maturation for 44 hr. The treated oocytes were then fertilized, electroporated at 30 V/mm with five 1 msec unipolar pulses, and subsequently cultured in vitro until development into the blastocyst stage. Without electroporation, the treatment with 50 μmol/L CGA had useful effects on the maturation rate of oocytes, the total cell number, and the apoptotic nucleus indices of blastocysts. When the oocytes were electroporated after in vitro fertilization, the treatment with 50 μmol/L CGA supplementation significantly improved the rate of oocytes that developed into blastocysts and reduced the apoptotic nucleus indices (4.7% and 7.6, respectively) compared with those of the untreated group (1.4% and 13.0, respectively). These results suggested that supplementation with 50 μmol/L CGA during maturation improves porcine embryonic development and quality of electroporation‐treated embryos.
Immediate placement and provisionalization of implants in the aesthetic zone with or without a connective tissue graft: A 1‐year randomized controlled trial and volumetric study
Authors: van Nimwegen Wouter G. , Raghoebar Gerry M. , Zuiderveld Elise G. , Jung Ronald E. , Meijer Henny J. A. , Mühlemann Sven 
Published: May 2018

AbstractObjectiveTo volumetrically compare peri‐implant mid‐facial soft tissue changes in immediately placed and provisionalized implants in the aesthetic zone, with or without a connective tissue graft.Material and methodsSixty patients were included. All implants were placed immediately after extraction. After randomization, in one group, a connective tissue graft (test group, n = 30) was inserted at the buccal aspect of the implant. The other group (control group, n = 30) received no connective tissue graft. Clinical parameters, digital photographs and conventional impressions were obtained before extraction (Tpre) and at 12 months following definitive crown placement (T12). The casts were digitized by a laboratory scanner, and a volumetric analysis was performed between Tpre and T12.ResultsTwenty‐five patients in each group were available for analysis at T12. Volumetric change, transformed to a mean (±SD) change in thickness, was −0.68 ± 0.59 mm (test) and −0.49 ± 0.54 mm (control) with a non‐significant difference between groups (p = .189). The mid‐facial mucosa level was significantly different between both groups (p = .014), with a mean (±SD) change of +0.20 ± 0.70 mm (test) and −0.48 ± 1.13 mm (control). The Pink Esthetic Score was similar between both groups.ConclusionsThe use of a CTG in immediately placed and provisionalized implants in the aesthetic zone did not result in less mucosal volume loss after 12 months, leading to the assumption that a CTG cannot fully compensate for the underlying facial bone loss, although a significantly more coronally located mid‐facial mucosa level was found when a CTG was performed.