bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Unit Level Small Area Model with Misclassified Covariates
Authors: Arima Serena , Polettini Silvia 
Published: May 2019

Summary
Model-based small area estimation relies on mixed effects regression models that link the small areas and borrow strength from similar domains. When the auxiliary variables that are used in the models are measured with error, small area estimators that ignore the measurement error may be worse than direct estimators. Alternative small area estimators accounting for measurement error have been proposed in the literature but only for continuous auxiliary variables. Adopting a Bayesian approach, we extend the unit level model to account for measurement error in both continuous and categorical covariates. For the discrete variables we model the misclassification probabilities and estimate them jointly with all the unknown model parameters. We test our model through a simulation study. The effect of the model proposed is emphasized through application to data from the Ethiopia Demographic and Health Survey where we focus on the women’s malnutrition issue: a dramatic problem in developing countries and an important indicator of the socio-economic progress of a country.
Estimating the Number of Serious Road Injuries Per Vehicle Type in the Netherlands by using Multiple Imputation of Latent Classes
Authors: Boeschoten Laura , Waal Ton , Vermunt Jeroen K. 
Published: May 2019

Summary
Statistics that are published by official agencies are often generated by using population registries, which are likely to contain classification errors and missing values. A method that simultaneously handles classification errors and missing values is multiple imputation of latent classes (MILC). We apply the MILC method to estimate the number of serious road injuries per vehicle type in the Netherlands and to stratify the number of serious road injuries per vehicle type into relevant subgroups by using data from two registries. For this specific application, the MILC method is extended to handle the large number of missing values in the stratification variable ‘region of accident’ and to include more stratification covariates. After applying the extended MILC method, a multiply imputed data set is generated that can be used to create statistical figures in a straightforward manner, and that incorporates uncertainty due to classification errors and missing values in the estimate of the total variance.
From sink to volcanic source: Unravelling missing terrestrial eruption records by characterization and high‐resolution chronology of lacustrine volcanic density flow deposits, Lake Inawashiro‐ko, Fukushima, Japan
Authors: Kataoka Kyoko S. , Nagahashi Yoshitaka 
Published: May 2019

AbstractEruption records in the terrestrial stratigraphy are often incomplete due to erosion after tephra deposition, limited exposure and lack of precise dating owing to discontinuity of strata. A lake system and sequence adjacent to active volcanoes can record various volcanic events such as explosive eruptions and subaqueous density flows being extensions of eruption triggered and secondary triggered lahars. A lacustrine environment can constrain precise ages of such events because of constant and continuous background sedimentation. A total of 71 subaqueous density flow deposits in a 28 m long core from Lake Inawashiro‐ko reveals missing terrestrial volcanic activity at Adatara and Bandai volcanoes during the past 50 kyr. Sedimentary facies, colour, grain size, petrography, clay mineralogy, micro X‐ray fluorescence analysis and chemistry of included glass shards characterize the flow event deposits and clarify their origin: (i) clay‐rich grey hyperpycnites, extended from subaerial cohesive lahars at Adatara volcano, with sulphide/sulphate minerals and high sulphur content which point to a source from hydrothermally altered material ejected by phreatic eruptions; and (ii) clay‐rich brown density flow deposits, induced by magmatic hydrothermal eruptions and associated edifice collapse at Bandai volcano, with the common presence of fresh juvenile glass shards and low‐grade hydrothermally altered minerals; whereas (iii) non‐volcanic turbidites are limited to the oldest large slope failure and the 2011 Tohoku‐oki earthquake events. The high‐resolution chronology of volcanic activity during the last 50 kyr expressed by lacustrine event deposits shows that phreatic eruption frequency at Adatara has roughly tripled and explosive eruptions at Bandai have increased by ca 50%. These results challenge hikers, ski‐fields and downstream communities to re‐evaluate the increased volcanic risks from more frequent eruptions and far‐reaching lahars, and demonstrate the utility of lahar and lacustrine volcanic density flow deposits to unravel missing terrestrial eruption records, otherwise the recurrence rate may be underestimated at many volcanoes.
Evaluation of rainfall kinetic energy and erosivity in northern Taiwan using kriging with climate characteristics
Authors: Liao Kuo‐Wei , Guo Jia‐Jun , Fan Jen‐Chen , Lee Cheng‐Chun , Huang Chien Lin 
Published: May 2019

AbstractA localized rainfall kinetic energy (E) equation and an erosivity map were developed, and the suitability of the universal soil loss equation (USLE) for assessing the soil erosion of a non‐US region was investigated. After accurately measuring and gathering data regarding raindrop size using disdrometers in four northern Taiwan locations, this study investigated the drop size distribution under different conditions by categorizing the rainfall patterns to develop regression equations for estimating the unit volume‐specific kinetic energy (KEmm) and the unit time‐specific kinetic energy (KEtime) of northern Taiwan. Climate zoning, which is not considered in currently used designs, was then implemented along with two‐stage cluster analysis to construct a rainfall erosivity (R) distribution map using the kriging model. The binary polynomial regression function of KEtime, which had the highest correlation (R2 = 0.98), was suggested to estimate E in northern Taiwan. It was found that the pattern and intensity (I) of rainfall will slightly affect E. The climatic influence on the root mean square of the semivariogram was significant, which suggests that climate zoning can help estimate the rainfall erosivity (R). The outcomes were extended to estimate R in areas without rainfall stations.
Multiple downy mildew effectors target the stress‐related NAC transcription factor LsNAC069 in lettuce
Authors: Meisrimler Claudia‐Nicole , Pelgrom Alexandra J. E. , Oud Bart , Out Suzan , Van den Ackerveken Guido 
Published: May 2019

SummaryTo cause disease in lettuce, the biotrophic oomycete Bremia lactucae secretes potential RxLR effector proteins. Here we report the discovery of an effector‐target hub consisting of four B. lactucae effectors and one lettuce protein target by a yeast‐two‐hybrid (Y2H) screening. Interaction of the lettuce tail‐anchored NAC transcription factor, LsNAC069, with B. lactucae effectors does not require the N‐terminal NAC domain but depends on the C‐terminal region including the transmembrane domain. Furthermore, in Y2H experiments, B. lactucae effectors interact with Arabidopsis and potato tail‐anchored NACs, suggesting that they are conserved effector targets. Transient expression of RxLR effector proteins BLR05 and BLR09 and their target LsNAC069 in planta revealed a predominant localization to the endoplasmic reticulum. Phytophthora capsici culture filtrate and polyethylene glycol treatment induced relocalization to the nucleus of a stabilized LsNAC069 protein, lacking the NAC‐domain (LsNAC069ΔNAC). Relocalization was significantly reduced in the presence of the Ser/Cys‐protease inhibitor TPCK indicating proteolytic cleavage of LsNAC069 allows for relocalization. Co‐expression of effectors with LsNAC069ΔNAC reduced its nuclear accumulation. Surprisingly, LsNAC069 silenced lettuce lines had decreased LsNAC069 transcript levels but did not show significantly altered susceptibility to B. lactucae. In contrast, LsNAC069 silencing increased resistance to Pseudomonas cichorii bacteria and reduced wilting effects under moderate drought stress, indicating a broad role of LsNAC069 in abiotic and biotic stress responses.
Stable native RIP9 complexes associate with C‐to‐U RNA editing activity, PPRs, RIPs, OZ1, ORRM1 and ISE2
Authors: Sandoval Rafael , Boyd Robert D. , Kiszter Alena N. , Mirzakhanyan Yeva , Santibańez Paola , Gershon Paul D. , Hayes Michael L. 
Published: May 2019

SummaryThe mitochondrial and chloroplast mRNAs of the majority of land plants are modified through cytidine to uridine (C‐to‐U) RNA editing. Previously, forward and reverse genetic screens demonstrated a requirement for pentatricopeptide repeat (PPR) proteins for RNA editing. Moreover, chloroplast editing factors OZ1, RIP2, RIP9 and ORRM1 were identified in co‐immunoprecipitation (co‐IP) experiments, albeit the minimal complex sufficient for editing activity was never deduced. The current study focuses on isolated, intact complexes that are capable of editing distinct sites. Peak editing activity for four sites was discovered in size‐exclusion chromatography (SEC) fractions ≥ 670 kDa, while fractions estimated to be approximately 413 kDa exhibited the greatest ability to convert a substrate containing the editing site rps14 C80. RNA content peaked in the ≥ 670 kDa fraction. Treatment of active chloroplast extracts with RNase A abolished the relationship of editing activity with high‐MW fractions, suggesting a structural RNA component in native complexes. By immunoblotting, RIP9, OTP86, OZ1 and ORRM1 were shown to be present in active gel filtration fractions, though OZ1 and ORRM1 were mainly found in low‐MW inactive fractions. Active editing factor complexes were affinity‐purified using anti‐RIP9 antibodies, and orthologs to putative Arabidopsis thaliana RNA editing factor PPR proteins, RIP2, RIP9, RIP1, OZ1, ORRM1 and ISE2 were identified via mass spectrometry. Western blots from co‐IP studies revealed the mutual association of OTP86 and OZ1 with native RIP9 complexes. Thus, RIP9 complexes were discovered to be highly associated with C‐to‐U RNA editing activity and other editing factors indicative of their critical role in vascular plant editosomes.
Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids
Authors: Chu Candice P. , Nabity Mary B. 
Published: May 2019

BackgroundSmall RNA sequencing (RNA‐seq) of biofluids is challenging due to the relative scarcity of microRNAs (miRNAs), limited sample volumes, and the lack of a gold standard isolation method. Additionally, few comparisons exist for the RNA isolation and sequencing methods of biofluids.ObjectivesWe aimed to compare the performance of six commercial RNA isolation kits and two library preparation methods for small RNA‐seq using canine serum and urine.MethodsSerum and urine were collected from seven dogs with protein‐losing nephropathy, and the samples were pooled. Total RNA from serum (2 mL) and urine (10 mL) was isolated in triplicate using three methods each for serum (Zymo Direct‐zol, mirVana PARIS, miRCURY Biofluids) and urine (Qiagen exoRNeasy, Norgen Urine Exosome, miRCURY Exosome). For each sample type, the two kits yielding the highest RNA concentration were selected, and small RNA‐seq was performed using TruSeq and NEXTflex library preparations. Data were analyzed by CPSS 2.0 and DESeq2.ResultsFor serum, Zymo Direct‐zol combined with NEXTflex was the only combination that enabled successful library preparation, while for urine, Qiagen exoRNeasy combined with NEXTflex outperformed other combinations for detecting miRNAs. The total number of miRNAs detected in serum and urine was 198 and up to 115, respectively. miRNA expression in serum was distinct from urine. Furthermore, the library preparation method introduced a higher variation of urine results than the RNA isolation method.ConclusionsDifferent isolation and library preparation methods show significant differences in miRNA results that could affect biomarker discovery. Small RNA‐seq provides an unbiased, global assessment to compare these methods in canine biofluids.
Circulating pig‐specific DNA as a novel biomarker for monitoring xenograft rejection
Authors: Zhou Ming , Lu Ying , Zhao Chengjiang , Zhang Junfang , Cooper David K. C. , Xie Chongwei , Song Zongpei , Gao Hanchao , Qu Zepeng , Lin Shan , Deng YangYang , Hara Hidetaka , Zhan Yongqiang , Jiang Zhengda , Dai Yifan , Wu Changyou , Cai Zhiming , Mou Lisha 
Published: May 2019

AbstractMonitoring for immune rejection is crucial for long‐term survival of pig xenografts. Circulating DNA is a promising non‐invasive biomarker for either organ injury or response to therapy. In this study, circulating pig‐specific DNA (cpsDNA) was monitored during xenograft rejection. Potential targets of cpsDNA were selected by in silico analysis, and species specificity of selected primers was confirmed by PCR. Subsequently, cpsDNA as a biomarker was evaluated using a complement‐dependent cytotoxicity (CDC) assay in vitro. Then, early diagnosis and response to rapamycin were assessed by an in vivo imaging model of pig‐to‐mouse cell transplantation. Finally, cpsDNA was monitored in a pig‐to‐monkey artery patch transplantation model. The results showed that (a) a method of cpsDNA quantitation was established for application in mouse and nonhuman primate models; (b) cpsDNA reflected CDC in vitro; (c) cpsDNA in vivo mirrored xenograft rejection, and correlated with xenograft loss in pig‐to‐mouse cell transplantation; (d) cpsDNA was significantly reduced when rapamycin was administered; and (e) dynamic cpsDNA was detectable in pig‐to‐monkey artery patch transplantation. In conclusion, measurement of cpsDNA could prove to be a less invasive, but more specific and sensitive low‐cost biomarker enabling monitoring of xenograft rejection and the response to immunosuppressive therapy.
Comparing neck extensor muscle function in asymptomatic Canadian adults and adults with tension-type headache: a cross-sectional study
Authors: Marchand Andrée-Anne , Houle Mariève , Girard Marie-Pier , Hébert Marie-Ève , Descarreaux Martin 
Published: May 2019

AimTo further the understanding of the pathophysiological mechanisms underlying tension-type headache (TTH) by comparing the endurance and strength of neck extensor muscles under acute muscle fatigue in participants with TTH and asymptomatic participants.MethodsWe conducted a cross-sectional analysis of neck extensor muscle performance. Asymptomatic participants and participants with TTH were recruited via social media platforms and from the Université du Québec à Trois-Rivières community and employees. A total of 44 participants with TTH and 40 asymptomatic participants took part in an isometric neck extensor endurance task performed at 60% of their maximum voluntary contraction. Inclusion criteria for the headache group were to be older than 18 years old and to fulfil the International Headache Society classification’s criteria for either frequent episodic or chronic TTH. Clinical (self-efficacy, anxiety, neck disability and kinesiophobia) and physical parameters (neck extensors maximum voluntary contraction, endurance time, muscle fatigue) as well as characteristics of headache episodes (intensity, frequency and associated disability) were collected for all participants. Surface electromyography was used to document upper trapezius, splenius capitis and sternocleidomastoids muscle activity and muscle fatigue.ResultsBoth groups displayed similar neck extensor muscle endurance capacity with a mean difference of 6.2 s (p>0.05) in favour of the control group (control=68.1±32.3; TTH=61.9±20.1). Similarly, participants in the headache group showed comparable neck extensor muscle strength (95.9±30.4 N) to the control group (111.3±38.7 N). Among participants with TTH, those scoring as severely incapacitated by headaches were the ones with higher neck-related disability (F[1,44]=10.77; p=0.002), the more frequent headache episodes (F[1,44]=6.70; p=0.01) and higher maximum headache intensity (F[1,44]=10.81; p=0.002).ConclusionA fatigue task consisting of isometric neck extension cannot efficiently differentiate participants with TTH from asymptomatic participants.
Is neighbourhood social cohesion associated with subjective well-being for older Chinese people? The neighbourhood social cohesion study
Authors: Yu Ruby , Cheung Osbert , Leung Jason , Tong Cecilia , Lau Kevin , Cheung Johnny , Woo Jean 
Published: May 2019

ObjectivesTo evaluate the psychometric properties of the Hong Kong version of Neighbourhood Cohesion Instrument (HK-NCI) and examine whether neighbourhood social cohesion as measured using HK-NCI would be associated with evaluative, hedonic and eudaemonic well-being.DesignA validation analysis followed by a cross-sectional analysis of a community-based survey.SettingCommunities in two districts (Sha Tin and Tai Po) in Hong Kong.Participants301 community-dwelling Chinese men and women aged 60 years and older normally residing in Sha Tin or Tai Po for not less than six consecutive months at the time of participation in the study were interviewed.MeasurementsNeighbourhood social cohesion was measured using the 15-item HK-NCI. The Social Cohesion Scale (SCS) and the Brief Sense of Community Scale (BSCS) were administered for assessing the validity of the HK-NCI. Evaluative (life satisfaction), hedonic (feelings of happiness) and eudaemonic well-being (sense of purpose and meaning in life) were examined. Socio-demographic characteristics, lifestyle and health behaviours, medical history, and neighbourhood characteristics were used as covariates.ResultsFor homogeneity, internal consistency of HK-NCI (α=0.813) was good. For stability (test–retest reliability), the averages of mean scores of the 15 items suggested an acceptable repeatability with an intra-class correlation coefficient=0.701(95% CI 0.497 to 0.832). HK-NCI was correlated with SCS (r=0.515–0.635, p<0.001) and BSCS (r=0.500–0.612, p<0.001). Neighbourhood social cohesion was positively and independently associated with life satisfaction, feelings of happiness and sense of purpose and meaning in life (all p values <0.05). Stratified analyses indicated that neighbourhood social cohesion was more strongly associated with all dimensions of subjective well-being in ‘young-old’ subgroup, and with sense of purpose and meaning in life for women.ConclusionThe HK-NCI has adequate levels of internal consistency and test–retest reliability. In addition, higher levels of neighbourhood social cohesion were associated with better subjective well-being among older Chinese people.
What works best when implementing a physical activity intervention for teenagers? Reflections from the ACTIVE Project: a qualitative study
Authors: James Michaela , Christian Danielle , Scott Samantha , Todd Charlotte , Stratton Gareth , Demmler Joanne , McCoubrey Sarah , Halcox Julian , Audrey Suzanne , Ellins Elizabeth A , Irvine Elizabeth , Brophy Sinead 
Published: May 2019

ObjectiveThis paper explores what aspects of a multicomponent intervention were deemed strengths and weaknesses by teenagers and the local council when promoting physical activity to young people.DesignQualitative findings at 12 months from a mixed method randomised control trial.MethodsActive Children Through Incentive Vouchers—Evaluation (ACTIVE) gave teenagers £20 of activity enabling vouchers every month for a year. Peer mentors were also trained and a support worker worked with teenagers to improve knowledge of what was available. Semistructured focus groups took place at 12 months to assess strengths and weaknesses of the intervention. Eight focus groups (n=64 participants) took place with teenagers and one additional focus group was dedicated to the local council’s sport development team (n=8 participants). Thematic analysis was used to analyse the data.ResultsTeenagers used the vouchers on three main activities: trampolining, laser tag or the water park. These appeal to both genders, are social, fun and require no prior skill or training. Choice and financial support for teenagers in deprived areas was considered a strength by teenagers and the local council. Teenagers did not engage with a trained peer mentor but the support worker was considered helpful.ConclusionsThe ACTIVE Project’s delivery had both strengths and weakness that could be used to underpin future physical activity promotion. Future interventions should focus on improving access to low cost, fun, unstructured and social activities rather than structured organised exercise/sport. The lessons learnt from this project can help bridge the gap between what is promoted to teenagers and what they actually want from activity provision.Trial registration numberISRCTN75594310
Associations between anthropometric indicators and both refraction and ocular biometrics in a cross-sectional study of Chinese schoolchildren
Authors: Ye Sheng , Liu Shengxin , Li Wenlei , Wang Qifan , Xi Wei , Zhang Xin 
Published: May 2019

ObjectiveTo identify associations between anthropometric indicators (height, weight and body mass index (BMI)) and both refraction and ocular biometrics in Chinese schoolchildren in Tianjin, China.DesignCross-sectional study.ParticipantsA total of 482 (86.07%) students (6–15 years old) with no history of ocular or systemic pathologies were enrolled in this study.MethodologyHeight and weight were measured using standardised protocols. Ocular biometrics (axial length (AL), vitreous chamber depth (VCD) and corneal curvature (CC)) were measured by a low-coherence optical reflectometry device. Cycloplegic refraction was measured using autorefraction. The AL/CC ratio and spherical equivalent refraction (SER) were calculated. Myopia was defined as SER ≤−0.50 dioptres (D). Multiple linear regression analysis was performed to explore the associations between anthropometric indicators (height, weight and BMI) and both refraction and ocular biometrics.ResultsThe overall prevalence of myopia was 71.16%. Overall, only height was associated with ALs, VCDs, AL/CC ratios and refractions after controlling for age, gender, parental myopia, family income, reading and writing distance and time spent outdoors. Furthermore, age-specific results demonstrated that height and weight were independently associated with refraction in participants aged 6–8 years and 9–11 years participants. Higher heights in schoolchildren were associated with longer ALs (regression coefficientb=+0.25 for each 10 cm difference in height, p<0.01), deeper VCDs (b=+0.23, p<0.01), higher AL/CC ratios (b=+0.04, p<0.01) and more negative refractions (b=−0.48, p<0.01). Heavier weights were also associated with longer ALs (+0.29 mm, p<0.01), deeper VCDs (+0.29 mm, p<0.01), higher AL/CC ratios (+0.04, p<0.01) and more negative refractions (−0.48 D, p<0.01).ConclusionsHeight and weight remained independently related to refraction and various ocular biometrics during the early adolescent growth period after adequately controlling for covariates, which could support the idea that a shared mechanism may regulate the coordinated growth of body and eye size in children.