bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of a neutral peptide aptamer scaffold to anchor BH3 peptides constitutes a viable approach to studying their function
Authors: Stadler L K J , Tomlinson D C , Lee T , Knowles M A , Ko Ferrigno P 
Published: January 2014

AbstractThe B-cell CLL/lymphoma-2 (Bcl-2) family of proteins are important regulators of the intrinsic pathway of apoptosis, and their interactions, driven by Bcl-2 homology (BH) domains, are of great interest in cancer research. Particularly, the BH3 domain is of clinical relevance, as it promotes apoptosis through activation of Bcl-2-associated x protein (Bax) and Bcl-2 antagonist killer (Bak), as well as by antagonising the anti-apoptotic Bcl-2 family members. Although investigated extensively in vitro, the study of the BH3 domain alone inside cells is more problematic because of diminished secondary structure of the unconstrained peptide and a lack of stability. In this study, we report the successful use of a novel peptide aptamer scaffold – Stefin A quadruple mutant – to anchor and present the BH3 domains from Bcl-2-interacting mediator of cell death (Bim), p53 upregulated modulator of apoptosis (Puma), Bcl-2-associated death promoter (Bad) and Noxa, and demonstrate its usefulness in the study of the BH3 domains in vivo. When expressed intracellularly, anchored BH3 peptides exhibit much the same binding specificities previously established in vitro, however, we find that, at endogenous expression levels, Bcl-2 does not bind to any of the anchored BH3 domains tested. Nonetheless, when expressed inside cells the anchored PUMA and Bim BH3 α-helices powerfully induce cell death in the absence of efficient targeting to the mitochondrial membrane, whereas the Noxa helix requires a membrane insertion domain in order to kill Mcl-1-dependent myeloma cells. Finally, the binding of the Bim BH3 peptide to Bax was the only interaction with a pro-apoptotic effector protein observed in this study.
A microarray for assessing transcription from pelagic marine microbial taxa
Authors: Shilova Irina N , Robidart Julie C , Tripp H James , Turk-Kubo Kendra , Wawrik Boris , Post Anton F , Thompson Anne W , Ward Bess , Hollibaugh James T , Millard Andy , Ostrowski Martin , Scanlan David J , Paerl Ryan W , Stuart Rhona , Zehr Jonathan P 
Published: January 2014

AbstractMetagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world’s oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
Conditional inference tree‐based analysis of hazardous traffic conditions for rear‐end and sideswipe collisions with implications for control strategies on freeways
Authors: Li Zhibin , Wang Wei , Chen Ruoyun , Liu Pan 
Published: January 2014

Identifying hazardous traffic conditions related to traffic collisions is important to the development of real‐time traffic control measures for preventing collision occurrences. The primary objective of this study is to explore the hazardous traffic situations on freeways for rear‐end and sideswipe collisions to assist the development of control strategies for mitigating collision risks using the conditional inference tree method. Based on the 3‐year crash data and traffic data from a freeway corridor on the Interstate 880 in California, the conditional inference tree was developed and validated for each collision type separately. Results showed that the hazardous traffic conditions were different between different types of collisions. The occurrence of rear‐end collision was mainly related to the magnitude of lengthwise traffic variation between upstream and downstream locations. The occurrence of sideswipe collision was related to the type of freeway segment as well as the crosswise traffic variation between adjacent lanes. The control strategies for the mitigation of collision potentials were discussed according to the appearances of the conditional inference trees developed in this study.
Calcium chloride electron injection/extraction layers in organic electronic devices
Authors: Qu Bo , Gao Zhi , Yang Hongsheng , Xiao Lixin , Chen Zhijian , Gong Qihuang 
Published: January 2014

Nontoxic calcium chloride (CaCl2) was introduced into organic electronic devices as cathode buffer layer (CBL). The turn-on voltage and maximum luminance of organic light-emitting diode (OLED) with 1.5 nm CaCl2 was 3.5 V and 21 960 cd/m2, respectively. OLED with 1.5 nm CaCl2 possessed comparable electroluminescent characteristics to that of the commonly used LiF. Moreover, the performance of the organic photovoltaic device with 0.5 nm CaCl2 was comparable to that of the control device with LiF. Therefore, CaCl2 has the potential to be used as the CBL for organic electronic devices.
Physical constraints determine the logic of bacterial promoter architectures
Authors: Ezer Daphne , Zabet Nicolae Radu , Adryan Boris 
Published: January 2014

Abstract
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA) when searching for their target sites. Using computer simulations of this search process, we show that the organization of the binding sites, in conjunction with TF copy number and binding site affinity, plays an important role in determining not only the steady state of promoter occupancy, but also the order at which TFs bind. These effects can be captured by facilitated diffusion-based models, but not by standard thermodynamics. We show that the spacing of binding sites encodes complex logic, which can be derived from combinations of three basic building blocks: switches, barriers and clusters, whose response alone and in higher orders of organization we characterize in detail. Effective promoter organizations are commonly found in the E. coli genome and are highly conserved between strains. This will allow studies of gene regulation at a previously unprecedented level of detail, where our framework can create testable hypothesis of promoter logic.
The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria
Authors: Gunnelius Liisa , Hakkila Kaisa , Kurkela Juha , Wada Hajime , Tyystjärvi Esa , Tyystjärvi Taina 
Published: January 2014

AbstractThe eubacterial RNA polymerase core, a transcription machinery performing DNA-dependent RNA polymerization, consists of two α subunits and β, β′ and ω subunits. An additional σ subunit is recruited for promoter recognition and transcription initiation. Cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the RNA polymerase (RNAP) core due to splitting of the β′ subunit to N-terminal γ and C-terminal β′ subunits. The physiological roles of the small ω subunit of RNAP, encoded by the rpoZ gene, are not yet completely understood in any bacteria. We found that although ω is non-essential in cyanobacteria, it has a major impact on the overall gene expression pattern. In ΔrpoZ strain, recruitment of the primary σ factor into the RNAP holoenzyme is inefficient, which causes downregulation of highly expressed genes and upregulation of many low-expression genes. Especially, genes encoding proteins of photosynthetic carbon concentrating and carbon fixing complexes were down, and the ΔrpoZ mutant showed low light-saturated photosynthetic activity and accumulated photoprotective carotenoids and α-tocopherol. The results indicate that the ω subunit facilitates the association of the primary σ factor with the RNAP core, thereby allowing efficient transcription of highly expressed genes.
Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data
Authors: Sun Guoli , Krasnitz Alexander 
Published: January 2014

AbstractBackgroundOne of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measure, applicable to all branches and across multiple scales of dissimilarity.ResultsWe formulate a method termed Tree Branches Evaluated Statistically for Tightness (TBEST) for identifying significantly distinct tree branches in hierarchical clusters. For each branch of the tree a measure of distinctness, or tightness, is defined as a rational function of heights, both of the branch and of its parent. A statistical procedure is then developed to determine the significance of the observed values of tightness. We test TBEST as a tool for tree-based data partitioning by applying it to five benchmark datasets, one of them synthetic and the other four each from a different area of biology. For each dataset there is a well-defined partition of the data into classes. In all test cases TBEST performs on par with or better than the existing techniques.ConclusionsBased on our benchmark analysis, TBEST is a tool of choice for detection of significantly distinct branches in hierarchical trees grown from biological data. An R language implementation of the method is available from the Comprehensive R Archive Network:cran.r-project.org/web/packages/TBEST/index.html.
Learn and thou shall thrive: advancing a model of workplace familism and organizational learning capability in small and medium enterprise (SMEs) manufacturers in Malaysia
Authors: Char Fei Ho Theresa , Hazlina Ahmad Noor , Thurasamy Ramayah 
Published: January 2014

Purpose
– This paper proposes a conceptual framework that would be able to explain the importance of workplace familism on business performance through an organizational learning capability as a mediator.

Design/methodology/approach
– A conceptual approach is taken whereby this paper is based on an extensive literature review of workplace familism and organizational learning capability. Four prepositions were proposed to highlight the focus of this study which is how workplace familism can be capitalized through organizational learning capability to enhance SMEs business performance.

Findings
– This paper provides a theoretical discussion on the importance of organizational learning capability in ensuring the survival of the family business. The concept of workplace familism are relatively new, hence, it offers an interesting avenue for further research especially in the Malaysian context.

Practical implications
– The paper draws attention to the importance of workplace familism and learning organization in fostering entrepreneurial survival and performance among SMEs.

Originality/value
– This paper shed some insight on the subject on workplace familism and organizational learning capability in small and medium enterprise (SMEs) which hopefully would attract scholars and researchers to pursue more research on this area.
How much did the return of rural migrant labor affect China's national economy?
Authors: Jia Wei , Liu Xiaoyun 
Published: January 2014

Purpose
– What this paper aims to tackle is how much did the return of rural migrant labor during the financial crisis affect China's GDP and the growth rate of the national economy.

Design/methodology/approach
– This paper constructs a computable general equilibrium (CGE) model and uses data of China's 2007 Input-Output Table to analyze the impact of the return of rural migrant labor on China's economy during the financial crisis.

Findings
– The results show that the return of rural migrant labor during the financial crisis had substantial impacts on China's economy. The national GDP decreased by about 0.499-1.463 percent, mainly due to the number of rural labor who migrated from the non-agricultural sector to agriculture. Of the major sectors of economy, the manufacturing, construction and other services sectors were the most affected.

Originality/value
– This paper assesses the impacts of return of rural migrant labor during the financial crisis on China's GDP and the growth rate of the national economy.
Rural-urban income gap and agricultural growth in China
Authors: Gao Yanyan , Zheng Jianghuai , Bu Maoliang 
Published: January 2014

Purpose– This paper aims to investigate the effect of rural-urban income gap on agricultural growth in China and its dynamics over time and across regions since reform and opening up.Design/methodology/approach– Two types of indices are constructed to measure the rural-urban income gap: the intra-provincial index and the inter-provincial index. A provincial panel data from 1978 to 2010 and growth accounting method are used to estimate the size of the adverse effect of rural-urban income gap on agricultural growth in China.Findings– The empirical results show that both indices of rural-urban income gaps are negatively associated with agriculture output, but the inter-provincial rural-urban income gap produces a larger adverse effect than the intra-provincial rural-urban income gap. Growth accounting analysis further shows that such adverse effects are decreasing over time and are larger in the central provinces. The results represent resource diversion effects of rural-urban income gap on agriculture.Originality/value– This paper bridges the gap in existing literature on the relationship between sectoral income gaps and agricultural growth, which confirms Schultz's argument that agricultural activities are efficient even in developing countries and the rural resources diverted out by income gap are not surplus. The results imply that equalized rural-urban and regional policies are required to maintain sustainable agricultural growth in China.
Study on the survival of China agri-food export trade relationships
Authors: Tian Dongwen , Li Rui , Yao Wei , Huang Li 
Published: January 2014

Purpose
– The purpose of this paper is to study whether, of China's food and agriculture (agri-food) export, the trade relationships along the extensive margin can transform into short-term ones, and further convert into long-term ones along the intensive margin with survival and maintenance, especially, under what kind of conditions these transformation realize successfully, and what the factors are and how they impact on the length of the trade relationships duration.

Design/methodology/approach
– The paper comprises three stages: decomposing China's agricultural export data (1999-2008) into highly disaggregated three distinct parts; with the Kaplan-Meier (KM) nonparametric estimation, discovering the practical source of stable and long-term export growth, and the threshold at which the short-run trade relationships deriving from newly established ones convert into long-run ones successfully; by semi parametric estimation through Cox proportional hazard model, preliminarily examining the possible impact of different factors on the trade relationship's hazard rate and duration.

Findings
– The paper reveals that China agri-food trade pattern at the product level is surprisingly dynamic with newly established trade relations being more likely to fail. While the frequent volatilities of short-term relations at the extensive margin could be used to evaluate the source of short-term export growth especially and effectively, the pattern of negative dependence together with the threshold effect of duration indicates, only when these short-term relations live longer than four years will they substantially contribute to a stable and prolonged export growth. Simultaneously, trade duration significantly correlates to importing country's development status, region it belongs to, product processing degree, export experience and geographical space between trading partners.

Research limitations/implications
– To avoid the likelihood of misleading when estimating quantitatively the source of long-term export growth, researchers should be cautious in accurately evaluating the impacts of all possible factors on the two trade margins' performances, which is beyond the scope of this paper though, and a matter of ongoing work on the research agenda.

Practical implications
– The study presents a set of important policy implications. Now that turnovers along the extensive margin have little impact on long-term China agri-food export growth, it turns out that improving export survival would result in significantly higher and stable export growth.

Originality/value
– By distinguishing the survival of trade relationship channels from their deepening, the discoveries in the paper are crucial to understand the different role the intensive and extensive margins play in China agri-food export growth. The diversified hazard rates of export relations in different duration intervals suggest that the constant hazard rate assumption in Melitz and Bernard et al. is in some sense not appropriate.
Steadying the ladder
Authors: Z. Chen Kevin , Hsu Claire , Fan Shenggen 
Published: January 2014

Purpose– This paper aims to draw lessons from China's development experiences, particularly in the areas of agricultural and rural development, to increase growth and reduce poverty in Africa South of the Sahara. It also examines China's rising economic involvement in Africa and makes recommendations for how the win-win outcomes from this engagement can be strengthened.Design/methodology/approach– In this paper, the authors compare the trends in economic and agricultural growth, as well as poverty and hunger reduction, in China and Africa South of the Sahara. The authors then examine strategies for development – in particular agricultural and rural development – and poverty reduction. Next, the authors review China's economic engagement in Africa in the areas of trade, investment, aid, and technical cooperation.Findings– Having conducted a comparative review of China and Africa's distinct development paths and current policy contexts, the authors discuss China's development lessons for Africa South of the Sahara and policy recommendations for China-Africa engagement related to agricultural and rural development, openness and liberalization, evidence-based policymaking, pro-poor policies, institutions and capacity, rising inequality, and environmental degradation.Originality/value– This paper rigorously integrates China's positive and negative development lessons for Africa in light of the most recent research on emerging domestic and international development strategies.
Assessing Korean consumers' valuation for domestic, Chinese, and US rice
Authors: Yong Lee Ji , Bong Han Doo , M. Nayga Jr Rodolfo , Min Yoon Jong 
Published: January 2014

Purpose
– The purpose of this paper is to assess Korean consumers' valuation for domestic rice and imported rice from China and the USA.

Design/methodology/approach
– In order to identify Korean consumers' willingness to pay (WTP) for domestic, Chinese, and US rice, the non-hypothetical experimental auction approach (i.e. the random nth price auction) was utilized. Auction participants were randomly assigned to three treatments: no labelling information, country of origin labelling information, and food miles labelling information to analyze the effects of differing labelling information on consumers' valuation.

Findings
– The results suggest that Korean consumers have a positive perception of and preference for domestic rice, particularly when country of origin information is provided. However, food miles information alone may not help consumers to distinguish between domestic and Chinese rice.

Originality/value
– The marketing of imported rice will increase since Korea will be opening its rice market under tariffication after 2015. Therefore, it is necessary for Korea and other exporting countries to identify the feasibility of marketing both domestic and imported rice, and also to investigate which rice from specific countries Korean consumers prefer. Therefore, the authors conducted the random nth price auction using real rice products and cash in transactions.
Quantifying the benefits associated with the use of alternative marketing arrangements by US farmers
Authors: Hu Wu-Yueh , Phaneuf Daniel , Zheng Xiaoyong 
Published: January 2014

Purpose
– The purpose of this paper is to quantify the benefits to farmers from using alternative marketing arrangements (AMAs) in the USA. The authors first estimate a behavioral model explaining farmers' joint decisions on which commodities to produce and which marketing channels to use when selling their outputs. The authors then use the estimated model to quantify the benefits to farmers from using AMAs.

Design/methodology/approach
– The authors use the discrete choice random utility maximization model to examine farmers' choices on production regimes, where a regime is defined as a possible combination of all the individual commodity/marketing arrangement channels that the farmer can choose to use. The farmer is assumed to compare the utilities he gets from each of the possible production regimes and then selects the production regime that yields the highest utility to him. The benefit of having access to a particular AMA is measured as the negative of the welfare loss associated with forcing the farmer to abandon that particular AMA.

Findings
– The results indicate that AMAs yield an economically significant amount of benefits to farmers who rely on them to market their outputs. At the national level, the benefit of using production contracts to hog farmers is valued at $336.4 million. The benefits of using marketing contracts are valued at $374.2, $156.6 and $92.1 million for corn, soybeans and wheat producers.

Originality/value
– The paper is the first study that uses the farm-level data to study the welfare effects of marketing contracts in the grain sector. The results show that considering a multi-enterprises farm, farmers' welfare loss might be smaller when the hog production contract is no longer existed.