bluuebunny/crossref_metadata_2025 huggingface dataset:
Facilitating patients with disorders of consciousness to sit without trunk support: a qualitative study
Authors: Miyata Kumiko , Yoshimura Sadako , Hayashi Yuko
Published: March 2015

Aims and objectives

This study aimed to clarify why and how clinical nurses facilitate sitting without trunk support among patients with disorders of consciousness.

Background

Recent attention has focused on encouraging patients with disorders of consciousness to sit without trunk support, but no reports describe this intervention among patients with poor awareness and physical disuse.

Design

Qualitative research design.

Methods

We enrolled five clinical nurses with interventional experience in rehabilitating patients with disorders of consciousness to sit without trunk support. Participant observation and semi‐structured interviews were used to collect data. The data were analysed by text‐mining method.

Results

Three reasons for nursing in the sitting position were identified: to raise the patient's body to assess the recovery of activities of daily living, to adjust their circadian rhythm and encourage the will to sit, and to make it easier to breathe. Five practices were identified: moving the patient to the prone position to sit in safety and comfort, developing postural stability by improving the flexibility of the lower limbs, improving the flexibility of the hip joints, developing trunk balance and encouraging hand use for stability, and ensuring safety by terminating the sitting practice when symptoms of respiratory failure, heart failure, or excessive tiredness developed.

Conclusions

The rationale for nursing patients with disorders of consciousness to sit without trunk support was to establish a foundation for independent living. This was achieved by preparing patient's disused body for activity by improving the flexibility of hip joint in the prone position. This represents a new intervention for patients with disorders of consciousness that could facilitate independent living.

Relevance to clinical practice

This study provides empirical and practical evidence from nurses who perform novel clinical interventions that specifically promote independent living. Further accumulation of quantitative clinical results and physiological verification are required.
Phorate‐induced Host Defence Responses Condition Acquired Resistance to Tomato Spotted Wilt in Cultivated Peanut (Arachis hypogaea L.)
Authors: Jain Mukesh , Gallo Maria , Chengalrayan Kudithipudi , Shaikh Nasir P. , MacDonald Gregory E. , Davis John M.
Published: March 2015

Phorate is an acetylcholinesterase‐inhibiting organophosphate pesticide used for the control of insects, mites and nematodes. In cultivated peanut (Arachis hypogaea L.), phorate is often used as an in‐furrow, systemic insecticide to reduce thrips populations which vector tomato spotted wilt tospovirus (TSWV). However, phorate‐induced suppression of disease incidence and severity is not solely due to thrips control because other pesticides control thrips but not TSWV. The present research was focused on understanding the biochemical and molecular components of the phorate‐induced host responses that may condition acquired resistance to TSWV in peanut. Phorate treatments adversely affected maximal quantum yield of the light reactions (Fv/Fm). A dose‐dependent increase in ascorbic acid content and in activities of the oxidative stress‐related enzymes, catalase and superoxide dismutase was evident following phorate treatment, whereas the level of glutathione reductase was not affected. An RT‐PCR differential display screen identified 35 expressed sequence tags (ESTs) responsive to phorate treatment in peanut leaves. Functional annotations revealed transcriptional regulation of ESTs implicated in primary and secondary metabolism including photosynthesis‐related genes, mitigation of oxidative stress, signalling pathways and pathogenesis‐ and defence‐related proteins. Two ESTs encoding membrane trafficking functions were downregulated, which may reflect reduced internalization and/or subsequent replication of viral particles in phorate‐treated leaves. Time‐course quantitative RT‐PCR analyses further verified fidelity and sensitivity of the mRNA differential display screen and corroborated that systemic spread of TSWV in field‐grown plants is reduced following phorate application. The mélange of differentially regulated gene functions is consistent with a model in which a phorate‐induced breach of redox control culminates in hypersensitive cell death and subsequent induction of systemic acquired resistance.
The plastid genome of the red alga Laurencia
Authors: Verbruggen Heroen , Costa Joana F.
Published: March 2015

We present the 174,935 nt long plastid genome of the red alga Laurencia sp. JFC0032. It is the third plastid genome characterized for the largest order of red algae (Ceramiales). The circular‐mapping plastid genome is small compared to most florideophyte red algae, and our comparisons show a trend toward smaller plastid genome sizes in the family Rhodomelaceae, independent from a similar trend in Cyanidiophyceae. The Laurencia genome is densely packed with 200 annotated protein‐coding genes (188 widely conserved, 3 open reading frames shared with other red algae and 9 hypothetical coding regions). It has 29 tRNAs, a single‐copy ribosomal RNA cistron, a tmRNA, and the RNase P RNA.
Sexual size dimorphism mediates effects of spatial resource variability onAmerican black bear space use
Authors: Hiller T. L. , Belant J. L. , Beringer J.
Published: March 2015

The distribution of animals is influenced by numerous factors including spatial distribution and temporal availability of resources. We tested the spatial resource variability hypothesis (increasing landscape heterogeneity results in increasing amount of space use) and the temporal resource variability hypothesis (temporal variation in resources reduces amount of space use) using location data from radiomarkedAmerican black bearsUrsus americanusinMissouri andArkansas,USA. We used 95% utilization distributions (UDs) to define individual seasonal space use and constructed 22 models using covariates that described composition, spatial arrangement and diversity of land cover types (an index of heterogeneity or patchiness); seasonal hard mast production; and seasonal use of land cover to test our hypotheses using linear modeling and small‐sample Akaike information criterion (AICc) model selection approaches. TheAICcbest performing model supported the spatial resource variability hypothesis and included Shannon diversity index [95% confidence limit (CL) of coefficient = 1.56–2.42] and sex (male; 95%CLof coefficient = 0.05–0.49) as covariates that explained variation in transformed values ofUDsize. Predicted and observed values during model evaluation were highly correlated (r = 0.90). As land cover heterogeneity increased,UDsize increased, likely a consequence of bears responding to greater patchiness to maintain sufficient resources. Further, theShannon diversity index was greater for malesthan females, suggesting larger bodied males used larger areas to meet their higher energetic costs due to landscape fragmentation. Studies of resource hypotheses in solitary species should consider intraspecific allometric relationships such as sexual size dimorphism as has been addressed using group size in social species.
Water‐related bird assemblages in an urban pond ‘archipelago’: Winter patterns of bird species occurrence, abundance and richness
Authors: Di Santo Maria Paola , Carpaneto Giuseppe M. , Battisti Corrado
Published: March 2015

This study reports on the patterns of species occurrence, abundance and richness of a wintering water‐related bird assemblage in an ‘archipelago’ of 70 small artificial urban ponds (AUPs) embedded in a metropolitan landscape (Rome, central Italy). A total of 20 species in 26 AUPs were sampled. Only the largest AUPs (>0.1 ha) contained all these species, except for Gallinula chloropus. The highest total mean species abundance was observed in the largest ponds, with statistically significant differences evident among size classes. Two significant spatial thresholds in species abundance and richness were observed (between 0.01 and 0.1 ha; between 0.1 and 1 ha in size). The abundance of single species was correlated with their frequency of occurrence. Ponds in urban areas must be larger than 0.1 ha to host a rich winter assemblage of birds, with a further increase in richness noted with a surface area larger than 1 ha. The highest number of species was observed in the larger ponds (>1 ha). The species richness of each AUP is directly correlated to their size (log‐transformed species–area relationship: log S = 3.515 + 0.497 log A; R2 = 0.76). Further research should be conducted to confirm these patterns and to implement information useful for planning and management of artificial ponds in urban areas for this purpose.
Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species
Authors: van Schaik J. , Dekeukeleire D. , Kerth G.
Published: March 2015

Host–parasite interactions are ubiquitous in nature. However, how parasite population genetic structure is shaped by the interaction between host and parasite life history remains understudied. Studies comparing multiple parasites infecting a single host can be used to investigate how different parasite life history traits interplay with host behaviour and life history. In this study, we used 10 newly developed microsatellite loci to investigate the genetic structure of a parasitic bat fly (Basilia nana). Its host, the Bechstein's bat (Myotis bechsteinii), has a social system and roosting behaviour that restrict opportunities for parasite transmission. We compared fly genetic structure to that of the host and another parasite, the wing‐mite, Spinturnix bechsteini. We found little spatial or temporal genetic structure in B. nana, suggesting a large, stable population with frequent genetic exchange between fly populations from different bat colonies. This contrasts sharply with the genetic structure of the wing‐mite, which is highly substructured between the same bat colonies as well as temporally unstable. Our results suggest that although host and parasite life history interact to yield similar transmission patterns in both parasite species, the level of gene flow and eventual spatiotemporal genetic stability is differentially affected. This can be explained by the differences in generation time and winter survival between the flies and wing‐mites. Our study thus exemplifies that the population genetic structure of parasites on a single host can vary strongly as a result of how their individual life history characteristics interact with host behaviour and life history traits.
Soil microbiome responses to the short‐term effects of Amazonian deforestation
Authors: Navarrete Acacio A. , Tsai Siu M. , Mendes Lucas W. , Faust Karoline , de Hollander Mattias , Cassman Noriko A. , Raes Jeroen , van Veen Johannes A. , Kuramae Eiko E.
Published: March 2015

Slash‐and‐burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear‐cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism‐related functions. Co‐occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash‐and‐burning deforestation in the Amazon region.
Dangers of broth after transplantation
Authors: Aggarwal Shikha , Sukkar Louisa , Wynter Lucy , Richards Kate , Cheung Jason , Chadban Steve J
Published: March 2015

Serum creatinine is routinely used to monitor renal function in transplant recipients. External factors including diet, exercise and hydration status can also influence serum creatinine concentration on a day‐to‐day basis. We describe a case of a patient whose serum creatinine increased from 128 to 171 μmol/L after ingestion of creatinine‐rich (3098 μmol/L) soup. A renal biopsy was performed but revealed no cause for the rise in creatinine and by the next day, serum creatinine had returned to baseline. We conducted two experiments to examine the effect of soup ingestion by healthy volunteers. We measured the creatinine concentration of various store‐bought stock preparations and found creatinine concentrations less than one‐quarter of that contained in our patient's homemade soup. A creatinine‐rich soup (4334 μmol/L) was ingested by six healthy volunteers age 33 (± 6.5) years with baseline normal serum creatinine 68 (± 14) μmol/L. Mean (standard deviation) serum creatinine increased to 77 (± 11) μmol/L 4 hours after soup ingestion (P = 0.0015, paired t‐test). Mean (standard deviation) creatinine clearance, extrapolated from the 4 hour urine collection following soup ingestion, was high (267 ± 198 mL/min) exhibiting a supra‐normal creatinine clearance. The rate of serum creatinine rise was lower in volunteers compared with the transplant patient, consistent with the concept of renal functional reserve. Our case highlights the importance of taking dietary changes into account when interpreting serum creatinine as a measure of allograft function.
A Simple Improvement of the IV‐estimator for the Classical Errors‐in‐Variables Problem
Authors: Andersson Jonas , Møen Jarle
Published: March 2015

Two measures of an error‐ridden variable make it possible to solve the classical errors‐in‐Variable problem by using one measure as an instrument for the other. It is well known that a second IV‐estimate can be obtained by reversing the roles of the two measures. We explore the optimal linear combination of these two estimates. In a Monte Carlo study, we show that the gain in precision is significant. The proposed estimator also compares well with full information maximum likelihood under normality. We illustrate the method by estimating the capital elasticity in the Norwegian ICT‐industry.
The impact of dental appearance and anxiety on self‐esteem in adult orthodontic patients
Authors: Romero‐Maroto M. , Santos‐Puerta N. , González Olmo M. J. , Peñacoba‐Puente C.
Published: March 2015

Structured Abstract

Objectives

To analyse the relationship between different dimensions of dental appearance impact and self‐esteem in adult patients undergoing orthodontic treatment, with special attention to the possible mediating role of anxiety.

Setting and Sample Population

A quasi‐experimental design was used with a matched control group (without orthodontic treatment). In each group (experimental and control), there were 85 patients.

Material and Methods

The impact of dental appearance was measured using the Psychosocial Impact of Dental Aesthetics Questionnaire (PIDAQ). State anxiety was assessed with the State Anxiety Inventory (STAI‐S) and self‐esteem with Rosenberg's self‐esteem scale.

Results

In both groups (experimental and control), self‐esteem correlates negatively, ranging between 0.26 and 0.43, with all dimensions of dental appearance impact (except for the positive dental self‐confidence dimension, where all correlations were positive). Anxiety correlates positively, ranges between 0.35 and 0.44, with social impact, psychological impact and aesthetic concern, although it maintains no significant correlations with dental self‐confidence. Nevertheless, in patients undergoing orthodontic treatment, anxiety plays a mediating role between dental impact dimensions and self‐esteem, whilst for the control group anxiety only plays a mediator role between psychological impact and self‐esteem.

Conclusion

Anxiety plays a fundamental role in the effect of perceived dental impact on self‐esteem in adult patients undergoing orthodontic treatment. These results have important practical implications for the design of bio‐psycho‐social intervention programs that contemplate cognitive‐affective variables as an essential part of orthodontic treatment in adults.
The heterotrimeric G‐protein β subunit, AGB1, plays multiple roles in the Arabidopsis salinity response
Authors: Yu Yunqing , Assmann Sarah M.
Published: March 2015

Salinity stress includes both osmotic and ionic toxicity. Sodium homeostasis is influenced by Na+ uptake and extrusion, vacuolar Na+ compartmentation and root to shoot Na+ translocation via transpiration. The knockout mutant of the Arabidopsis heterotrimeric G‐protein Gβ subunit, agb1, is hypersensitive to salt, exhibiting a leaf bleaching phenotype. We show that AGB1 is mainly involved in the ionic toxicity component of salinity stress and plays roles in multiple processes of Na+ homeostasis. agb1 mutants accumulate more Na+ and less K+ in both shoots and roots of hydroponically grown plants, as measured by inductively coupled plasma atomic emission spectrometry. agb1 plants have higher root to shoot translocation rates of radiolabelled 24Na+ under transpiring conditions, as a result of larger stomatal apertures and increased stomatal conductance. 24Na+ tracer experiments also show that 24Na+ uptake rates by excised roots of agb1 and wild type are initially equal, but that agb1 has higher net Na+ uptake at 90 min, implicating possible involvement of AGB1 in the regulation of Na+ efflux. Calcium alleviates the salt hypersensitivity of agb1 by reducing Na+ accumulation to below the toxicity threshold. Our results provide new insights into the regulatory pathways underlying plant responses to salinity stress, an important agricultural problem.
An insecure base: Attachment style and orienting response to positive stimuli
Authors: Yee Claire I. , Shiota Michelle N.
Published: March 2015

In adults as in infants, psychological attachment to close others provides a “secure base” for exploration and pursuit of opportunities. Insecure attachment is likely to interfere with this function. The present study examined the association of individual differences in adult attachment style with peripheral physiological measures of automatic orienting to several kinds of positive, rewarding stimuli. Attachment style was largely unrelated to extent of heart rate deceleration in response to the appearance of positive emotion‐eliciting images. However, attachment avoidance was associated with reduced skin conductance responding to the onset of several kinds of positive stimuli. These findings suggest that working models of relationships with close others have complex implications for the early stages of responding to opportunities for reward presented by the environment.
Evidence of a full West Antarctic Ice Sheet back to the early Oligocene: insight from double dating of detrital apatites in Ross Sea sediments.
Authors: Olivetti Valerio , Balestrieri Maria Laura , Rossetti Federico , Thomson Stuart N. , Talarico Franco M. , Zattin Massimiliano
Published: March 2015

The West Antarctic Ice Sheet is the most unstable component of the Antarctic cryosphere. Its fluctuations are well documented since the Pliocene, but its behaviour over the last 35 Ma is more controversial, particularly during periods of past high global pCO2 values similar to those predicted in future global climate scenarios. Here, we present new U–Pb dating of detrital apatite grains (previously dated by the fission‐track method) from Cape Roberts Project Oligocene to Pliocene marine sediments in the Ross Sea. Two past ice‐flow patterns were identified: one formed by outlet glaciers sourcing short‐travelled apatites and one, northerly directed, bringing far‐travelled apatite grains. The latter provides the first robust physical evidence for the presence and repeated expansion of an Oligocene West Antarctic Ice Sheet.
A cluster of rotavirus enteritis in pediatric liver recipients
Authors: Cui H. , Bai S. , Huo Z. , Li J. , Sun J. , An X.
Published: March 2015

We observed a cluster of 4 pediatric liver recipients who developed diarrhea in a liver transplant unit within 5 days. Feces from these 4 patients were rotavirus positive when tested with Colloidal Gold Diagnostic Kit. Nucleic acid from 3 fecal specimens was extracted and reverse transcribed. Two were amplified positively. The complementary DNAs were sequenced. Alignment and phylogenetic analysis were performed with MEGA 6.06. Although involving only 4 pediatric liver recipients, this cluster was caused by at least 2 distinct G9P[8] rotavirus strains and included community infection and nosocomial infection.
Brokered Pathways to Justice and Cracks in the Law: A Closer Look at the Claims‐Making Experiences of Low‐Wage Workers
Authors: Gleeson Shannon
Published: March 2015

This article examines the factors that shape low‐wage workers' decision to mobilize their legal rights following a workplace violation. I discuss the diverse mechanisms of employer retaliation, including the role of employer sanctions, the role of community social networks, and the myriad challenges that claimants face in navigating the labor standards enforcement bureaucracy.Idemonstrate how, although unauthorized status is formally not a barrier for accessing many key benefits inCalifornia, the structural position of unauthorized workers place them at a particular disadvantage, significantly so for subcontracted and seasonal workers. These data are based on a of survey of 453 claimants who have sought assistance from a nonprofit legal aid clinic for low‐wage workers in theSanFranciscoBayArea, and in‐depth follow‐up interviews with a representative subsample of 90 respondents, 12–30 months later. Five years of participant observation at a legal aid clinic focused on workers' compensation claims, and interviews with 24 injured workers, also inform these findings.
From Racism to International Solidarity: The Journey of UAW Local 879, 1980–1995
Authors: Rachleff Peter
Published: March 2015

This commentary is based on a paper presented as part of a panel on “Working Class Self‐Activity in Transnational Contexts” at the 2013 North American Labor History Conference. It is largely based on the author's personal experiences with United Automobile Workers' Union (UAW) Local 879, an industrial union at the Ford Truck Assembly plant in Saint Paul, Minnesota. In this commentary, Rachleff traces the transformation of consciousness among white union members from racism and nationalism to new militancy, internationalism, and anti‐racism. He identifies several key turning points in the rank‐and‐file's experiences: the arrival of several hundred workers of color from other Ford plants; the Hormel strike of the mid‐1980s; Ford management's push for labor‐management cooperation in the early 1990s; and the North American Free Trade Agreement. At each of these points, local leadership, education, and activism helped workers engage new ideas, perspectives, and self‐awareness.
Two-Bar Thermal Ratcheting for Alloy 617—Part I: Scoping Tests
Authors: Wang Yanli , Sham T.-L. , Jetter R. I.
Published: March 2015

A two-bar thermal ratcheting procedure has been implemented to Alloy 617 at very high temperatures. The procedure is based on two bars tested on two coupled servo hydraulic machines to achieve equal displacement and constant total applied load, mimicking the behavior of a pressurized cylinder subjected to through wall thermal transients. The bars were heated and cooled out of phase to generate thermally induced loading superimposed on a constant mean stress. Scoping test results at slow heating and cooling rates are presented for different mean stresses and thermal histories.
Computational Investigation of Drug Action on Human-Induced Stem Cell-Derived Cardiomyocytes
Authors: Frotscher Ralf , Koch Jan-Peter , Staat Manfred
Published: March 2015

We compare experimental and computational results for the actions of the cardioactive drugs Lidocaine, Verapamil, Veratridine, and Bay K 8644 on a tissue monolayer consisting of mainly fibroblasts and human-induced pluripotent stem cell-derived cardiomyocytes (hiPSc-CM). The choice of the computational models is justified and literature data is collected to model drug action as accurately as possible. The focus of this work is to evaluate the validity and capability of existing models for native human cells with respect to the simulation of pharmaceutical treatment of monolayers and hiPSc-CM. From the comparison of experimental and computational results, we derive suggestions for model improvements which are intended to computationally support the interpretation of experimental results obtained for hiPSc-CM.
Three-Dimensional Local Measurements of Bone Strain and Displacement: Comparison of Three Digital Volume Correlation Approaches
Authors: Palanca Marco , Tozzi Gianluca , Cristofolini Luca , Viceconti Marco , Dall'Ara Enrico
Published: March 2015

Different digital volume correlation (DVC) approaches are currently available or under development for bone tissue micromechanics. The aim of this study was to compare accuracy and precision errors of three DVC approaches for a particular three-dimensional (3D) zero-strain condition. Trabecular and cortical bone specimens were repeatedly scanned with a micro-computed tomography (CT). The errors affecting computed displacements and strains were extracted for a known virtual translation, as well as for repeated scans. Three DVC strategies were tested: two local approaches, based on fast-Fourier-transform (DaVis-FFT) or direct-correlation (DaVis-DC), and a global approach based on elastic registration and a finite element (FE) solver (ShIRT-FE). Different computation subvolume sizes were tested. Much larger errors were found for the repeated scans than for the virtual translation test. For each algorithm, errors decreased asymptotically for larger subvolume sizes in the range explored. Considering this particular set of images, ShIRT-FE showed an overall better accuracy and precision (a few hundreds microstrain for a subvolume of 50 voxels). When the largest subvolume (50–52 voxels) was applied to cortical bone, the accuracy error obtained for repeated scans with ShIRT-FE was approximately half of that for the best local approach (DaVis-DC). The difference was lower (250 microstrain) in the case of trabecular bone. In terms of precision, the errors shown by DaVis-DC were closer to the ones computed by ShIRT-FE (differences of 131 microstrain and 157 microstrain for cortical and trabecular bone, respectively). The multipass computation available for DaVis software improved the accuracy and precision only for the DaVis-FFT in the virtual translation, particularly for trabecular bone. The better accuracy and precision of ShIRT-FE, followed by DaVis-DC, were obtained with a higher computational cost when compared to DaVis-FFT. The results underline the importance of performing a quantitative comparison of DVC methods on the same set of samples by using also repeated scans, other than virtual translation tests only. ShIRT-FE provides the most accurate and precise results for this set of images. However, both DaVis approaches show reasonable results for large nodal spacing, particularly for trabecular bone. Finally, this study highlights the importance of using sufficiently large subvolumes, in order to achieve better accuracy and precision.
Mechanically Driven Branching of Bacterial Colonies
Authors: Giverso Chiara , Verani Marco , Ciarletta Pasquale
Published: March 2015

A continuum mathematical model with sharp interface is proposed for describing the occurrence of patterns in initially circular and homogeneous bacterial colonies. The mathematical model encapsulates the evolution of the chemical field characterized by a Monod-like uptake term, the chemotactic response of bacteria, the viscous interaction between the colony and the underlying culture medium and the effects of the surface tension at the boundary. The analytical analysis demonstrates that the front of the colony is linearly unstable for a proper choice of the parameters. The simulation of the model in the nonlinear regime confirms the development of fingers with typical wavelength controlled by the size parameters of the problem, whilst the emergence of branches is favored if the diffusion is dominant on the chemotaxis or for high values of the friction parameter. Such results provide new insights on pattern selection in bacterial colonies and may be applied for designing engineered patterns.
A Vine-Copula-Based Reliability Analysis Method for Structures With Multidimensional Correlation
Authors: Jiang C. , Zhang W. , Han X. , Ni B. Y. , Song L. J.
Published: March 2015

This paper proposed a vine-copula-based structural reliability analysis method which is an effective approach for performing a reliability analysis on complex multidimensional correlation problems. A joint probability distribution function (PDF) among multidimensional random variables was established using a vine copula function, based on which a reliability analysis model was constructed. Two solution algorithms were proposed to solve this reliability analysis model: one was based on Monte Carlo simulation (MCS) and another one was based on the first-order reliability method (FORM). The former method provides a generalized computational method for a reliability analysis based on vine copula functions and can provide so-called “precise solutions”; the latter method has high computational efficiency and can be used to solve actual complex engineering problems. Finally, three numerical examples were provided to verify the effectiveness of the method.
Thickness modulation effects of Al2O3 capping layers on device performance for the top-gate thin-film transistors using solution-processed poly(4-vinyl phenol)/Zn-Sn-O gate stacks
Authors: Kim Kyeong-Ah , Bak Jun-Yong , Yoon Sung-Min , Kim Seong Jip , Jeong Sunho , Choi Youngmin , Jung Soon-Won
Published: March 2015

Solution-processed Zn-Sn-O (ZTO) top-gate thin-film transistors with Al2O3/poly(4-vinyl phenol) (PVP) double-layered gate insulators (GI) were fabricated and characterized. ZTO active channel was formed by spin-coating method and activated at a temperature as low as 350 °C. The chemical damages for the PVP films, which were induced during the photolithography-based patterning process were effectively suppressed by the introduction of Al2O3 capping layer. This capping layer also played an important role in improving the drain current hysteretic behaviors caused by intrinsic properties of the PVP film by modulating the capacitance coupling in the double-layered GI. The carrier mobility, subthreshold swing, and on/off ratio were obtained as approximately 5.13 cm2V−1s−1, 0.36 V/dec, 7.03 × 106, respectively, with hysteresis-free characteristics when the thickness values of Al2O3 capping and PVP GI layers were designed to be 90 and 220 nm, respectively.
Adaptive beamlet‐based finite‐size pencil beam dose calculation for independent verification of IMRT and VMAT
Authors: Park Justin C. , Li Jonathan G. , Arhjoul Lahcen , Yan Guanghua , Lu Bo , Fan Qiyong , Liu Chihray
Published: March 2015

Purpose:

The use of sophisticated dose calculation procedure in modern radiation therapy treatment planning is inevitable in order to account for complex treatment fields created by multileaf collimators (MLCs). As a consequence, independent volumetric dose verification is time consuming, which affects the efficiency of clinical workflow. In this study, the authors present an efficient adaptive beamlet‐based finite‐size pencil beam (AB‐FSPB) dose calculation algorithm that minimizes the computational procedure while preserving the accuracy.

Methods:

The computational time of finite‐size pencil beam (FSPB) algorithm is proportional to the number of infinitesimal and identical beamlets that constitute an arbitrary field shape. In AB‐FSPB, dose distribution from each beamlet is mathematically modeled such that the sizes of beamlets to represent an arbitrary field shape no longer need to be infinitesimal nor identical. As a result, it is possible to represent an arbitrary field shape with combinations of different sized and minimal number of beamlets. In addition, the authors included the model parameters to consider MLC for its rounded edge and transmission.

Results:

Root mean square error (RMSE) between treatment planning system and conventional FSPB on a 10 × 10 cm2 square field using 10 × 10, 2.5 × 2.5, and 0.5 × 0.5 cm2 beamlet sizes were 4.90%, 3.19%, and 2.87%, respectively, compared with RMSE of 1.10%, 1.11%, and 1.14% for AB‐FSPB. This finding holds true for a larger square field size of 25 × 25 cm2, where RMSE for 25 × 25, 2.5 × 2.5, and 0.5 × 0.5 cm2 beamlet sizes were 5.41%, 4.76%, and 3.54% in FSPB, respectively, compared with RMSE of 0.86%, 0.83%, and 0.88% for AB‐FSPB. It was found that AB‐FSPB could successfully account for the MLC transmissions without major discrepancy. The algorithm was also graphical processing unit (GPU) compatible to maximize its computational speed. For an intensity modulated radiation therapy (∼12 segments) and a volumetric modulated arc therapy fields (∼90 control points) with a 3D grid size of 2.0 × 2.0 × 2.0 mm3, dose was computed within 3–5 and 10–15 s timeframe, respectively.

Conclusions:

The authors have developed an efficient adaptive beamlet‐based pencil beam dose calculation algorithm. The fast computation nature along with GPU compatibility has shown better performance than conventional FSPB. This enables the implementation of AB‐FSPB in the clinical environment for independent volumetric dose verification.
Spectra of clinical CT scanners using a portable Compton spectrometer
Authors: Duisterwinkel H. A. , van Abbema J. K. , van Goethem M. J. , Kawachimaru R. , Paganini L. , van der Graaf E. R. , Brandenburg S.
Published: March 2015

Purpose:

Spectral information of the output of x‐ray tubes in (dual source) computer tomography (CT) scanners can be used to improve the conversion of CT numbers to proton stopping power and can be used to advantage in CT scanner quality assurance. The purpose of this study is to design, validate, and apply a compact portable Compton spectrometer that was constructed to accurately measure x‐ray spectra of CT scanners.

Methods:

In the design of the Compton spectrometer, the shielding materials were carefully chosen and positioned to reduce background by x‐ray fluorescence from the materials used. The spectrum of Compton scattered x‐rays alters from the original source spectrum due to various physical processes. Reconstruction of the original x‐ray spectrum from the Compton scattered spectrum is based on Monte Carlo simulations of the processes involved. This reconstruction is validated by comparing directly and indirectly measured spectra of a mobile x‐ray tube. The Compton spectrometer is assessed in a clinical setting by measuring x‐ray spectra at various tube voltages of three different medical CT scanner x‐ray tubes.

Results:

The directly and indirectly measured spectra are in good agreement (their ratio being 0.99) thereby validating the reconstruction method. The measured spectra of the medical CT scanners are consistent with theoretical spectra and spectra obtained from the x‐ray tube manufacturer.

Conclusions:

A Compton spectrometer has been successfully designed, constructed, validated, and applied in the measurement of x‐ray spectra of CT scanners. These measurements show that our compact Compton spectrometer can be rapidly set‐up using the alignment lasers of the CT scanner, thereby enabling its use in commissioning, troubleshooting, and, e.g., annual performance check‐ups of CT scanners.
Therapeutics to block autoantibody initiation and propagation in systemic lupus erythematosus and rheumatoid arthritis
Authors: Suurmond Jolien , Zou Yong Rui , Kim Sun Jung , Diamond Betty
Published: March 2015

Recent advances in lupus and rheumatoid arthritis suggest new approaches for damping autoimmunity.
Advances in allergen immunotherapy: Aiming for complete tolerance to allergens
Authors: Akdis Cezmi A. , Akdis Mübeccel
Published: March 2015

Allergen-specific immunotherapy is a tolerance-inducing therapy for allergic disease.
Good-in-good-out: Diet modification in chronic kidney disease
Authors: Chitalia Vipul
Published: March 2015

Low-protein diet with or without ketoacids retards renal failure progression without increasing mortality.
The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins
Authors: Koskimäki Janne J. , Pirttilä Anna Maria , Ihantola Emmi-Leena , Halonen Outi , Frank A. Carolin
Published: March 2015

Endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. While endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells,
Methylobacterium extorquens
strain DSM13060 is a facultatively intracellular symbiont of the meristematic cells of Scots pine (Pinus sylvestris L.) shoot tips. The bacterium promotes host growth and development without the production of known plant growth-stimulating factors. Our objective was to examine intracellular colonization by M. extorquens DSM13060 of Scots pine and sequence its genome to identify novel molecular mechanisms potentially involved in intracellular colonization and plant growth promotion. Reporter construct analysis of known growth promotion genes demonstrated that these were only weakly active inside the plant or not expressed at all. We found that bacterial cells accumulate near the nucleus in intact, living pine cells, pointing to host nuclear processes as the target of the symbiont's activity. Genome analysis identified a set of eukaryote-like functions that are common as effectors in intracellular bacterial pathogens, supporting the notion of intracellular bacterial activity. These include ankyrin repeats, transcription factors, and host-defense silencing functions and may be secreted by a recently imported type IV secretion system. Potential factors involved in host growth include three copies of phospholipase A2, an enzyme that is rare in bacteria but implicated in a range of plant cellular processes, and proteins putatively involved in gibberellin biosynthesis. Our results describe a novel endophytic niche and create a foundation for postgenomic studies of a symbiosis with potential applications in forestry and agriculture.

IMPORTANCE
All multicellular eukaryotes host communities of essential microbes, but most of these interactions are still poorly understood. In plants, bacterial endophytes are found inside all tissues. M. extorquens DSM13060 occupies an unusual niche inside cells of the dividing shoot tissues of a pine and stimulates seedling growth without producing cytokinin, auxin, or other plant hormones commonly synthesized by plant-associated bacteria. Here, we tracked the bacteria using a fluorescent tag and confocal laser scanning microscopy and found that they localize near the nucleus of the plant cell. This prompted us to sequence the genome and identify proteins that may affect host growth by targeting processes in the host cytoplasm and nucleus. We found many novel genes whose products may modulate plant processes from within the plant cell. Our results open up new avenues to better understand how bacteria assist in plant growth, with broad implications for plant science, forestry, and agriculture.
The Number of Alphaherpesvirus Particles Infecting Axons and the Axonal Protein Repertoire Determines the Outcome of Neuronal Infection
Authors: Koyuncu Orkide O. , Song Ren , Greco Todd M. , Cristea Ileana M. , Enquist Lynn W.
Published: March 2015

Infection by alphaherpesviruses invariably results in invasion of the peripheral nervous system (PNS) and establishment of either a latent or productive infection. Infection begins with long-distance retrograde transport of viral capsids and tegument proteins in axons toward the neuronal nuclei. Initial steps of axonal entry, retrograde transport, and replication in neuronal nuclei are poorly understood. To better understand how the mode of infection in the PNS is determined, we utilized a compartmented neuron culturing system where distal axons of PNS neurons are physically separated from cell bodies. We infected isolated axons with fluorescent-protein-tagged pseudorabies virus (PRV) particles and monitored viral entry and transport in axons and replication in cell bodies during low and high multiplicities of infection (MOIs of 0.01 to 100). We found a threshold for efficient retrograde transport in axons between MOIs of 1 and 10 and a threshold for productive infection in the neuronal cell bodies between MOIs of 1 and 0.1. Below an MOI of 0.1, the viral genomes that moved to neuronal nuclei were silenced. These genomes can be reactivated after superinfection by a nonreplicating virus, but not by a replicating virus. We further showed that viral particles at high-MOI infections compete for axonal proteins and that this competition determines the number of viral particles reaching the nuclei. Using mass spectrometry, we identified axonal proteins that are differentially regulated by PRV infection. Our results demonstrate the impact of the multiplicity of infection and the axonal milieu on the establishment of neuronal infection initiated from axons.

IMPORTANCE
Alphaherpesvirus genomes may remain silent in peripheral nervous system (PNS) neurons for the lives of their hosts. These genomes occasionally reactivate to produce infectious virus that can reinfect peripheral tissues and spread to other hosts. Here, we use a neuronal culture system to investigate the outcome of axonal infection using different numbers of viral particles and coinfection assays. We found that the dynamics of viral entry, transport, and replication change dramatically depending on the number of virus particles that infect axons. We demonstrate that viral genomes are silenced when the infecting particle number is low and that these genomes can be reactivated by superinfection with UV-inactivated virus, but not with replicating virus. We further show that viral invasion rapidly changes the profiles of axonal proteins and that some of these axonal proteins are rate limiting for efficient infection. Our study provides new insights into the establishment of silent versus productive alphaherpesvirus infections in the PNS.
The Soil Microbiome Influences Grapevine-Associated Microbiota
Authors: Zarraonaindia Iratxe , Owens Sarah M. , Weisenhorn Pamela , West Kristin , Hampton-Marcell Jarrad , Lax Simon , Bokulich Nicholas A. , Mills David A. , Martin Gilles , Taghavi Safiyh , van der Lelie Daniel , Gilbert Jack A.
Published: March 2015

Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g.,
Rhizobiaceae
and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.

IMPORTANCE
Vine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.
Web search activity data accurately predict population chronic disease risk in the USA
Authors: Nguyen Thin , Tran Truyen , Luo Wei , Gupta Sunil , Rana Santu , Phung Dinh , Nichols Melanie , Millar Lynne , Venkatesh Svetha , Allender Steve
Published: March 2015

Background

The WHO framework for non-communicable disease (NCD) describes risks and outcomes comprising the majority of the global burden of disease. These factors are complex and interact at biological, behavioural, environmental and policy levels presenting challenges for population monitoring and intervention evaluation. This paper explores the utility of machine learning methods applied to population-level web search activity behaviour as a proxy for chronic disease risk factors.

Methods

Web activity output for each element of the WHO's Causes of NCD framework was used as a basis for identifying relevant web search activity from 2004 to 2013 for the USA. Multiple linear regression models with regularisation were used to generate predictive algorithms, mapping web search activity to Centers for Disease Control and Prevention (CDC) measured risk factor/disease prevalence. Predictions for subsequent target years not included in the model derivation were tested against CDC data from population surveys using Pearson correlation and Spearman's r.

Results

For 2011 and 2012, predicted prevalence was very strongly correlated with measured risk data ranging from fruits and vegetables consumed (r=0.81; 95% CI 0.68 to 0.89) to alcohol consumption (r=0.96; 95% CI 0.93 to 0.98). Mean difference between predicted and measured differences by State ranged from 0.03 to 2.16. Spearman's r for state-wise predicted versus measured prevalence varied from 0.82 to 0.93.

Conclusions

The high predictive validity of web search activity for NCD risk has potential to provide real-time information on population risk during policy implementation and other population-level NCD prevention efforts.