bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome
Authors: Carosso Giovanni A. , Boukas Leandros , Augustin Jonathan J. , Nguyen Ha Nam , Winer Briana L. , Cannon Gabrielle H. , Robertson Johanna D. , Zhang Li , Hansen Kasper D. , Goff Loyal A. , Bjornsson Hans T. 
Published: December 2018

AbstractChromatin modifiers act to coordinate gene expression changes critical to neuronal differentiation from neural stem/progenitor cells (NSPCs). Lysine-specific methyltransferase 2D (KMT2D) encodes a histone methyltransferase that promotes transcriptional activation, and is frequently mutated in cancers and in the majority (>70%) of patients diagnosed with the congenital, multisystem intellectual disability (ID) disorder Kabuki syndrome 1 (KS1). Critical roles for KMT2D are established in various non-neural tissues, but the effects of KMT2D loss in brain cell development have not been described. We conducted parallel studies of proliferation, differentiation, transcription, and chromatin profiling in KMT2D-deficient human and mouse models to define KMT2D-regulated functions in neurodevelopmental contexts, including adult-born hippocampal NSPCs in vivo and in vitro. We report cell-autonomous defects in proliferation, cell cycle, and survival, accompanied by early NSPC maturation in several KMT2D-deficient model systems. Transcriptional suppression in KMT2D-deficient cells indicated strong perturbation of hypoxia-responsive metabolism pathways. Functional experiments confirmed abnormalities of cellular hypoxia responses in KMT2D-deficient neural cells, and accelerated NSPC maturation in vivo. Together, our findings support a model in which loss of KMT2D function suppresses expression of oxygen-responsive gene programs important to neural progenitor maintenance, resulting in precocious neuronal differentiation in a mouse model of KS1.Graphical Abstract
Decoding functional regulatory maps via genomic evolutionary footprints in 63 green plants
Authors: Tian Feng , Yang De-Chang , Meng Yu-Qi , Jin Jinpu , Gao Ge 
Published: December 2018

AbstractSystematic identification of functional transcriptional regulatory interactions is essential for understanding regulatory systems. Here, we firstly established genome-wide conservation landscapes for 63 green plants of seven lineages and then developed an algorithm FunTFBS to screen for functional regulatory elements and interactions by coupling base-varied binding affinities of transcription factors with the evolutionary footprints on their binding sites. Using the FunTFBS and the conservation landscapes, we further identified over two million functional interactions for 21,346 TFs, charting functional regulatory maps of these 63 plants. Our work provides plant community with valuable resources to decode plant transcriptional regulatory system and genome sequences.
A cross-cancer metastasis signature in the microRNA-mRNA axis of paired tissue samples
Authors: Lee Samuel C. , Quinn Alistair , Nguyen Thin , Venkatesh Svetha , Quinn Thomas P. 
Published: December 2018

AbstractIn the progression of cancer, cells acquire genetic mutations that cause uncontrolled growth. Over time, the primary tumour may undergo additional mutations that allow for the cancerous cells to spread throughout the body as metastases. Since metastatic development typically results in markedly worse patient outcomes, research into the identity and function of metastasisassociated biomarkers could eventually translate into clinical diagnostics or novel therapeutics. Although the general processes underpinning metastatic progression are understood, no consistent nor clear cross-cancer biomarker profile has yet emerged. However, the literature suggests that some microRNAs (miRNAs) may play an important role in the metastatic progression of several cancer types. Using a subset of The Cancer Genome Atlas (TCGA) data, we performed an integrated analysis of mRNA and miRNA expression with paired metastatic and primary tumour samples to interrogate how the miRNA-mRNA regulatory axis influences metastatic progression. From this, we successfully built mRNAand miRNA-specific classifiers that can discriminate pairs of metastatic and primary samples across 11 cancer types. In addition, we identified a number of miRNAs whose metastasis-associated dysregulation could predict mRNA metastasis-associated dysregulation. Among the most predictive miRNAs, we found several previously implicated in cancer progression, including miR-301b, miR-1296, and miR-423. Taken together, our results suggest that cross-cancer metastatic samples have unique biomarker signatures when compared with paired primary tumours, and that these miRNA biomarkers can be used to predict both metastatic status and mRNA expression.
Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis
Authors: Nisthal Alex , Wang Connie Y. , Ary Marie L. , Mayo Stephen L. 
Published: December 2018

AbstractThe accurate prediction of protein stability upon sequence mutation is an important but unsolved challenge in protein engineering. Large mutational datasets are required to train computational predictors, but traditional methods for collecting stability data are either low-throughput or measure protein stability indirectly. Here, we develop an automated method to generate thermodynamic stability data for nearly every single mutant in a small 56-residue protein. Analysis reveals that most single mutants have a neutral effect on stability, mutational sensitivity is largely governed by residue burial, and unexpectedly, hydrophobics are the best tolerated amino acid type. Correlating the output of various stability prediction algorithms against our data shows that nearly all perform better on boundary and surface positions than for those in the core, and are better at predicting large to small mutations than small to large ones. We show that the most stable variants in the single mutant landscape are better identified using combinations of two prediction algorithms, and that including more algorithms can provide diminishing returns. In most cases, poor in silico predictions were tied to compositional differences between the data being analyzed and the datasets used to train the algorithm. Finally, we find that strategies to extract stabilities from high-throughput fitness data such as deep mutational scanning are promising and that data produced by these methods may be applicable toward training future stability prediction tools.Significance StatementUsing liquid-handling automation, we constructed and measured the thermodynamic stability of almost every single mutant of protein G (Gβ1), a small domain. This self-consistent dataset is the largest of its kind and offers unique opportunities on two fronts: (i) insight into protein domain properties such as positional sensitivity and incorporated amino acid tolerance, and (ii) service as a validation set for future efforts in protein stability prediction. As Gβ1 is a model system for protein folding and design, and its single mutant landscape has been measured by deep mutational scanning, we expect our dataset to serve as a reference for studies aimed at extracting stability information from fitness data or developing novel high-throughput stability assays.
Neuroblast-specific chromatin landscapes allow integration of spatial and temporal cues to generate neuronal diversity in Drosophila
Authors: Sen Sonia Q , Chanchani Sachin , Southall Tony D , Doe Chris Q 
Published: December 2018

AbstractDuring early neurogenesis in flies and mice, spatial and temporal cues interact to specify neuronal diversity, yet in no organism is it known how spatial and temporal cues are integrated. We used Targeted DamID (TaDa) to identify the genomic binding sites of the temporal transcription factor Hunchback in two adjacent Drosophila neuroblasts (NB5-6 and NB7-4). Hunchback targets were different in each neuroblast. Profiling chromatin accessibility showed that each neuroblast had a distinct chromatin landscape: Hunchback-bound loci in NB5-6 were in open chromatin, but the same loci in NB7-4 were in closed chromatin. Moreover, binding of the spatial factor Gsb/Pax3, essential for NB5-6 specification, was correlated with open chromatin and Hunchback-enriched loci in NB5-6, but not NB7-4. We propose early-acting spatial factors establish a unique chromatin landscape in each neuroblast, thereby restricting temporal factor binding to different loci in each neuroblast, resulting in different neurons in each neuroblast lineage.Impact statementIntegration of spatial and temporal identity during Drosophila neurogenesis is due to spatial factors generating neuroblast-specific chromatin thereby biasing subsequent temporal transcription factor binding and producing neuroblast-specific neurons.
Value creation and value maintenance
Authors: Chen Jiawen , Yao Xiaotao , Liu Linlin 
Published: November 2018

PurposeThis paper aims to examine how a firm’s capability affects its political networking in emerging economies and how the institutional environment influences the relationship between a firm’s capability and its political networking.Design/methodology/approachThe authors test the theoretical model by analyzing a database from a World Bank survey in China.FindingsThe results show a nonlinear (U-shaped) relationship between a firm’s capability and its efforts in political networking. The relationship between a firm’s capability and political networking is contingent on the institutional environment, as reflected in institutional development and industry regulation.Originality/valueThis study elucidates political networking in emerging economies and contributes to research on corporate political strategy.
Ontology-based heuristic patent search
Authors: Phan Cong-Phuoc , Nguyen Hong-Quang , Nguyen Tan-Tai 
Published: December 2018

Purpose
Large collections of patent documents disclosing novel, non-obvious technologies are publicly available and beneficial to academia and industries. To maximally exploit its potential, searching these patent documents has increasingly become an important topic. Although much research has processed a large size of collections, a few studies have attempted to integrate both patent classifications and specifications for analyzing user queries. Consequently, the queries are often insufficiently analyzed for improving the accuracy of search results. This paper aims to address such limitation by exploiting semantic relationships between patent contents and their classification.

Design/methodology/approach
The contributions are fourfold. First, the authors enhance similarity measurement between two short sentences and make it 20 per cent more accurate. Second, the Graph-embedded Tree ontology is enriched by integrating both patent documents and classification scheme. Third, the ontology does not rely on rule-based method or text matching; instead, an heuristic meaning comparison to extract semantic relationships between concepts is applied. Finally, the patent search approach uses the ontology effectively with the results sorted based on their most common order.

Findings
The experiment on searching for 600 patent documents in the field of Logistics brings better 15 per cent in terms of F-Measure when compared with traditional approaches.

Research limitations/implications
The research, however, still requires improvement in which the terms and phrases extracted by Noun and Noun phrases making less sense in some aspect and thus might not result in high accuracy. The large collection of extracted relationships could be further optimized for its conciseness. In addition, parallel processing such as Map-Reduce could be further used to improve the search processing performance.

Practical implications
The experimental results could be used for scientists and technologists to search for novel, non-obvious technologies in the patents.

Social implications
High quality of patent search results will reduce the patent infringement.

Originality/value
The proposed ontology is semantically enriched by integrating both patent documents and their classification. This ontology facilitates the analysis of the user queries for enhancing the accuracy of the patent search results.
“It’s not black and white”
Authors: Crawford Sharinne , Hokke Stacey , Nicholson Jan M. , Zion Lawrie , Lucke Jayne , Keyzer Patrick , Hackworth Naomi 
Published: December 2018

PurposeThe internet offers an opportunity for researchers to engage participants in research in a cost-effective and timely manner. Yet the use of the internet as a research tool (internet research) comes with a range of ethical concerns, and the rapidly changing online environment poses challenges for both researchers and ethics committees. The purpose of this paper is to highlight the key ethical issues of using the internet to recruit, retain and trace participants in public health research, from the perspectives of researchers and human research ethics committee (HREC) members.Design/methodology/approachThis study employed a qualitative design using semi-structured interviews with eight public health researchers and seven HREC members in Australia to explore the key ethical issues of using the internet to engage research participants.FindingsThe study identified commonalities between researchers and HREC members regarding the utility and ethical complexity of using the internet to recruit, retain and trace research participants. The need for guidance and support regarding internet research, for both groups, was highlighted, as well as the need for flexibility and responsiveness in formal ethical processes.Originality/valueThis research contributes to the understanding of how the internet is used to engage participants in public health research and the ethical context in which that occurs. Supporting the ethical conduct of internet research will benefit those involved in research, including researchers, HRECs, organisations and research participants.
Online product category and pricing strategies of land-based retailers
Authors: Wu Jin-Feng , Chang Ya Ping , Yan Jun , Hou De-Lin 
Published: December 2018

Purpose
The purpose of this paper is to understand how two online marketing orientations of land-based retailers in product category and price could change retail brand attitude when retail brand familiarities differ.

Design/methodology/approach
This paper proposes a research model with two orientations in product category and price as antecedents of retail brand attitude change and retail brand familiarity as a moderator. Empirical data were collected from 684 shoppers across three land-based retailers to test the research hypotheses.

Findings
Both orientations in product category and price can improve customers’ retail brand attitudes. Retail brand familiarity plays a significant moderator in some of the situations. Online-offline product category congruence and online-prototypical price congruence have significantly positive effects on retail brand attitude change whether retail brand familiarity is high or low. The effect of online-offline price congruence is significant only among high-familiarity customers, while the effect of online-prototypical product category congruence is found to be significant only among low-familiarity customers.

Research limitations/implications
The study identifies the moderating effects of retail brand familiarity on the relationships between two online marketing orientations in product category and price and retail brand attitude change. Based on the moderating effects, this study will help researchers to better understand the effectiveness of two online marketing orientations subject to varying degrees of retail brand familiarity in a multichannel retailing context.

Practical implications
The findings of this study can guide land-based retailers to focus on the right orientations in product category and price to improve customers’ attitudes toward the retail brand when existing or new customers are targeted.

Originality/value
This study provides a first study to empirically assess the change in retail brand attitude prompted by homogenous and prototypical orientations in product category and price and subject to varying degrees of retail brand familiarity. Overall, the results offer insights of how land-based retailers could manage their overall performance by designing more effective online product category and pricing strategies for existing or new customers.
The impact of GST implementation on the Malaysian stock market index volatility
Authors: Haron Razali , Ayojimi Salami Mansurat 
Published: December 2018

Purpose
The purpose of this paper is to examine the impact of the Goods and Service Tax (GST) implementation on Malaysian stock market index.

Design/methodology/approach
This study used daily closing prices of the Malaysian stock index and futures markets for the period ranging from June 2009 to November 2016. Empirical estimation is based on the generalised autoregressive conditional heteroscedasticity (1, 1) model for pre- and post-announcement of the GST.

Findings
Result shows that volatility of Malaysian stock market index increases in the post-announcement than in the pre-announcement of the GST which indicates that educative programs employed by the government before the GST announcement did not yield meaningful result. The volatility of the Malaysian stock market index is persistent during the GST announcement and highly persistent after the implementation. Noticeable increase in post-announcement is in support with the expectation of the market about GST policy in Malaysia.

Practical implications
The finding of this study is consistent with expectation of the market that GST policy will increase the price of the goods and services and might reduce standard of living. This is supported by a noticeable increase in the volatility of the Malaysian stock market index in the post-announcement of GST which is empirically shown during the announcement and after the implementation of GST. Although the GST announcement could be classified as a scheduled announcement, unwillingness to accept the policy prevails in the market as shown by the increase in the market volatility.

Originality/value
Past studies on Malaysian stock market index volatility focus on the impact of Asian and global financial crisis whereas this study examines the impact of the GST announcement and implementation on the volatility of the Malaysian stock market index.
A new weighted fuzzy information axiom method in production research
Authors: Cebi Selcuk , Kahraman Cengiz 
Published: December 2018

Purpose
The purpose of this paper is to propose a novel weighting algorithm for fuzzy information axiom (IA) and to apply it to the evaluation process of 3D printers.

Design/methodology/approach
As a decision-making tool, IA method is presented to evaluate the performance of any design. Then, weighted IA methods are investigated and a new weighting procedure is introduced to the literature. Then, the existing axiomatic design methods and the proposed new method are classified into two groups: weighting based on information content and weighting based on design ranges. The weighting based on information content approach consists of four methods including pessimistic and optimistic approaches. The philosophy of the weighting based on design ranges is to narrow design ranges in order to decrease fuzziness in the model. To prove the robustness and the performance of the proposed weighting method, the results are compared with the existing methods in the literature. Then, the new approach is applied to evaluate 3D printers.

Findings
The results of the proposed study show that the proposed weighting algorithm has better performance than the old ones for IA. Therefore, the proposed weighting algorithm should be used for the weighting tool of IA thereafter.

Originality/value
An effective weighting method compatible with the philosophy of IA method has been proposed. Furthermore, the performances of 3D printers are compared by using the proposed method.
Facing disruptive technologies: aligning purchasing maturity to contingencies
Authors: Søgaard Britta , Skipworth Heather Dawn , Bourlakis Michael , Mena Carlos , Wilding Richard 
Published: December 2018

PurposeThis paper aims to explore how purchasing could respond to disruptive technologies by examining the assumptions underlying purchasing strategic alignment and purchasing maturity through a contingency lens.Design/methodology/approachThis study uses a systematic review across purchasing maturity and purchasing strategic alignment literature. This is supplemented with exploratory case studies to include practitioners’ views.FindingsThis research demonstrates that neither purchasing maturity nor purchasing strategic alignment are suitable approaches to respond to disruptive technologies. Purchasing maturity does not allow purchasing managers to select relevant practices. It also shows no consideration of any contingencies, which practitioners highlight as important for the selection of practices. Purchasing strategic alignment includes the company strategy as a contingency but does not provide any practices to choose from. It does not include any other contextual contingencies considered important by practitioners. The findings indicate that linking the two research streams may provide a more suitable approach to responding to disruptive technologies.Research limitations/implicationsThis research demonstrates the requirement to develop a new approach to responding to disruptive technologies, by linking purchasing maturity and purchasing strategic alignment to contextual contingencies. This is a currently unexplored approach in academic literature, which refutes the generally accepted premise that higher maturity unilaterally supports a better positioning towards technological disruption. This research also highlights a requirement for practitioners to shift their approach to “best practices”.Originality/valueThis is the first research to systematically review the relationships between purchasing maturity and purchasing strategic alignment. It adds to contingency theory by suggesting that purchasing maturity models can support the achievement of strategic alignment. Also, future research directions are suggested to explore these relationships.