bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for estimating spikelet number per panicle: Integrating image analysis and a 5-point calibration model
Authors: Zhao Sanqin , Gu Jiabing , Zhao Youyong , Hassan Muhammad , Li Yinian , Ding Weimin 
Published: November 2015

AbstractSpikelet number per panicle (SNPP) is one of the most important yield components used to estimate rice yields. The use of high-throughput quantitative image analysis methods for understanding the diversity of the panicle has increased rapidly. However, it is difficult to simultaneously extract panicle branch and spikelet/grain information from images at the same resolution due to the different scales of these traits. To use a lower resolution and meet the accuracy requirement, we proposed an interdisciplinary method that integrated image analysis and a 5-point calibration model to rapidly estimate SNPP. First, a linear relationship model between the total length of the primary branch (TLPB) and the SNPP was established based on the physiological characteristics of the panicle. Second, the TLPB and area (the primary branch region) traits were rapidly extracted by developing image analysis algorithm. Finally, a 5-point calibration method was adopted to improve the universality of the model. The number of panicle samples that the error of the SNPP estimates was less than 10% was greater than 90% by the proposed method. The estimation accuracy was consistent with the accuracy determined using manual measurements. The proposed method uses available concepts and techniques for automated estimations of rice yield information.
Protection of soil carbon within macro-aggregates depends on intra-aggregate pore characteristics
Authors: Kravchenko Alexandra N. , Negassa Wakene C. , Guber Andrey K. , Rivers Mark L. 
Published: November 2015

AbstractSoil contains almost twice as much carbon (C) as the atmosphere and 5–15% of soil C is stored in a form of particulate organic matter (POM). Particulate organic matter C is regarded as one of the most labile components of the soil C, such that can be easily lost under right environmental settings. Conceptually, micro-environmental conditions are understood to be responsible for protection of soil C. However, quantitative knowledge of the specific mechanisms driving micro-environmental effects is still lacking. Here we combined CO2respiration measurements of intact soil samples with X-ray computed micro-tomography imaging and investigated how micro-environmental conditions, represented by soil pores, influence decomposition of POM. We found that atmosphere-connected soil pores influenced soil C’s and especially POM’s, decomposition. In presence of such pores losses in POM were 3–15 times higher than in their absence. Moreover, we demonstrated the presence of a feed-forward relationship between soil C decomposition and pore connections that enhance it. Since soil hydrology and soil pores are likely to be affected by future climate changes, our findings indicate that not-accounting for the influence of soil pores can add another sizable source of uncertainty to estimates of future soil C losses.
Dense sampling reveals behavioral oscillations in rapid visual categorization
Authors: Drewes Jan , Zhu Weina , Wutz Andreas , Melcher David 
Published: November 2015

AbstractPerceptual systems must create discrete objects and events out of a continuous flow of sensory information. Previous studies have demonstrated oscillatory effects in the behavioral outcome of low-level visual tasks, suggesting a cyclic nature of visual processing as the solution. To investigate whether these effects extend to more complex tasks, a stream of “neutral” photographic images (not containing targets) was rapidly presented (20 ms/image). Embedded were one or two presentations of a randomly selected target image (vehicles and animals). Subjects reported the perceived target category. On dual-presentation trials, the ISI varied systematically from 0 to 600 ms. At randomized timing before first target presentation, the screen was flashed with the intent of creating a phase reset in the visual system. Sorting trials by temporal distance between flash and first target presentation revealed strong oscillations in behavioral performance, peaking at 5 Hz. On dual-target trials, longer ISIs led to reduced performance, implying a temporal integration window for object category discrimination. The “animal” trials exhibited a significant oscillatory component around 5 Hz. Our results indicate that oscillatory effects are not mere fringe effects relevant only with simple stimuli, but are resultant from the core mechanisms of visual processing and may well extend into real-life scenarios.
Reversible superconductor-insulator transition in LiTi2O4 induced by Li-ion electrochemical reaction
Authors: Yoshimatsu K. , Niwa M. , Mashiko H. , Oshima T. , Ohtomo A. 
Published: November 2015

AbstractTransition metal oxides display various electronic and magnetic phases such as high-temperature superconductivity. Controlling such exotic properties by applying an external field is one of the biggest continuous challenges in condensed matter physics. Here, we demonstrate clear superconductor-insulator transition of LiTi2O4 films induced by Li-ion electrochemical reaction. A compact electrochemical cell of pseudo-Li-ion battery structure is formed with a superconducting LiTi2O4 film as an anode. Li content in the film is controlled by applying a constant redox voltage. An insulating state is achieved by Li-ion intercalation to the superconducting film by applying reduction potential. In contrast, the superconducting state is reproduced by applying oxidation potential to the Li-ion intercalated film. Moreover, superconducting transition temperature is also recovered after a number of cycles of Li-ion electrochemical reactions. This complete reversible transition originates in difference in potentials required for deintercalation of initially contained and electrochemically intercalated Li+ ions.
A high risk of osteosarcoma in individuals who are homozygous for the p.D104N in endostatin
Authors: Bi Wen-Zhi , Li Dian-Wei , Luo Song , Song Zhi-Gang , Wang Yun , Jin Hua , Wang Yan , Li Qing , Li Meng-Xia , Wang Dong , Sun Bo , Xu Meng , Xu Cheng-Xiong 
Published: November 2015

AbstractThe D104N polymorphism (p.D104N) in endostatin has been previously identified in many types of cancer and this polymorphism is believed to be a phenotypic modulator in some tumors. However, it is unknown whether endostatin p.D104N affects the risk and progression of osteosarcoma (OS). Here, we analyzed the p.D104N endostatin variant in 236 patients with OS and 418 healthy individuals. Similar frequencies of wild type and heterozygous p.104DN endostatin were observed in controls and OS patients. Interestingly, the frequency of the homozygous p.D104N (p.104NN) genotype was higher in OS patients group compared to control group, suggesting that individuals with p.104NN endostatin have a significantly increased risk for OS. In addition, OS patients with p.104NN endostatin had a shorter survival time and a higher rate of metastasis than OS patients with wild type endostatin. Animal experiments revealed that overexpression of p.104NN endostatin did not significantly inhibit OS lung metastasis. Interestingly, administration of endostatin dramatically inhibited OS lung metastasis in the p.104NN endostatin xenograft model. Together, these results suggest that p.104NN of endostatin is associated with the risk of OS and demonstrates predictive significance for clinical outcome in OS patients. In addition, endostatin therapy may be necessary for OS patients harboring p.104NN endostatin.
Ethical Challenges: Less About Moral Wrongdoing and More About Communication Breakdown
Authors: Leslie Paula , Casper Mary 
Published: November 2015

“My patient refuses thickened liquids, should I discharge them from my caseload?” A version of this question appears at least weekly on the American Speech-Language-Hearing Association's Community pages. People talk of respecting the patient's right to be non-compliant with speech-language pathology recommendations. We challenge use of the word “respect” and calling a patient “non-compliant” in the same sentence: does use of the latter term preclude the former?
In this article we will share our reflections on why we are interested in these so called “ethical challenges” from a personal case level to what our professional duty requires of us. Our proposal is that the problems that we encounter are less to do with ethical or moral puzzles and usually due to inadequate communication. We will outline resources that clinicians may use to support their work from what seems to be a straightforward case to those that are mired in complexity. And we will tackle fears and facts regarding litigation and the law.
Visible emission spectroscopy of highly charged tungsten ions in LHD: II. Evaluation of tungsten ion temperature
Authors: Fujii K , Takahashi Y , Nakai Y , Kato D , Goto M , Morita S , Hasuo M 
Published: November 2015

Abstract
We demonstrated a polarization-resolved high resolution spectroscopy of a visible emission line of highly charged tungsten ions (λ
0 = 668.899 nm, Shinohara et al Phys. Scr.

90 125402) for the large helical device (LHD) plasma, where the tungsten ions were introduced by a pellet injection. Its spectral profile shows broadening and polarization dependence, which are attributed to the Doppler and Zeeman effects, respectively. The tungsten ion temperature was evaluated for the first time from the broadening of visible the emission line, with its emission location determined by the Abel inversion of the chord-integrated emission intensities observed with multiple chords. The tungsten ion temperature was found to be close to the helium-like argon ion temperature, which is used as an ion temperature monitor in LHD.
Shape component analysis: structure-preserving dimension reduction on biological shape spaces
Authors: Lee Hao-Chih , Liao Tao , Zhang Yongjie Jessica , Yang Ge 
Published: November 2015

AbstractMotivation: Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques.Results: We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins.Availability and implementation: Source code and data for reproducing results of this article are freely available at https://github.com/ccdlcmu/shape_component_analysis_Matlab. The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS.Contact: geyang@andrew.cmu.edu
TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates
Authors: Höhna Sebastian , May Michael R. , Moore Brian R. 
Published: November 2015

Abstract
Summary: Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation–extinction) that are modeled using birth–death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. We enable both statistical inference and efficient simulation under these models. We also provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.
Availability and implementation: The source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/.
Contact: Sebastian.Hoehna@gmail.com
Use of Placebo in Pediatric Inflammatory Bowel Diseases
Authors: Turner Dan , Koletzko Sibylle , Griffiths Anne M. , Hyams Jeffrey , Dubinsky Marla , de Ridder Lissy , Escher Johanna , Lionetti Paolo , Cucchiara Salvatore , Lentze Michael J. , Koletzko Berthold , van Rheenen Patrick , Russell Richard K. , Mack David , Veereman Gigi , Vermeire Séverine , Ruemmele Frank 
Published: November 2015

ABSTRACTPerforming well‐designed and ethical trials in pediatric inflammatory bowel diseases (IBD) is a priority to support optimal therapy and reduce the unacceptable long lag between adult and pediatric drug approval. Recently, clinical trials in children have been incorporating placebo arms into their protocols under conditions that created controversy. Therefore, 4 organizations (the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition; European Crohn's and Colitis Organization; the Canadian Children IBD Network; and the Global Pediatric IBD Network) jointly provide a statement on the role of placebo in pediatric IBD trials. Consensus was achieved by 94 of 100 (94%) voting committees’ members that placebo should only be used if there is genuine equipoise between the active treatment and placebo; for example, this may be considered in trials of drugs with new mechanisms of action without existing adult data, especially when proven effective alternatives do not exist outside the trial. Placebo may also be used in situations where it is an “add‐on” to an effective therapy or to evaluate exit‐strategies of maintenance therapy after long‐term deep remission. It has been, however, agreed that no child enrolled in a trial should receive a known inferior treatment both within and outside the trial. This also includes withholding therapy in children who show clinical response after a short induction therapy. Given the similarity between pediatric and adult IBD regarding pathophysiology and response to treatments, drugs generally cannot be considered being in genuine equipoise with placebo if it has proven efficacy in adults. Continued collaboration of all stakeholders is needed to facilitate drug development and evaluation in pediatric IBD.
Decreased Expression of Enterocyte Nutrient Assimilation Genes and Proteins in the Small Intestine of Cystic Fibrosis Mouse
Authors: De Lisle Robert C. 
Published: November 2015

ABSTRACTObjectives:Cystic fibrosis (CF) has major effects on the intestinal tract with potential consequences on nutrition, but these are not fully understood. I investigated the possibility of altered enterocyte maturation in CF, as suggested by decreased enterocyte nutrient assimilation gene expression in published transcriptome analysis of the small intestine of CF mouse.Methods:In CF and wild‐type (WT) mice, enterocyte gene/protein expression was analyzed by quantitative realtime polymerase chain reaction (qRT‐PCR), enzyme histochemistry, immunohistochemistry, and Western blot. One group of mice was maintained on a control liquid diet; to manipulate the gut microbiota, a second group was treated with oral antibiotics; to improve hydration of the gut lumen, a third group was given a laxative drinking solution.Results:On the control diet in the CF intestine, there were decreased levels (67%–85% reduction of WT levels) of enterocyte genes/proteins. Antibiotics did not normalize the expression of enterocyte markers in the CF mouse. In contrast, the laxative treatment of CF mice significantly increased expression to near WT levels.Conclusions:These studies suggest that the environment of the CF intestinal lumen plays a role in reduced maturation of enterocytes. Because changing the gut lumen environment can affect enterocyte maturation, this is not a cell‐autonomous effect of loss of CF transmembrane conductance regulator.
Endoscopic Versus Histological Disease Extent at Presentation of Paediatric Inflammatory Bowel Disease
Authors: Ashton James J. , Coelho Tracy , Ennis Sarah , Vadgama Bhumita , Batra Akshay , Afzal Nadeem A. , Beattie R. Mark 
Published: November 2015

ABSTRACTObjectives:The Paris classification (PC) of paediatric inflammatory bowel disease categorises disease extent and therefore affects treatment decisions. Histological (microscopic) disease extent is not incorporated, and endoscopic (macroscopic) findings may underrepresent disease extent when compared with histological findings; this study compares disease extent at presentation.Methods:Data were obtained of patients <17 years of age diagnosed with inflammatory bowel disease from 2010 to 2013 at University Hospital Southampton. Data are presented as percentage of patients undergoing endoscopy. PC was performed alongside a modified PC by histological disease location.Results:A total of 172 patients were identified (median age at diagnosis 13.5 years, 115 boys); Crohn disease (CD) 107, ulcerative colitis (UC) 50, inflammatory bowel disease unclassified (IBDU) 15; 159 had undergone upper gastrointestinal (GI) endoscopy, 163 had undergone lower GI endoscopy. Histological disease was more extensive at all points for CD, UC, and IBDU. CD—endoscopic ileal disease in 49% of patients compared with histological disease in 71.3%. Comparing PC—a 10% increase in L3 disease (ileocolonic), a 24% increase in L3 + L4a disease (ileocolonic plus upper GI), and a 27% increase in all of the upper GI involvement if histological disease extent was used. UC—the most common disease location was the rectum (endoscopic 91.5% vs histological 93.6%) and descending colon (endoscopic 89.4% vs histological 95.7%). Comparing PC—a 19% increase in E4 disease (pancolitis) if histological disease extent was used.Conclusions:These data confirm that histological disease extent is greater than endoscopic disease extent. This should be considered when the PC is used. Further study is needed to elucidate which classification would better predict disease outcome.
On characterizing membrane protein clusters withmodel-freespatial correlation approaches
Authors: Shivanandan Arun , Unnikrishnan Jayakrishnan , Radenovic Aleksandra 
Published: November 2015

AbstractSpatial aggregation or clustering of membrane proteins could be important for their functionality, e.g., in signaling, and nanoscale imaging can be used to study its origins, structure and function. Such studies require accurate characterization of clusters, both for absolute quantification and hypothesis testing. A set ofmodel-freequantification approaches —freeof specific cluster models— have been proposed for this purpose. They include the radius of maximal aggregationraobtained from the maxima of the empirical BesagL(r) –rfunction as an estimator of cluster size, and the estimation of various cluster parameters based on an exponential approximation for the Pair Correlation Function(PCF). However, the parameter identifiability and bias and scaling due to theirmodel-freenature are not clear. In practice, the clusters might exhibit specific patterns, and the behavior of these estimators in such cases must be studied. Here, we theoretically analyze these approaches for a set of cluster models, and obtain information about their identifiability and bias. We find that theratiobetweenraand true cluster size depends on both the true size as well as the number of clusters per unit area, or other corresponding parameters, in a model-dependent manner. In particular,rascales with respect to the true size by a factor that can be arbitrarily large, depending on models and parameter values. For the method based on PCF approximation, for most models we analyzed, the ratios between approximate and true model parameters were found to be constants that depend only on models and independent of other parameters. For the models analyzed, this ratio was within ±100%. Our theoretical approach was validated by means of simulations. We also discuss some general issues in inference using second-order spatial properties. While precision could also be key, such information on identifiability and accuracy provides clarity on estimation, can lead to better inference, and can also fuel more accurate method development.
Monitoring earnings management in emerging markets
Authors: Hessayri Manel , Saihi Malek 
Published: November 2015

Purpose
– The purpose of this paper is to examine whether International Financial Reporting Standards (IFRS) adoption complements corporate governance factors (e.g. ownership structure) in monitoring managers’ discretional behavior in an emerging market context.

Design/methodology/approach
– The paper relies on a sample of listed companies in the United Arab Emirates, Morocco, South Africa and the Philippines during an eight-year period on average (four years of pre-adoption period and four years of post-adoption period).

Findings
– The authors find no evidence of lower earnings management after the switch to IFRS reporting, suggesting that managerial discretional behavior is insensitive to a firm’s IFRS adoption. However, the authors document effective monitoring role of a firm’s ownership structure on earnings management. More interestingly, institutional investors are effective in constraining earnings management when holding a high level of ownership. Moreover, the effect of blockholders and institutional blockholders varies as their ownership rises following a non-linear pattern.

Research limitations/implications
– First, the assumption that discretionary accruals are adequate measure of earnings management may be criticized in different ways. Second, the findings, performed on listed companies in the United Arab Emirates, Morocco, South Africa and the Philippines, should be interpreted with caution and cannot be generalized to all emerging market countries.

Practical implications
– Standards setters and market authorities should be aware of earnings management determinants to set adequate and fitting accounting standards limiting opportunistic behavior of managers and mainly to set up training programs to accounting professionals improving the IFRS implementation. Moreover, considering specific features of firms in emerging market countries related to ownership structure, international investors may rely on such criteria to evaluate firms. Finally, auditors should be aware of different incentives for earnings management in order to be able to detect eventual manipulation of accounting earnings.

Originality/value
– This paper provides a timely contribution to the continuous debate of the effect of IFRS adoption on earnings management in a poorly exploited setting, emerging market context. When investigating, additionally, the eventual non-linear effect of institutional ownership, block ownership, institutional block ownership and non-institutional block ownership on earnings management, a major contribution is that it brings to light the finding of a differential influence of ownership levels on earnings management.