bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
Authors: Sundaramoorthy Ramasubramanian , Hughes Amanda L. , Singh Vijender , Wiechens Nicola , Ryan Daniel P. , El-Mkami Hassane , Petoukhov Maxim , Svergun Dmitri I. , Treutlein Barbara , Fischer Monika , Michaelis Jens , Böttcher Bettina , Norman David G. , Owen-Hughes Tom 
Published: November 2016

AbstractThe yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.
Kinetics of multi-substrate inBeauveriabassiana JUCHE22
Authors: Mondal Subhoshmita , Majumdar Sarangam 
Published: November 2016

ABSTRACTThe pattern of the biomass specific growth rate is an important focus for many biotechnological applications. Several control strategies have been employed to describe version of the exponential phase of growth of microorganisms. Moreover, in some bioprocesses there is more than one feeding substrates required for the specific growth. Hence, the problem of estimating multiple substrate consumption rates together with the specific growth rate of the microorganism becomes applicable. In this context, the dynamics behaviour of fed-batch process with multiple substrates (dextrose and peptone) and kinetics is further investigated inBeauveria bassiana. Different features of the proposed model are assessed by numerical simulation in different scenarios.
Ecological Interactions and the Netflix Problem
Authors: Desjardins-Proulx Philippe , Laigle Idaline , Poisot Timothée , Gravel Dominique 
Published: November 2016

0AbstractSpecies interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore theKnearest neighbour approach, with a special emphasis on recommendation, along with other machine learning techniques. Recommenders are algorithms developed for companies like Netflix to predict if a customer would like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. We also explore how theKnearest neighbour approach can be used with both positive and negative information, in which case the goal of the algorithm is to fill missing entries from a matrix (imputation). By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for theKnearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized to ecology to improve theKNN algorithms and using richer data to capture indirect relationships between species.
Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacteriumProteus mirabilisstrain SCDR1
Authors: Saeb Amr T. M. , Al-Rubeaan Khalid A. , Abouelhoda Mohamed , Selvaraju Manojkumar , Tayeb Hamsa T. 
Published: November 2016

AbstractBackgroundP. mirabilisis a common uropathogenic bacterium that can cause major complications in patients with long-standing indwelling catheters or patients with urinary tract anomalies. In addition,P. mirabilisis a common cause of chronic osteomyelitis in Diabetic foot ulcer (DFU) patients. We isolatedP. mirabilis SCDR1from a Diabetic ulcer patient. We examinedP. mirabilisSCDR1 levels of resistance against Nano-silver colloids, the commercial Nano-silver and silver containing bandages and commonly used antibiotics. We utilized next generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis and pathogenomics in the characterization of the infectious pathogen.ResultsP. mirabilis SCDR1is a multi-drug resistant isolate that also showed high levels of resistance against Nano-silver colloids, Nano-silver chitosan composite and the commercially available Nano-silver and silver bandages. TheP. mirabilis-SCDR1 genome size is 3,815,621 bp. with G+C content of 38.44%.P. mirabilis-SCDR1 genome contains a total of 3,533 genes, 3,414 coding DNA sequence genes, 11, 10, 18 rRNAs (5S, 16S, and 23S), and 76 tRNAs. Our isolate contains all the required pathogenicity and virulence factors to establish a successful infection.P. mirabilisSCDR1 isolate is a potential virulent pathogen that despite its original isolation site, wound, it can establish kidney infection and its associated complications.P. mirabilis SCDR1contains several mechanisms for antibiotics and metals resistance including, biofilm formation, swarming mobility, efflux systems, and enzymatic detoxification.ConclusionP. mirabilis SCDR1is the first reported spontaneous Nanosilver resistant bacterial strain.P. mirabilisSCDR1 possesses several mechanisms that may lead to the observed Nanosilver resistance.
Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation
Authors: Belaghzal Houda , Dekker Job , Gibcus Johan H. 
Published: November 2016

ABSTRACTChromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and TADs, as well as high-resolution conformational features such as DNA loops.
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance
Authors: Emad Amin , Woese Carl R. , Cairns Junmei , Kalari Krishna R. , Wang, M.D. Liewei , Sinha Saurabh 
Published: November 2016

ABSTRACTBackgroundIdentification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characterization of the mechanism of action of drugs. Furthermore, screening the expression of these genes in the tumor tissue may suggest the best course of chemotherapy or a combination of drugs to overcome drug resistance.ResultsWe developed a computational method called ProGENI to identify genes most associated with the variation of drug response across different individuals, based on gene expression data. In contrast to existing methods, ProGENI also utilizes prior knowledge of protein-protein and genetic interactions, using random walk techniques. Analysis of two relatively new and large datasets including gene expression data on hundreds of cell lines and their cytotoxic responses to a large compendium of drugs reveals a significant improvement in prediction of drug sensitivity using genes identified by ProGENI compared to other methods. Our siRNA knockdown experiments on ProGENI-identified genes confirmed the role of many new genes in sensitivity to three chemotherapy drugs: cisplatin, docetaxel and doxorubicin. Based on such experiments and extensive literature survey, we demonstrate that about 73% our top predicted genes modulate drug response in selected cancer cell lines. In addition, global analysis of genes associated with groups of drugs uncovered pathways of cytotoxic response shared by each group.ConclusionsOur results suggest that knowledge-guided prioritization of genes using ProGENI gives new insight into mechanisms of drug resistance and identifies genes that may be targeted to overcome this phenomenon.
Arusha women entrepreneur: reducing poverty through job creation and sustainable income for smallholder farmers
Authors: Calvo Sara , Morales Andres 
Published: November 2016

Subject area
Social enterprise.

Study level/applicability
This case study can be used on modules on social enterprise (SE) and international business for undergraduate and postgraduate studies.

Case overview
Arusha Women Entrepreneur (AWE) is a SE established in 2008 in Tanzania that employs low-income women from peri-urban Arusha and provides technical and management skills training to smallholder farmers. AWE has created a value supply chain from the production and marketing of aflatoxin-free, natural peanut butter, having a strong vision of delivering social and development benefits for smallholder peanut farmers and unemployed women.

Expected learning outcomes
This case is the basis for class discussion rather than for illustrating either effective or ineffective handling of a business. From this case, students will learn about the emergence and development of SEs and the challenges they encounter to grow.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS: 3: Entrepreneurship.
Staff perceptions and changing role of pre-hospital profession in the UK ambulance services
Authors: Wankhade Paresh 
Published: November 2016

PurposeThere is a growing academic interest in the examination and exploration of work intensification in a wide range of healthcare settings. The purpose of this paper is to explore the differing staff perceptions in emergency ambulance services in the UK. It provides evidence on the challenges for the paramedic professionalisation agenda and managing operational demands and work intensity in emotionally challenging circumstances, with significant implications for patient safety.Design/methodology/approachDrawing on the evidence from an empirical study in a large National Health Service ambulance trust in England, this paper examines the challenges and differing staff perceptions of the changing scope and practice of ambulance personnel in the UK. Amidst the progress on the professionalisation of the paramedic agenda, individual trusts are facing challenges in form of staff attitudes towards meeting performance targets, coupled with rising demand, fear of loss of contracts and private competition.FindingsResearch findings highlight differing perceptions from various sub-cultural groups and lack of clarity over the core values which are reinforced by cultural and management differences. Need for greater management to explore the relationship between high sickness levels and implications for patient safety including the need for policy and research attention follows from this study. The implications of work intensity on gender equality within the ambulance settings are also discussed.Research limitations/implicationsAmbulance services around the world are witnessing a strain on their operational budgets with increasing demand for their services. Study evidence support inconclusive evidence for patent safety despite the growing specialist paramedic roles. Organisational implications of high staff sickness rates have been largely overlooked in the management literature. This study makes an original contribution while building upon the earlier conceptions of work intensification.Practical implicationsThe study findings have significant implications for the ambulance services for better understanding of the staff perceptions on work intensity and implications for patient safety, high sickness absence rates amidst increasing ambulance demand. Study findings will help prepare the organisational policies and design appropriate response.Social implicationsSocietal understanding about the organisational implications of the work intensity in an important emergency response service will encourage further debate and discussion.Originality/valueThis study makes an original contribution by providing insights into the intra-organisational dynamics in an unusual organisational setting of the emergency ambulance services. Study findings have implications for further research inquiry into staff illness, patient safety and gender issues in ambulance services. Evidence cited in the paper has further relevance to ambulance services globally.
Assessment of emergency/disaster preparedness and awareness for animal owners in Canada
Authors: Onukem Mary 
Published: November 2016

PurposeThe purpose of this paper is to review the vulnerability and challenges faced by Canadian pet owners in times of disaster and evaluate emergency preparedness measures put in place to address the identified issues.Design/methodology/approachEmergency preparedness strategies from different countries were identified to weigh against Canada’s state of preparedness.FindingsPet/animal owners without emergency plans for their animals are more vulnerable than non-pet owners when they need to flee from disaster; and as Canada faces disaster challenges, proactive preparedness in emergency demands awareness, cooperation and commitment from everyone –governments, corporations, community groups and individuals become a necessity.Originality/valueBased on the identified need, the paper reviews strategies that engages pet owners in preparing for emergency in order to keep individuals and their communities safe. This paper will be beneficial to policy makers, researchers, health educators, scholars and emergency management professionals that read the journal.
Managerial and leadership implications of the retained duty system in English fire and rescue services
Authors: West Damien , Murphy Peter 
Published: November 2016

Purpose
The purpose of this paper is to explore the managerial and leadership challenges faced when managing personnel in the retained duty system (RDS) within English fire and rescue services. It examines the key areas of motivation, commitment, culture, relationships and practical management arrangements.

Design/methodology/approach
This exploratory research, using primary and secondary sources, adopted a deductive approach, incorporating questionnaires, interviews, focus groups and document analysis.

Findings
The research identified issues agreed upon by both employees and managers, and as well as areas of disparity and conflict. It also highlighted matters that appear to be pivotal to the successful management of a RDS, and in particular the importance of how roles are deployed, and managed by senior management, as well as how employees perceive them.

Practical implications
This paper offers recommendations regarding the managerial understanding and appreciation of an RDS as some managers in this research appear to have little or no knowledge of (or indeed a misconception of) key issues in the effective management of the RDS It suggests recommendations for the wider support and engagement of RDS personnel.

Originality/value
This paper offers a contemporary assessment of the challenges faced when managing RDS personnel. While firefighters and whole-time unionised firefighters in particular, have attracted interest from scholars of industrial relations, there has been relatively little academic research from a public management perspective.
Export market expansion through indirect learning: evidence from Korean exporters
Authors: Oh Han-Mo , Arnett Dennis B. , An Sang Bong 
Published: November 2016

PurposeA appreciable number of exporters have successfully developed their markets in foreign countries although they have little prior experience in those countries. Advocating that indirect learning plays a crucial role in explaining this phenomenon, the purpose of this paper is attempted to investigate whether and how learning indirectly from competitors and interfirm relationships enables exporters to successful expand their business into foreign markets.Design/methodology/approachDrawing on the knowledge-based theory of the firm and the late-mover advantage theory, the authors developed an empirically testable model that explains and predicts the effects of indirect learning on the success of export market expansion. The model was tested using a complied archival data set in regard to exporters’ market expansion events and international accounting. The sampling frame was the events of Korean exporters’ market expansion.FindingsEmpirical evidence shows that exporters’ indirect learning from domestic, local, global competitors and from interfirm relationships influence their success of market expansion. In addition, indirect learning from domestic rivals and from interfirm relationships has a more positive effect on the success of expansion into emerging markets than into developed markets.Research limitations/implicationsBecause the authors employed an event-study method, the limitations of this method can be applied to the present research. In addition, because of the empirical context, the results of the research may lack generalizability. The authors, however, provided an understanding how an exporter can succeed in a foreign market specifically when it has lack of direct experience in the market.Practical implicationsThe results of the current research suggested that an exporter should try to learn from local, domestic, and global rivals experienced in a foreign market in order to succeed in the market. In addition, exporters should be affiliated with business groups or partnerships because these affiliations can strengthen the information-sharing mechanisms. Moreover, an exporter should focus first on learning from local rivals and then domestic rivals in order to develop proper expansion strategies. Finally, an exporter should attempt to more actively learn from rivals and interfirm relationships when it targets an emerging market than a developed market.Originality/valuePrior studies have emphasized the effects of a firm’s direct learning on market development success. The authors, however, filled a knowledge gap of the impacts of learning in two aspects. First, the authors provided an understanding of the effects of indirect learning on market expansion success. Second, the authors demonstrated these effects in the context of export.
Impact of application factors of the AEO program on its performance
Authors: Chang-Bong Kim , Chun Hong-Uk , Kwon Seung-Ha 
Published: November 2016

Purpose
In a changing trade landscape, global trade transaction relies on a global supply-chain network. Customs clearance to cross borders is critical to enhancing the competitiveness of both importers and exporters. As such, each country has adopted an authorized economic operator (AEO) program to promote the security of both imported and exported cargo as well as expedite freight movements. The purpose of this paper is to discover the factors which should be taken into account to utilize an AEO program, and to look at the causal relations between these factors.

Design/methodology/approach
This study conducted a survey on 201 AEO programs in Korea. With partial least squares, the structure model is tested using the coefficient value of the determination of the dependent variable, explained by the sign and scale of the path coefficient, statistical significance, and leading variable. Moreover, this study performed bootstrap re-sampling to verify all paths and significance.

Findings
It was found that AEO external pressure, training capacity, and sustainability are shown to have a significant impact on AEO performance. Furthermore, for the group with a high level of AEO application, training capacity and AEO sustainability are shown to have a greater effect on AEO performance. For the group with a low level of AEO application, internal regulation is shown to have a bigger impact on AEO performance.

Originality/value
This study sets itself apart from previous ones in that it examines AEO application for trade security and facilitation with regard to customs, which would affect global supply-chain management.
Handling of production disturbances in the manufacturing industry
Authors: Bokrantz Jon , Skoogh Anders , Ylipää Torbjörn , Stahre Johan 
Published: November 2016

Purpose
A common understanding of what events to regard as production disturbances (PD) are essential for effective handling of PDs. Therefore, the purpose of this paper is to answer the two questions: how are individuals with production or maintenance management positions in industry classifying different PD factors? Which factors are being measured and registered as PDs in the companies monitoring systems?

Design/methodology/approach
A longitudinal approach using a repeated cross-sectional survey design was adopted. Empirical data were collected from 80 companies in 2001 using a paper-based questionnaire, and from 71 companies in 2014 using a web-based questionnaire.

Findings
A diverging view of 21 proposed PD factors is found between respondents in manufacturing industry, and there is also a lack of correspondence with existing literature. In particular, planned events are not classified and registered to the same extent as downtime losses. Moreover, the respondents are often prone to classify factors as PDs compared to what is actually registered. This diverging view has been consistent for over a decade, and hinders companies to develop systematic and effective strategies for handling of PDs.

Originality/value
There has been no in-depth investigation, especially not from a longitudinal perspective, of the personal interpretation of PDs from people who play a central role in achieving high reliability of production systems.