bluuebunny/crossref_metadata_2025 huggingface dataset:
The Relationship of Depressive Symptoms and Vitamin D Intake to Cardiac Event–Free Survival in Patients With Heart Failure
Authors: Song Eun Kyeung , Kang Seok-Min
Published: September 2016

Background:

Low vitamin D and depressive symptoms are associated with inflammation activation that predicts cardiovascular disease. Little is known about the relationships among vitamin D intake, depressive symptoms, and cardiac events in heart failure (HF).

Purpose:

The aim of this study is to determine the relationships among vitamin D deficiency, depressive symptoms, and cardiac events.

Methods:

A total of 204 HF patients completed a 3-day food diary to determine average daily intake of vitamin D. Patients completed the Patient Health Questionnaire-9 to assess somatic and cognitive depressive symptoms and were split into 2 groups using the Patient Health Questionnaire-9 cut-point score of 10 (< 10, no depressive symptoms; ≥ 10, depressive symptoms). Data on cardiac events during 1 year were obtained through medical record review. Hierarchical Cox and logistic regressions were used for data analyses.

Results:

Sixty patients (29.4%) had depressive symptoms and 106 (52.0%) had vitamin D deficiency. Depressive symptoms (hazard ratio [HR], 1.93; P = .031) and vitamin D deficiency (HR, 1.84, P = .036) predicted shorter cardiac event–free survival in Cox regression. Depressive symptoms predicted shorter cardiac event–free survival in patients with vitamin D deficiency (HR, 2.16; P = .038), but not those with vitamin D adequacy. Somatic depressive symptoms were associated with vitamin D deficiency (odds ratio, 1.12; P = .028) in logistic regression, whereas cognitive depressive symptoms were not.

Conclusions:

Vitamin D deficiency and depressive symptoms predicted shorter cardiac event–free survival. Depressive symptoms did not predict cardiac events in HF patients with vitamin D adequacy. Somatic depressive symptoms predicted vitamin D deficiency, but cognitive depressive symptoms did not. Additional research is necessary to determine the protective role of vitamin D in the link between somatic depressive symptoms and cardiac events.
The Mental Health Parity and Addiction Equity Act Evaluation Study
Authors: Harwood Jessica M. , Azocar Francisca , Thalmayer Amber , Xu Haiyong , Ong Michael K. , Tseng Chi-Hong , Wells Kenneth B. , Friedman Sarah , Ettner Susan L.
Published: September 2016

Objective:

The federal Mental Health Parity and Addiction Equity Act (MHPAEA) sought to eliminate historical disparities between insurance coverage for behavioral health (BH) treatment and coverage for medical treatment. Our objective was to evaluate MHPAEA’s impact on BH expenditures and utilization among “carve-in” enrollees.

Methods:

We received specialty BH insurance claims and eligibility data from Optum, sampling 5,987,776 adults enrolled in self-insured plans from large employers. An interrupted time series study design with segmented regression analysis estimated monthly time trends of per-member spending and use before (2008–2009), during (2010), and after (2011–2013) MHPAEA compliance (N=179,506,951 member-month observations). Outcomes included: total, plan, patient out-of-pocket spending; outpatient utilization (assessment/diagnostic evaluation visits, medication management, individual and family psychotherapy); intermediate care utilization (structured outpatient, day treatment, residential); and inpatient utilization.

Results:

MHPAEA was associated with increases in monthly per-member total spending, plan spending, assessment/diagnostic evaluation visits [respective immediate increases of: $1.05 (P=0.02); $0.88 (P=0.04); 0.00045 visits (P=0.00)], and individual psychotherapy visits [immediate increase of 0.00578 visits (P=0.00) and additional increases of 0.00017 visits/mo (P=0.03)].

Conclusions:

MHPAEA was associated with modest increases in total and plan spending and outpatient utilization; for example, in July 2012 predicted per-enrollee plan spending was $4.92 without MHPAEA and $6.14 with MHPAEA. Efforts should focus on understanding how other barriers to BH care unaddressed by MHPAEA may affect access/utilization. Future research should evaluate effects produced by the Affordable Care Act’s inclusion of BH care as an essential health benefit and expansion of MHPAEA protections to the individual and small group markets.
A Novel Model for Predicting Rehospitalization Risk Incorporating Physical Function, Cognitive Status, and Psychosocial Support Using Natural Language Processing
Authors: Greenwald Jeffrey L. , Cronin Patrick R. , Carballo Victoria , Danaei Goodarz , Choy Garry
Published: September 2016

Background:

With the increasing focus on reducing hospital readmissions in the United States, numerous readmissions risk prediction models have been proposed, mostly developed through analyses of structured data fields in electronic medical records and administrative databases. Three areas that may have an impact on readmission but are poorly captured using structured data sources are patients’ physical function, cognitive status, and psychosocial environment and support.

Objective of the Study:

The objective of the study was to build a discriminative model using information germane to these 3 areas to identify hospitalized patients’ risk for 30-day all cause readmissions.

Research Design:

We conducted clinician focus groups to identify language used in the clinical record regarding these 3 areas. We then created a dataset including 30,000 inpatients, 10,000 from each of 3 hospitals, and searched those records for the focus group-derived language using natural language processing. A 30-day readmission prediction model was developed on 75% of the dataset and validated on the other 25% and also on hospital specific subsets.

Results:

Focus group language was aggregated into 35 variables. The final model had 16 variables, a validated C-statistic of 0.74, and was well calibrated. Subset validation of the model by hospital yielded C-statistics of 0.70–0.75.

Conclusions:

Deriving a 30-day readmission risk prediction model through identification of physical, cognitive, and psychosocial issues using natural language processing yielded a model that performs similarly to the better performing models previously published with the added advantage of being based on clinically relevant factors and also automated and scalable. Because of the clinical relevance of the variables in the model, future research may be able to test if targeting interventions to identified risks results in reductions in readmissions.
Alterations in Aerobic Exercise Performance and Gait Economy Following High-Intensity Dynamic Stepping Training in Persons With Subacute Stroke
Authors: Leddy Abigail L. , Connolly Mark , Holleran Carey L. , Hennessy Patrick W. , Woodward Jane , Arena Ross A. , Roth Elliot J. , Hornby T. George
Published: September 2016

Background and Purpose:

Impairments in metabolic capacity and economy (O2cost) are hallmark characteristics of locomotor dysfunction following stroke. High-intensity (aerobic) training has been shown to improve peak oxygen consumption in this population, with fewer reports of changes in O2cost. However, particularly in persons with subacute stroke, inconsistent gains in walking function are observed with minimal associations with gains in metabolic parameters. The purpose of this study was to evaluate changes in aerobic exercise performance in participants with subacute stroke following high-intensity variable stepping training as compared with conventional therapy.

Methods:

A secondary analysis was performed on data from a randomized controlled trial comparing high-intensity training with conventional interventions, and from the pilot study that formed the basis for the randomized controlled trial. Participants 1 to 6 months poststroke received 40 or fewer sessions of high-intensity variable stepping training (n = 21) or conventional interventions (n = 12). Assessments were performed at baseline (BSL), posttraining, and 2- to 3-month follow-up and included changes in submaximal

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submax) and O2cost at fastest possible treadmill speeds and peak speeds at BSL testing.

Results:

Significant improvements were observed in

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submax with less consistent improvements in O2cost, although individual responses varied substantially. Combined changes in both

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submax and

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2 at matched peak BSL speeds revealed stronger correlations to improvements in walking function as compared with either measure alone.

Discussion and Conclusions:

High-intensity stepping training may elicit significant improvements in

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submax, whereas changes in both peak capacity and economy better reflect gains in walking function. Providing high-intensity training to improve locomotor and aerobic exercise performance may increase the efficiency of rehabilitation sessions.

Video Abstract available for more insights from the authors (see Supplemental Digital Content, http://links.lww.com/JNPT/A142).
The Perception and Costs of the Interview Process for Plastic Surgery Residency Programs: Can the Process Be Streamlined?
Authors: Susarla Srinivas M. , Swanson Edward W. , Slezak Sheri , Lifchez Scott D. , Redett Richard J.
Published: September 2016

Background:

The purpose of this study was to assess applicant perceptions and costs associated with the interview process for plastic surgery residency positions.

Methods:

This was a cross-sectional survey of applicants to the integrated- and independent-track residencies at the authors’ institution. All applicants who were interviewed were invited to complete a Web-based survey on costs and perceptions of various components of the interview process. Descriptive and bivariate statistics were computed to compare applicants to the two program tracks.

Results:

Fifty-three applicants were interviewed for residency positions; 48 completed a survey (90.5 percent response rate). Thirty-four applicants were candidates for the integrated program; 16 applicants were candidates for the independent program. The program spent $2763 per applicant interviewed; 63 percent of applicants spent more than $5000 on the interview process. More than 70 percent of applicants missed more than 7 days of work to attend interviews. Independent applicants felt less strongly that interviews were critical to the selection process and placed less value on physically visiting the hospital and direct, in-person interaction. Applicants placed little value on program informational talks. Applicants who had experience with virtual interviews felt more positively about the format of a video interview relative to those who did not.

Conclusions:

The residency interview process is resource intensive for programs and applicants. Removing informational talks may improve the process. Making physical tours and in-person interviews optional are other alternatives that merit future study.
Using a structural root system model to evaluate and improve the accuracy of root image analysis pipelines
Authors: Lobet Guillaume , Koevoets Iko T. , Noll Manuel , Meyer Patrick E. , Tocquin Pierre , Pagès Loïc , Périlleux Claire
Published: September 2016

Root system analysis is a complex task, often performed with fully automated image analysis pipelines. However, the outcome is rarely verified by ground-truth data, which might lead to underestimated biases.

We have used a root model, ArchiSimple, to create a large and diverse library of ground-truth root system images (10,000). For each image, three levels of noise were created. This library was used to evaluate the accuracy and usefulness of several image descriptors classically used in root image analysis softwares.

Our analysis highlighted that the accuracy of the different traits is strongly dependent on the quality of the images and the type, size and complexity of the root systems analysed. Our study also demonstrated that machine learning algorithms can be trained on a synthetic library to improve the estimation of several root system traits.

Overall, our analysis is a call to caution when using automatic root image analysis tools. If a thorough calibration is not performed on the dataset of interest, unexpected errors might arise, especially for large and complex root images. To facilitate such calibration, both the image library and the different codes used in the study have been made available to the community.
Identification of important amino acid replacements in the 2013-2016 Ebola virus outbreak
Authors: Olabode Abayomi S , Gatherer Derek , Jiang Xiaowei , Matthews David , Hiscox Julian A , Gunther Stephan , Carroll Miles W , Lovell Simon C , Robertson David L
Published: September 2016

The phylogenetic relationships of Zaire ebolavirus have been intensively analysed over the course of the 2013-2016 outbreak. However, there has been limited consideration of the functional impact of this variation. Here we describe an analysis of the available sequence data in the context of protein structure and phylogenetic history. Amino acid replacements are rare and predicted to have minor effects on protein stability. Synonymous mutations greatly outnumber nonsynonymous mutations, and most of the latter fall into unstructured intrinsically disordered regions, indicating that purifying selection is the dominant mode of selective pressure. However, one replacement, occurring early in the outbreak in Gueckedou in Guinea on 31st March 2014 (alanine to valine at position 82 in the GP protein), is close to the site where the virus binds to the host receptor NPC1 and is located in the phylogenetic tree at the origin of the major B lineage of the outbreak. The functional and evolutionary evidence indicates this A82V change likely has consequences for EBOV's host specificity and hence adaptation to humans.
Catalyzed Synthesis of Zinc Clays by Prebiotic Central Metabolites
Authors: Zhou Ruixin , Basu Kaustuv , Hartman Hyman , Matocha Christopher J. , Sears S. Kelly , Vali Hojatollah , Guzman Marcelo I.
Published: September 2016

How primordial metabolic networks such as the reverse tricarboxylic acid (rTCA) cycle and clay mineral catalysts coevolved remains a mystery in the puzzle to understand the origin of life. While prebiotic reactions from the rTCA cycle were accomplished via photochemistry on semiconductor minerals, the synthesis of clays was demonstrated at low temperature and ambient pressure catalyzed by oxalate. Herein, the crystallization of clay minerals is catalyzed by succinate, an example of a photoproduced intermediate from central metabolism. The experiments connect the synthesis of sauconite, a model for clay minerals, to prebiotic photochemistry. We report the temperature, pH, and concentration dependence on succinate for the synthesis of sauconite identifying new mechanisms of clay formation in surface environments of rocky planets. The work demonstrates that seeding induces nucleation at low temperatures accelerating the crystallization process. Cryogenic and conventional transmission electron microscopies, X-ray diffraction, diffuse reflectance Fourier transformed infrared spectroscopy, and measurements of total surface area are used to build a three-dimensional representation of the clay. These results suggest the coevolution of clay minerals and early metabolites in our planet could have been facilitated by sunlight photochemistry, which played a significant role in the complex interplay between rocks and life over geological time.
ENVIREM: An expanded set of bioclimatic and topographic variables increases flexibility and improves performance of ecological niche modeling
Authors: Title Pascal O , Bemmels Jordan B
Published: September 2016

Species distribution modeling is a valuable tool with many applications across ecology and evolutionary biology. The selection of biologically meaningful environmental variables that determine relative habitat suitability is a crucial aspect of the modeling pipeline. The 19 bioclimatic variables from WorldClim are frequently employed, primarily because they are easily accessible and available globally for past, present and future climate scenarios. Yet, the availability of relatively few other comparable environmental datasets potentially limits our ability to select appropriate variables that will most successfully characterize a species’ distribution. We identified a set of 16 climatic and two topographic variables in the literature, which we call theenviremdataset, many of which are likely to have direct relevance to ecological or physiological processes determining species distributions. We generated this set of variables at the same resolutions as WorldClim, for the present, mid-Holocene, and Last Glacial Maximum (LGM). For 20 North American vertebrate species, we then assessed whether including theenviremvariables led to improved species distribution models compared to models using only the existing WorldClim variables. We found that including the ENVIREM dataset in the pool of variables to select from led to substantial improvements in niche modeling performance in 17 out of 20 species. We also show that, when comparing models constructed with different environmental variables, differences in projected distributions were often greater in the LGM than in the present. These variables are worth consideration in species distribution modeling applications, especially as many of the variables have direct links to processes important for species ecology. We provide these variables for download at multiple resolutions and for several time periods at envirem.github.io. Furthermore, we have written the ‘envirem’ R package to facilitate the generation of these variables from other input datasets.
Online ion-exchange chromatography for small-angle X-ray scattering
Authors: Hutin Stephanie , Brennich Martha , Maillot Benoit , Round Adam
Published: September 2016

Biological small-angle X-ray scattering (BioSAXS) is a powerful technique to determine the solution structure, particle size, shape and surface-to-volume ratio of macromolecules. However, a drawback is that the sample needs to be monodisperse. To ensure this, size-exclusion chromatography (SEC) has been implemented on many BioSAXS beamlines. Here, the integration of ion-exchange chromatography (IEC) using both continuous linear and step gradients on a beamline is described. Background subtraction for continuous gradients by shifting a reference measurement and two different approaches for step gradients, which are based on interpolating between two background measurements, are discussed. The results presented here serve as a proof of principle for online IEC and subsequent data treatment.
Empirical power laws for the radii of gyration of protein oligomers
Authors: Tanner John J.
Published: September 2016

The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2–6 and 8. The power-law exponents for oligomers span a narrow range of 0.38–0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.
Workforce and destination influence over hospitality industry performance
Authors: Alonso-Almeida María del Mar , Llach Josep , Barquero Jose Daniel , Bremser Kerstin
Published: September 2016

Purpose

As part of the recent global financial crisis, Europe has experienced a double crisis (financial crisis and Euro crisis) leading to a double dip recession, meaning that the effects of the crisis have been longer and more severe. Tourism, specifically the hospitality industry, is important for the economy of Southern European countries, where the crisis has been the worst. Spain especially depends on tourism as important source of GDP. Therefore, the purpose of this paper is to identify the contributing factors to better manage the crisis impacts and anticipate future impacts.

Design/methodology/approach

The authors examine the performance of a sample of 7,293 Spanish hospitality companies based on data from 2008 to 2011. With the aim of testing the hypotheses, a multivariate regression analysis was performed.

Findings

Results show the importance of a direct effect over both internal (workforce as well as hotel characteristics) and external factors (destination-related GDP spending) for growth, with varying influence across factors. Nevertheless, the most influenced are the moderated effects among the workforce and external variables.

Research limitations/implications

This study contributes to the literature by providing a firm-level analysis (rather than an industry-level analysis) and offers an almost complete picture of a specific geographical area. Future research should address the performance of other tourism industries in times of crisis, such as restaurants and travel agencies, and the relationships between performances in different tourism industries. Regarding the limitations of the paper, the main limitation is associated with the use of panel data from an official database. These include problems in the design, data collection and data management of panel surveys.

Practical implications

These findings help the hospitality industry to understand the relevant drivers and coping strategies associated with the hospitality industry during a financial crisis.

Originality/value

This study is focused on the firm-level analysis instead of an industry-level analysis and can thus give advice to the strategic behaviour of companies.
International diversification and firm performance: a four-stage model
Authors: Ferraris Alberto , Bresciani Stefano , Del Giudice Manlio
Published: September 2016

Purpose

The purpose of this paper is to investigate the relationship between international diversification (ID) and performance in multinational firms by proposing a new and unified theory of multinationality that incorporates, integrates and extends previous concepts and hypotheses.

Design/methodology/approach

The study relies on data concerning the world’s largest companies, derived from the Fortune Global 500. An OLS regression analysis has been carried out in order to test a four-stage relationship between ID and performance.

Findings

On a final sample of 391 multinationals, this paper provides an empirical evidence that support the existence of a four-stage theory by using a relevant sample of “top” multinational firms.

Research limitations/implications

This study has two main limitations: first, a single indicator was used to measure ID; second, some potential variables have had to be excluded due to data availability.

Practical implications

This paper offers some intriguing practical implications, as well: first, it points out to some thresholds where performances are higher at certain level of ID; second, it highlights that performance will face two kinds of decreases due to intra-regional and inter-regional liability of foreignness; finally, it individuates differences with regard to some firms’ characteristics such as home or host country’s behaviors and about the kind of industries in which they operate, as well.

Originality/value

This is one of the first studies that tests and finds positive evidences about a four-stage theory, regarding to the relationship between ID and performance. Moreover, it proposes other interesting results with regard to the differences between home vs host country-oriented firms and between manufacturing vs services multinational firms.
Show me a strathspey: taking steps to digitize tune collections
Authors: McAulay Karen
Published: September 2016

Purpose

The present paper describes an Arts and Humanities Research Council (AHRC) research project into Scottish fiddle music and the important considerations of music digitization, access and discovery in designing the website that will be one of the project’s enduring outcomes.

Design/methodology/approach

The paper is a general review of existing online indices to music repertoires and some of the general problems associated with selecting metadata and indexing such material and is a survey of the various recent and contemporary projects into the digital encoding of musical notation for online use.

Findings

The questions addressed during the design of the Bass Culture project database serve to highlight the importance of cooperation between musicologists, information specialists and computer scientists, and the benefits of having researchers with strengths in more than one of these disciplines. The Music Encoding Initiative proves an effective means of providing digital access to the Scottish fiddle tune repertoire.

Originality/value

The digital encoding of music notation is still comparatively cutting-edge; the Bass Culture project is thus a useful exemplar for interdisciplinary collaboration between musicologists, information specialists and computer scientists, and it addresses issues which are likely to be applicable to future projects of this nature.
Precipitation, not air temperature, drives functional responses of trees in semi‐arid ecosystems
Authors: Grossiord Charlotte , Sevanto Sanna , Adams Henry D. , Collins Adam D. , Dickman Lee T. , McBranch Natalie , Michaletz Sean T. , Stockton Elizabeth A. , Vigil Miguel , McDowell Nate G.
Published: September 2016

Model scenarios of climate change predict that warming and drought will occur simultaneously in the future in many regions. The capacity of woody species to modify their physiology and morphology in response to environmental conditions is widely recognized, but little is known about the responses of trees to reduced precipitation and increased temperature acting simultaneously.

In a semi‐arid woodland, we assessed the responses in physiological (needle emergence, maximum photosynthesis, stomatal conductance, water use efficiency (WUE) and shoot elongation) and morphological (needle length and thickness, and leaf mass per area (LMA)) foliar traits of piñon pine (Pinus edulis) in response to three years of a 45% reduction in precipitation, a 4.8 °C increase in air temperature and their simultaneous effects.

A strong change in physiological and morphological traits in response to reduced precipitation was observed. Precipitation reduction delayed needle emergence, decreased photosynthesis and stomatal conductance, increased WUE, decreased shoot elongation and induced shorter needles with a higher LMA. Trees subjected to simultaneous reductions in precipitation and warming demonstrated a similar response. However, atmospheric warming did not induce a response in any of the measured traits.

Physiological and morphological traits of trees in this semi‐arid climate were more responsive to changes in soil moisture than air temperature. Long‐term exposure to seasonal drought stress in arid sites may have resulted in strong plastic responses to this first stressor. However, atmospheric warming probably was not experienced as a stress for trees in this warm and dry climate. Overall, our results indicate that in semi‐arid ecosystems where tree functioning is already highly limited by soil water availability, atmospheric warming as anticipated with climate change may have less impact on foliar trait responses than previously thought.
An overview of the biological metal uptake pathways in Pseudomonas aeruginosa
Authors: Schalk Isabelle J. , Cunrath Olivier
Published: September 2016

Biological metal ions, including Co, Cu, Fe, Mg, Mn, Mo, Ni and Zn ions, are necessary for the survival and the growth of all microorganisms. Their biological functions are linked to their particular chemical properties: they play a role in structuring macromolecules and/or act as co‐factors catalyzing diverse biochemical reactions. These metal ions are also essential for microbial pathogens during infection: they are involved in bacterial metabolism and various virulence factor functions. Therefore, during infection, bacteria need to acquire biological metal ions from the host such that there is competition for these ions between the bacterium and the host. Evidence is increasingly emerging of “nutritional immunity” against pathogens in the hosts; this includes strategies making access to metals difficult for infecting bacteria. It is clear that biological metals play key roles during infection and in the battle between the pathogens and the host. Here, we summarize current knowledge about the strategies used by Pseudomonas aeruginosa to access the various biological metals it requires. P. aeruginosa is a medically significant Gram‐negative bacterial opportunistic pathogen that can cause severe chronic lung infections in cystic fibrosis patients and that is responsible for nosocomial infections worldwide.
A monotonically declining elevational pattern of bacterial diversity in freshwater lake sediments
Authors: Zeng Jin , Zhao Dayong , Li Huabing , Huang Rui , Wang Jianjun , Wu Qinglong L.
Published: September 2016

The distribution patterns of bacterial communities along elevational gradients remain unexplored in aquatic ecosystems. This study investigated the diversity and community composition of bacteria in the sediments of lakes along a mountainside elevational gradient from 525 to 4 490 m in western China. The bacterial alpha diversity (taxonomic richness and phylogenetic diversity) at different sediment depths decreased monotonically with the increasing elevation, and the beta diversity (dissimilarity between lakes) increased significantly with the increasing elevation distance. Both elevation and chemical variables including pH and carbon/nitrogen ratio were identified as major factors affecting the bacterial diversity. Especially, bacterial alpha/beta diversity was significantly related to both chemical and elevational gradients in the surface sediments, whereas elevation overwhelmed chemical factors in influencing the bacterial alpha/beta diversity in the subsurface sediments. Phylogenetic structure analysis demonstrated that environmental filtering was the most important process affecting the bacterial community assembly along the elevational gradient, and the strength of environmental filtering increased towards high elevations. In summary, we observed for the first time a monotonically decreasing elevational pattern in bacterial diversity of freshwater lake sediments, which is mainly driven by elevation associated environmental factors.
Plant phenolic acids induce programmed cell death of a fungal pathogen: MAPK signaling and survival of Cochliobolus heterostrophus
Authors: Shalaby Samer , Larkov Olga , Lamdan Netta‐Li , Goldshmidt‐Tran Orit , Horwitz Benjamin A.
Published: September 2016

Plant aromatic compounds provide signals and a nutrient source to pathogens, and also act as stressors. Structure‐activity relationships suggest two pathways sensing these compounds in the maize pathogen Cochliobolus heterostrophus, one triggering a stress response, and one inducing enzymes for their degradation. Focusing on the stress pathway, we found that ferulic acid causes rapid appearance of TUNEL‐positive nuclei, dispersion of histone H1:GFP, hyphal shrinkage, and eventually membrane damage. These hallmarks of programmed cell death (PCD) were not seen upon exposure to caffeic acid, a very similar compound. Exposure to ferulic acid dephosphorylated two MAP kinases: Hog1 (stress activated) and Chk1 (pathogenicity related), while increasing phosphorylation of Mps1 (cell integrity related). Mutants lacking Hog1 or Chk1 are hypersensitive to ferulic acid while Mps1 mutants are not. These results implicate three MAPK pathways in the stress response. Ferulic acid and the antifungal fludioxonil have opposite additive effects on survival and on dephosphorylation of Hog1, which is thus implicated in survival. The results may explain why some fungal pathogens of plants undergo cell death early in host invasion, when phenolics are released from plant tissue.
Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol
Authors: Atashgahi Siavash , Lu Yue , Zheng Ying , Saccenti Edoardo , Suarez‐Diez Maria , Ramiro‐Garcia Javier , Eisenmann Heinrich , Elsner Martin , J.M. Stams Alfons , Springael Dirk , Dejonghe Winnie , Smidt Hauke
Published: September 2016

Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study, glycerol was injected in an aquifer contaminated with cis‐dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance of Firmicutes, Bacteriodetes and sulfate reducing Deltaproteobacteria. In line with 13C cDCE enrichment and increased Dehalococcoides mccartyi (Dcm) numbers, dechlorination was observed toward the end of the field experiment, albeit being incomplete with accumulation of vinyl chloride. This was concurrent with (i) decreased concentrations of dissolved organic carbon (DOC), reduced relative abundances of fermenting and sulfate reducing bacteria that have been suggested to promote Dcm growth by providing electron donor (H2) and essential corrinoid cofactors, (ii) increased sulfate concentration and increased relative abundance of Epsilonproteobacteria and Deferribacteres as putative oxidizers of reduced sulfur compounds. Strong correlations of DOC, relative abundance of fermenters and sulfate reducers, and dechlorination imply the importance of syntrophic interactions to sustain robust dechlorination. Tracking microbial and environmental parameters that promote/preclude enhanced reductive dechlorination should aid development of sustainable bioremediation strategies.
Effects and mechanisms of Bacillus thuringiensis crystal toxins for mosquito larvae
Authors: Zhang Qi , Hua Gang , Adang Michael J.
Published: September 2016

Bacillus thuringiensis is a Gram‐positive aerobic bacterium that produces insecticidal crystalline inclusions during sporulation phases of the mother cell. The virulence factor, known as parasporal crystals, is composed of Cry and Cyt toxins. Most Cry toxins display a common 3‐domain topology. Cry toxins exert intoxication through toxin activation, receptor binding and pore formation in a suitable larval gut environment. The mosquitocidal toxins of Bt subsp. israelensis (Bti) were found to be highly active against mosquito larvae and are widely used for vector control. Bt subsp. jegathesan is another strain which possesses high potency against broad range of mosquito larvae. The present review summarizes characterized receptors for Cry toxins in mosquito larvae, and will also discuss the diversity and effects of 3‐D mosquitocidal Cry toxin and the ongoing research for Cry toxin mechanisms generated from investigations of lepidopteran and dipteran larvae.
Photokinesis and Djopsin gene expression analysis during the regeneration of planarian eyes
Authors: DONG Zimei , YUWEN Yanqing , SIMA Yingxu , DONG Yanping , ZHAN Huina , CHEN Guangwen , LIU Dezeng
Published: September 2016

Planarians provide the ideal model for studying eye development, with their simple eye structure and exceptionally rapid regeneration. Here, we observed the eye morphogenesis, photophobic behavior, spectral sensitivity and expression pattern of Djopsin in the freshwater planarian Dugesia japonica. The results showed that: (i) Djopsin encoding the putative protein belonged to the rhabdomeric opsins group and displayed high conservation during animal evolution; (ii) planarians displayed diverse photophobic response to different visible wavelengths and were more sensitive to light blue (495 nm) and yellow (635 nm); (iii) the morphogenesis and functional recovery of eyes were related to the expression pattern of Djopsin during head regeneration; and (iv) Djopsin gene plays a major role in functional recovery during eye regeneration and visual system maintenance in adult planarians.
MicroRNAs as biomarkers and regulators of nonalcoholic fatty liver disease
Authors: Liu Xiao Lin , Cao Hai Xia , Fan Jian Gao
Published: September 2016

Nonalcoholic fatty liver disease (NAFLD) is a complicated disease affected by the interaction of environmental and genetic factors; however, the precise pathogenesis of the disease has not been fully determined. There is a need to better understand the pathogenesis of NAFLD and to identify non‐invasive diagnostic modalities. Recent advances in systematic biology and epigenetics have improved our understanding of the genotype–phenotype relationships in NAFLD. MicroRNAs (miRNAs) are important regulators of a wide range of biological processes. MiRNAs are extremely stable and protect from RNAase‐mediated degradation in body fluids, making them attractive candidate biomarkers for the early detection of the disease and the monitoring of disease progression. In this review, we summarized the current knowledge on miRNAs as potential biomarkers of NAFLD at different stages and for the prognosis of advanced diseases. Furthermore, we discussed the implications of miRNAs that functioning in lipid metabolism and hepatic steatosis as well as in hepatic inflammation and fibrosis with regard to the pathogenesis of NAFLD.
Health Policy and Shared Decision Making in Emergency Care: A Research Agenda
Authors: Maughan Brandon C. , Meisel Zachary F. , Venkatesh Arjun K. , Lin Michelle P. , Perry Warren M. , Schuur Jeremiah D. , Pines Jesse M. , Kizzie‐Gillett Constance L. , Vaughan William , Grudzen Corita R.
Published: September 2016

Although the Patient Protection and Affordable Care Act and other laws have promoted the use of shared decision making (SDM) in recent years, few specific policies have addressed the opportunities and challenges of utilizing SDM in the emergency department (ED). Policies relating to physician payment, quality measurement, and medical–legal risks each present unique challenges to adoption of SDM in the ED. This article summarizes findings from a health policy breakout session of the 2016 Academic Emergency Medicine Consensus Conference “Shared Decision Making in the Emergency Department: Development of a Policy‐relevant, Patient‐centered Research Agenda.” The objectives were to 1) describe federal and state policies that influence utilization or assessment of SDM; 2) identify policies and policy‐focused knowledge gaps that serve as barriers to adoption of ED SDM; and 3) to define a consensus‐based, policy‐focused research agenda to support adoption of SDM in emergency care.
A survey of various endodontic procedures related to mineral trioxide aggregate usage by members of the Australian Society of Endodontology
Authors: Ha William N. , Duckmanton Peter , Kahler Bill , Walsh Laurence J.
Published: September 2016

This study aims to assess education on the use of mineral trioxide aggregate (MTA) and Biodentine among members of the Australian Society of Endodontology (ASE), a society of specialist endodontists (ED) and general dentists with an interest in endodontics (GD). The study also aims to compare the procedural preferences relating to perforation repair, apical barrier, root‐end filling and regenerative endodontics. A structured online questionnaire was used, which sought details of the education in the use of MTA and the procedural steps involved in perforation repair, apical barrier, root‐end filling and regenerative endodontics. Fisher's exact test was performed to compare the GD with ED. Responses were received from 208 out of 499 ASE members. Some 40% of the total respondents were ED. Almost all ED (98.8%) and some GD (39.8%) used MTA for perforation repairs. Likewise, almost all ED (96.3%) and some GD (42.7%) used MTA for apical barrier procedures. Lack of experience was more of a barrier to its use for GD (48.7%) than its high cost (31.6%). Few members used Biodentine. Significant differences exist in how MTA is used between GD and ED. Experience in handling MTA is a larger barrier to its widespread use in endodontics than its cost.
Prospective study comparing video‐endoscopic radical inguinal lymph node dissection (VEILND) with open radical ILND (OILND) for penile cancer over an 8‐year period
Authors: Kumar Vivekanandan , Sethia K. Krishna
Published: September 2016

Objective

To compare the complications and oncological outcomes between video‐endoscopic inguinal lymph node dissection (VEILND) and open ILND (OILND) in men with carcinoma of the penis.

Patients and methods

A prospectively collected institutional database was used to determine the outcomes in 42 consecutive patients undergoing ILND between 2008 and 2015 in a centre for treating penile cancer. Before 2013 all procedures were OILNDs. Since 2013 we have performed VEILND on all patients in need of ILND. The wound‐related and non‐wound‐related complications, length of stay, and oncological safety between OILND and VEILND groups were compared. The mean duration of follow‐up was 71 months for OILND and 16 months for the VEILND groups.

Results

In the study period 42 patients underwent 68 ILNDs (OILND 35, VEILND 33). The patients’ demographics, primary stage and grade, and indications were comparable in both groups. There were no intraoperative complications in either group. The wound complication rate was significantly lower in the VEILND group at 6% compared to 68% in the OILND group. Lymphocoele rates were similar in both the groups (27% and 20%). The VEILND group had a better or the same lymph node yield, mean number of positive lymph nodes, and lymph node density confirming oncological safety. There were no groin recurrences in either group of patients. VEILND significantly reduced the mean length of stay by 4.8 days (P < 0.001).

Conclusion

VEILND is an oncologically safe procedure with considerably low morbidity and reduced length of stay, at a mean (range) follow‐up of 16 (4–35) months.
Recent developments of genetically encoded optical sensors for cell biology
Authors: Bolbat Andrey , Schultz Carsten
Published: September 2016

Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high‐end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer‐based sensors, sensors utilising bioluminescence, sensors using self‐labelling SNAP‐ and CLIP‐tags, and finally tetracysteine‐based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
Genetic Moderation of Intervention Efficacy: Dopaminergic Genes, The Incredible Years, and Externalizing Behavior in Children
Authors: Chhangur Rabia R. , Weeland Joyce , Overbeek Geertjan , Matthys Walter , Orobio de Castro Bram , van der Giessen Danielle , Belsky Jay
Published: September 2016

This study investigated whether children scoring higher on a polygenic plasticity index based on five dopaminergic genes (DRD4, DRD2, DAT1, MAOA, and COMT) benefited the most from the Incredible Years (IY) parent program. Data were used from a randomized controlled trial including 341 Dutch families with 4‐ to 8‐year‐old children (55.7% boys) showing moderate to high levels of problem behavior. IY proved to be most effective in decreasing parent‐reported (but not observed) externalizing behavior in boys (but not girls) carrying more rather than fewer dopaminergic plasticity alleles; this Gene × Intervention effect was most pronounced in the case of boys whose parents’ manifested the most positive change in parenting in response to the intervention. These results proved robust across a variety of sampling specifications (e.g., intention to treat, ethnicity).
Repair of transperineal recto‐urethral fistula using a fibrin sealant haemostatic patch
Authors: Giuliani G. , Guerra F. , Coletta D. , La Torre M. , Franco G. , Leonardo C. , Infantino A. , La Torre F.
Published: September 2016

Aim

Recto‐urethral fistula (RUF) is a rare complication of radical prostatectomy. We report a transperineal approach using a fibrin sealant haemostatic patch.

Method

Five consecutive patients who developed RUF following radical prostatectomy had a direct transperineal repair with a haemostatic patch (TachoSil®) and were assessed at a median follow‐up of 35.5 (21–45) months.

Results

There were no early postoperative complications. The average length of hospital stay was 5 (4–7) days. One patient developed recurrence 4 weeks after removal of the urethral catheter. Following healing in four patients the stoma was reversed at a median interval of 3 months, and 9.5 (7–10) months following the prostatic surgery. In the four patients with successful closure there was no case of recurrence or anorectal or urinary dysfunction at a median follow‐up of 35.5 (21–45) months.

Conclusion

Direct transperineal repair of RUF reinforced with a fibrin haemostatic patch of TachoSil is safe and effective.
New perylene dyes, derivatives of 1,6,7,12‐tetrachloroperylene‐3,4,9,10‐tetracarboxylic acid: synthesis and application
Authors: Paluszkiewicz Joanna , Stolarski Roland , Stanczyk Wlodzimierz A. , Martynski Tomasz , Rutowicz Joanna
Published: September 2016

New dyes – aliphatic esters of 1,6,7,12‐tetrachloroperylene‐3,4,9,10‐tetracarboxylic acid – were prepared as potential fluorescent light‐stable colorants for high‐visibility safety wear. The structure of the 15 perylenes was confirmed by 1H and 13C nuclear magnetic resonance spectroscopy and mass spectrometry, and their spectroscopic and physicochemical properties were determined. An attempt was made to apply the synthesised products as disperse dyes in the coloration of polyester as well as in the mass coloration of polystyrene and poly(methyl methacrylate). The light, wash, and rubbing fastness of the dyeings were determined, and chromaticity coordinates of selected samples were measured and discussed.