bluuebunny/crossref_metadata_2025 huggingface dataset:
Intensive and Specific Feedback Self-control of the Argonautes and MicroRNA Targeting Activity
Authors: Wang Degeng , Gill Audrey , Zhang Fangyuan
Published: September 2018

The miRNA pathway consists of three segments – biogenesis, targeting and downstream regulatory effectors. How the cells control their activities remains incompletely understood. This study explored the intrinsically complex miRNA-mRNA targeting relationships, and suggested differential mechanistic control of the three segments. We first analyzed evolutionarily conserved sites for conserved miRNAs in the human transcriptome. Strikingly, AGO1, AGO2 and AGO3 are all among the top 14 mRNAs with highest numbers of unique conserved miRNA sites, and so is ANKRD52, the phosphatase regulatory subunit of the recently identified AGO phosphorylation cycle (AGOs, CSNK1A1, ANKRD52 and PPP6C). The mRNAs for TNRC6, which acts together with loaded AGO to channel miRNA-mediated regulation actions onto specific mRNAs, are also heavily miRNA-targeted. Moreover, mRNAs of the AGO phosphorylation cycle share much more than expected miRNA binding sites. In contrast, upstream miRNA biogenesis mRNAs do not display these characteristics, and neither do the downstream regulatory effector mRNAs. In a word, miRNAs heavily and directly feedback-regulate their targeting machinery mRNAs, but neither upstream biogenesis nor downstream regulatory effector mRNAs. The observation was then confirmed with experimentally determined miRNA-mRNA target relationships. In summary, our exploration of the miRNA-mRNA target relationship uncovers intensive, and specific, feedback auto-regulation of miRNA targeting activity directly by miRNAs themselves, i.e., segment-specific feedback auto-regulation of miRNA pathway. Our results also suggest that the complexity of miRNA-mRNA targeting relationship – a defining feature of miRNA biology – should be a rich source for further functional exploration.
Relationships of trainee dentists’ empathy and communication characteristics with simulated patients’ assessment in medical interviews
Authors: Watanabe Sho , Yoshida Toshiko , Kono Takayuki , Taketa Hiroaki , Shiotsu Noriko , Shirai Hajime , Torii Yasuhiro
Published: September 2018

Objectives

We aimed to clarify the characteristics of communication between trainee dentists and simulated patients (SPs) and to examine how the level of trainee dentists’ self-reported empathy influences assessment by SPs in medical interviews.

Materials and methods

The study involved 100 trainee dentists at Okayama University Hospital and eight SPs. The trainee dentists conducted initial interviews with the SPs after completing the Japanese version of the Jefferson Scale of Empathy. Their interviews were recorded and analyzed using the Roter Interaction Analysis System. The SPs assessed the trainees’ communication immediately after each interview. The trainee dentists were classified into two groups (more positive and less positive groups) according to SP assessment scores.

Results

Compared with the less positive trainees, the more positive trainees scored higher on the [Emotional expression] and lower on the [Medical data gathering] Roter Interaction Analysis System categories. There was no difference in [Dental data gathering] between the two groups. The SPs of more positive trainees had higher rates of [Positive talk] and [Emotional expression] and lower rates of [Medical information giving] and [Dental information giving]. The trainees with more positive ratings from SPs had significantly higher Jefferson Scale of Empathy total scores.

Conclusion

The results of this study suggest that responding to the SPs’ emotions is a relevant characteristic of dentist–SP communication to SPs’ positive assessment in medical interviews. Further, trainees’ self-reported empathy was related with the SPs’ assessment of trainees’ communication, which indicated that patient satisfaction can be improved by increasing the dentist’s empathy. Thus, an empathic attitude among dentists is a significant determinant of patient satisfaction.
Metagenomic profiling of ticks: identification of novel rickettsial genomes and detection of tick borne canine parvovirus
Authors: Ravi Anuradha , Ereqat Suheir , Al-Jawabreh Amer , Abdeen Ziad , Shamma Omar Abu , Hall Holly , Pallen Mark J. , Nasereddin Abedelmajeed
Published: September 2018

Background

Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors.

Methodology/Principal Findings

We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genusRickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar toRickettsia massiliaestrain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogenCandidatusRickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of strains of the Coxiella-like endosymbiontCandidatusCoxeilla mudrowiae. A sheep tick yielded sequences from the sheep pathogenAnaplasma ovis, whileHyalommaticks from camels yielded sequences belonging toFrancisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus.

Significance

Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (CandidatusRickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.

Author Summary

We have shown how DNA sequencing can be used to detect and characterise potentially pathogenic microorganisms carried by ticks. We surveyed hard ticks collected from domesticated animals across the West Bank territory of Palestine. All the ticks came from species that are also capable of feeding on humans. We detected several important pathogens, including two species ofRickettsia, the sheep pathogenAnaplasma ovisand canine parvovirus. These findings highlight the importance of hard ticks and the hazards they present for human and animal health in Palestine and the opportunities presented by high-throughput sequencing and bioinformatics analyses of DNA sequences in this setting.
Gp78 E3 ubiquitin ligase mediates both basal and damage-induced mitophagy
Authors: Joshi Bharat , Mohammadzadeh Yayha , Gao Guang , Nabi Ivan R.
Published: September 2018

Mitophagy, the elimination of mitochondria by the autophagy machinery, evolved to monitor mitochondrial health and maintain mitochondrial integrity. PINK1 is a sensor of mitochondrial health that recruits Parkin and other mitophagy-inducing ubiquitin ligases to depolarized mitochondria. However, mechanisms underlying mitophagic control of mitochondrial homeostasis, basal mitophagy, remain poorly understood. The Gp78 E3 ubiquitin ligase, an endoplasmic reticulum membrane protein, induces mitochondrial fission, endoplasmic reticulum-mitochondria contacts and mitophagy of depolarized mitochondria. CRISPR/Cas9 knockout of Gp78 in HT-1080 fibrosarcoma cells results in reduced ER-mitochondria contacts, increased mitochondrial volume and resistance to CCCP-induced mitophagy. Knockdown (KD) of the essential autophagy protein ATG5 increased mitochondrial volume of wild-type cells but did not impact mitochondrial volume of Gp78 knockout cells. This suggests that endogenous Gp78 actively eliminates mitochondria by autophagy in wild-type HT-1080 cells. Damage-induced mitophagy of depolarized mitochondria, in the presence of CCCP, but not basal mitophagy was prevented by knockdown of PINK1. This suggests that endogenous Gp78 plays dual roles in mitophagy induction: 1) control of mitochondrial homeostasis through mitophagy of undamaged mitochondria; and 2) elimination of damaged mitochondria through PINK1.
X-ray structure of alisporivir in complex with cyclophilin A at 1.5 Å resolution
Authors: Dujardin Marie , Bouckaert Julie , Rucktooa Prakash , Hanoulle Xavier
Published: September 2018

Alisporivir (ALV) is an 11-amino-acid hydrophobic cyclic peptide withN-methyl-D-alanine andN-ethyl-L-valine (NEV) residues at positions 3 and 4, respectively. ALV is a non-immunosuppressive cyclosporin A (CsA) derivative. This inhibitor targets cyclophilins (Cyps), a family of proteins with peptidyl-prolylcis/transisomerase enzymatic activity. Cyps act as protein chaperones and are involved in numerous cellular functions. Moreover, Cyps have been shown to be an essential cofactor for the replication of many viruses, includingHepatitis C virusandHuman immunodeficiency virus, and have also been shown to be involved in mitochondrial diseases. For these reasons, cyclophilins represent an attractive drug target. The structure of ALV in complex with cyclophilin A (CypA), the most abundant Cyp in humans, has been determined at 1.5 Å resolution. This first structure of the CypA–ALV complex shows that the binding of ALV is highly similar to that of CsA. The high resolution allowed the unambiguous determination of the conformations of residues 3 and 4 in ALV when bound to its target. In particular, the side-chain conformation of NEV4 precludes the interaction of the CypA–ALV complex with calcineurin, a cellular protein phosphatase involved in the immune response, which explains the non-immunosuppressive property of ALV. This study provides detailed molecular insights into the CypA–ALV interaction.
Application of differential resonant high-energy X-ray diffraction to three-dimensional structure studies of nanosized materials: A case study of Pt–Pd nanoalloy catalysts
Authors: Petkov Valeri , Shastri Sarvjit , Kim Jong-Woo , Shan Shiyao , Luo Jin , Wu Jinfang , Zhong Chuan-Jian
Published: September 2018

Atoms in many of the increasingly complex nanosized materials of interest to science and technology do not necessarily occupy the vertices of Bravais lattices. The atomic scale structure of such materials is difficult to determine by traditional X-ray diffraction and so their functional properties remain difficult to optimize by rational design. Here, the three-dimensional structure of PtxPd100−xnanoalloy particles is determined, wherex= 0, 14, 36, 47, 64 and 100, by a non-traditional technique involving differential resonant high-energy X-ray diffraction experiments conducted at theKedge of Pt and Pd. The technique is coupled with three-dimensional modeling guided by the experimental total and element-specific atomic pair distribution functions. Furthermore, using DFT (density functional theory) calculation based on the positions of atoms in the obtained three-dimensional structure models, the catalytic performance of Pt–Pd particles is explained. Thus, differential resonant high-energy X-ray diffraction is shown to be an excellent tool for three-dimensional structure studies of nanosized materials. The experimental and modeling procedures are described in good detail, to facilitate their wider usage.
X-ray reflectivity of chemically vapor-deposited diamond single crystals in the Laue geometry
Authors: Stoupin S. , Ruff J. P. C. , Krawczyk T. , Finkelstein K. D.
Published: September 2018

The absolute X-ray reflectivity of chemically vapor-deposited (CVD) single-crystal diamond plates was measured in the Laue geometry in the double-crystal non-dispersive setting with an asymmetric Si beam-conditioner crystal. The measurements were supplemented by rocking-curve topography. The measured reflectivity curves are examined in the framework of the Darwin–Hamilton approach using a set of two independent parameters: the characteristic thickness of mosaic blocks and their average angular misorientation. Owing to strong extinction effects, the width of the reflectivity curves does not directly represent the average misorientation of the blocks. Two different sets of parameters were found for the 111 asymmetric reflection in the two different scattering configurations (beam compression and beam expansion). Analysis of the rocking-curve topographs shows that this discrepancy can be attributed to inhomogeneity of the diamond crystal microstructure.
The real part of the dispersion surface in X-ray dynamical diffraction in the Laue case for perfect crystals
Authors: Saka Takashi
Published: September 2018

The real part of the dispersion surface in X-ray dynamical diffraction in the Laue case for perfect crystals is analysed using a Riemann surface. In the conventional two-beam approximation, each branch or wing of the dispersion surface is specified by one sheet of the Riemann surface. The characteristic features of the dispersion surface are analytically revealed using four parameters, which are the real and imaginary parts of two quantities that specify the degree of departure from the exact Bragg condition and the reflection strength. The present analytical method is generally applicable, irrespective of the magnitudes of the parameters with no approximation. Characteristic features of the dispersion surface are also revealed by geometrical considerations with respect to the Riemann surface.
Crystal structure of theAcinetobacter baumanniiouter membrane protein Omp33
Authors: Abellón-Ruiz Javier , Zahn Michael , Baslé Arnaud , van den Berg Bert
Published: September 2018

Acinetobacter baumanniiis becoming a major threat to human health due to its multidrug resistance. This is owing in a large part to the low permeability of its outer membrane (OM), which prevents high internal antibiotic concentrations and makes antibiotic-resistance mechanisms more effective. To exploit OM channels as potential delivery vehicles for future antibiotics, structural information is required. One abundant OM protein inA. baumanniiis Omp33. This protein has been reported to be important for thein vivofitness and virulence ofA. baumannii, but its structure is not known. Here, the X-ray crystal structure of Omp33 is reported at a resolution of 2.1 Å. Omp33 has a 14-β-stranded barrel without stable extracellular loop constrictions. Instead, an extended and unusual periplasmic turn connecting β-strands 2 and 3 is present, which folds into the pore lumen and completely blocks the aqueous channel. The Omp33 structure helps in understanding howA. baumanniiOM proteins contribute to the low permeability of the cell envelope of this bacterium and suggests that Omp33 might function as a gated channel.
Ovule bet‐hedging at high elevation in the South American Andes: Evidence from a phylogenetically controlled multispecies study
Authors: Arroyo Mary T. K. , Pérez Fernanda , Jara‐Arancio Paola , Pacheco Diego , Vidal Paula , Flores María Francisca
Published: September 2018

How animal‐pollinated plants support low and stochastic pollination in the high alpine is a key question in plant ecology. The ovule bet‐hedging hypothesis proposes compensation for stochastic pollination via ovule oversupply in flowers allowing the benefits of windfall pollination events to be reaped. Under this hypothesis, ovule number is expected to increase from tree line upward on high mountains characterized by steep declines in flower visitation rates and increasingly more variable pollination.

Ovule/floret number was investigated for a total of 174 simple‐flowered and pseudanthial species in the central Chilean Andes (2,100–3,650 m.a.s.l.). Phylogenetic reconstruction was undertaken using ITS sequences and a constrained ordinal‐level backbone reflecting the APG‐IV topology. Ovule/floret number was modelled with ordinary least squares regression (OLS) and phylogenetic generalized least squares regression (PGLS) with elevation, floral biomass, life history, pollinator efficiency, pollination generalization, and seasonal flowering period as explanatory variables.

The best performing OLS and PGLS models for simple‐flowered species consistently included vegetation belt and floral biomass, and with PGLS, pollination efficiency and flowering period. For pseudanthial species, explanatory variables were always floral biomass and its interaction with elevation. Effects of life history and generalized pollination was not found. Ovule/floret number showed high phylogenetic signal, increased with floral biomass and was generally higher in the upper alpine belt in both floral categories. Simple‐flowered species with efficient pollination and flowering early, respectively, had larger ovule numbers.

Synthesis. Ovule number increases with elevation in the central Chilean alpine in two separate floral groups independently of some effects of flowering period and pollinator efficiency. Greater disparity in pollen deposition on stigmas than with inefficient pollination under low visitation rates might explain the association between efficient pollination and higher ovule numbers. Our study provides the first empirical evidence for ovule bet‐hedging in the alpine environment. Future studies on the ovule bet‐hedging hypothesis should include a measure of flower size.
Heterotrophic substrate specificity in the aquatic environment: The role of microscale patchiness investigated using modelling
Authors: Hellweger Ferdi L.
Published: September 2018

Recent observations of natural bacterial communities show high genetic diversity in organic carbon uptake systems (microdiversity) and specificity in substrate species taken up. This seemingly contradicts a large body of literature from laboratory experiments under nutrient‐limiting conditions, where mixed substrate use is the rule. This apparent discrepancy can be resolved by realizing that bacteria in the natural aquatic environment encounter nutrients as high‐concentration patches. They may live in an ecologically nutrient‐limiting environment, but they are rarely in a biologically nutrient‐limited state. Rather they switch between non‐growing and nutrient‐replete states. During nutrient‐replete growth the metabolism is saturated and assimilating additional substrates does not increase the growth rate, but carrying the assimilation system constitutes a cost. Consequently, the specialist strategy is beneficial, which is consistent with observations from laboratory experiments. When the bacteria are not growing, the added cost also reduces the fitness of the generalist species. A simple mathematical model encompassing the relevant mechanisms is developed and parameterized realistically based on the literature. The model predicts that, under pulsed conditions, specialization is beneficial when the metabolic cost of an additional uptake system is more than ~0.5% of the total metabolic cost, which is a reasonable estimate and illustrates that this is a plausible hypothesis.
A Social‐Ecological Systems Approach to Enhance Sustainable Farming and Forestry in the EU
Authors: Dwyer Janet , Berriet‐Solliec Marielle , Lataste François Gaël , Short Chris , Maréchal Anne , Hart Kaley
Published: September 2018

The two concepts of public goods and ecosystem services are often used to describe the same welfare benefits potentially generated by agriculture and forestry, but they originate from different perspectives and each offer only partial analysis of these relationships. A more holistic approach – Social‐Ecological Systems (SES) – has been adapted and applied in new research to understand more fully how the relationships can best be characterised, and beneficial change promoted, through policy reforms and practical action. An important and novel part of the description of a SES, as developed under the PEGASUS project, is the assessment of its ‘valorisation cascade’. Through the mapping and consideration of assets, actors, interactions, drivers and the nature of the valorisation cascade in 34 diverse case studies, the project highlighted the importance of multi‐actor approaches and social processes to foster beneficial change. These include collective action, co‐learning and trust between actors, promoting experimentation and innovation, developing public and/or consumer awareness and identifying new valorisation options, including via commercial supply chains and enhanced community involvement.
Influence of pain score measured by a visual analog scale (PS‐VAS) on the Health Assessment Questionnaire Disability Index and 28‐joint Disease Activity Index with C‐reactive protein in rheumatoid arthritis patients
Authors: Yoshii Ichiro , Chijiwa Tatsumi , Sawada Naoya
Published: September 2018

Background

Pain is a serious burden for rheumatoid arthritis (RA) patients. However, the effect on Health Assessment Questionnaire Disability Index (HAQ‐DI) and 28‐joint Disease Activity Score (DAS28) has not been presented. The aim of this study is to evaluate them in a case series.

Methods

Three hundred and eighty‐two RA patients who were treated for more than 5 years were studied. The parameters assessed included average value of the DAS28 with C‐reactive protein (DAS28‐CRP), the HAQ‐DI score, the Sharp/van der Heijde Score (SvdHS), age, and the pain score measured by a visual analog scale (PS‐VAS). Relationships among these factors and the relationships between the HAQ‐DI score and the other factors, and the relationships between the change in HAQ‐DI scores and the changes in other factors were evaluated statistically with multivariate linear regression analysis. The effect of PS‐VAS on HAQ‐DI was compared with that of DAS28‐CRP on the overlapping data of each parameter.

Results

HAQ‐DI demonstrated significant positive correlations with all parameters. However, PS‐VAS demonstrated a stronger effect than DAS28‐CRP, also demonstrated without overlapping data. After minimizing the effects of DAS28‐CRP, age and SvdHS, there was a significant correlation between HAQ‐DI and PS‐VAS in all analyses. The change in HAQ‐DI demonstrated a significant correlation with the change in PS‐VAS.

Conclusions

These results suggested that HAQ‐DI is deeply influenced by PS‐VAS. The effect of DAS28‐CRP overlapped with the effect of PS‐VAS in a major way. Pain control for RA patients is the most important factor contributing to activities of daily living, as well as disease activity control.
Ex‐post moral hazard in prevented planting
Authors: Kim Taehoo , Kim Man‐Keun
Published: September 2018

This article analyzes the existence of moral hazard in prevented planting (PP) in the United States. The PP provision is defined as the “failure to plant an insured crop by the final planting date due to adverse events.” If the farmer decides not to plant a crop, the farmer receives a PP indemnity. Late planting (LP) is an option for farmers to plant a crop while maintaining crop insurance after the final planting date. Crop insurance may alter farmers’ behavior in selecting PP or LP and could increase the likelihood of PP claims even though farmers can choose LP. This study finds evidence that a farmer with higher insurance coverage tends to choose PP more often (ex‐post moral hazard). Spatial panel models attest to the existence of the ex‐post moral hazard in PP empirically. Empirical results show that the PP ratio has a positive relationship with insurance coverage in the case of corn production.
Mental health literacy among Nigerian teachers
Authors: Aluh Deborah Oyine , Dim Obinna Felix , Anene‐Okeke Chigozie Gloria
Published: September 2018

Introduction

Teachers are frontline professionals who have daily contact with children and are therefore most likely to have the biggest impact on their students. Findings in this study should inform the development of teacher training programs, and more broadly, assist in the success of a strategic plan addressing mental health in classrooms. This study aims to assess mental health literacy among teachers with focus on their knowledge of depression.

Methods

The study was a cross‐sectional descriptive survey conducted among teachers in five secondary schools (high school) in southeast Nigeria. All consenting teachers were recruited, making a total of 120 participants. The participants were presented with a questionnaire designed to elicit the participants' recognition of the disorder depicted in two vignettes and their recommendation about the appropriate source of help seeking. One vignette was of a clinically depressed case while the other vignette was about a girl undergoing normal life crisis.

Results

Out of the 120 teachers recruited into the study, 104 questionnaires were adequately completed indicating a response rate of 86.7%. A total of 16.3% (n = 17) participants correctly identified and labeled the depression vignette. Only 14 teachers (13.5%) recommended professional help from a psychiatrist or psychologist. Diminished ability to concentrate was the most identified symptom of distress for depression (30.8%). Counsellors were the most recommended source of help.

Discussion

Mental health literacy was poor among the teachers surveyed. There is an urgent need to improve mental health literacy among teachers in Nigeria.
A new method to measure and decrease the online social networking addiction
Authors: Esmaeili Rad Mahsa , Ahmadi Farid
Published: September 2018

Introduction

The online social networking addiction is a type of technology addiction that can lead to distraction, depression, anxiety, and lower academic performance. In this research, an android mobile application was designed based on the previous literature as well as authors' previous works to measure and decrease social networking addiction level.

Methods

This research is a randomized controlled trial. Participants were the students in Urmia University of Technology. The mobile application was designed and sent to 100 (35 males and 65 females) students randomly as an intervention group and was sent to 100 (38 males and 62 females) students randomly as a control group. In order to evaluate the efficacy of treatment, data were collected before and after 2‐week treatment.

Results

The results indicated that the designed mobile application can measure the online social networking addiction level with online social networking addiction scale, it can also decrease the online social networking addiction, depression, anxiety level, and the time spent on online social networks, and it can improve the sleep quality and life satisfaction level.

Discussion

Therefore, the designed mobile application can be used as an appropriate instrument to measure and decrease the online social networking addiction level of college students.
Trends in suicide methods by age group
Authors: Demir Mustafa
Published: September 2018

Introduction

This study investigates the trends in suicide methods by age group in Turkey.

Method

Secondary data on suicide from 2007 to 2015 were obtained from the Turkish Statistical Institute. The direct standardization method was used to calculate suicide rates. Correlation test was used to show the trends in suicide methods by age.

Results

Statistically significant changes in suicide methods were seen for persons aged 15 to 24 years and 25 to 44 years, where jumping increased; among persons aged 15 to 24 years, cutting/burning decreased.

Discussion

The most popular suicide method is jumping.
Development of a carbon calculator tool for riparian forest restoration
Authors: Matzek Virginia , Stella John , Ropion Pearce
Published: September 2018

Aim(s)

Methods for estimating carbon sequestration in riparian forest biomass are needed to qualify riparian restoration and conservation projects for funding through carbon credits. As part of a proposed accounting methodology for California's cap‐and‐trade system, we described five riparian vegetation associations and created a tool to predict their rates of carbon accumulation under different restoration and land‐use scenarios.

Location

California, USA.

Methods

We assembled a database of 654 forest inventory plots of known age (3–108 years) from replanted and naturally recruiting California riparian forests. We then used detrended correspondence analysis and agglomerative hierarchical clustering to detect vegetation structure in the plots and delineate distinct forest types. We used allometric equations to estimate biomass from individual trees’ diameters and calculate total biomass for each plot. Next, we fitted sigmoid growth functions to the plot biomass data to generate expected values for live‐tree biomass over a 100‐year period for each forest type. Finally, we created an algorithm to match user‐inputted data for an intended restoration project with a look‐up table that predicts carbon accumulation appropriate to the user's scenario.

Results

California riparian vegetation was divided into willow scrub, cottonwood–willow, mixed riparian, upland riparian and riparian woodland types. Total carbon sequestration in riparian vegetation and soil varied from 75.7 to 137.4 Mg C/ha at 30 years post‐restoration and from 95.1 to 175.8 Mg C/ha 100 years after stand initiation. Vegetation types dominated by taller, more shade‐tolerant trees developed more slowly than scrubby and pioneer stands, but came to a higher maximum biomass. Our models put riparian biomass accumulation in the range of the few extant literature values for mediterranean systems, but uncertainties are high, and soil carbon may be underestimated.

Conclusions

Our workflow and methods should be transferable to the development of carbon accounting tools for any other woody vegetation type. However, our difficulty in finding appropriate published data for the analysis suggests a critical need for field surveys appropriate to biomass estimation in woodland and forest communities not exploited for timber. The most important measurements are the age of the stand and a census of tree species, height and diameter.
Human disturbance promotes herbivory by leaf‐cutting ants in the Caatinga dry forest
Authors: Siqueira Felipe F. S. , Ribeiro‐Neto José Domingos , Tabarelli Marcelo , Andersen Alan N. , Wirth Rainer , Leal Inara R.
Published: September 2018

Anthropogenic disturbances are known to modify plant–animal interactions such as those involving the leaf‐cutting ants, the most voracious and proliferating herbivore across human‐modified landscapes in the Neotropics. Here, we evaluate the effect of chronic anthropogenic disturbance (e.g., firewood collection, livestock grazing) and vegetation seasonality on foraging area, foliage availability in the foraging area, leaf consumption and herbivory rate of the leaf‐cutting ant Atta opaciceps in the semiarid Caatinga, a mosaic of dry forest and scrub vegetation in northeast Brazil. Contrary to our initial expectation, the foraging area was not affected by either disturbance intensity or the interaction between season and disturbance intensity. However, leaf consumption and herbivory rate were higher in more disturbed areas. We also found a strong effect of seasonality, with higher leaf consumption and herbivory rate in the dry season. Our results suggest that the foraging ecology of leaf‐cutting ants is modulated by human disturbance and seasonality as these two drivers affect the spectrum and the amount of resources available for these ants in the Caatinga. Despite the low productivity of Caatinga vegetation, the annual rates of biomass consumption by A. opaciceps are similar to those reported from other leaf‐cutting ants in rain forests and savannas. This is made possible by maintaining high foraging activity even in the peak of the dry season and taking benefit from any resource available, including low‐quality items. Such compensation highlights the adaptive capacity of LCA to persist or even proliferate in human‐modified landscapes from dry to rain forests.
The impact of hurricanes Irma and Maria on the forest ecosystems of Saba and St. Eustatius, northern Caribbean
Authors: Eppinga Maarten B. , Pucko Carolyn A.
Published: September 2018

In September 2017, Irma became the first recorded category 5 hurricane to hit the Caribbean Windward Islands. The second category 5, Maria, followed two weeks later. In November 2017, we assessed the structural impact of this disturbance on highly valued Caribbean forest ecosystems. We recorded the status of 935 tree stems on Saba and St. Eustatius in stands at different elevations. Tree damage was substantial on both islands, with 93 percent of stems being defoliated, 84 percent having lost primary and/or secondary branches and 36 percent having structural stem damage. Average tree mortality was 18 percent, with mortality being nearly twice as high on St. Eustatius than on Saba. Surprisingly, we found that neither individual stem size nor community size distributions mediated the forests’ response to the hurricanes. Our results show that these hurricanes comprised a density‐independent disturbance, which may become more common as the frequency of strong hurricanes is projected to increase.
Associations of adverse childhood experiences and suicidal behaviors in adulthood in a U.S. nationally representative sample
Authors: Thompson Martie P. , Kingree J. B. , Lamis Dorian
Published: September 2018

Background

Suicide is a leading cause of death among adolescents and young adults. The current study extends the research linking adverse childhood experiences (ACEs) to suicidal behaviors by testing these associations using a nationally representative sample, assessing for suicide ideation and attempts in adulthood, controlling for established risk factors for suicidality, and measuring a broad array of ACEs.

Methods

The sample included 9,421 participants from the National Longitudinal Study of Adolescent Health who participated in four waves of assessments spanning 13 years. We examined longitudinal associations between eight different ACEs (physical, sexual, and emotional abuse, neglect, parental death, incarceration, alcoholism, and family suicidality) with suicidal ideation and suicide attempts in adulthood, while controlling for depression, problem alcohol use, drug use, delinquency, impulsivity, gender, race, age, and urbanicity. We also tested for cumulative associations of ACEs with suicide ideation and attempts.

Results

Logistic regression analyses indicated that physical, sexual, and emotional abuse, parental incarceration, and family history of suicidality each increased the risk by 1.4 to 2.7 times for suicidal ideation and suicide attempts in adulthood. The accumulation of ACEs increased the odds of suicide ideation and attempts. Compared with those with no ACEs, the odds of seriously considering suicide or attempting suicide in adulthood increased more than threefold among those with three or more ACEs.

Conclusions

Intervention strategies need to prevent ACEs from occurring and, if they do occur, should take into account the impact of cumulative ACEs on suicide risk. Future research should focus on identifying mediating mechanisms for the ACEs‐suicidality association using longitudinal research designs and determine which ACEs are most important to include in a cumulative ACE measure.
The effect of cause, timing, kidney function recovery, and recurrent events on the prognosis of acute kidney injury in kidney transplant recipients
Authors: van Dijk Tuvya Y. , Rahamimov Ruth , Chagnac Avry , van Dijk David J. , Mor Eytan , Shlomai Amir , Rozen‐Zvi Benaya
Published: September 2018

Aim

To assess the incidence of acute kidney injury (AKI) and its common etiologies in kidney transplant recipients and the effect of AKI's characteristics on graft survival.

Methods

In a retrospective longitudinal cohort study, all serum creatinine (SCr) values of patients that had kidney transplantation between 01/2002‐12/2010 were retrieved. AKI was defined as a 50% increase in SCr. Etiologies, recurrence, timing, and kidney function dynamics during the event were evaluated. The primary endpoint was defined as graft loss. Time‐varying Cox model was used for the analysis.

Results

Of 659 patients, 208 (31.6%) patients had 321 documented AKI events. Of these, 138 (66.4%) patients had one event, and 70 (33.6%) patients had recurrent events. The leading etiologies of the first AKI event were as follows: infection (33.4%), hypovolemia (14.3%), and unknown etiology (16.8%). Both first and recurrent AKI events were associated with an increased risk of graft loss (HR: 2.76, 95% CI: 1.95‐3.89) and (HR: 4.54, 95% CI: 2.59‐7.93), respectively. This deleterious association was lower within three months after transplantation, compared to later events. Patients in whom kidney function returned to baseline were less prone to graft loss.

Conclusions

Late‐onset, incomplete recovery, and recurrent AKI events are associated with increased graft loss.
A novel case of an aggressive superficial spindle cell sarcoma in an adult resembling fibrosarcomatous dermatofibrosarcoma protuberans and harboring an EML4‐NTRK3 fusion
Authors: Olson Nicholas , Rouhi Omid , Zhang Linsheng , Angeles Christina , Bridge Julia , Lopez‐Terrada Dolores , Royce Thomas , Linos Konstantinos
Published: September 2018

A subset of soft tissue sarcomas often harbors recurrent fusions involving protein kinases. While some of these fusion events have shown utility in arriving at a precise diagnosis, novel fusions in otherwise difficult to classify sarcomas continue to be identified. We present a case of a 40‐year‐old female who noted a lower back nodule in 2010 that was initially labeled as a dermatofibrosarcoma protuberans with fibrosarcomatous transformation. The lesion recurred the following year and metastasized to the groin 6 years later. Because of some morphologic peculiarities, molecular characterization was pursued in the metastatic focus, which revealed the neoplasm was negative for the COL1A1‐PDGFB fusion. However, anchored multiplex polymerase chain reaction for targeted next‐generation sequencing (Archer Dx) detected an EML4‐NTRK3 fusion, which was confirmed by reverse transcription‐PCR, Sanger sequencing and RNA sequencing analysis of the recurrent and metastatic specimens. Although various soft tissue neoplasms involving fusions with NTRK genes are well‐reported, the current case could not be easily classified in any of the established entities. Nevertheless, it raises interesting questions regarding the importance of classification, prognosis, and treatment for some of these tyrosine kinase fusion‐driven sarcomas.
Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood
Authors: Goodman Sarah J. , Roubinov Danielle S. , Bush Nicole R. , Park Mina , Farré Pau , Emberly Eldon , Hertzman Clyde , Essex Marilyn J. , Kobor Michael S. , Boyce W. Thomas
Published: September 2018

A growing body of research has documented associations between adverse childhood environments and DNA methylation, highlighting epigenetic processes as potential mechanisms through which earlyexternalcontexts influence health across the life course. The present study tested a complementary hypothesis: indicators of children's earlyinternal, biological, and behavioral responses to stressful challenges may also be linked to stable patterns of DNA methylation later in life. Children's autonomic nervous system reactivity, temperament, and mental health symptoms were prospectively assessed from infancy through early childhood, and principal components analysis (PCA) was applied to derive composites of biological and behavioral reactivity. Buccal epithelial cells were collected from participants at 15 and 18 years of age. Findings revealed an association between early life biobehavioral inhibition/disinhibition and DNA methylation across many genes. Notably, reactive, inhibited children were found to have decreased DNA methylation of theDLX5andIGF2genes at both time points, as compared to non‐reactive, disinhibited children. Results of the present study are provisional but suggest that the gene's profile of DNA methylation may constitute a biomarker of normative or potentially pathological differences in reactivity. Overall, findings provide a foundation for future research to explore relations among epigenetic processes and differences inbothindividual‐level biobehavioral risk and qualities of the early, external childhood environment.
How User‐centric Innovation is Affecting Stakeholder Marketing Strategies: Exploratory Findings from the Music Industry
Authors: Gamble Jordan Robert , McAdam Rodney , Brennan Michael
Published: September 2018

This paper empirically explores how user‐centric innovation (UCI) in the music industry is affecting how key stakeholder groups are approaching and developing their marketing (and associated management) strategies. The three‐stage interview‐based research methodology consisted of 52 semi‐structured in‐depth interviews with UCI experts and artist managers, as well as representatives from major record labels. The findings make four substantial contributions to theory and practice in the interrelated fields of UCI, marketing and the music industry. First, they provide practical and pragmatic insights for industry practitioners on how different UCI marketing approaches are affecting their management strategies. Second, they take steps towards answering many of the identified gaps in research and knowledge relating to the concept of UCI. Third, they present theoretical models as a foundation for which new UCI marketing theory can be built upon. Last, they offer directions for future research to advance our empirical findings.
Chironomid incorporation of methane‐derived carbon in plankton‐ and macrophyte‐dominated habitats in a large shallow lake
Authors: Agasild Helen , Kisand Anu , Ainelo Epp , Feldmann Tõnu , Timm Henn , Karus Katrit , Kisand Veljo , Jones Roger I. , Nõges Tiina
Published: September 2018

While 13C‐depleted carbon derived from biogenic methane can substantially contribute to the benthic secondary production in deep stratified lakes, its role in shallow lakes is less clear. We investigated the dynamics of δ13C and δ15N in the larvae of Chironomus plumosus throughout an annual cycle in two ecologically distinct basins (open‐water plankton‐dominated and sheltered macrophyte‐covered) of a large (270 km2), shallow, polymictic and eutrophic lake (Võrtsjärv, Estonia, North Europe). The larval stable isotopic compositions were linked to the presence of methane‐oxidising bacteria (MOB) in larval guts and sediments.

Molecular detection of MOB revealed their presence in various sediment types, but stable isotope (SI) analysis revealed clear differences in the feeding of chironomid larvae between the plankton‐ and macrophyte‐dominated habitats.

In the plankton‐dominated habitat, the mean δ13C values of larvae remained relatively constant (−38.3‰ to −35.5‰) and corresponded closely to the sediment δ13C values. Mean δ13C values of chironomid larvae were generally lower in macrophyte‐dominated habitats (−43.4‰ to −33.0‰), and both seasonal and individual variation in larval δ13C values were more pronounced. MOB presence in larval guts proved a dietary contribution from biogenic methane in macrophyte‐dominated habitats. Both the SI and molecular results indicated that MOB could help support larvae even during the cold temperature‐limited and ice‐covered periods.

Our study indicates that methane‐derived carbon makes a low but steady contribution to the larval chironomids throughout an annual cycle in large shallow Võrtsjärv. However, this contribution can be substantially higher in the lake habitats with abundant macrophytes. The study provides further evidence that a carbon flow pathway from biogenic methane can contribute to the benthic food web under variable habitat conditions in a shallow polymictic lake.
Ecosystem‐scale methane flux in tropical peat swamp forest in Indonesia
Authors: Sakabe Ayaka , Itoh Masayuki , Hirano Takashi , Kusin Kitso
Published: September 2018

Data on ecosystem‐scale methane (CH4) fluxes in tropical peatlands are currently lacking in the globalCH4budget. Although the waterlogged Indonesian peatlands contain the largest share of peat carbon in South‐East Asia, ecosystem‐scaleCH4budgets have not yet been reported, although these peatlands have the potential to emitCH4. We observed 1‐year variations in the ecosystem‐scaleCH4flux in an undrained secondary peat swamp forest in central Kalimantan, Indonesia, using the eddy covariance method. We found that the peat swamp forest switched from being aCH4sink during the dry season (as low as −8.9 mg C m−2 day−1) to a source ofCH4during the wet season (up to 10.7 mg C m−2 day−1), and this was dependent on changes in the groundwater level (GWL). The highGWLduring the wet season enhanced the anaerobicCH4production in the surface layer that had more labile organic matter. However, theCH4emission also increased when theGWLdropped during dry spells in the wet season. The annualCH4budget in the studied tropical peat swamp forest (0.09–0.17 g C m−2 year−1) was much lower than that in northern, temperate, and subtropical wetlands. We found thatCH4fluxes had almost no effect on the global warming gas budget of the peat swamp forest, and values were only a few percent less than theCO2fluxes at the same site. In addition, we conducted anaerobic soil incubation experiments to examine the effect of land‐use change onCH4production. The results indicated much higherCH4production potential in undrained forest soil than in drained or drained and burned ex‐forest soils. However, althoughCH4production decreased in drained soils relative to undrained soils, conserving pristine peat swamp forests with highGWLs is important to suppress global warming becauseCO2emissions increase in drained peatlands.
Explaining institutional amnesia in government
Authors: Stark Alastair
Published: September 2018

This article explains why different government agencies experience variations in organizational memory loss. It first explains institutional amnesia theoretically by expanding the formal‐institutional view of organizational memory to include agential and structural‐contextual properties, revealing a broader range of novel explanations for amnesia. Institutional amnesia is then explained empirically through an international analysis of memory loss in four Westminster systems (Australia, Canada, New Zealand, and the United Kingdom). This analysis, which principally relies on 100 interviews with ministers, policy officials, and public‐sector leaders across the four countries, leads to the introduction of four explanations for amnesia, relating to: organizational churn, absorptive capacity, strategic‐instrumental decision making, and historical storytelling.
Discerning Penal Values and Judicial Decision Making: The Case of Whole Life Sentencing in Europe and the United States of America
Authors: ROGAN MARY
Published: September 2018

Interpretive policy analysis has shown the need for multifactorial accounts of the influences on penal policy and its underlying penal values. To date, it has focused largely on political and administrative decision making. This article argues that judicial decisions interpreting the compliance of penal policies with the constitutional and legal frameworks applicable in a state must also be considered when seeking to discern the nature of approaches to penal policy. The article posits that judicial decisions are important and useful indicators of penal values. To illustrate the point, the article examines the approaches of the European Court of Human Rights and the Supreme Court of the United States to whole life sentencing. By exploring the differences in penal values between Europe and the United States of America through the prism of judicial decisions, the article considers the possibilities and limits offered by examinations of judicial action as sources of understanding of penal values.