bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Value of Coexisting Lobular Carcinoma In Situ With Invasive Lobular Carcinoma
Authors: Harbhajanka Aparna , Lamzabi Ihab , Syed Sahr , Jain Richa , Ghai Ritu , Reddy Vijaya B. , Bitterman Pincas , Gattuso Paolo 
Published: November 2015

Aims and Objectives:
Recent studies show that lobular carcinoma in situ (LCIS) and invasive lobular carcinoma (ILC) share similar genetic molecular biology. There are increasing concerns regarding the biological significance of LCIS. The aim of this study is to investigate whether the presence of coexisting LCIS in ILC affects tumor biology and behavior and to correlate it with other clinicopathologic parameters.

Materials and Methods:
In this study, 254 cases of ILC were included. Clinicopathologic parameters and immunohistochemical stains for estrogen receptor (ER), progesterone receptor (PR), E-cadherin, human epidermal growth factor receptor (HER2), and MIB-1 of 254 ILC cases were retrieved. The patient with ILC and coexisting LCIS were compared with pure ILC cases with respect to different clinicopathologic parameters.

Results:
Of the 254 cases, 107 cases were pure ILC and 147 cases were ILC with coexisting LCIS. Seventy-six (76/184, 41.32%) cases showed axillary lymph node metastases. Lymph node metastasis was absent in 108 cases, micrometastasis was present in 5 cases, and stage N1, N2, N3 in 51, 5, and 15 cases, respectively. Nodal involvement, locoregional and distant recurrence of ILC with LCIS were less frequent compared with ILC without LCIS with P-value of 0.034 and 0.007, respectively. The presence of coexisting LCIS in ILC predicted higher disease-free survival (DFS) compared with pure ILC (P=0.034, log-rank test). When divided into different strata, ER-positive ILC cases with associated LCIS cases showed better DFS than ER-positive pure ILC cases (P=0.021, log-rank test). Similarly, ILC cases with LCIS in patient less than 50 years showed better DFS than the patient less than 50 years with pure ILC (P=0.045, log-rank test).

Conclusions:
In conclusion, ILC coexisting with lobular carcinoma in situ (ILC+LCIS) is characterized by less nodal involvement, lower locoregional, and distant recurrence and better DFS than pure ILC. When divided into different strata, ER-positive and less than 50-year groups with ILC+LCIS show even significant better DFS than pure ILC. These findings suggest that there is biological significance of coexisting LCIS in ILC and that this may have more effect on tumor aggressiveness in certain strata of ILC.
Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties
Authors: Wolfe Marnin D. , Kulakow Peter , Rabbi Ismail Y. , Jannink Jean-Luc 
Published: November 2015

ABSTRACTIn clonally propagated crops, non-additive genetic effects can be effectively exploited by the identification of superior genetic individuals as varieties. Cassava(Manihot esculentaCrantz) is a clonally propagated staple food crop that feeds hundreds of millions. We quantified the amount and nature of non-additive genetic variation for key traits in a breeding population of cassava from sub-Saharan Africa using additive and non-additive genome-wide marker-based relationship matrices. We then assessed the accuracy of genomic prediction of additive compared to total (additive plus non-additive) genetic value. We confirmed previous findings based on diallel populations, that non-additive genetic variation is significant, especially for yield traits. Further, we show that we total genetic value correlated more strongly to observed phenotypes than did additive value, although this is constrained by low broad-sense heritability and is not beneficial for traits with already high heritability. We address the implication of these results for cassava breeding and put our work in the context of previous results in cassava, and other plant and animal species.
Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in theChlamydomonas reinhardtiiplastid genome
Authors: Ness Rob W. , Kraemer Susanne A. , Colegrave Nick , Keightley Peter D. 
Published: November 2015

AbstractPlastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input ofde novomutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterizede novomutation inChlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies inC. reinhardtiiand demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.
A statistical approach to genome size evolution: Observations and explanations
Authors: Li Dirson Jian 
Published: November 2015

AbstractGenome size evolution is a fundamental problem in molecular evolution. Statistical analysis of genome sizes brings new insight into the evolution of genome size. Although the variation of genome sizes is complicated, it is indicated that the genome size evolution can be explained more clearly at taxon level than at species level. I find that the genome size distribution for species in a taxon fits log-normal distribution. And I find a relationship between the phylogeny of life and the statistical features of genome size distributions among taxa. I observed different statistical features of genome size distributions between animal taxa and plant taxa. A log-normal stochastic process model is developed to simulate the genome size evolution. The simulation results on the log-normal distributions of genome sizes and their statistical features agree with the observations.
Mass graphs and their applications in top-down proteomics
Authors: Kou Qiang , Wu Si , Tolić Nikola , Pasa-Tolić Ljiljana , Liu Xiaowen 
Published: November 2015

AbstractAlthough proteomics has made rapid progress in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird view” of intact proteoforms. The combinatorial explosion of possible proteoforms, which may result in billions of possible proteoforms for one protein, makes proteoform identification a challenging computational problem. Here we propose a new data structure, called the mass graph, for efficiently representing proteoforms. In addition, we design mass graph alignment algorithms for proteoform identification by top-down mass spectrometry. Experiments on a histone H4 mass spectrometry data set showed that the proposed methods outperformed MS-Align-E in identifying complex proteoforms.
Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls
Authors: Hu Yi-Juan , Liao Peizhou , Johnston H. Richard , Allen Andrew S. , Satten Glen A. 
Published: November 2015

AbstractNext-generation sequencing of DNA provides an unprecedented opportunity to discover rare genetic variants associated with complex diseases and traits. However, when testing the association between rare variants and traits of interest, the current practice of first calling underlying genotypes and then treating the called values as known is prone to false positive findings, especially when genotyping errors are systematically different between cases and controls. This happens whenever cases and controls are sequenced at different depths or on different platforms. In this article, we provide a likelihood-based approach to testing rare variant associations that directly models sequencing reads without calling genotypes. We consider the (weighted) burden test statistic, which is the (weighted) sum of the score statistic for assessing effects of individual variants on the trait of interest. Because variant locations are unknown, we develop a simple, computationally efficient screening algorithm to estimate the loci that are variants. Because our burden statistic may not have mean zero after screening, we develop a novel bootstrap procedure for assessing the significance of the burden statistic. We demonstrate through extensive simulation studies that the proposed tests are robust to a wide range of differential sequencing qualities between cases and controls, and are at least as powerful as the standard genotype calling approach when the latter controls type I error. An application to the UK10K data reveals novel rare variants in geneBTBD18associated with childhood onset obesity. The relevant software is freely available.
Commodity prices, the exchange rate and manufacturing in South Africa: what do the data say?
Authors: Hodge Duncan 
Published: November 2015

Purpose
– The purpose of this paper is to investigate the empirical relationships between changes in OECD output, commodity prices, the real exchange rate, real money supply, unit labour costs and manufacturing in South Africa. In particular, to test a version of the Dutch disease argument that increases in the prices of South Africa’s main commodity exports have had a negative effect on domestic manufacturing against the alternative hypothesis that there is a positive relationship between such changes in commodity prices and domestic manufacturing output.

Design/methodology/approach
– Construction of a model including real manufacturing output in South Africa as the dependent variable and the following independent variables: OECD output, an international real metals price index, a real effective exchange rate index, real M3 money supply and manufacturing unit labour costs. The time series sample data comprise 124 quarterly observations for the period 1980-2010. The model equation was tested and estimated using a Johansen cointegration approach.

Findings
– The main findings are: OECD output is the single most important determinant of domestic manufacturing output; while the real exchange rate has the predicted negative sign, rising commodity prices are associated with increases rather than decreases in domestic manufacturing and; large increases in unit labour costs since the early 1980s have dragged down manufacturing over the sample period.

Originality/value
– The finding of a positive relationship between commodity prices and domestic manufacturing means that the Dutch disease argument must be revised when applied to South Africa. While rising commodity prices may lead to a negative exchange rate effect on manufacturing competitiveness, this is more than offset by the positive growth effects associated with upswings in the commodity price cycle.
Achieving food and nutrition security under rapid transformation in China and India
Authors: Fan Shenggen , Rue Christopher 
Published: November 2015

Purpose
– The purpose of this paper is to set the stage for the proceeding articles with background of the impressive yet incomplete progress made in eliminating hunger and malnutrition in China and India.

Design/methodology/approach
– The paper provides background of the progress and challenges to achieving food security and nutrition in China and India. It then highlights the lessons learned from this special issue, and concludes with remaining knowledge gaps.

Findings
– The paper summarizes findings from each article in the special issue.

Originality/value
– Comparing the experiences of these two countries is essential to share knowledge and accelerate progress in eliminating poverty, hunger, and malnutrition both within these countries and globally.
KnowingGuanxifrom the perspective of Tao: a mixed methodological approach
Authors: Tian Longwei , Ma Yucheng , Hu Wei , Li Yuan 
Published: November 2015

Purpose– This paper aims to, from a Taoism perspective, one of Chinese inveterate cultures and mindsets, add knowledge into how Chinese indigenous cultures and mindsets will affect the way of Chinese people perceive and process guanxi. Specifically, this paper outlines the mechanism of guanxi from a culture perspective. Cultures significantly affect local people behavior.Design/methodology/approach– A mixed-methods survey (Study 1) – analyzed with one-way ANOVA – and interview (Study 2) – analyzed with grounded theory – were used to answer the research questions. In total, 248 surveys were collected for Study 1, and 34 interviews for Study 2 that were transcribed into a word file, which consists of 609 pages with 327,463 Chinese characters, were processed.Findings– The findings show that guanxi is determined by positive and negative forces between instrumental and affective components. Further, two essential conditions – fitness of personality and clear contract, which would determine when a positive or negative force would emerge in a guanxi – were identified.Originality/value– The main contribution is that this paper clarifies the guanxi mechanism based upon one of the most significant Chinese cultures and mindsets. Or guanxi is viewed from a new perspective – how Taoism affects Chinese people’s perception and evaluation of guanxi. This paper also finds evidence for the main arguments based upon the two studies.
The boat is rocked – Employees' grumbles: a decision dilemma
Authors: Bin Shamsuri Abd Latiff Sukri , Alagappar Ponmalar N. , Kumar Dileep 
Published: November 2015

Subject area
Entrepreneurship, Strategic Management, Organizational Change Management.

Study level/applicability
Postgraduate and undergraduate students.

Case overview
Restoran Minang Plus is a self-styled family-owned and managed restaurant featuring a gamut of Malaysian Negeri Sembilan and Indonesian Padang dishes. The eatery establishment has sailed the food industry waters successfully since 2004 and currently has five branches. However, there are certain imperatives they have to institute to integrate their entrepreneurial challenges with organizational change management. The nature of the forces in the competitive restaurant landscape requires a continuous rethinking of current strategic actions, organizational change, communication systems, motivation, asset deployment and strategic flexibility to respond quickly to changing conditions and thereby develop and maintain a competitive advantage. The question is how do they integrate this organizational change management to their entrepreneurial challenges with a view to achieve and maintain competitive advantage?

Expected learning outcomes
The expected learning outcomes are as follows: understanding managing diversity by looking at the different categories of diversity, that is, generic characteristics and learned characteristics that influence work attitudes; explaining how fostering learning and reinforcement can help in increasing job satisfaction; describing the basic motivational needs of the employees and how it can help in increasing job performance; understanding how an entrepreneurial firm can maximize its firm performance through effective change management; and understanding the importance of strategic management in an entrepreneurial firm.

Supplementary materials
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Increasing testing efficiency through the development of an IT-based adaptive testing tool for competency measurement
Authors: Kleinhans Janne , Schumann Matthias 
Published: November 2015

Purpose
– This paper investigates the potential of computerized adaptive testing for CMs to reduce test time. In the context of education and training, competency measurement (CM) is a central challenge in competency management. For complex CMs, a compromise must be addressed between the time available and the quality of the measurements. Increasing the efficiency of existing tests therefore poses a key challenge.

Design/methodology/approach
– Results from a market analysis show a lack of integrated adaptive testing tools for CMs. The implementation, integration and evaluation of an appropriate adaptive component are presented for the example of the learning management system ILIAS used for a CM of health workers. The textbook scenario of a linear testing implementation is compared with results from the adaptive testing tool implementation. A simulation component is created to investigate the robustness of the adaptive test regarding answers that are inconsistent with the test person’s ability.

Findings
– A test time reduction of 40 per cent is achieved by the adaptive test. The test shows high stability for up to 20 per cent of the answers being inconsistent with the test person’s ability.

Originality/value
– Results indicate the high potential of computerized adaptive testing for CMs. The developed tool could be used for the implementation of combined multimedia computerized adaptive tests. Time savings could be utilized to improve measurement quality. Large-scale empirical studies on the interaction between competency dimensions could be facilitated. No other tool could be identified possessing these capabilities.
Molecular and functional characterization of a candidate sex pheromone receptor OR1 in Spodoptera litura
Authors: Zhang Qin‐Hui , Wu Zhong‐Nan , Zhou Jing‐Jiang , Du Yong‐Jun 
Published: November 2015

AbstractOlfaction is primarily mediated by highly specified olfactory receptors (ORs). Here, we cloned and identified an olfactory receptor, named SlituOR1 (Genbank no. JN835269), from Spodoptera litura and found evidence that it is a candidate pheromone receptor. It exhibited male‐biased expression in the antennae, where it was localized at the base of sensilla trichoidea, the antennal sensilla mainly responsive to pheromones in moths. Conserved orthologues of this receptor, found among known pheromone receptors within the Lepidoptera, and SlituOR1 were placed among a clade of candidate pheromone receptors in a phylogeny tree of insect OR gene sequences. SlituOR1 showed differential expression in S. litura populations attracted to traps baited with different ratios of the two sex pheromone components (9Z,11E)‐tetradecadienyl acetate (Z9E11‐14:OAc) and (9Z,12E)‐tetradecadienyl acetate (Z9E12‐14:OAc). Knocking down of SlituOR1 by RNA interference reduced the electroantennogram (EAG) response to Z9E11‐14:OAc, and this result is consistent with the field trapping experiment. We infer that variation in transcription levels of olfactory receptors may modulate sex pheromone perception in male moths and could provide some of the flexibility required to maintain the functionality of communication with females when a population is adapting to a new niche and reproductive isolation becomes an advantage.
Comparative Effectiveness Research: Alternatives to “Traditional” Computed Tomography Use in the Acute Care Setting
Authors: Moore Christopher L. , Broder Joshua , Gunn Martin L. , Bhargavan‐Chatfield Mythreyi , Cody Dianna , Cullison Kevin , Daniels Brock , Gans Bradley , Kennedy Hall M. , Gaines Barbara A. , Goldman Sarah , Heil John , Liu Rachel , Marin Jennifer R. , Melnick Edward R. , Novelline Robert A. , Pare Joseph , Repplinger Michael D. , Taylor Richard A. , Sodickson Aaron D. 
Published: November 2015

AbstractComputed tomography (CT) scanning is an essential diagnostic tool and has revolutionized care of patients in the acute care setting. However, there is widespread agreement that overutilization of CT, where benefits do not exceed possible costs or harms, is occurring. The goal was to seek consensus in identifying and prioritizing research questions and themes that involve the comparative effectiveness of “traditional” CT use versus alternative diagnostic strategies in the acute care setting. A modified Delphi technique was used that included input from emergency physicians, emergency radiologists, medical physicists, and an industry expert to achieve this.
Autophosphorylation of alpha isoform of calcium/calmodulin‐dependent kinase II regulates alcohol addiction‐related behaviors
Authors: Mijakowska Zofia , Łukasiewicz Kacper , Ziółkowska Magda , Lipiński Michał , Trąbczyńska Anna , Matuszek Żaneta , Łęski Szymon , Radwanska Kasia 
Published: November 2015

AbstractThe development of addiction is associated with a dysregulation of glutamatergic transmission in the brain reward circuit. α isoform of calcium/calmodulin‐dependent kinase II (αCaMKII) is one of the key proteins that regulates structural and functional plasticity of glutamatergic synapses. αCaMKII activity can be controlled by the autophosphorylation of threonine 286. The role of this autophosphorylation in the regulation of addiction‐related behaviors has been proposed but is still poorly understood. Here, using αCaMKII autophosphorylation‐deficient mutant mice (T286A), we show that, in comparison with wild‐type animals, they are less resistant to high doses of alcohol and do not show psychostimulant response neither to alcohol injections nor during voluntary alcohol drinking. T286A mutants are also less prone to develop alcohol addiction‐related behaviors including an increased motivation for alcohol, persistent alcohol seeking during withdrawal and alcohol consumption on relapse. Finally, we demonstrate that αCaMKII autophosphorylation regulates also alcohol‐induced remodeling of glutamatergic synapses in the hippocampus and amygdala. In conclusion, our data suggest that αCaMKII autophosphorylation‐dependent remodeling of glutamatergic synapses is a plausible mechanism for the regulation of the alcohol addiction‐related behaviors.