bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cascading spatial and trophic impacts of oak decline on the soil food web
Authors: Domínguez‐Begines Jara , De Deyn Gerlinde B. , García Luis V. , Eisenhauer Nico , Gómez‐Aparicio Lorena 
Published: November 2018

Abstract

Tree defoliation and mortality have considerably increased world‐wide during the last decades due to global change drivers such as increasing drought or invasive pests and pathogens. However, the effects of this tree decline on soil food webs are poorly understood.

In this study, we evaluated the impacts of Quercus suber decline on soil food webs of Mediterranean mixed forests invaded by the exotic oomycete pathogen Phytophthora cinnamomi, using soil nematodes as bioindicator taxa. We used a spatially explicit neighbourhood approach to predict the characteristics of the nematode community (diversity, trophic structure, and several indices indicative of soil food web conditions) as a function of the characteristics of the tree and shrub community (species composition, size, and health status).

Our results indicate that the process of defoliation and mortality of Q. suber caused significant alterations in the nematode trophic structure increasing the abundance of lower trophic levels (bacterivores, fungivores, and herbivores) and decreasing the abundance of higher levels (predators and omnivores). Furthermore, Q. suber decline altered the functional composition of soil communities, producing a setback of the ecological succession in the soil food web to an earlier stage (decrease in the maturity index and increase in the plant parasitic index), simplified soil food webs (decrease in the structure index), and shifts in the predominant decomposition channel (increase in the fungivores/bacterivores ratio).

We also detected contrasting characteristics of the nematode community in neighbourhoods dominated by coexisting woody species, which suggests potential for long‐term indirect effects on soil food webs due to the substitution of Q. suber by non‐declining species.

Synthesis. Our study provides novel results that show the major impacts that ongoing health deterioration of dominant tree species can have on the structure and composition of soil food webs in forest systems invaded by exotic pathogens, with cascading consequences for soil biogeochemical processes in both the short‐ and long term.
Evaluation Of A Powder‐Free DNA Extraction Method For Skeletal Remains
Authors: Harrel Michelle , Mayes Carrie , Gangitano David , Hughes‐Stamm Sheree 
Published: November 2018

AbstractBones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality.
Effects of fluctuating thermal regimes on cold survival and life history traits of the spotted wing Drosophila (Drosophila suzukii)
Authors: Enriquez Thomas , Ruel David , Charrier Maryvonne , Colinet Hervé 
Published: November 2018

AbstractDrosophila suzukii is an invasive pest causing severe damages to a large panel of cultivated crops. To facilitate its biocontrol with strategies such as sterile or incompatible insect techniques, D. suzukii must be mass‐produced and then stored and transported under low temperature. Prolonged cold exposure induces chill injuries that can be mitigated if the cold period is interrupted with short warming intervals, referred to as fluctuating thermal regimes (FTR). In this study, we tested how to optimally use FTR to extend the shelf life of D. suzukii under cold storage. Several FTR parameters were assessed: temperature (15, 20, 25 °C), duration (0.5, 1, 2, 3 h), and frequency (every 12, 24, 36, 48 h) of warming intervals, in two wild‐type lines and in two developmental stages (pupae and adults). Generally, FTR improved cold storage tolerance with respect to constant low temperatures (CLT). Cold mortality was lower when recovery temperature was 20 °C or higher, when duration was 2 h per day or longer, and when warming interruptions occurred frequently (every 12 or 24 h). Applying an optimized FTR protocol to adults greatly reduced cold mortality over long‐term storage (up to 130 d). Consequences of FTR on fitness‐related traits were also investigated. For adults, poststorage survival was unaffected by FTR, as was the case for female fecundity and male mating capacity. On the other hand, when cold storage occurred at pupal stage, poststorage survival and male mating capacity were altered under CLT, but not under FTR. After storage of pupae, female fecundity was lower under FTR compared to CLT, suggesting an energy trade‐off between repair of chill damages and egg production. This study provides detailed information on the application and optimization of an FTR‐based protocol for cold storage of D. suzukii that could be useful for the biocontrol of this pest.
Long‐term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis
Authors: Fischer Martin Alexander , Güllert Simon , Refai Sarah , Künzel Sven , Deppenmeier Uwe , Streit Wolfgang R. , Schmitz Ruth Anne 
Published: November 2018

SummaryAmmonia caused disturbance of biogas production is one of the most frequent incidents in regular operation of biogas reactors. This study provides a detailed insight into the microbial community of a mesophilic, full‐scale biogas reactor (477 kWh h−1) fed with maize silage, dried poultry manure and cow manure undergoing initial process disturbance by increased ammonia concentration. Over a time period of 587 days, the microbial community of the reactor was regularly monitored on a monthly basis by high‐throughput amplicon sequencing of the archaeal and bacterial 16S rRNA genes. During this sampling period, the total ammonia concentrations varied between 2.7 and 5.8 g l−1 [NH4+–N]. To gain further inside into the active metabolic pathways, for selected time points metatranscriptomic shotgun analysis was performed allowing the quantification of marker genes for methanogenesis, hydrolysis and syntrophic interactions. The results obtained demonstrated a microbial community typical for a mesophilic biogas plant. However in response to the observed changing process conditions (e.g. increasing NH4+ levels, changing feedstock composition), the microbial community reacted highly flexible by changing and adapting the community composition. The Methanosarcina‐dominated archaeal community was shifted to a Methanomicrobiales‐dominated archaeal community in the presence of increased ammonia conditions. A similar trend as in the phylogenetic composition was observed in the transcription activity of genes coding for enzymes involved in acetoclastic methanogenesis and syntrophic acetate oxidations (Codh/Acs and Fthfs). In accordance, Clostridia simultaneously increased under elevated ammonia concentrations in abundance and were identified as the primary syntrophic interaction partner with the now Methanomicrobiales‐dominated archaeal community. In conclusion, overall stable process performance was maintained during increased ammonia concentration in the studied reactor based on the microbial communities’ ability to flexibly respond by reorganizing the community composition while remaining functionally stable.
MiR‐145‐targeted HBXIP modulates human breast cancer cell proliferation
Authors: Jiang Yang , Wang Dan , Ren Hui , Shi Ying , Gao Yufei 
Published: November 2018

BackgroundMiR‐145 has been identified as a tumor suppressive microRNA in multiple cancers. In this current investigation, we searched for new direct targets of miR‐145 and evaluated their effect on breast cancer development.MethodsTargetscan was used to predict the target genes of miR‐145. The targeting of miR‐145 on oncogenic HBXIP was verified by luciferase reporter gene analysis. The effect of miR‐145 on the level of messenger RNA and protein of HBXIP was evaluated by quantitative real‐time PCR and immunoblotting. Correlations between miR‐145 and HBXIP, as well as miR‐145 expression, were analyzed in 30 paired breast cancer and noncancerous tissues by quantitative real‐time PCR. Methyl thiazol tetrazolium and colony formation assays were applied to determine the cell proliferation ability.Results
HBXIP was identified as a novel target gene of miR‐145 in breast cancer. MiR‐145 was found to dose‐dependently decrease messenger RNA and protein expression of HBXIP in breast cancer MCF‐7 cells. Notably, miR‐145 expression was negatively related to HBXIP expression and was obviously reduced in breast cancer samples. Finally, miR‐145 suppressed cell proliferation while its inhibitor, anti‐miR‐145, accelerated cell proliferation. Interestingly, silencing of HBXIP reversed the acceleration of cell proliferation induced by anti‐miR‐145 in breast cancer.ConclusionOncogenic HBXIP is a new direct target of tumor suppressive miR‐145. Our findings reveal that miR‐145‐targeting HBXIP could be a potential therapeutic target in breast cancer.
Functional traits and community composition: A comparison among community‐weighted means, weighted correlations, and multilevel models
Authors: Miller Jesse E. D. , Damschen Ellen I. , Ives Anthony R. 
Published: November 2018

Abstract

Of the several approaches that are used to analyse functional trait–environment relationships, the most popular is community‐weighted mean regressions (CWMr) in which species trait values are averaged at the site level and then regressed against environmental variables. Other approaches include model‐based methods and weighted correlations of different metrics of trait–environment associations, the best known of which is the fourth‐corner correlation method.

We investigated these three general statistical approaches for trait–environment associations: CWMr, five weighted correlation metrics (Peres‐Neto, Dray, & ter Braak, Ecography, 40, 806–816, 2017), and two multilevel models (MLM) using four different methods for computing p‐values. We first compared the methods applied to a plant community dataset. To determine the validity of the statistical conclusions, we then performed a simulation study.

CWMr gave highly significant associations for both traits, whereas the other methods gave a mix of support. CWMr had inflated type I errors for some simulation scenarios, implying that the significant results for the data could be spurious. The weighted correlation methods had generally good type I error control but had low power. One of the multilevel models, that from Jamil, Ozinga, Kleyer, and ter Braak (Journal of Vegetation Science, 24, 988–1000, 2013) had both good type I error control and high power when an appropriate method was used to obtain p‐values. In particular, if there was no correlation among species in their abundances among sites, a parametric bootstrap likelihood ratio test (LRT) gave the best power. When there was correlation among species in their abundances, a conditional parametric LRT had correct type I errors but had lower power.

There is no overall best method for identifying trait–environment associations. For the simple task of testing associations between single environmental variables and single traits, the weighted correlations with permutation tests all had good type I error control, and their ease of implementation is an advantage. For the more complex task of multivariate analyses and model fitting, and when high statistical power is needed, we recommend MLM2 (Jamil et al., 2013). However, care must be taken to ensure against inflated type I errors for both weighted correlations and MLM2. Because CWMr exhibited highly inflated type I error rates, it should always be avoided.
Tracking Assault‐injured, Drug‐using Youth in Longitudinal Research: Follow‐up Methods
Authors: Roche Jessica S. , Clery Michael J. , Carter Patrick M. , Dora‐Laskey Aaron , Walton Maureen A. , Ngo Quyen M. , Cunningham Rebecca M. 
Published: November 2018

AbstractObjectivesViolence is one of the leading causes of death among youth ages 14 to 24. Hospital‐ and emergency department (ED)‐based violence prevention programs are increasingly becoming a critical part of public health efforts; however, evaluation of prevention efforts is needed to create evidence‐based best practices. Retention of study participants is key to evaluations, although little literature exists regarding optimizing follow‐up methods for violently injured youth. This study aims to describe the methods for retention in youth violence studies and the characteristics of hard‐to‐reach participants.MethodsThe Flint Youth Injury (FYI) Study is a prospective study following a cohort of assault‐injured, drug‐using youth recruited in an urban ED, and a comparison population of drug‐using youth seeking medical or non–violence‐related injury care. Validated survey instruments were administered at baseline and four follow‐up time points (6, 12, 18, and 24 months). Follow‐up contacts used a variety of strategies and all attempts were coded by type and level of success. Regression analysis was used to predict contact difficulty and follow‐up interview completion at 24 months.ResultsA total of 599 patients (ages 14–24) were recruited from the ED (mean ± SD age = 20.1 ± 2.4 years, 41.2% female, 58.2% African American), with follow‐up rates at 6, 12, 18, and 24 months of 85.3%, 83.7% 84.2%, and 85.3%, respectively. Participant contact efforts ranged from two to 53 times per follow‐up time frame to complete a follow‐up appointment, and more than 20% of appointments were completed off site at community locations (e.g., participants’ homes, jail/prison). Participants who were younger (p < 0.05) and female (p < 0.01) were more likely to complete their 24‐month follow‐up interview. Participants who sought care in the ED for assault injury (p < 0.05) and had a substance use disorder (p < 0.01) at baseline required fewer contact attempts to complete their 24‐month follow‐up, while participants reporting a fight within the immediate 3 months before their 24‐month follow‐up (p < 0.01) required more intensive contact efforts.ConclusionsThe FYI study demonstrated that achieving high follow‐up rates for a difficult‐to‐track, violently‐injured ED population is feasible through the use of established contact strategies and a variety of interview locations. Results have implications for follow‐up strategies planned as part of other violence prevention studies.
A Machine Learning Approach to Predicting Need for Hospitalization for Pediatric Asthma Exacerbation at the Time of Emergency Department Triage
Authors: Patel Shilpa J. , Chamberlain Daniel B. , Chamberlain James M. 
Published: November 2018

AbstractObjectivesPediatric asthma is a leading cause of emergency department (ED) utilization and hospitalization. Earlier identification of need for hospital‐level care could triage patients more efficiently to high‐ or low‐resource ED tracks. Existing tools to predict disposition for pediatric asthma use only clinical data, perform best several hours into the ED stay, and are static or score‐based. Machine learning offers a population‐specific, dynamic option that allows real‐time integration of available nonclinical data at triage. Our objective was to compare the performance of four common machine learning approaches, incorporating clinical data available at the time of triage with information about weather, neighborhood characteristics, and community viral load for early prediction of the need for hospital‐level care in pediatric asthma.MethodsRetrospective analysis of patients ages 2 to 18 years seen at two urban pediatric EDs with asthma exacerbation over 4 years. Asthma exacerbation was defined as receiving both albuterol and systemic corticosteroids. We included patient features, measures of illness severity available in triage, weather features, and Centers for Disease Control and Prevention influenza patterns. We tested four models: decision trees, LASSO logistic regression, random forests, and gradient boosting machines. For each model, 80% of the data set was used for training and 20% was used to validate the models. The area under the receiver operating characteristic (AUC) curve was calculated for each model.ResultsThere were 29,392 patients included in the analyses: mean (±SD) age of 7.0 (±4.2) years, 42% female, 77% non‐Hispanic black, and 76% public insurance. The AUCs for each model were: decision tree 0.72 (95% confidence interval [CI] = 0.66–0.77), logistic regression 0.83 (95% CI = 0.82–0.83), random forests 0.82 (95% CI = 0.81–0.83), and gradient boosting machines 0.84 (95% CI = 0.83–0.85). In the lowest decile of risk, only 3% of patients required hospitalization; in the highest decile this rate was 100%. After patient vital signs and acuity, age and weight, followed by socioeconomic status (SES) and weather‐related features, were the most important for predicting hospitalization.ConclusionsThree of the four machine learning models performed well with decision trees preforming the worst. The gradient boosting machines model demonstrated a slight advantage over other approaches at predicting need for hospital‐level care at the time of triage in pediatric patients presenting with asthma exacerbation. The addition of weight, SES, and weather data improved the performance of this model.
Alcohol Use Among Never‐Deployed U.S. Army Reserve and National Guard Soldiers: The Effects of Nondeployment Emotions and Sex
Authors: Hoopsick Rachel A. , Homish D. Lynn , Vest Bonnie M. , Homish Gregory G. 
Published: November 2018

BackgroundLimited research shows that mental health problems are prevalent among never‐deployed soldiers and many experience negative emotions related to their nondeployment. U.S. Army Reserve/National Guard (USAR/NG) soldiers are also at high risk for alcohol misuse. However, it is not known if nondeployment emotions contribute to an increased risk of alcohol misuse among never‐deployed USAR/NG soldiers.MethodsData are from Operation: SAFETY (Soldiers and Families Excelling Through the Years), an ongoing study of USAR/NG soldiers. We used regression models to examine the relations between nondeployment emotions, assessed by the Non‐Deployment Emotions (NDE) Questionnaire, and a range of alcohol use outcomes, assessed by the Alcohol Use Disorders Identification Test and standard quantity and frequency questions, among a sample of never‐deployed soldiers who were partnered at baseline (N = 174). Final models controlled for years of military service, current number of close military friends in the social network, marital satisfaction, and depression. We also tested for potential differences in these associations by sex.ResultsNondeployment emotions were associated with frequency of getting drunk (adjusted risk ratio [aRR] = 1.02, 95% CI: 1.01, 1.04; p < 0.05) and typical number of drinks consumed during a drinking episode (aRR = 1.03, 95% CI: 1.01, 1.04; p < 0.01). Nondeployment emotions had a trend‐level association with percent of days drinking (adjusted odds ratio = 1.05, 95% CI: 1.00, 1.11; p = 0.055). Nondeployment emotions had a significant interaction with sex (p < 0.05) on the likelihood of alcohol problems, such that only male soldiers experienced a greater likelihood of alcohol problems when they had highly negative nondeployment emotions. There was no relation between nondeployment emotions and alcohol problems among female soldiers.ConclusionsFindings demonstrate that greater nondeployment emotions are associated with increased alcohol use among never‐deployed USAR/NG soldiers. The NDE Questionnaire may assist in identifying those at highest risk for alcohol problems.
Parental perception on the effects of early exposure to anaesthesia on neurodevelopment
Authors: Koh J. H. , Daniel P. , Bong C. L. 
Published: November 2018

SummarySeveral studies have investigated the effects of general anaesthesia on neurodevelopment in children, with conflicting results. The potential for early general anaesthesia exposure to impact neurodevelopment in children may cause significant concern for parents. Administering a questionnaire in 200 parents, we aimed to explore their knowledge, concerns and perceptions, and determine factors which influence parents’ willingness for their children to participate in relevant research studies. A significant proportion of parents (40%) were concerned that general anaesthesia may affect their child's neurodevelopment. Generally these concerns arose from the parents’ own beliefs or preconceived ideas and only 25.5% had encountered prior information in this domain. Parents with children aged 2 years or younger, those whose children had previous general anaesthesia exposure, and those who had encountered information about potential neurodevelopmental effects were most likely to be concerned. The majority of parents (68%) would agree to participate in research studies, especially if they were able to receive the test results. Anaesthetists should pre‐emptively initiate discussions to address any potential misconceptions regarding the effects of general anaesthesia on neurodevelopment in children.
The therapeutic space and doctor–parent relationship in paediatrics: trainees’ experiences and perspectives
Authors: Arzuaga Bonnie H. , Petty Carter , Janvier Annie 
Published: November 2018

AbstractAimTo explore paediatric trainees’ experiences and perspectives regarding interactions and relationships between physicians and patients’ parents.MethodsEmail survey was sent to AAP Section of Pediatric Trainees members. Trainees were asked about 40 interactions with parents as well as perceived benefits/risks and potential influences. Analysis of associations between variables and perspectives/experiences used chi‐square and Fisher exact.ResultsThree hundred and seventy surveys were completed. Respondents participated in a median of nine interactions (IQR 7–13; range 0–37): 99.7% participated in at least one; 52% in 5–10; 41% in >10. 50% reported refusing to participate in at least one interaction following parental request; 8% refused 5–10; 1% refused >10. Electronic communication/social media domain had highest refusals and most interactions respondents believed should never be allowed. 94% agreed that interactions may be beneficial to providers: 75% identified at least one benefit; 86% one risk. Respondents who are parents or female reported increased interactions.ConclusionA variety of interactions with patient's parents are common amongst paediatric trainees, who identify risks and benefits. Disagreements relative to acceptability of certain interactions points to the need for additional research. A reflective educational approach, rather than a prescriptive one, may help trainees better manage these relationships.