bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
Authors: Yu Fengchao , Li Ning , Yu Weichuan 
Published: December 2016

AbstractChemical cross-linking coupled with mass spectrometry is a powerful tool to study protein-protein interactions and protein conformations. Two linked peptides are ionized and fragmented to produce a tandem mass spectrum. In such an experiment, a tandem mass spectrum contains ions from two peptides. The peptide identification problem becomes a peptide-peptide pair identification problem. Currently, most existing tools don’t search all possible pairs due to the quadratic time complexity. Consequently, a significant percentage of linked peptides are missed. In our earlier work, we developed a tool named ECL to search all pairs of peptides exhaustively. While ECL does not miss any linked peptides, it is very slow due to the quadratic computational complexity, especially when the database is large. Furthermore, ECL uses a score function without statistical calibration, while researchers1,2have demonstrated that using a statistical calibrated score function can achieve a higher sensitivity than using an uncalibrated one.Here, we propose an advanced version of ECL, named ECL 2.0. It achieves a linear time and space complexity by taking advantage of the additive property of a score function. It can analyze a typical data set containing tens of thousands of spectra using a large-scale database containing thousands of proteins in a few hours. Comparison with other five state-of-the-art tools shows that ECL 2.0 is much faster than pLink, StavroX, ProteinProspector, and ECL. Kojak is the only one tool that is faster than ECL 2.0. But Kojak does not exhaustively search all possible peptide pairs. We also adopt ane-value estimation method to calibrate the original score. Comparison shows that ECL 2.0 has the highest sensitivity among the state-of-the-art tools. The experiment using a large-scalein vivocross-linking data set demonstrates that ECL 2.0 is the only tool that can find PSMs passing the false discovery rate threshold. The result illustrates that exhaustive search and well calibrated score function are useful to find PSMs from a huge search space.
Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography
Authors: Kim Doyeon , Oh Nuri , Kim Kyoohyun , Lee SangYun , Pack Chan-Gi , Park Ji-Ho , Park YongKeun 
Published: December 2016

AbstractDelivery of gold nanoparticles (GNPs) into live cells has high potentials, ranging from molecular-specific imaging, photodiagnostics, to photothermal therapy. However, studying the long-term dynamics of cells with GNPs using conventional fluorescence techniques suffers from phototoxicity and photobleaching. Here, we present a method for 3-D imaging of GNPs inside live cells exploiting refractive index (RI) as imaging contrast. Employing optical diffraction tomography, 3-D RI tomograms of live cells with GNPs are precisely measured for an extended period with sub-micrometer resolution. The locations and contents of GNPs in live cells are precisely addressed and quantified due to their distinctly high RI values, which was validated by confocal fluorescence imaging of fluorescent dye conjugated GNPs. In addition, we perform quantitative imaging analysis including the segmentations of GNPs in the cytosol, the volume distributions of aggregated GNPs, and the temporal evolution of GNPs contents in HeLa and 4T1 cells.AbbreviationsGNPsgold nanoparticlesRIrefractive indexODToptical diffraction tomographyDMDdigital micromirror device
Delivery of BACE1 siRNA mediated by TARBP-BTP fusion protein reduces β-amyloid deposits in a transgenic mouse model of Alzheimer’s Disease
Authors: Haroon Mohamed M , Saba Kamal , Boddeda Venkata H , Kumar Jerald M , Patel Anant Bahadur , Gopal Vijaya 
Published: December 2016

AbstractSystemic delivery of nucleic acids to the central nervous system (CNS) is a major challenge for the development of RNA interference-based therapeutics due to absence of stability, target specificity, non-permeability to the blood-brain barrier (BBB), and mainly due to lack of suitable carriers. Using a designed bi-functional fusion protein TARBP-BTP, very recently we demonstrated knockdown of target genes in the brain of both AβPP-PS1 (Alzheimer’s disease, AD) and wildtype C57BL/6 mice upon systemic delivery of a single dose of siRNA. In this report, we further substantiate this hypothesis through an extended study in AβPP-PS1 mice, which upon treatment with seven doses of β-secretase APP cleaving Enzyme 1 (BACE1) siRNA, led to target-specific effects in the mouse brain. Concomitant gene silencing and consequent reduction in plaque load in the cerebral cortex and hippocampus (>60%) in mice treated with TARBP-BTP:siRNA complex further led to improvement in spatial learning and memory, which was assessed and verified through Morris Water Maze test that revealed significant improvement in cognitive function. Moreover, the treatment did not induce any adverse effects as revealed by the histopathology of different organs. The work validates the efficiency of TARBP-BTP fusion protein as an efficient mediator of RNAi giving considerable scope for future intervention of neurodegenerative disorders of the CNS through the use of short nucleic acids as gene specific inhibitors.
The hippocampus as a predictive map
Authors: Stachenfeld Kimberly L. , Botvinick Matthew M. , Gershman Samuel J. 
Published: December 2016

ABSTRACTA cognitive map has long been the dominant metaphor for hippocampal function, embracing the idea that place cells encode a geometric representation of space. However, evidence for predictive coding, reward sensitivity, and policy dependence in place cells suggests that the representation is not purely spatial. We approach this puzzle from a reinforcement learning perspective: what kind of spatial representation is most useful for maximizing future reward? We show that the answer takes the form of a predictive representation. This representation captures many aspects of place cell responses that fall outside the traditional view of a cognitive map. Furthermore, we argue that entorhinal grid cells encode a low-dimensional basis set for the predictive representation, useful for suppressing noise in predictions and extracting multiscale structure for hierarchical planning.
Postmodern patriotism: teachers’ perceptions of loyalty to Singapore
Authors: Chua Shuyi , Sim Jasmine B.-Y. 
Published: December 2016

PurposeThe purpose of this paper is to explore humanities teachers’ perceptions of patriotism in Singapore by addressing two questions. First, what are teachers’ understandings of patriotism? Second, what are teachers’ attitudes toward patriotism as a quality of good citizenship?Design/methodology/approachThe qualitative case study approach was used, with semi-structured interviews and classroom observations as data sources. The participants were four teachers from diverse backgrounds with distinct perceptions of patriotism. Data analysis methods included writing teacher profiles and thematic coding.FindingsTeachers were generally positive toward patriotism and understood it in four ways: cosmopolitan, nationalistic, social-movement and person oriented. These themes were not mutually exclusive but distributed across the participants in varying extents. These findings show that patriotism is susceptible to individual meaning-making, and there are different scales and expressions of patriotism.Research limitations/implicationsThe results from this small case study cannot be generalized. However, owing to globalization, it is likely that alternative ways of understanding patriotism might become more widespread and salient in citizenship education. Hence, the authors recommend that more studies be conducted on larger samples and using other methods.Originality/valueThis study goes in-depth into a case where teachers had positive feelings toward patriotism, and it draws on the context of Singapore to understand how and why this is so. It also revealed conceptions of patriotism that differ from the more common constructs in the educational literature, suggesting that people from post-colonial countries with different histories, might conceive of patriotism differently from others.
Institutions do matter
Authors: Lui Luen Tim Percy 
Published: December 2016

Purpose
The purpose of this paper is to examine how institutional designs governing the executive-legislative relations in the Hong Kong Special Administrative Region (HKSAR) have weakened the government’s capacity to effectively govern the HKSAR.

Design/methodology/approach
This paper examines institutional designs and rules that govern Hong Kong’s executive-legislative relations. It uses the case of the HKSAR Legislative Council (LegCo) to illustrate the impacts of institutional designs and rules on the performance of political institutions and government performance.

Findings
This paper finds that institutional designs and rules do affect the performance of a political institution. This paper suggests changes to the institutional designs and rules that govern the operation of the HKSAR LegCo, and the interaction between the legislature and the executive so as to create a facilitative context for good governance.

Originality/value
Studies on governance in Hong Kong mostly focus on individual institution’s behavior and performance. This paper studies the problem of governance in Hong Kong from the perspective of executive-legislative relations. It adopts the institutional theory to examine the behavior, performance, and interaction between the legislative and executive branches.
The roles of internships in encouraging university students to join political parties
Authors: Ng Hoi-Yu 
Published: December 2016

PurposePolitical parties in Hong Kong are eager to recruit university students and internship programs are a major recruitment channel for them. However, studies on the influences of political internship programs on university students are few and have mainly been conducted in Western democracies. Therefore, the purpose of this paper is to explore the roles of political party internship programs in encouraging university and community college students to join political parties in Hong Kong, a semi-democratic autonomous region of China.Design/methodology/approachThis study is based on the insights gained from semi-structured interviews with a small sample of former party interns.FindingsThis paper found that party internship programs can play three major roles in encouraging students at higher education institutions to join a political party. They are: exposing students to the recruitment efforts of the party, helping students who have no political aspirations to generate a desire to join, and providing an opportunity for those already considering joining to ascertain if the party is really suitable for them.Originality/valueThis paper shows that political internships in semi-democratic regimes like Hong Kong can play similar roles as those in Western democracies to stimulate some university students to pursue a career in politics and help those already considering a political career to ascertain their goals. This paper also shows that these stimulating and confirming effects could also apply to the application for party membership.
Meta-analysis of business-related research in the former Warsaw Pact and the Soviet Union countries
Authors: Bureš Vladimír 
Published: December 2016

Purpose
Research focussed on various issues or perspectives of business can be considered as an important driving force for business development. The purpose of this paper is to identify the main topics and trends associated with business-related research conducted in Belarus, the Czech Republic, Estonia, Hungary, Latvia, Lithuania, Poland, Russia, Slovakia and Ukraine. The study results contribute to a context-aware explanation of the dynamics of business-oriented research in individual countries.

Design/methodology/approach
This study both quantitatively and semantically analyses 6,166 abstracts indexed and abstracted in the Scopus database. Three main research questions and associated hypotheses are investigated. Three text-mining techniques were applied in the analysis of available resources, namely, word clustering, collocation statistics and correspondence analysis.

Findings
There is a growing trend in the quantity of business-related research publications associated with each country. Similarly, there is an increasing internationalisation and intensification process of research networks. It is possible to identify both general and specific business topics that are investigated in individual countries.

Research limitations/implications
The time spans investigated do not always correspond with the main events occurring at the national level. From the semantic analysis perspective, the shortage of records for specific time periods prevents a valid semantic analysis, and the results are dependent on the quality of the abstracts provided by the authors. The study results might be used as support for funding decisions or context-aware evaluation of research outcomes at both institutional and national level.

Originality/value
This study provides a unique insight into the development and mutual comparison of business-related research in the countries investigated.
Impacts and adaptation to climate change in Malaysian real estate
Authors: Shahid Shamsuddin , Pour Sahar Hadi , Wang Xiaojun , Shourav Sabbir Ahmed , Minhans Anil , Ismail Tarmizi bin 
Published: December 2016

PurposeThere is a growing concern in recent years regarding climate change risks to real estate in the developed and developing countries. It is anticipated that the property sector could be affected by variable climate and related extremes as well as by the strategies adopted to combat greenhouse gas (GHG) emissions. This paper aims to analyse the current knowledge regarding future climate changes to understand their possible impacts on the real estate sector of Malaysia with an aim to help stakeholders to adopt necessary responses to reduce negative impacts.Design/methodology/approachAvailable literature is reviewed and data related to climatic influences on buildings and structures are analysed to understand the climate change impacts on real estate in Malaysia.FindingsThe study reveals that temperature in the Peninsular Malaysia will increase by 1.1 to 3.6°C, rainfall will be more variable and river discharge in some river basins will increase up to 43 per cent during the northeast monsoon season by the end of this century. These changes in turn will pose risks of property damage and increase property lifecycle costs. Furthermore, property prices and the overall growth of the property sector may be affected by the government policy of GHG emission reduction by up to 45 per cent by the year 2030. This study concludes that the property sector of Malaysia will be most affected by the implementation of GHG emission reduction policy in the short term and due to the physical risk posed by variable climate and related extremes in the long term.Originality/valueThe study in general will assist in guiding the operational responses of various authorities, especially in terms of those interventions aimed at climate change risk reduction in the property sector of Malaysia.
An investigation into the major environment and climate change policy issues in southwest coastal Bangladesh
Authors: Roy Anjan Kumer Dev 
Published: December 2016

Purpose
This paper aims to examine the issues of environment and climate change policy gaps and their impacts on the natural resources and ecosystems in southwest coastal Bangladesh. The effects of the increasing human activities as well as natural disasters due to the environment and climate change are analysed. The policy options as a response to mitigation, adaptation and possible human suffering as consequences are explored through discourse analysis.

Design/methodology/approach
This study applied focus group discussions, workshop and field visits to collect the data and information to explore environment and climate change policy-related problems.

Findings
It was found that there is a need for major policy reform to guide development interventions to reverse salinity, waterlogging, migration and groundwater recharging problems for sustainable environmental and ecosystem management in the region.

Originality/value
The paper then underscores the need for governments at all levels to adequately fund geo-information-based development interventions as adequate and proactive responses to environmental management and development to combat future environmental and climate change problems in the region.
Innovative approach to build a “no regret” framework for reinforcing agricultural water resilience under climate risks and change in Burkina Faso
Authors: Gahi Narcisse Zegbé , Dongo Kouassi , Koudou Aimé , Badolo Mathieu 
Published: December 2016

Purpose
This paper aims to propose, for the very first time in Burkina Faso, a “no regret” reference tool to improve policies and processes which could strengthen agricultural water resilience under climate risks and change for sustained food security. Such a framework consists of five pillars derived from the agricultural water vulnerability analysis.

Design/methodology/approach
The method combined a new designed tool “ClimProspect”, adapted to the Sahelian climatic context, participatory and analogue approaches.

Findings
Innovative “no regret” framework to overcome current and future climate risks on agricultural water requirements has been built.

Research limitations/implications
The paper proposes a new way to assess vulnerability and build resilience for a given system and brings climate and disaster risks together. In fact, in the country, disaster and climate risks are closely associated.

Practical implications
The proposed measures will reinforce water security under climate variability and change and disaster risks, boost the farmers’ participation in water governance and secure the adaptation investment for the long term.

Social implications
Implementing the proposed measures should provide farmers with agricultural water needs at any time over the year, having access to social protection and sustainably increase their food security.

Originality/value
Method used explicitly allows for paying attention, at the same time, to climate variability and change, disaster risks and social issues. The “no regret” framework is a practical secured tool for policy makers and planners, and it gives them a new way to secure sustainable water requirements.
Using nutraceuticals in the management of major depressive disorder (MDD)
Authors: Khalifa Nahlaa , Aljaaly Elham Abbas 
Published: December 2016

PurposeThe purpose of this paper is to study evidence-based records on the impact of some effective nutraceuticals on major depression disorder management; and describe the antidepressant properties of nutraceuticals to achieve health policy targets and maintain a sustainable healthcare system.Design/methodology/approachThe literature was searched using MEDLINE (PubMed), Google Scholar, PsycINFO and Quertile databases and retrieving relevant published articles in peer-reviewed journals.FindingsThe results provided evidence of a range of nutraceuticals with potential benefits in the management of depression. Studies support the anti-depressant properties of S-adenosyl methionine, folnic acid, 5-hydroxytryptophan and omega-3 fatty acids. The results might represent evidence for an innovative adjunctive neurobiological line for the management and treatment of depression.Practical implicationsRandomized-controlled trials and evaluations continue to provide evidence for the use of nutraceuticals in the treatment of depression.Social implicationsNutraceuticals emphasize the personalized medicine, which offers a psychophysical balance to the individual.Originality/valueNutraceuticals have specific antidepressant properties that may be beneficial in psychiatric populations and reduce pharmacotherapeutic side effects.
Artisanal gold mining’s impact on local livelihoods and the mining industry in Ivory Coast
Authors: Kouame Kouame Joseph Arthur , Jiang Fuxing , Sitao Zhu 
Published: December 2016

PurposeIn rural regions, mining is an activity that employs many people due to the fact that the barriers to entry are sometimes trivial, with very low technology, capital fund, and no specialized skills required. Many people including children are engaged in artisanal mining in Ivory Coast because they can earn higher incomes in mining than through other traditional activities such as agriculture, which is the main activity in the country. Artisanal mining contributes to reduce abject poverty prevalent in the country and it offers many others opportunities. However, this activity has many negative social impacts. Local people including miners are risking their lives everyday as they are exposed to unsanitary conditions, prostitution, chemical contaminants, and alcoholism, and also due to the large degradation of lands. The paper aims to discuss these issues.Design/methodology/approachAll the data collected during this study were analyzed before some of it was corrected. For data analysis and interpretation, the authors used Word and Excel and other software, and other statistical tools for maps, graphs, and tables.FindingsThe main objective of this paper is to understand how artisanal gold mining in the Ivory Coast affects local livelihoods and the environment.Research limitations/implicationsThis study was carried out during the author’s study in China. The data collection between the two countries was too difficult due to the long distance. Many times the network was not reliable for any call and discuss with miners when we are not in the country. The hesitation of miners to give real information to the authors was also a main problem because most of them are illegal miners. Some of the guided questionnaires stayed without feedback for almost three months. The production was sold on a day-to-day basis by the miners in the illegal mining sites, so the authors could not obtain with precision the monthly and annual production to calculate income of the miners.Originality/valueSome key recommendations for addressing artisanal mining activities in order to have a good option for sustainable management of mineral resources in the country are proposed.