bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete physical mapping of IL6 reveals a new marker associated with chronic periodontitis
Authors: Farhat S. B. , de Souza C. M. , Braosi A. P. R. , Kim S. H. , Tramontina V. A. , Papalexiou V. , Olandoski M. , Mira M. T. , Luczyszyn S. M. , Trevilatto P. C. 
Published: May 2016

Background and ObjectiveInterleukin‐6 (IL‐6) is a powerful stimulator of osteoclast differentiation and bone resorption. Production of IL‐6 is modulated by polymorphisms, and higher levels of this cytokine are found locally in patients with chronic periodontitis. In this study we performed a modern approach – Complete physical mapping of the IL6 gene – to identify the polymorphisms associated with chronic periodontitis in a southern Brazilian population sample.Material and MethodsOne‐hundred and nine individuals of both genders (mean age: 41.5 ± 8.5 years) were divided into a study group (56 participants with periodontitis) and a control group (53 individuals without periodontitis). After collection and purification of DNA, nine tag single nucleotide polymorphisms (SNPs; rs1524107, rs2069835, rs2069837, rs2069838, rs2069840, rs2069842, rs2069843, rs2069845 and rs2069849) covering the entire gene were selected according to the information available on the International HapMap Project website and evaluated using real‐time PCR.ResultsDifferences in the distribution of the following parameters were statistically significant between study and control groups: number of teeth (p = 0.030); probing depth (p < 0.001); clinical attachment level (p < 0.001); gingival index (p < 0.001); plaque index (p = 0.003); calculus index (p < 0.001); and dental mobility (p < 0.001). It was found that marker rs2069837 (located in intron 2 of IL6) under G dominant was associated with protection against chronic periodontitis in a Brazilian population in the presence of clinical variables, such as visible plaque, dentist visit frequency and dental floss use, and was suggested for the first time as a marker of susceptibility to chronic periodontitis.ConclusionComplete physical mapping of IL6 (using tag SNPs) was carried out for the first time, unveiling allele G of polymorphism rs2069837 (located in the second intron of IL6) as a suggestive marker of protection against chronic periodontitis in a Brazilian population.
Writing creatively in a museum: tracing lines through persons, art objects and texts
Authors: Sabeti Shari 
Published: May 2016

AbstractCreative writing is often thought of as an individual and solitary pursuit. This is partly owing to Romantic (and still popular) notions of creativity as residing in highly gifted individuals, but also to the widely held belief that writing is a lonely rather than a social activity. The research presented in this paper provides a unique insight into the creative process by tracing the way one poem is produced by a member of a creative writing class based on a major urban art gallery. Based on a 5‐year ethnographic study of this class, it employs interview material, field notes, photographs and creative writing as data. Using theories from both the “anthropology of writing” (Barton and Papen, ; Latour and Woolgar, 1986) and the “anthropology of creativity” (Ingold, ; Hallam and Ingold, ), I argue that creative writing is a relational and temporal process involving complex and multiple claims for agency. I also go on to show that when the text moves from a private to a public context, these multiple agencies are encompassed and erased under the umbrella of individual authorship.
Digital writing practices: a close look at one grade three author
Authors: Kervin Lisa , Mantei Jessica 
Published: May 2016

AbstractThis paper reports on the digital writing practices of a Grade Three primary school student as he used an iPad to plan, produce and share digital texts. The case study acknowledges that writing is undergoing a period of great change in many classrooms and works to show how a student author has interpreted and produced digital texts with new technologies. In particular, the specific practices, digital materials and literacy concepts will be explicated through analyses of two digital texts created by this author. This focus acknowledges the ways texts can be planned, produced and shared using multiple modes and media. These social practices and the wider learning opportunities afforded through the flexible and recursive ways students produce text have yet to be fully explored. This paper also extends current understandings about digital writing practices through its examination of the connections between and among multiple apps as an author crafts digital text.
Colletotrichum higginsianum extracellular LysM proteins play dual roles in appressorial function and suppression of chitin‐triggered plant immunity
Authors: Takahara Hiroyuki , Hacquard Stéphane , Kombrink Anja , Hughes H. Bleddyn , Halder Vivek , Robin Guillaume P. , Hiruma Kei , Neumann Ulla , Shinya Tomonori , Kombrink Erich , Shibuya Naoto , Thomma Bart P. H. J. , O'Connell Richard J. 
Published: May 2016

Summary

The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large repertoire of candidate‐secreted effectors containing LysM domains, but the role of such proteins in the pathogenicity of any Colletotrichum species is unknown.

Here, we characterized the function of two effectors, ChELP1 and ChELP2, which are transcriptionally activated during the initial intracellular biotrophic phase of infection.

Using immunocytochemistry, we found that ChELP2 is concentrated on the surface of bulbous biotrophic hyphae at the interface with living host cells but is absent from filamentous necrotrophic hyphae. We show that recombinant ChELP1 and ChELP2 bind chitin and chitin oligomers in vitro with high affinity and specificity and that both proteins suppress the chitin‐triggered activation of two immune‐related plant mitogen‐activated protein kinases in the host Arabidopsis. Using RNAi‐mediated gene silencing, we found that ChELP1 and ChELP2 are essential for fungal virulence and appressorium‐mediated penetration of both Arabidopsis epidermal cells and cellophane membranes in vitro.

The findings suggest a dual role for these LysM proteins as effectors for suppressing chitin‐triggered immunity and as proteins required for appressorium function.
Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation
Authors: Zhang Laining , Yang Xiaoyu , Tian Li , Chen Lei , Yu Weichang 
Published: May 2016

Summary

The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling.

In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)‐based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives.

Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH‐based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties.

The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
Genetic background of hyperphenylalaninemia in Nagasaki, Japan
Authors: Dateki Sumito , Watanabe Satoshi , Nakatomi Akiko , Kinoshita Eiichi , Matsumoto Tadashi , Yoshiura Koh‐ichiro , Moriuchi Hiroyuki 
Published: May 2016

AbstractPhenylketonuria (PKU) and related hyperphenylalaninemia (HPA) are caused by a deficiency in hepatic phenylalanine hydroxylase (PAH). The incidence of PKU in Nagasaki prefecture is higher than that in all parts of Japan (1/15 894 vs 1/120 000). To investigate the genetic background of patients with HPA in Nagasaki prefecture, mutation analysis was done in 14 patients with PKU or mild HPA. Homozygous or compound heterozygous PAH mutations were identified in all the patients. The spectrum of PAH mutations in the cohort was broad and similar to those in all parts of Japan and East Asian countries. R53H is the most common mutation in patients with mild HPA. The present results provide further support for genotype–phenotype correlations in patients with HPA. The high incidence of PKU in Nagasaki, the westernmost part of Japan, might be due to migration of people with PAH mutations from China and Korea, and geographic factors.
Can Microfiltered Seminal Plasma Preserve the Morphofunctional Characteristics of Porcine Spermatozoa in the Absence of Antibiotics? A Preliminary Study
Authors: Barone F , Ventrella D , Zannoni A , Forni M , Bacci ML 
Published: May 2016

ContentsArtificial insemination is extensively performed in pig farms in Europe, the United States and Canada. Antibiotics are typically added to the inseminating dose to limit bacterial growth during liquid phase storage at 16°C, as bacterial contamination is unavoidable. The World Organization for Animal Health (OIE) and the Food and Agriculture Organization (FAO) take action to control and reduce antibiotic use in animals as more bacteria are becoming resistant to antimicrobials. To avoid the use of antibiotics, we prepared inseminating doses using microfiltered seminal plasma (SP). Microfiltration is a common technology used to reduce bacterial contamination but may retain seminal substances, influencing sperm quality during storage. Therefore, the aim of this study was to evaluate the morphofunctional parameters of spermatozoa during storage at 16°C in doses prepared with or without microfiltered SP, with or without the addition of antibiotics, in a Latin square design. Artificial insemination doses with microfiltered SP and without antibiotic addition preserved spermatozoa viability, mitochondrial membrane potential, acrosome integrity and objective motility, with absolute values equal or even better than those observed in conventional doses. In conclusion, although the results could be considered preliminary due to the small sample size, this study suggests that microfiltration of SP can be a simple method, feasible on farms, to replace antibiotic use in extended doses stored in the liquid phase at 16°C for up to 7 days.
Effect of long‐term treatment with corticosteroids on skeletal muscle strength, functional exercise capacity and health status in patients with interstitial lung disease
Authors: Hanada Masatoshi , Sakamoto Noriho , Ishimatsu Yuji , Kakugawa Tomoyuki , Obase Yasushi , Kozu Ryo , Senjyu Hideaki , Izumikawa Koichi , Mukae Hiroshi , Kohno Shigeru 
Published: May 2016

AbstractBackground and objectiveCorticosteroids are occasionally used in the treatment of ILD. Chronic corticosteroid administration induces skeletal muscle weakness. However, it is unclear whether chronic corticosteroid treatment could further reduce skeletal muscle strength in patients with ILD who are weaker than healthy controls. The aim of this study was to determine the effects of chronic corticosteroid administration on skeletal muscle strength, exercise capacity, activities of daily living (ADL) and health status in ILD patients.MethodsForty‐seven ILD patients treated with corticosteroids and 51 Medical Research Council dyspnea grade‐matched ILD patients not treated with corticosteroids were assessed by isometric quadriceps muscle force (QF) and handgrip force (HF), pulmonary function, 6‐min walk distance, ADL score and health status (Medical Outcomes Study 36‐Item Short‐Form Health Survey), and the two groups' results were compared.ResultsQF and HF were significantly lower in subjects on corticosteroids than in the control patients (QF, 52.6 ± 25.6 vs 77.1 ± 33.3 %predicted, P < 0.001; HF, 63.8 ± 22.4 vs 81.8 ± 28.3 %predicted, P < 0.001, respectively). There were no significant differences in the 6MWD, ADL score and all subscales of the SF‐36 between the groups. Inverse correlations were found between skeletal muscle strength and total amount of corticosteroids administered (QF, r = −0.401, P = 0.005; HF, r = −0.403, P = 0.005). On multiple regression analysis, the total amount of corticosteroids was an independent predictor of HF.ConclusionChronic cor3ticosteroid treatment contributes to muscle weakness in ILD patients, and muscle weakness is inversely correlated to the total amount of corticosteroids administered.
Asymptotic Theory of Outlier Detection Algorithms for Linear Time Series Regression Models
Authors: Johansen Søren , Nielsen Bent 
Published: May 2016

AbstractOutlier detection algorithms are intimately connected with robust statistics that down‐weight some observations to zero. We define a number of outlier detection algorithms related to the Huber‐skip and least trimmed squares estimators, including the one‐step Huber‐skip estimator and the forward search. Next, we review a recently developed asymptotic theory of these. Finally, we analyse the gauge, the fraction of wrongly detected outliers, for a number of outlier detection algorithms and establish an asymptotic normal and a Poisson theory for the gauge.
The Grid Method for In‐plane Displacement and Strain Measurement: A Review and Analysis
Authors: Grédiac M. , Sur F. , Blaysat B. 
Published: May 2016

AbstractThe grid method is a technique suitable for the measurement of in‐plane displacement and strain components on specimens undergoing a small deformation. It relies on a regular marking of the surfaces under investigation. Various techniques are proposed in the literature to retrieve these sought quantities from images of regular markings, but recent advances show that techniques developed initially to process fringe patterns lead to the best results. The grid method features a good compromise between measurement resolution and spatial resolution, thus making it an efficient tool to characterise strain gradients. Another advantage of this technique is the ability to establish closed‐form expressions between its main metrological characteristics, thus enabling to predict them within certain limits. In this context, the objective of this paper is to give the state of the art in the grid method, the information being currently spread out in the literature. We propose first to recall various techniques that were used in the past to process grid images, to focus progressively on the one that is the most used in recent examples: the windowed Fourier transform. From a practical point of view, surfaces under investigation must be marked with grids, so the techniques available to mark specimens with grids are presented. Then we gather the information available in the recent literature to synthesise the connection between three important characteristics of full‐field measurement techniques: the spatial resolution, the measurement resolution and the measurement bias. Some practical information is then offered to help the readers who discover this technique to start using it. In particular, programmes used here to process the grid images are offered to the readers on a dedicated website. We finally present some recent examples available in the literature to highlight the effectiveness of the grid method for in‐plane displacement and strain measurement in real situations.
Does Presentation Order Impact Choice After Delay?
Authors: Berger Jonah 
Published: May 2016

AbstractOptions are often presented incidentally in a sequence, but does serial position impact choice after delay, and if so, how? We address this question in a consequential real‐world choice domain. Using 25 years of citation data, and a unique identification strategy, we examine the relationship between article order (i.e., position in a journal issue) and citation count. Results indicate that mere serial position affects the prominence that research achieves: Earlier‐listed articles receive more citations. Furthermore, our identification strategy allows us to cast doubt on alternative explanations (i.e., editorial placement) and instead indicate that the effect is driven by psychological processes of attention and memory. These findings deepen the understanding of how presentation order impacts choice, suggest that subtle presentation factors can bias an important scientific metric, and shed light on how psychological processes shape collective outcomes.
Declining blood collection and utilization in the United States
Authors: Chung Koo‐Whang , Basavaraju Sridhar V. , Mu Yi , van Santen Katharina L. , Haass Kathryn A. , Henry Richard , Berger James , Kuehnert Matthew J. 
Published: May 2016

BACKGROUNDThe Department of Health and Human Services National Blood Collection and Utilization Survey (NBCUS) has been conducted biennially since 1997. Data are used to estimate national blood collection and utilization.STUDY DESIGN AND METHODSThe 2013 Department of Health and Human Services NBCUS is a cross‐sectional survey of all US blood collection centers and hospitals as listed in the 2012 American Hospital Association Annual Survey database that perform at least 100 inpatient surgical procedures annually. The study objective was to estimate, with 95% confidence intervals (CIs), the number of blood and blood components collected and transfused in the United States.RESULTSIn 2013, a total of 14,237,000 whole blood and apheresis red blood cell (RBC) units (95% CI, 13,639,000‐14,835,000) were collected with 13,395,000 available for transfusion. Of these, 13,180,000 (95% CI, 12,389,000‐13,972,000) whole blood and RBC units were transfused. This represented a 4.4% decline in the number of transfused units compared to 2011. Outdated (i.e., expired without being transfused) whole blood and RBC units declined by 17.3%. Apheresis (2,318,000; 95% CI, 2,154,000‐2,482,000) and whole blood–derived platelet (PLT; 130,000; 95% CI, 23,000‐237,000) distribution declined in 2013. Total PLT transfusions increased in 2013 (2,281,000) in comparison to 2011 (2,169,000). Total plasma units distributed (4,338,000) and transfused (3,624,000) declined.CONCLUSIONBoth blood collection and utilization have declined, but the gap between collection and utilization is narrowing. As collections decline further and hospitals decrease transfusions and manage products more efficiently, the decline in surplus inventory may be a concern for disaster preparedness or other unexpected utilization needs.
Combination of voxel‐based and projection‐based methods in terms of convergence for CT reconstruction
Authors: Chukanov Viacheslav , Bergner Frank 
Published: May 2016

Purpose:Recent applications of iterative image reconstruction algorithms to multislice helical CT have shown that iterative reconstruction can significantly improve image quality and reduce artifacts. In this paper, the authors introduce a combination of two different algorithms with different convergence properties: ordered subsets separable paraboloidal surrogates (OS‐SPS) and iterative coordinate descent (ICD). The first one updates image voxels simultaneously, slightly changing attenuation values iteration by iteration. The second algorithm updates image voxel by voxel, each time performing full forward and backward projections of the voxel. It has been shown that ICD converges better at high‐frequency areas and requires more iterations to reconstruct low‐frequency components of the image. In contrast to ICD, SPS requires multiple iterations to reconstruct high‐frequency areas. In this paper, the authors introduce an algorithm which leverages the benefits of both ICD and SPS.Methods:The idea is to update the entire image with SPS, determine high‐frequency components, and focus ICD computations on it using nonhomogeneous ICD update.Results:The authors have successfully implemented OS‐SPS, ICD, their hybrid approach, and few variations of ICD based on spatially nonuniform updates.Conclusions:The authors have examined the convergence of different algorithms and found that proposed algorithm converges better than OS‐SPS, ICD, as well as various improved variants of ICD.
Characterization and Sequencing of an H6N6 Avian Influenza Virus Isolated from Sansui Sheldrake Ducks in Guizhou, Southwestern China
Authors: Duan Zhiqiang , Chen Jiaqi , Ji Xinqin , Xu Houqiang , Ruan Yong , Zhao Jiafu 
Published: May 2016

ABSTRACT
Here, we report the complete genome sequence of an H6N6 avian influenza virus (AIV) isolated from Sansui Sheldrake ducks in Guizhou Province, China, in 2014. Phylogenetic analysis showed that the H6N6 virus was a reassortant virus derived from three different H6 subtype lineages. The finding of this study will help us understand the epidemiology and the evolutionary characteristics of H6 subtypes of AIV in ducks in southwestern China.
Draft Genome Sequence of Hydrocarbon-Degrading Enterobacter cloacae Strain S1:CND1, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil Refinery, Guwahati, Assam, India
Authors: Mukherjee Arghya , Chettri Bobby , Langpoklakpam James S. , Singh Arvind K. , Chattopadhyay Dhrubajyoti 
Published: May 2016

ABSTRACT

We report here the 4.57-Mb draft genome sequence of hydrocarbon-degrading
Enterobacter cloacae
strain S1:CND1 isolated from oil-contaminated soil in Guwahati, India. S1:CND1 contains 4,205 coding sequences and has a G+C content of 57.45%. This is the first report of the genome sequence of an
E. cloacae
adapted to an oil-contaminated environment.
Draft Genome Sequence of
Branchiibius
sp. NY16-3462-2, Isolated from a Mixed Clinical Sample
Authors: Lapierre Pascal , Halse Tanya A. , Shea Joseph , Escuyer Vincent E. , Musser Kimberlee A. 
Published: May 2016

ABSTRACT

Here, we report the release of a draft genome assembly of a Gram-positive cocci
Branchiibius
sp. NY16-3462-2 with a high-GC content, sequenced from a mixed clinical sample containing
Mycobacterium tuberculosis
. This genome is the first publicly available sequence from a representative of the genus
Branchiibius
.