bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the optical absorption of BiFeO3 for photovoltaic applications via uniaxial compression or biaxial tension
Authors: Dong Huafeng , Wu Zhigang , Wang Shanying , Duan Wenhui , Li Jingbo
Published: February 2013

First-principles computations are employed to investigate the electronic structures and optical absorption of rhombohedral BiFeO3 under uniaxial compression and biaxial tension. We find that the bandgap of BiFeO3 is reduced under uniaxial compression, and it can be tuned to the ideal value for photovoltaic applications; furthermore, the indirect-to-direct bandgap transition occurs, which would lead to much enhanced optical absorption near the band edge. Similar results are found for biaxial tensile strain. Strong optical absorption is critical to build efficient solar cells based on ferroelectric thin films; strain engineering is thus a practical route towards realizing this scheme, in which no junction is needed to separate charge carriers.
Evidence of martensitic phase transitions in magnetic Ni-Mn-In thin films
Authors: Sokolov A. , Zhang Le , Dubenko I. , Samanta T. , Stadler S. , Ali N.
Published: February 2013

Ni50Mn35In15 Heusler alloy thin films (with thicknesses of about 10 nm) have been grown on single crystal MgO and SrTiO3 (STO) (100) substrates using a laser-assisted molecular beam epitaxy method. Films of mixed austenitic and martensitic phases and of pure martensitic phase have been detected for those grown on MgO and STO substrates, respectively. Thermomagnetic curves were measured using a SQUID magnetometer and are consistent with those of off-stoichiometric In-based bulk Heusler alloys, including a martensitic transition at T = 315 K for films grown on MgO. The differences in the properties of the films grown on MgO and STO are discussed.
Toroidal modeling of interaction between resistive wall mode and plasma flow
Authors: Liu Yueqiang , Sun Youwen
Published: February 2013

The non-linear interplay between the resistive wall mode (RWM) and the toroidal plasma flow is numerically investigated in a full toroidal geometry, by simultaneously solving the initial value problems for the n = 1 RWM and the n = 0 toroidal force balance equation. Here, n is the toroidal mode number. The neoclassical toroidal viscous torque is identified as the major momentum sink that brakes the toroidal plasma flow during the non-linear evolution of the RWM. This holds for a mode that is initially either unstable or stable. For an initially stable RWM, the braking of the flow, and hence the eventual growth of the mode, depends critically on the initial perturbation amplitude.
Pattern discovery and cancer gene identification in integrated cancer genomic data
Authors: Mo Qianxing , Wang Sijian , Seshan Venkatraman E. , Olshen Adam B. , Schultz Nikolaus , Sander Chris , Powers R. Scott , Ladanyi Marc , Shen Ronglai
Published: February 2013

Large-scale integrated cancer genome characterization efforts including the cancer genome atlas and the cancer cell line encyclopedia have created unprecedented opportunities to study cancer biology in the context of knowing the entire catalog of genetic alterations. A clinically important challenge is to discover cancer subtypes and their molecular drivers in a comprehensive genetic context. Curtis et al. [Nature(2012) 486(7403):346–352] has recently shown that integrative clustering of copy number and gene expression in 2,000 breast tumors reveals novel subgroups beyond the classic expression subtypes that show distinct clinical outcomes. To extend the scope of integrative analysis for the inclusion of somatic mutation data by massively parallel sequencing, we propose a framework for joint modeling of discrete and continuous variables that arise from integrated genomic, epigenomic, and transcriptomic profiling. The core idea is motivated by the hypothesis that diverse molecular phenotypes can be predicted by a set of orthogonal latent variables that represent distinct molecular drivers, and thus can reveal tumor subgroups of biological and clinical importance. Using the cancer cell line encyclopedia dataset, we demonstrate our method can accurately group cell lines by their cell-of-origin for several cancer types, and precisely pinpoint their known and potential cancer driver genes. Our integrative analysis also demonstrates the power for revealing subgroups that are not lineage-dependent, but consist of different cancer types driven by a common genetic alteration. Application of the cancer genome atlas colorectal cancer data reveals distinct integrated tumor subtypes, suggesting different genetic pathways in colon cancer progression.
Poisson factor models with applications to non-normalized microRNA profiling
Authors: Lee Seonjoo , Chugh Pauline E. , Shen Haipeng , Eberle R. , Dittmer Dirk P.
Published: February 2013

Motivation: Next-generation (NextGen) sequencing is becoming increasingly popular as an alternative for transcriptional profiling, as is the case for micro RNAs (miRNA) profiling and classification. miRNAs are a new class of molecules that are regulated in response to differentiation, tumorigenesis or infection. Our primary motivating application is to identify different viral infections based on the induced change in the host miRNA profile. Statistical challenges are encountered because of special features of NextGen sequencing data: the data are read counts that are extremely skewed and non-negative; the total number of reads varies dramatically across samples that require appropriate normalization. Statistical tools developed for microarray expression data, such as principal component analysis, are sub-optimal for analyzing NextGen sequencing data.

Results: We propose a family of Poisson factor models that explicitly takes into account the count nature of sequencing data and automatically incorporates sample normalization through the use of offsets. We develop an efficient algorithm for estimating the Poisson factor model, entitled Poisson Singular Value Decomposition with Offset (PSVDOS). The method is shown to outperform several other normalization and dimension reduction methods in a simulation study. Through analysis of an miRNA profiling experiment, we further illustrate that our model achieves insightful dimension reduction of the miRNA profiles of 18 samples: the extracted factors lead to more accurate and meaningful clustering of the cell lines.

Availability: The PSVDOS software is available on request.

Contact:  ddittmer@med.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p
Authors: Han Kihoon , Gennarino Vincenzo Alessandro , Lee Yoontae , Pang Kaifang , Hashimoto-Torii Kazue , Choufani Sanaa , Raju Chandrasekhar S. , Oldham Michael C. , Weksberg Rosanna , Rakic Pasko , Liu Zhandong , Zoghbi Huda Y.
Published: February 2013

Proper neurological function in humans requires precise control of levels of the epigenetic regulator methyl CpG-binding protein 2 (MeCP2). MeCP2 protein levels are low in fetal brains, where the predominant MECP2 transcripts have an unusually long 3′ untranslated region (UTR). Here, we show that miR-483-5p, an intragenic microRNA of the imprinted IGF2, regulates MeCP2 levels through a human-specific binding site in the MECP2 long 3′ UTR. We demonstrate the inverse correlation of miR-483-5p and MeCP2 levels in developing human brains and fibroblasts from Beckwith-Wiedemann syndrome patients. Importantly, expression of miR-483-5p rescues abnormal dendritic spine phenotype of neurons overexpressing human MeCP2. In addition, miR-483-5p modulates the levels of proteins of the MeCP2-interacting corepressor complexes, including HDAC4 and TBL1X. These data provide insight into the role of miR-483-5p in regulating the levels of MeCP2 and interacting proteins during human fetal development.
Electron backscatter diffraction investigation of local misorientations and orientation gradients in connection with evolution of grain boundary structures in deformed and annealed zirconium. A new approach in grain boundary analysis
Authors: Jedrychowski Mariusz , Tarasiuk Jacek , Bacroix Brigitte , Wronski Sebastian
Published: February 2013

The main aim of the present work is to study the relation between microstructural features – such as local misorientations, grain orientation gradients and grain boundary structures – and thermomechanical treatment of hexagonal zirconium (Zr702α). Electron backscatter diffraction (EBSD) topological maps are used to analyze the aforementioned material parameters at the early stages of plastic deformation imposed by channel-die compression, as well as at a partial recrystallization state achieved by brief annealing. The evolution of local misorientations and orientation gradients is investigated using the so-called kernel average misorientation (KAM) and grain orientation spread (GOS) statistics implemented in the TSLOIMdata analysis software [TexSEM Laboratories (2004), Draper, UT, USA]. In the case of grain boundaries (GBs) a new method of analysis is presented. As an addition to the classical line segments method, where the grain boundary is represented by line segments that separate particular pairs of neighboring points, an approach that focuses on grain boundary areas is proposed. These areas are represented by sets of EBSD points, which are specially selected from a modified calculation procedure for the KAM. Different evolution mechanisms of intragranular boundaries, low-angle grain boundaries and high-angle grain boundaries are observed depending on the compression direction. The observed differences are consistent with the results obtained from KAM and GOS analysis. It is also concluded that the proposed method of grain boundary characterization seems to be promising, as it provides new and interesting analysis tools such as textures, absolute fractions and other EBSD statistics of the GB areas. This description may be more compatible with a real deformed microstructure, especially for grain boundaries with very small misorientation, which are indeed clustered areas of lattice defect accumulation.
Evaluating the polymorphic phase transition in calcium-doped Ba(Zr0.05Ti0.95)O3: a lead-free piezoelectric ceramic
Authors: Singh Gurvinderjit , Tiwari V. S. , Gupta P. K.
Published: February 2013

Structural and dielectric investigations were carried out on a perovskite lead-free (Ba1−xCax)(Zr0.05Ti0.95)O3ferroelectric ceramic forx= 0.03, 0.05, 0.08, 0.10, 0.12 and 0.15. The room-temperature structural analysis reveals a crossover from orthorhombic to tetragonal crystal structure nearx= 0.10. A coexistence of tetragonal (P4mm) and orthorhombic (Pmm2) structure is observed in the composition range 0.05 ≤x≤ 0.10. The fraction of tetragonal phase increases from 27% forx= 0.05 to 71% forx= 0.10. The dielectric measurements show that the tetragonal to orthorhombic and rhombohedral to orthorhombic transition temperatures decrease with an increase in Ca2+content, while the cubic to tetragonal transition temperature remains the same. It is also shown that for the tetragonal to orthorhombic transition a phase coexistence occurs over a temperature range of about 18 K. The coexistence range covers room temperature for intermediate compositions:x= 0.05, 0.08 and 0.10. Therefore, higher dielectric and piezoelectric properties are observed in these compositions.
Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities
Authors: Rodriguez Jose A. , Xu Rui , Chen Chien-Chun , Zou Yunfei , Miao Jianwei
Published: February 2013

Coherent diffraction imaging (CDI) is high-resolution lensless microscopy that has been applied to image a wide range of specimens using synchrotron radiation, X-ray free-electron lasers, high harmonic generation, soft X-ray lasers and electrons. Despite recent rapid advances, it remains a challenge to reconstruct fine features in weakly scattering objects such as biological specimens from noisy data. Here an effective iterative algorithm, termed oversampling smoothness (OSS), for phase retrieval of noisy diffraction intensities is presented. OSS exploits the correlation information among the pixels or voxels in the region outside of a support in real space. By properly applying spatial frequency filters to the pixels or voxels outside the support at different stages of the iterative process (i.e.a smoothness constraint), OSS finds a balance between the hybrid input–output (HIO) and error reduction (ER) algorithms to search for a global minimum in solution space, while reducing the oscillations in the reconstruction. Both numerical simulations with Poisson noise and experimental data from a biological cell indicate that OSS consistently outperforms the HIO, ER–HIO and noise robust (NR)–HIO algorithms at all noise levels in terms of accuracy and consistency of the reconstructions. It is expected that OSS will find application in the rapidly growing CDI field, as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed. TheMATLAB(The MathWorks Inc., Natick, MA, USA) source code of the OSS algorithm is freely available from http://www.physics.ucla.edu/research/imaging.
Long‐term Changes in Fruit Phenology in a West African Lowland Tropical Rain Forest are Not Explained by Rainfall
Authors: Polansky Leo , Boesch Christophe
Published: February 2013

Decreases in rainfall have been proposed to have a negative impact on tropical rain forests, and West Africa is currently experiencing a decline in rainfall at the multi‐decadal scale. Here, we present analyses of a long‐term dataset on the plant fruiting status from individuals of 44 species of the tropical rain forest of Taï National Park, Côte d'Ivoire. This study includes records of 1401 individuals collected at monthly intervals for over 12 yr, 984 of which survived throughout the entire study period. The aims of this study were to: (1) quantitate inter‐annual trends in species and forest scale fruit presence; and (2) test the importance of rainfall in explaining inter‐annual fruit presence variability. Long‐term upward trends in the expected proportion of individuals with fruits were found for the majority of species, while no significant downward trends were detected, driving a significant upward trend at the community level. Peak production months of the upward trending species were not associated with the dry or wet season. Significant rainfall correlations with the total proportion of individuals showing fruit were generally negative, with only five species showing significant positive correlations. Taken together, these results suggest that the observed inter‐annual trends and variability of fruit abundance are currently not associated with rainfall. We discuss several parsimonious and complex alternative explanations.
Tear down this wall: on the persistence of borders in trade
Authors: Nitsch Volker , Wolf Nikolaus
Published: February 2013

Abstract Why do borders still matter for economic activity? The reunification of Germany in 1990 provides a unique natural experiment for examining the effect of political borders on trade. With the fall of the Berlin Wall and the rapid formation of a political and economic union, strong and strictly enforced administrative barriers to trade between East Germany and West Germany were eliminated completely within a very short period of time. Remarkable persistence in intra‐German trade patterns along the former East‐West border suggests that border effects are neither statistical artefacts nor driven by administrative barriers to trade, but arise from economic fundamentals.
Genetic Moderation of Early Child‐Care Effects on Social Functioning Across Childhood: A Developmental Analysis
Authors: Belsky Jay , Pluess Michael
Published: February 2013

Data from 508 Caucasian children in the NICHD Study of Early Child Care and Youth Development shows that the DRD4 (but not 5‐HTTLPR) polymorphism moderates the effect of child‐care quality (but not quantity or type) on caregiver‐reported externalizing problems at 54 months and in kindergarten and teacher‐reported social skills at kindergarten and first grade—but not thereafter. Only children carrying the 7‐repeat allele proved susceptible to quality‐of‐care effects. The behavior–problem interactions proved more consistent with diathesis‐stress than differential‐susceptibility thinking, whereas the reverse was true of the social‐skills' results. Finally, the discerned Gene × Environment interactions did not account for previously reported parallel ones involving difficult temperament in infancy.
Immunization with 60 kD Ro peptide produces different stages of preclinical autoimmunity in a Sjögren's syndrome model among multiple strains of inbred mice
Authors: Kurien B T , Dsouza A , Igoe A , Lee Y J , Maier-Moore J S , Gordon T , Jackson M , Scofield R H
Published: February 2013

Sjögren's syndrome is a chronic illness manifested characteristically by immune injury to the salivary and lacrimal glands, resulting in dry mouth/eyes. Anti-Ro [Sjögren's syndrome antigen A (SSA)] and anti-La [Sjögren's syndrome antigen B (SSB)] autoantibodies are found frequently in Sjögren's subjects as well as in individuals who will go on to develop the disease. Immunization of BALB/c mice with Ro60 peptides results in epitope spreading with anti-Ro and anti-La along with lymphocyte infiltration of salivary glands similar to human Sjögren's. In addition, these animals have poor salivary function/low saliva volume. In this study, we examined whether Ro-peptide immunization produces a Sjögren's-like illness in other strains of mice. BALB/c, DBA-2, PL/J, SJL/J and C57BL/6 mice were immunized with Ro60 peptide-274. Sera from these mice were studied by immunoblot and enzyme-linked immunosorbent assay for autoantibodies. Timed salivary flow was determined after pharmacological stimulation, and salivary glands were examined pathologically. We found that SJL/J mice had no immune response to the peptide from Ro60, while C57BL/6 mice produced antibodies that bound the peptide but had no epitope spreading. PL/J mice had epitope spreading to other structures of Ro60 as well as to La, but like C57BL/6 and SJL/J had no salivary gland lymphocytic infiltration and no decrement of salivary function. DBA-2 and BALB/c mice had infiltration but only BALB/c had decreased salivary function. The immunological processes leading to a Sjögren's-like illness after Ro-peptide immunization were interrupted in a stepwise fashion in these differing mice strains. These data suggest that this is a model of preclinical disease with genetic control for epitope spreading, lymphocytic infiltration and glandular dysfunction.
Mitochondrial optic neuropathies: our travels from bench to bedside and back again
Authors: Sadun Alfredo A , La Morgia Chiara , Carelli Valerio
Published: February 2013

The standard scientific method requires that you make an interesting observation, generate a hypothesis and then design an experiment to test the hypothesis. In ophthalmology, as in most fields of medicine, the observations and hypotheses tend to have more degrees of freedom, and the interpretation of experiments is also more complicated and often indeterminate. But sometimes it works out, going back and forth from bench to bedside to bench, in reiterative cycles. A successful example of alternating bench and bedside studies was presented (AAS) at the 2012 Alper Memorial given at the Washington Hospital Medical Center, illustrating a series of questions and investigations that pertain to mitochondrial optic neuropathies, beginning two decades ago, before the concept of mitochondrial optic neuropathies had much meaning. Basic science questions are often best answered by that extraordinary experiment of nature that we call clinical disease, and clinical questions are often best tested in the laboratory.
Relationship between macular ganglion cell complex thickness and macular outer retinal thickness: a spectral‐domain optical coherence tomography study
Authors: Kita Yoshiyuki , Kita Ritsuko , Takeyama Asuka , Anraku Ayako , Tomita Goji , Goldberg Ivan
Published: February 2013

Background

To assess the relationship between macular ganglion cell complex and macular outer retinal thicknesses.

Design

Case–control study.

Participants

Forty‐two normal eyes and 91 eyes with primary open‐angle glaucoma were studied.

Methods

Spectral‐domain optical coherence tomography (RTVue‐100) was used to measure the macular ganglion cell complex and macular outer retinal thickness. Ganglion cell complex to outer retinal thickness ratio was also calculated.

Main Outcome Measures

The relationships between the ganglion cell complex and outer retinal thicknesses and between the ganglion cell complex to outer retinal thickness ratio and outer retinal thickness were evaluated.

Results

There was a positive correlation between ganglion cell complex and outer retinal thicknesses in the normal group and the glaucoma group (r = 0.53, P < 0.001 and r = 0.42, P < 0.001, respectively). In that respect, there was no correlation between ganglion cell complex to outer retinal thickness ratio and outer retinal thickness in the both groups (r = −0.07, P = 0.657, and r = 0.04, P = 0.677, respectively). The ganglion cell complex to outer retinal thickness ratio was 55.65% in the normal group, 45.07% in the glaucoma group. This difference was statistically significant.

Conclusions

The ganglion cell complex thickness may be affected by outer retinal thickness, and there is individual variation in the outer retinal thickness. Therefore, when determining the ganglion cell complex, it seems necessary to consider the outer retinal thickness as well. We propose the ratio as a suitable parameter to account for individual variations in outer retinal thickness.
An analysis of two island groups as potential sites for trials of transgenic mosquitoes for malaria control
Authors: Marsden Clare D. , Cornel Anthony , Lee Yoosook , Sanford Michelle R. , Norris Laura C. , Goodell Parker B. , Nieman Catelyn C. , Han Sarah , Rodrigues Amabelia , Denis Joao , Ouledi Ahmed , Lanzaro Gregory C.
Published: February 2013

Considerable technological advances have been made towards the generation of genetically modified mosquitoes for vector control. In contrast, less progress has been made towards field evaluations of transformed mosquitoes which are critical for evaluating the success of, and hazards associated with, genetic modification. Oceanic islands have been highlighted as potentially the best locations for such trials. However, population genetic studies are necessary to verify isolation. Here, we used a panel of genetic markers to assess for evidence of genetic isolation of two oceanic island populations of the African malaria vector, Anopheles gambiae s.s. We found no evidence of isolation between the Bijagós archipelago and mainland Guinea‐Bissau, despite separation by distances beyond the known dispersal capabilities of this taxon. Conversely, the Comoros Islands appear to be genetically isolated from the East African mainland, and thus represent a location worthy of further investigation for field trials. Based on assessments of gene flow within and between the Comoros islands, the island of Grande Comore was found to be genetically isolated from adjacent islands and also exhibited local population structure, indicating that it may be the most suitable site for trials with existing genetic modification technologies.
Venous thromboembolism (VTE) risk assessment: Rural nurses' knowledge and use in a rural acute care hospital
Authors: Gaston Sherryl , White Sarahlouise
Published: February 2013

It is estimated that about 2000 people die as a result of venous thromboembolism (VTE) each year, with a further 30 000 being hospitalized. Prophylaxis significantly reduces VTE morbidity and mortality, and thus represents a real long‐term health‐care benefit. The aim of this study was twofold: (i) to assess the current level of compliance to VTE risk assessment and prophylaxis best practice guidelines within an Australian rural hospital; and (ii) to determine the effectiveness of nurse education on that compliance. VTE compliance information was obtained from auditing patient notes for a 3‐month period prior to nurse education and was repeated after the education. Nurse knowledge of VTE risk assessment and prophylaxis use was also measured. Both compliance with and knowledge of best practice VTE risk assessment and prophylaxis increased following nurse education. Although the sample size was relatively small, this study has shown nurse education to be effective at increasing VTE compliance and awareness within an Australian rural hospital. This relatively inexpensive and simple intervention bears consideration and could lead to reductions in the morbidity and mortality associated with VTE, as well as reduction in associated health‐care costs.
Antimicrobial susceptibility and genetic characteristics of Propionibacterium acnes isolated from patients with acne
Authors: Schafer Fabiola , Fich Felix , Lam Marusella , Gárate Cynthia , Wozniak Aniela , Garcia Patricia
Published: February 2013

Background  Propionibacterium acnes is an important target in acne management. Antibiotic resistance has increased, reducing its clinical efficiency.

Objective  To study the prevalence, antimicrobial susceptibility patterns, and resistance mechanisms of P. acnes isolated from patients with acne.

Methods  Skin swabs were collected from 83 patients. Agar dilution determined the minimum inhibitory concentrations of five antibiotics. Polymerase chain reaction and DNA sequencing were used to identify mutations.

Results  P. acnes was isolated in 80 of 83 patients (96%), and 27 patients had resistance to antibiotics (33.7%). The mean age was older in the antibiotic‐resistant group (20.8 ± 5.8 vs. 18.3 ± 3.7, P = 0.02). Resistance to trimethoprim–sulfamethoxazole was 26.3%, erythromycin 12.5%, and clindamycin 7.5%. All clindamycin‐resistant strains had cross‐resistance to erythromycin, and 40% erythromycin‐resistant strains had cross‐resistance to trimethoprim–sulfamethoxazole. All strains were sensitive to tetracycline and doxycycline. The use of topical erythromycin or clindamycin was a risk factor to carry resistant strains (P = 0.02, P = 0.04, respectively). Resistance to trimethoprim–sulfamethoxazole was associated with acne severity (P = 0.02). Six of the 10 erythromycin‐resistant strains had a mutation in the peptidyl transferase region of the 23S rRNA gene: one A2058G and five A2059G. No strain carrying mutation G2057A was found.

Conclusions  Resistance to trimethoprim–sulfamethoxazole was the most common pattern found, and further studies are required to clarify its resistance mechanism. A certain tetracycline resistance was expected, but interestingly all strains remained sensitive. Resistance to erythromycin and clindamycin were influenced using topical formulations. Mutation A2059G was related to high resistance to erythromycin. Antibiotic resistance is increasing, and new strategies are needed.
Nephrectomy Via Ventral Median Celiotomy in Equids
Authors: Arnold Carolyn E. , Taylor Tex , Chaffin M. Keith , Schott Harold C. , Caron John P.
Published: February 2013

Objective

To report technique for, and outcome after, nephrectomy through a ventral median celiotomy in equids.

Study Design

Case series.

Animals

Equids with unilateral renal disease (n = 6), aged 2 months to 18 years, weighing 90–434 kg.

Methods

A ventral median celiotomy was used to access the left or right kidney. To facilitate surgical exposure, the small intestine was reflected towards the diaphragm using laparotomy sponges and the ascending colon was exteriorized and in some cases evacuated. The peritoneum over the affected kidney was incised and blunt dissection used to free the kidney from the retroperitoneal fat, then the renal artery, vein, and ureter were isolated and ligated. Abdominal lavage with sterile saline solution was performed before abdominal closure.

Results

Four horses, 1 donkey, and 1 mule had unilateral nephrectomy to treat verminous nephritis (1), idiopathic hematuria (1), and ectopic ureter (4). A ventral median approach provided adequate access to the kidney in all 6 cases. Two horses had postoperative complications (peritonitis, chylous abdominal effusion) that resolved with medical therapy. No complications attributable to nephrectomy were reported by the owners upon follow‐up 1–8 years after surgery.

Conclusions

A ventral median approach for nephrectomy can be used for unilateral nephrectomy in equids weighing up to 434 kg.
Influence of Information on Consumers' Evaluations Using Check‐All‐That‐Apply Questions and Sorting: A Case Study with Milk Desserts
Authors: Vidal Leticia , Barreiro Cecilia , Gómez Beatriz , Ares Gastón , Giménez Ana
Published: February 2013

Consumer perception of food products is a very complex phenomenon that is influenced by a wide range of characteristics. In particular, consumer perception of the sensory characteristics of food products can be strongly affected by information and expectations. Thus, the comparison of product characterizations from blind and informed conditions can provide a valuable insight about the impact of information on consumer perception of food products. In this context, the aim of the present work was to present a case study in which the influence of information on results of product characterizations of milk desserts from two methodologies, check‐all‐that‐apply (CATA) questions and sorting, was studied. Six commercial vanilla milk desserts were evaluated under blind and informed conditions by two groups of 50 consumers using CATA questions and sorting. Results showed that information had a small impact on overall liking scores and product characterizations, suggesting that consumers' perception of the desserts was mainly determined by their sensory characteristics.

Practical Applications

The influence of information was larger for the sorting task than for check‐all‐that‐apply question, as expected, due to the fact that this last methodology was based exclusively on the perception of the sensory characteristics of the samples. Sorting tasks showed that consumers' categorizations under informed conditions were mainly related to the samples' sensory characteristics, and that information only had a limited influence. The comparison of blind and informed sorting tasks might enable one to determine the relative influence of package information on consumer perception of food products, which may be an interesting way of studying the impact of previous expectations and nonsensory variables on consumer perception.
Post‐natal changes inMCT1 expression in the forestomach of calves
Authors: Pfannkuche H. , Taifour F. , Steinhoff‐Wagner J. , Hammon H. M. , Gäbel G.
Published: February 2013

The monocarboxylate transporter 1 (MCT1) has been demonstrated to be involved in the transfer of short‐chain fatty acids (SCFA) and/or their intraepithelial metabolites from the rumen to the blood. AsMCT1 plays a role inSCFAtransfer, it is assumed thatSCFAare the main substrates influencing its expression. However, there are hints thatMCT1 may also be expressed during the early life of the animal whenSCFAare not released in the forestomach. To figure out whetherMCT1 expression in the forestomach is influenced independently ofSCFAduring that period, we studied post‐natalMCT1 expression immunohistochemically in the epithelia of omasum, atrium ruminis, saccus dorsalis ruminis, saccus ventralis ruminis and reticulum of calves born preterm and at term. The calves were nourished by colostrum or by milk‐based formula diet.MCT1 could be found in all the forestomach compartments tested, even in preterm calves. The protein was mainly oriented to the luminal side in the immature epithelium 24 h after birth. Orientation to the blood side of the cells developed during the first 4 days after birth. In the rumen epithelia (but not in the other forestomach compartments tested), orientation ofMCT1 to the blood side of the cells was paralleled by an increase in the overall expression rate during the first 4 days after birth. As lactate levels were very high directly after birth, a lactate‐dependent substrate induction may have been the underlying mechanism. However, non‐specific changes due to general differential processes might also be the cause. Both early upregulation ofMCT1 and high blood lactate levels may provide the epithelia with lactate as energy source.
A single‐nucleotide polymorphism of miR‐196a‐2 and vitiligo: an association study and functional analysis in a Han Chinese population
Authors: Huang Ye , Yi Xiuli , Jian Zhe , Wei Chao , Li Shuli , Cai Chuan , Zhang Ping , Li Kai , Guo Sen , Liu Ling , Shi Qiong , Gao Tianwen , Li Chunying
Published: February 2013

Recent evidence indicates that oxidative stress and genetic factors play an important role in the pathogenesis of vitiligo. SNPs in miRNAs involved in oxidative stress could potentially influence the development of vitiligo. In this case–control study, we investigated the association of a functional SNP of rs11614913 in miR‐196a‐2 with risk of vitiligo. A significantly lower risk of vitiligo was associated with the rs11614913 miR‐196a‐2 CC genotype (adjusted OR, 0.77; CI, 0.60–0.98). In addition, TYRP1 gene expression was considerably down‐regulated by the rs11614913 C allele in miR‐196a‐2, which lowered the levels of intracellular reactive oxygen species (ROS) and reduced the proportion of early apoptosis in human melanocytes in response to H2O2 treatment. Our data suggest that the rs11614913 C allele in miR‐196a‐2 confers potential protection against oxidative effects on human melanocytes through the modulation of the target gene, TYRP1, which may account for the decreased risk of vitiligo in this study population.
Lung stem cells: Do they exist?
Authors: Bertoncello Ivan , McQualter Jonathan L.
Published: February 2013

Recognition of the potential of stem cell‐based therapies for alleviating intractable lung diseases has provided the impetus for research aimed at identifying regenerative cells in the adult lung, understanding how they are organized and regulated, and how they could be harnessed in lung regenerative medicine. In this review, we describe the attributes of adult stem and progenitor cells in adult organs and how they are regulated by the permissive or restrictive microenvironment in which they reside. We describe the power and limitations of experimental models, cell separative strategies and functional assays used to model the organization and regulation of adult airway and alveolar stem cells in the adult lung. The review summarizes recent progress and obstacles in defining endogenous lung epithelial stem and progenitor cells in mouse models and in translational studies.
Whose Choice Is It? Shared Decision Making in Nephrology Care
Authors: Murray Mary Ann , Bissonnette Janice , Kryworuchko Jennifer , Gifford Wendy , Calverley Sharon
Published: February 2013

Patients living with end‐stage renal disease (ESRD) are faced with numerous decisions across the trajectory of their illness. Shared decision making (SDM) offers a patient‐centered approach to engage patients in decision making in meaningful ways. Using an SDM approach, patients and providers collaborate to make healthcare decisions by taking into account the best available empirical evidence, in conjunction with the patient’s values, preferences, and individual circumstances. In this article, we outline the principles of SDM; highlight the broad range and context of decisions faced by patients living with ESRD; review decision‐support interventions; and consider opportunities and challenges for implementing SDM into usual ESRD practice. A summary of current knowledge and areas for research and further investigation concludes the paper. Because nephrology team members spend a lot of time interacting with patients during treatments and follow‐up care, they are well positioned to engage in SDM. Healthcare systems need innovation in communication to ensure the ethical application of important technological improvements in renal treatments, and to ensure that patient decision‐support processes are available. SDM is a promising innovation to support the recalibration of care for patients living with end‐stage renal disease.
Epidemiology, outcomes, and mortality predictors of invasive mold infections among transplant recipients: a 10‐year, single‐center experience
Authors: Neofytos D. , Treadway S. , Ostrander D. , Alonso C.D. , Dierberg K.L. , Nussenblatt V. , Durand C.M. , Thompson C.B. , Marr K.A.
Published: February 2013

Background

The epidemiology of invasive mold infections (IMI) in transplant recipients differs based on geography, hosts, preventative strategies, and methods of diagnosis.

Methods

We conducted a retrospective observational study to evaluate the epidemiology of proven and probable IMI, using prior definitions, among all adult hematopoietic stem cell transplant (HSCT) and solid organ transplant (SOT) recipients in the era of “classic” culture‐based diagnostics (2000–2009). Epidemiology was evaluated before and after an initiative was begun to increase bronchoscopy in HSCT recipients after 2005.

Results

In total, 106 patients with one IMI were identified. Invasive aspergillosis (IA) was the most common IMI (69; 65.1%), followed by mucormycosis (9; 8.5%). The overall rate of IMI (and IA) was 3.5% (2.5%) in allogeneic HSCT recipients. The overall incidence for IMI among lung, kidney, liver, and heart transplant recipients was 49, 2, 11, and 10 per 1000 person‐years, respectively. The observed rate of IMI among human leukocyte antigen‐matched unrelated and haploidentical HSCT recipients increased from 0.6% annually to 3.0% after bronchoscopy initiation (P < 0.05). The 12‐week mortality among allogeneic HSCT, liver, kidney, heart, and lung recipients with IMI was 52.4%, 47.1%, 27.8%, 16.7%, and 9.5%, respectively. Among allogeneic HSCT (odds ratio [OR]: 0.07, P = 0.007) and SOT (OR: 0.22, P = 0.05) recipients with IA, normal platelet count was associated with improved survival. Male gender (OR: 14.4, P = 0.007) and elevated bilirubin (OR: 5.7, P = 0.04) were significant predictors of mortality for allogeneic HSCT and SOT recipients with IA, respectively.

Conclusions

During the era of culture‐based diagnostics, observed rates of IMI were low among all transplants except lung transplant recipients, with relatively higher mortality rates. Diagnostic aggressiveness and host variables impact the reported incidence and outcome of IMI and likely account for institutional variability in multicenter studies. Definitions to standardize diagnoses among SOT recipients are needed.
Leaching patterns from wood of different tree species and environmental implications related to wood storage areas
Authors: Svensson Henric , Marques Marcia , Kaczala Fabio , Hogland William
Published: February 2013

Batch tests were carried out with sawdust obtained from oak (Quercus robur), maple (Acer platanoides), pine (Pinus sylvestris), beech (Fagus sylvatica) and wood chips from oak and pine. Leaching of organic compounds expressed as dissolved organic carbon (DOC) in mg/kg of dry mass took place during the first 24 h. The following additional variables were analysed: pH, conductivity, colour, phenols, tannins and lignin, and biochemical oxygen demand (BOD7). When leachates obtained with oak wood chips and pine wood chips were compared, no significant difference was observed. However, in batch tests with sawdust, DOC released by oak (90 000 mg/kg) was significantly higher (P = 0.0001) than DOC released by pine (30 000 mg/kg). The results suggest that particle size is not the only variable affecting the leaching of organic compounds from wood. Regarding BOD, colour [platinum‐cobalt (Pt‐Co)], phenols, tannins and lignin, the leaching patterns differed among species, and oak was the species with the highest released values.
Limited potential of school textbooks to prevent tobacco use among students grade 1–9 across multiple developing countries: a content analysis study
Authors: Saito Junko , Nonaka Daisuke , Mizoue Tetsuya , Kobayashi Jun , Jayatilleke Achini C , Shrestha Sabina , Kikuchi Kimiyo , Haque Syed E , Yi Siyan , Ayi Irene , Jimba Masamine
Published: February 2013

Objective

To evaluate the content of school textbooks as a tool to prevent tobacco use in developing countries.

Design

Content analysis was used to evaluate if the textbooks incorporated the following five core components recommended by the WHO: (1)consequences of tobacco use; (2)social norms; (3)reasons to use tobacco; (4)social influencesand (5)resistance and life skills.

Setting

Nine developing countries: Bangladesh, Cambodia, Laos, Nepal, Sri Lanka, Benin, Ghana, Niger and Zambia.

Textbooks analysed

Of 474 textbooks for primary and junior secondary schools in nine developing countries, 41 were selected which contained descriptions about tobacco use prevention.

Results

Of the 41 textbooks, theconsequences of tobacco usecomponent was covered in 30 textbooks (73.2%) and thesocial normscomponent was covered in 19 (46.3%). The other three components were described in less than 20% of the textbooks.

Conclusions

A rather limited number of school textbooks in developing countries contained descriptions of prevention of tobacco use, but they did not fully cover the core components for tobacco use prevention. The chance of tobacco prevention education should be seized by improving the content of school textbooks.
Complexities of Horn Description Logics
Authors: Krötzsch Markus , Rudolph Sebastian , Hitzler Pascal
Published: February 2013

Description logics (DLs) have become a prominent paradigm for representing knowledge in a variety of application areas, partly due to their ability to achieve a favourable balance between expressivity of the logic and performance of reasoning. Horn description logics are obtained, roughly speaking, by disallowing all forms of disjunctions. They have attracted attention since their (worst-case) data complexities are in general lower than those of their non-Horn counterparts, which makes them attractive for reasoning with large sets of instance data (ABoxes). It is therefore natural to ask whether Horn DLs also provide advantages for schema (TBox) reasoning, that is, whether they also feature lower combined complexities. This article settles this question for a variety of Horn DLs. An example of a tractable Horn logic is the DL underlying the ontology language OWL RL, which we characterize as the Horn fragment of the description logic
SROIQ
without existential quantifiers. If existential quantifiers are allowed, however, many Horn DLs become intractable. We find that Horn-
ALC
already has the same worst-case complexity as
ALC
, that is,
ExpTime
, but we also identify various DLs for which reasoning is
PSpace
-complete. As a side effect, we derive simplified syntactic definitions of Horn DLs for which we exploit suitable normal form transformations.
Image retrieval with query-adaptive hashing
Authors: Liu Dong , Yan Shuicheng , Ji Rong-Rong , Hua Xian-Sheng , Zhang Hong-Jiang
Published: February 2013

Hashing-based approximate nearest-neighbor search may well realize scalable content-based image retrieval. The existing semantic-preserving hashing methods leverage the labeled data to learn a fixed set of semantic-aware hash functions. However, a fixed hash function set is unable to well encode all semantic information simultaneously, and ignores the specific user's search intention conveyed by the query. In this article, we propose a query-adaptive hashing method which is able to generate the most appropriate binary codes for different queries. Specifically, a set of semantic-biased discriminant projection matrices are first learnt for each of the semantic concepts, through which a semantic-adaptable hash function set is learnt via a joint sparsity variable selection model. At query time, we further use the sparsity representation procedure to select the most appropriate hash function subset that is informative to the semantic information conveyed by the query. Extensive experiments over three benchmark image datasets well demonstrate the superiority of our proposed query-adaptive hashing method over the state-of-the-art ones in terms of retrieval accuracy.
Level-3 Cholesky Factorization Routines Improve Performance of Many Cholesky Algorithms
Authors: Gustavson Fred G. , Waśniewski Jerzy , Dongarra Jack J. , Herrero José R. , Langou Julien
Published: February 2013

Four routines called DPOTF3i, i = a,b,c,d, are presented. DPOTF3i are a novel type of level-3 BLAS for use by BPF (
B
locked
P
acked
F
ormat) Cholesky factorization and LAPACK routine DPOTRF. Performance of routines DPOTF3i are still increasing when the performance of Level-2 routine DPOTF2 of LAPACK starts decreasing. This is our main result and it implies, due to the use of larger block size
nb
, that DGEMM, DSYRK, and DTRSM performance also increases! The four DPOTF3i routines use simple register blocking. Different platforms have different numbers of registers. Thus, our four routines have different register blocking sizes.

BPF is introduced. LAPACK routines for POTRF and PPTRF using BPF instead of full and packed format are shown to be trivial modifications of LAPACK POTRF source codes. We call these codes BPTRF. There are two variants of BPF: lower and upper. Upper BPF is “identical” to Square Block Packed Format (SBPF). “LAPACK” implementations on multicore processors use SBPF. Lower BPF is less efficient than upper BPF. Vector inplace transposition converts lower BPF to upper BPF very efficiently. Corroborating performance results for DPOTF3i versus DPOTF2 on a variety of common platforms are given for
n
≈
nb
as well as results for large
n
comparing DBPTRF versus DPOTRF.
Finite Element Integration on GPUs
Authors: Knepley Matthew G. , Terrel Andy R.
Published: February 2013

We present a novel finite element integration method for low-order elements on GPUs. We achieve more than 100GF for element integration on first order discretizations of both the Laplacian and Elasticity operators on an NVIDIA GTX285, which has a nominal single precision peak flop rate of 1 TF/s and bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.
A Runge-Kutta BVODE Solver with Global Error and Defect Control
Authors: Boisvert Jason J. , Muir Paul H. , Spiteri Raymond J.
Published: February 2013

Boundary value ordinary differential equations (BVODEs) are systems of ODEs with boundary conditions imposed at two or more distinct points. The global error (GE) of a numerical solution to a BVODE is the amount by which the numerical solution differs from the exact solution. The defect is the amount by which the numerical solution fails to satisfy the ODEs and boundary conditions. Although GE control is often familiar to users, the defect controlled numerical solution can be interpreted as the exact solution to a perturbation of the original BVODE. Software packages based on GE control and on defect control are in wide use.

The defect control solver, BVP_SOLVER, can provide an a posteriori estimate of the GE using Richardson extrapolation. In this article, we consider three more strategies for GE estimation based on (i) the direct use of a higher-order discretization formula (HO), (ii) the use of a higher-order discretization formula within a deferred correction (DC) framework, and (iii) the product of an estimate of the maximum defect and an estimate of the BVODE conditioning constant, and demonstrate that the HO and DC approaches have superior performance. We also modify BVP_SOLVER to introduce
GE control
.