bluuebunny/crossref_metadata_2025_split huggingface dataset:
Managing the protein folding demands in the endoplasmic reticulum of plants
Authors: Liu Jian‐Xiang , Howell Stephen H. 
Published: March 2016

SummaryEndoplasmic reticulum (ER) stress occurs in plants during certain developmental stages or under adverse environmental conditions, as a result of the accumulation of unfolded or misfolded proteins in the ER. To minimize the accumulation of misfolded proteins in the ER, a protein quality control (PQC) system monitors protein folding and eliminates misfolded proteins through either ER‐associated protein degradation (ERAD) or autophagy. ER stress elicits the unfolded protein response (UPR), which enhances the operation in plant cells of the ER protein folding machinery and the PQC system. The UPR also reduces protein folding demands in the ER by degrading mRNAs encoding secretory proteins. In plants subjected to severe or chronic stress, UPR promotes programmed cell death (PCD). Progress in the field in recent years has provided insights into the regulatory networks and signaling mechanisms of the ER stress responses in plants. In addition, novel physiological functions of the ER stress responses in plants for coordinating plant growth and development with changing environment have been recently revealed.
The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)
Authors: Lagomarsino Laura P. , Condamine Fabien L. , Antonelli Alexandre , Mulch Andreas , Davis Charles C. 
Published: March 2016

Summary

The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade.

We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model.

We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr.

Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.
Natural antigenic differences in the functionally equivalent extracellular DNABII proteins of bacterial biofilms provide a means for targeted biofilm therapeutics
Authors: Rocco C.J. , Davey M.E. , Bakaletz L.O. , Goodman S.D. 
Published: March 2016

SummaryBacteria that persist in the oral cavity exist within complex biofilm communities. A hallmark of biofilms is the presence of an extracellular polymeric substance (EPS), which consists of polysaccharides, extracellular DNA (eDNA), and proteins, including the DNABII family of proteins. The removal of DNABII proteins from a biofilm results in the loss of structural integrity of the eDNA and the collapse of the biofilm structure. We examined the role of DNABII proteins in the biofilm structure of the periodontal pathogen Porphyromonas gingivalis and the oral commensal Streptococcus gordonii. Co‐aggregation with oral streptococci is thought to facilitate the establishment of P. gingivalis within the biofilm community. We demonstrate that DNABII proteins are present in the EPS of both S. gordonii and P. gingivalis biofilms, and that these biofilms can be disrupted through the addition of antisera derived against their respective DNABII proteins. We provide evidence that both eDNA and DNABII proteins are limiting in S. gordonii but not in P. gingivalis biofilms. In addition, these proteins are capable of complementing one another functionally. We also found that whereas antisera derived against most DNABII proteins are capable of binding a wide variety of DNABII proteins, the P. gingivalis DNABII proteins are antigenically distinct. The presence of DNABII proteins in the EPS of these biofilms and the antigenic uniqueness of the P. gingivalis proteins provide an opportunity to develop therapies that are targeted to remove P. gingivalis and biofilms that contain P. gingivalis from the oral cavity.
Relative maturity and the development of immunity to gastrointestinal nematodes in sheep: an overlooked paradigm?
Authors: Greer A. W. , Hamie J. C. 
Published: March 2016

SummarySheep display considerable variation in both the timing and magnitude of development of immunity to gastrointestinal nematodes (GIN). Onset of immunity is dependent on a number of factors, including antigenic stimulus, nutrition supply, age and size of the animals, the latter of which are confounded. Here, we review the factors associated with the development of immunity to GIN in sheep, particularly in the context of the role that relative maturity may have through applying the rules of genetic size scaling based on examples from published literature. Comparing animals based on their metabolic age, rather than chronological age, may provide an explanation for the timing of immune development and may reduce the variation in immune development that frequently is observed both between and within breeds. Further, this approach may help explain the phenotypic differences in animal performance between animals of varying immunological capacity to GIN through influences on mature body weight. As such, when considering factors influencing immune development to GIN, physiological age or relative maturity may be considered an overlooked paradigm. We propose it may be worthwhile to consider metabolic age when comparing the immune competence of animals to ensure the subjects are at an analogous stage of physiological development.
End‐of‐life care in residential care homes: a retrospective study of the perspectives of family members using the VOICES questionnaire
Authors: Andersson Sofia , Lindqvist Olav , Fürst Carl‐Johan , Brännström Margareta 
Published: March 2016

BackgroundIn Europe, residential care homes (RCHs) are replacing hospitals as the place where death occurs, and they play an important role in end‐of‐life (EOL) care.ObjectiveThe aim was to describe the quality of care during the last 3 months and last 3 days of life of those who died in RCHs as reported by family members. We also investigated whether there were differences in the EOL care of younger patients (<85 years) vs. the oldest old patients (≥85 years) as reported by family members.DesignA retrospective survey design.MethodsDeaths (n = 189) at 19 RCHs in one municipality in Sweden were included. Family members were sent the VOICES questionnaire 1 month after their elderly relative had died. Descriptive statistics were used.ResultsIn the last 3 days before death, most family members reported there was enough help with nursing (93%) and personal care (78.5%). Among the family members, 86% were told that the resident was likely to die shortly. Most (94.1%) of residents were reported to have died at their preferred place. No significant difference was found between age groups. Family members also reported that about half of the elderly had pain (46.5%) and 86.4% received treatment; 55.9% had breathlessness and 39.7% received treatment. Breathlessness was significantly (p = 0.01) more common in the younger group, and they were treated more often (p = 0.006) than the oldest old.ConclusionThis study revealed an overall positive picture of personal and nursing care and communication. These findings indicate that the quality of EOL care at RCHs is high. Inadequate management was found for symptom relief the last days of life. This suggests that this subject merits further attention by care professionals. To achieve better quality of EOL care at RCHs, we emphasise the importance of systematically working to improve symptom relief.
Correlates of children's compliance with moderate‐to‐vigorous physical activity recommendations: a multilevel analysis
Authors: Pereira S. , Borges A. , Gomes T. N. , Santos D. , Souza M. , dos Santos F. K. , Chaves R. N. , Barreira T. V. , Hedeker D. , Katzmarzyk P. T. , Maia J. A. R. 
Published: March 2016

This study aimed to investigate the association between individual and school characteristics associated with the number of school days children comply with moderate‐to‐vigorous physical activity (MVPA) recommendations. Sample comprises 612 Portuguese children, aged 9–11 years, from 23 schools. Time spent in MVPA was measured by accelerometry, while individual‐level correlates were obtained by anthropometry and questionnaires. School‐level variables were collected by questionnaire, and accelerometer wear time and season were also considered. Maximum likelihood estimates of model parameters were obtained via a multilevel analysis with children as level‐1, and school as level‐2. Children who spent more time in sedentary activities and girls were less likely to comply with MVPA/daily. More mature children and those who use active transportation to school were more likely to attain the PA recommendation. Furthermore, greater accelerometer wear time and spring season increased the chance to achieve the recommended MVPA. In terms of school‐level correlates, a greater number of available facilities was negatively associated with children MVPA compliance. Given the set of variables, our results showed that individual characteristics seem to be more relevant for children's compliance rates with PA/day than school context variables, which should be taken into account in the implementation of school policies and practices.
Building Information Modelling for High‐rise Land Administration
Authors: Atazadeh Behnam , Kalantari Mohsen , Rajabifard Abbas , Ho Serene , Ngo Tuan 
Published: March 2016

AbstractCurrent land administration systems mainly use 2D plans to define and secure ownership rights associated with properties in high‐rise buildings. These 2D plans may not effectively communicate and manage the spatial complexity associated with multi‐layered and stacked properties in such buildings; additionally, multiple pages of plans (representing sections of the building) are required to represent all ownership boundaries. In response, land administration organizations have been investigating a 3D digital approach to managing information about ownership rights in high‐rise building structures. In this article, Building Information Modeling (BIM) is proposed as a feasible approach for managing land and property information in high‐rise buildings. BIM provides a collaborative, digital and intelligent 3D data environment for managing building information throughout the lifecycle of buildings. However, there is currently no capacity in BIM for recording and representing information about ownership and boundaries of properties, which is core land administration information. Therefore, this article proposes an extension to the BIM standard, which is implemented in a prototype BIM model of a complex building to showcase the potential capability of using BIM for high‐rise land administration and for modeling 3D ownership rights.
A Genetic Algorithm for Tributary Selection with Consideration of Multiple Factors
Authors: Zhang Ling , Guilbert Eric 
Published: March 2016

AbstractDrainage systems are important components in cartography and Geographic Information Systems (GIS), and achieve different drainage patterns based on the form and texture of their network of stream channels and tributaries due to local topography and subsurface geology. The drainage pattern can reflect the geographical characteristics of a river network to a certain extent. To preserve the drainage pattern during the generalization process, this article proposes a solution to deal with many factors, such as the tributary length and the order in river tributary selection. This leads to a multi‐objective optimization problem solved with a Genetic Algorithm. In the multi‐objective model, different weights are used to aggregate all objective functions into a fitness function. The method is applied on a case study to evaluate the importance of each factor for different types of drainage and results are compared with a manually generalized network. The result can be controlled by assigning different weights to the factors. From this work, different weight settings according to drainage patterns are proposed for the river network generalization.
A model‐based scatter artifacts correction for cone beam CT
Authors: Zhao Wei , Vernekohl Don , Zhu Jun , Wang Luyao , Xing Lei 
Published: March 2016

Purpose:Due to the increased axial coverage of multislice computed tomography (CT) and the introduction of flat detectors, the size of x‐ray illumination fields has grown dramatically, causing an increase in scatter radiation. For CT imaging, scatter is a significant issue that introduces shading artifact, streaks, as well as reduced contrast and Hounsfield Units (HU) accuracy. The purpose of this work is to provide a fast and accurate scatter artifacts correction algorithm for cone beam CT (CBCT) imaging.Methods:The method starts with an estimation of coarse scatter profiles for a set of CBCT data in either image domain or projection domain. A denoising algorithm designed specifically for Poisson signals is then applied to derive the final scatter distribution. Qualitative and quantitative evaluations using thorax and abdomen phantoms with Monte Carlo (MC) simulations, experimental Catphan phantom data, and in vivo human data acquired for a clinical image guided radiation therapy were performed. Scatter correction in both projection domain and image domain was conducted and the influences of segmentation method, mismatched attenuation coefficients, and spectrum model as well as parameter selection were also investigated.Results:Results show that the proposed algorithm can significantly reduce scatter artifacts and recover the correct HU in either projection domain or image domain. For the MC thorax phantom study, four‐components segmentation yields the best results, while the results of three‐components segmentation are still acceptable. The parameters (iteration number K and weight β) affect the accuracy of the scatter correction and the results get improved as K and β increase. It was found that variations in attenuation coefficient accuracies only slightly impact the performance of the proposed processing. For the Catphan phantom data, the mean value over all pixels in the residual image is reduced from −21.8 to −0.2 HU and 0.7 HU for projection domain and image domain, respectively. The contrast of the in vivo human images is greatly improved after correction.Conclusions:The software‐based technique has a number of advantages, such as high computational efficiency and accuracy, and the capability of performing scatter correction without modifying the clinical workflow (i.e., no extra scan/measurement data are needed) or modifying the imaging hardware. When implemented practically, this should improve the accuracy of CBCT image quantitation and significantly impact CBCT‐based interventional procedures and adaptive radiation therapy.
Draft Genome Sequences of 10
Bacillus subtilis
Strains That Form Spores with High or Low Heat Resistance
Authors: Berendsen Erwin M. , Wells-Bennik Marjon H. J. , Krawczyk Antonina O. , de Jong Anne , van Heel Auke , Eijlander Robyn T. , Kuipers Oscar P. 
Published: March 2016

ABSTRACT

Here, we report the draft genome sequences of 10 isolates of
Bacillus subtilis
, a spore forming Gram-positive bacterium. The strains were selected from food products and produced spores with either high or low heat resistance.
Epidemic potential ofEscherichia coliST131 andKlebsiella pneumoniaeST258: a systematic review and meta-analysis
Authors: Dautzenberg M J D , Haverkate M R , Bonten M J M , Bootsma M C J 
Published: March 2016

ObjectivesObservational studies have suggested thatEscherichia colisequence type (ST) 131 andKlebsiella pneumoniaeST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters forE. coliST131 andK. pneumoniaeST258, in order to investigate whetherE. coliST131 andK. pneumoniaeST258 are truly hyperendemic clones.Primary outcome measuresA systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity forE. coliST131 andK. pneumoniaeST258. Meta-regression was performed to quantify these characteristics.ResultsThe systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coliST131 n=9;K. pneumoniaeST258 n=10)), 2 on duration of infectiousness (E. coliST131 n=2), and 324 on pathogenicity (E. coliST131 n=285;K. pneumoniaeST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regressionE. coliisolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting thatE. coliST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131.E. coliST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. ForK. pneumoniaeST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence.ConclusionsWith the currently available data, it cannot be confirmed nor rejected, thatE. coliST131 orK. pneumoniaeST258 are hyperendemic clones.
Smoke-free homes: what are the barriers, motivators and enablers? A qualitative systematic review and thematic synthesis
Authors: Passey Megan E , Longman Jo M , Robinson Jude , Wiggers John , Jones Laura L 
Published: March 2016

ObjectiveTo thematically synthesise primary qualitative studies of the barriers, motivators and enablers of smoke-free homes (SFHs).DesignSystematic review and thematic synthesis.Data sourcesSearches of MEDLINE, EBM Reviews (Cochrane Database of Systematic Reviews), PsycINFO, Global Health, CINAHL, Web of Science, Informit and EMBASE, combining terms for families, households and vulnerable populations; SFH and secondhand smoke; and qualitative research, were supplemented by searches of PhD theses, key authors, specialist journals and reference lists.Study selectionWe included 22 articles, reporting on 18 studies, involving 646 participants. Inclusion criteria: peer-reviewed; English language; published from 1990 onwards (to week 3 of April 2014); used qualitative data collection methods; explored participants’ perspectives of home smoking behaviours; and the barriers, motivators and enablers to initiating and/or maintaining a SFH.Data extraction1 of 3 authors extracted data with checking by a second.Data synthesisA thematic synthesis was performed to develop 7 core analytic themes: (1) knowledge, awareness and risk perception; (2) agency and personal skills/attributes; (3) wider community norms and personal moral responsibilities; (4) social relationships and influence of others; (5) perceived benefits, preferences and priorities; (6) addiction and habit; (7) practicalities.ConclusionsThis synthesis highlights the complexity faced by many households in having a SFH, the practical, social, cultural and personal issues that need to be addressed and balanced by households, and that while some of these are common across study settings, specific social and cultural factors play a critical role in shaping household smoking behaviours. The findings can inform policy and practice and the development of interventions aimed at increasing SFHs.Trial registration numberCRD42014014115.
Do patients hospitalised in high-minority hospitals experience more diversion and poorer outcomes? A retrospective multivariate analysis of Medicare patients in California
Authors: Shen Yu-Chu , Hsia Renee Y 
Published: March 2016

ObjectiveWe investigated the association between crowding as measured by ambulance diversion and differences in access, treatment and outcomes between black and white patients.DesignRetrospective analysis.SettingWe linked daily ambulance diversion logs from 26 California counties between 2001 and 2011 to Medicare patient records with acute myocardial infarction and categorised patients according to hours in diversion status for their nearest emergency departments on their day of admission: 0, <6, 6 to <12 and ≥12 h. We compared the amount of diversion time between hospitals serving high volume of black patients and other hospitals. We then use multivariate models to analyse changes in outcomes when patients faced different levels of diversion, and compared that change between black and white patients.Participants29 939 Medicare patients from 26 California counties between 2001 and 2011.Main outcome measures(1) Access to hospitals with cardiac technology; (2) treatment received; and (3) health outcomes (30-day, 90-day, and 1-year death and 30-day readmission).ResultsHospitals serving high volume of black patients spent more hours in diversion status compared with other hospitals. Patients faced with the highest level of diversion had the lowest probability of being admitted to hospitals with cardiac technology compared with those facing no diversion, by 4.4% for cardiac care intensive unit, and 3.4% for catheterisation laboratory and coronary artery bypass graft facilities. Patients experiencing increased diversion also had a 4.3% decreased likelihood of receiving catheterisation and 9.6% higher 1-year mortality.ConclusionsHospitals serving high volume of black patients are more likely to be on diversion, and diversion is associated with poorer access to cardiac technology, lower probability of receiving revascularisation and worse long-term mortality outcomes.
Combining Epigenetic and Immunotherapy to Combat Cancer
Authors: Chiappinelli Katherine B. , Zahnow Cynthia A. , Ahuja Nita , Baylin Stephen B. 
Published: March 2016

Abstract
The most exciting recent advance for achieving durable management of advanced human cancers is immunotherapy, especially the concept of immune checkpoint blockade. However, with the exception of melanoma, most patients do not respond to immunotherapy alone. A growing body of work has shown that epigenetic drugs, specifically DNA methyltransferase inhibitors, can upregulate immune signaling in epithelial cancer cells through demethylation of endogenous retroviruses and cancer testis antigens. These demethylating agents may induce T-cell attraction and enhance immune checkpoint inhibitor efficacy in mouse models. Current clinical trials are testing this combination therapy as a potent new cancer management strategy. Cancer Res; 76(7); 1683–9. ©2016 AACR.