bluuebunny/crossref_metadata_2025_split huggingface dataset:
A maximum entropy framework for nonexponential distributions
Authors: Peterson Jack , Dixit Purushottam D. , Dill Ken A. 
Published: December 2013

SignificanceMany statistical distributions, particularly among social and biological systems, have “heavy tails,” which are situations where rare events are not as improbable as would have been guessed from more traditional statistics. Heavy-tailed distributions are the basis for the phrase “the rich get richer.” Here, we propose a basic principle underlying systems with heavy-tailed distributions. We show that it is the same principle (maximum entropy) used in statistical physics and statistics to estimate probabilistic models from relatively few constraints. The heavy-tail principle can be expressed in terms of shared costs and economies of scale. The probability distribution we derive is a mathematical digamma function, and we show that it accurately fits 13 real-world data sets.
Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection
Authors: Grady Sarah L. , Purdy John G. , Rabinowitz Joshua D. , Shenk Thomas 
Published: December 2013

Significance
Virus infection can trigger profound alterations in host cell metabolism, but the role of individual enzymes in this process is relatively unstudied. Here, we show that argininosuccinate synthetase 1 (AS1) antagonizes the production of herpes simplex virus 1 (HSV-1) in cultured fibroblasts. Infection reduces the level of AS1 protein, and further reduction induced by siRNA treatment enhances the production of HSV-1. AS1 deficiency mimics many of the metabolic changes induced by HSV-1 infection, demonstrating that a decrease in the activity of a single cellular enzyme is responsible for much of the metabolic reprogramming induced by HSV-1. These results underscore the dependence of HSV-1 replication on altered host cell metabolism.
Mortality among Patients with Methicillin-ResistantStaphylococcus aureusUSA300 versus Non-USA300 Invasive Infections: A Meta-Analysis
Authors: Nair Rajeshwari , Ammann Eric , Rysavy Matthew , Schweizer Marin L. 
Published: December 2013

Background.Community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) has been found to be epidemiologically and microbiologically distinct from healthcare-associated MRSA. Most CA-MRSA infections are not invasive; however, fatal outcomes have been reported among healthy people with CA-MRSA invasive infections. Epidemiological studies have attributed a major burden of CA-MRSA infections in the United States to the predominant clone USA300. We investigated the association between USA300 invasive infections and mortality by conducting a systematic review and meta-analysis of studies that reported mortality rates associated with USA300 strains.Methods.We searched PubMed, bibliographies of other publications, and gray literature between January 2001 and December 2013. Observational studies of patients with an invasive MRSA infection were included. The exposure of interest was presence of USA300 invasive infection. Studies were included only if they provided MRSA PFGE types and if corresponding mortality data were the measured outcome. We pooled crude odds ratios (cORs) using a random-effects model. Woolf test of homogeneity andQandI2statistics were assessed.Results.Of 574 articles identified by the search strategy, 8 met the inclusion criteria. Risk of mortality was significantly lower among patients with USA300 MRSA infections (pooled cOR, 0.63 [95% confidence interval (CI)], 0.49–0.81). There was a moderate degree of heterogeneity among study results (P= .29;I2= 18%). Results were observed to be heterogeneous due to study design, quality of studies, and definition of mortality.Conclusions.MRSA invasive infection with USA300 does not appear to be associated with higher mortality compared with infections due to non-USA300 strains. Nevertheless, larger well-designed studies are warranted to further evaluate this association.
Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies
Authors: Cattoni Diego I. , Thakur Shreyasi , Godefroy Cedric , Le Gall Antoine , Lai-Kee-Him Josephine , Milhiet Pierre-Emmanuel , Bron Patrick , Nöllmann Marcelo 
Published: December 2013

Abstract
SpoIIIE/FtsK are a family of ring-shaped, membrane-anchored, ATP-fuelled motors required to segregate DNA across bacterial membranes. This process is directional and requires that SpoIIIE/FtsK recognize highly skewed octameric sequences (SRS/KOPS for SpoIIIE/FtsK) distributed along the chromosome. Two models have been proposed to explain the mechanism by which SpoIIIE/FtsK interact with DNA. The loading model proposes that SpoIIIE/FtsK oligomerize exclusively on SpoIIIE recognition sequence/orienting polar sequences (SRS/KOPS) to accomplish directional DNA translocation, whereas the target search and activation mechanism proposes that pre-assembled SpoIIIE/FtsK hexamers bind to non-specific DNA, reach SRS/KOPS by diffusion/3d hopping and activate at SRS/KOPS. Here, we employ single-molecule total internal reflection imaging, atomic force and electron microscopies and ensemble biochemical methods to test these predictions and obtain further insight into the SpoIIIE–DNA mechanism of interaction. First, we find that SpoIIIE binds DNA as a homo-hexamer with neither ATP binding nor hydrolysis affecting the binding mechanism or affinity. Second, we show that hexameric SpoIIIE directly binds to double-stranded DNA without requiring the presence of SRS or free DNA ends. Finally, we find that SpoIIIE hexamers can show open and closed conformations in solution, with open-ring conformations most likely resembling a state poised to load to non-specific, double-stranded DNA. These results suggest how SpoIIIE and related ring-shaped motors may be split open to bind topologically closed DNA.
Exploring DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data
Authors: Sawaya Sterling , Boocock James , Black Michael A. , Gemmell Neil 
Published: December 2013

AbstractPausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA structure. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. We have developed a new way to examine polymerase kinetics and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.Author SummaryDNA can be found in various forms that differ from the double-helix first discovered by Watson and Crick in 1953. These alternative DNA structures depend on the DNA sequence, and researchers continue to explore which sequences have the potential to form alternative structures. Here we advance the use of Pacific Biosciences sequencer data to explore potential alternative DNA structures. The Pacific Bio-sciences sequencer provides an unprecedented way to examine the interaction between DNA polymerase and DNA by following a single polymerase in real time as it copies a DNA molecule. The pausing of DNA polymerase is a common method for exploring the DNA sequences that have the potential to form alternative DNA structures, and Pacific Biosciences data has previously been used to measure polymerase pausing at a slipped strand structure. DNA polymerase is known to pause at some of these alternative structures, such as the structure known as the G-quadruplex, a DNA structure that has potentially importing regulatory significance. We examine polymerase kinetics around a G-quadruplex, and find evidence of polymerase pausing in the Pacific Biosciences kinetics. We provide a method, with publicly available code, so that others can examine these polymerase kinetics for any sequence of interest.
Data fusion and sensor selection from imperfect sources with regards to the operating environment
Authors: El-Mahassni Edwin 
Published: December 2013

Purpose
– The purpose of this paper is to extend the work of fusing sensors with a Bayesian method to incorporate the sensor's reliability with regard to their operating environment. The results are then to be used with the expected decision formula, conditional entropy and mutual information for suboptimally selecting which types of sensors should be fused where there are operational constraints.

Design/methodology/approach
– The approach is an extension of previous work incorporating an environment parameter. The expected decision formula then forms the basis for sensor selection.

Findings
– The author found that the performance of the sensors is correlated to the environment of operation, given that the likelihood of error will be higher in a difficult terrain than would otherwise be the case. However, the author also shows the sensors for fusion will vary if the author knows specifically which terrain the sensors will be operating in.

Research limitations/implications
– The author notes that in order for this technique to be effective, a proper understanding of the limitations of the sensors, possible terrain types and targets have to be assumed.

Practical implications
– The practical implication of this work is the ability to assess the performance of fused sensors according to the environment or terrain they might be operating under, thus providing a greater level of sensitivity than would otherwise be the case.

Originality/value
– The author has extended previous ideas on sensor fusion from imprecise and uncertain sources using a Bayesian technique, as well as developed techniques regarding which sensors should be chosen for fusion given payload or other constraints.
Segregation of children worldwide: the human rights imperative to end institutionalization
Authors: Rosenthal Eric , Ahern Laurie 
Published: December 2013

Purpose
– The purpose of this paper is to emphasize the human rights imperative to end the segregation of children in orphanages and other residential institutions.

Design/methodology/approach
– The paper draws on international human rights standards under the UN Convention on the Rights of Persons with Disabilities and other treaties, as well as documentation gathered by Disability Rights International (DRI) over the past 20 years.

Findings
– DRI has found that institutionalization of children exposes them to high risk of physical, sexual and emotional abuse. Even clean and well-staffed orphanages are psychologically damaging. Well intentioned but misguided donors often perpetuate institutionalization by investing in the building or rebuilding of institutions instead of investing in community-based alternatives.

Originality/value
– Through the Worldwide Campaign to End the Institutionalization of Children, DRI is calling for a moratorium on all new placements of children in orphanages. No new institutions should be built. Research shows that children thrive in a family or family-like environment, and all children are capable of being supported to live in the community.
E-business and process change: two case studies (towards an assessment framework)
Authors: Wynn Martin George , Turner Phillip , Lau Erin 
Published: December 2013

Purpose
– The purpose of this research paper is to explore the impacts of e-business technology adoption at process level in SMEs.

Design/methodology/approach
– The paper reviews a range of literature and mainstream models relating to e-business impacts in SMEs and then focuses on two in-depth case studies. The cases draw their empirical material from the involvement of the authors in e-business project management in these two companies.

Findings
– The two case studies show significant impacts of e-business technology at process level. They also illustrate how contrasting information systems strategies can successfully embrace e-business process change, and suggest the importance of organisational issues in determining the degree of benefits delivery.

Research limitations/implications
– The paper suggests a framework for analysing the impact of e-business at process level that can be used with other SME case studies.

Practical implications
– The suggested assessment framework can be used for comparison with e-business implementations in other SMEs.

Originality/value
– The value of the case studies lies in their originality and the paper highlights the potential impacts and benefits of e-business at process level. The suggested assessment framework builds on existing models and concepts but provides an update and customisation relevant to today's e-business technologies and business environment.
E-commerce trading activity and the SME sector: an FSB perspective
Authors: Pickernell David , Jones Paul , Packham Gary , Thomas Brychan , White Gareth , Willis Robert 
Published: December 2013

Purpose
– This study aims to examine e-commerce within UK small and medium sized enterprises (SMEs). More specifically, it seeks to explore associations between e-commerce and internal and external antecedents including trading behaviour, owner/manager characteristics, innovation, public sector involvement, business advice and finance sources.

Design/methodology/approach
– An 8,500+ sample derived from the 2008 UK Federation of Small Businesses survey was utilised. An OLS regression equation was generated where the percentage of sales made using e-commerce constituted the dependent variable. Independent variables were constructed for several sets of factors including innovation, business advice and sources of finance, as well as a range of owner and SME typology variables.

Findings
– The results suggest that e-commerce is more strongly apparent in SMEs started from scratch and where they were involved in basic or high knowledge services or the tourist trade. SMEs undertaking e-commerce were also associated with innovation in the form of copyright, as well as public procurement with local authorities and the university sector. Specific business advice in the form of capacity, family and suppliers was also associated with e-commerce trading.

Research limitations/implications
– These results have implications for SMEs and public sector stakeholders. SMEs must recognise the importance of several potential antecedents such as intellectual property rights, specific business advice and finance to encourage e-commerce. Moreover, it was apparent that certain SME characteristics, namely locality and trading behaviour, were associated with effective e-commerce.

Originality/value
– This study will be of value to academia, SMEs and key public sector stakeholders in the formulation of policy for ICT development.
SMEs' adoption of enterprise applications
Authors: Ramdani Boumediene , Chevers Delroy , Williams Densil A. 
Published: December 2013

Purpose
– This paper aims to empirically explore the TOE (technology-organisation-environment) factors influencing small to medium-sized enterprises' (SMEs') adoption of enterprise applications (EA).

Design/methodology/approach
– Direct interviews were used to collect data from a random sample of SMEs located in the northwest of England. Using partial least squares (PLS) technique, 102 responses were analysed.

Findings
– Results indicate that technology, organisation and environment contexts impact SMEs' adoption of EA. This suggests that the TOE model is indeed a robust tool to predict the adoption of EA by SMEs.

Research limitations/implications
– Although this study focused on examining factors that influence SMEs' adoption of a set of systems such as CRM and e-procurement, it fails to differentiate between factors influencing each of these applications. The model used in this study can be used by software vendors not only in developing marketing strategies that can target potential SMEs, but also to develop strategies to increase the adoption of EA among SMEs.

Practical implications
– This model could be used by software vendors to determine which SMEs they should target with their products. It can also be used by policy makers to develop strategies to increase the rate of EA adoption among SMEs.

Originality/value
– This paper provides a model that can predict SMEs' adoption of EA. SMEs, adoption, enterprise applications, enterprise systems, ICT, PLS, technology-organisation-environment framework, TOE
Developing a cybernetic lifestyle
Authors: Ronald David MacGill Victor 
Published: December 2013

Purpose
– The dominant paradigms of the world today are reductionist and linear and have led us towards crises in the environment, economics, health and more. Cybernetics is one alternative paradigm, which moves beyond reductionist thought. The paper aims to investigate cybernetics and how it might move from a paradigm to a way of living. A cybernetic worldview enables us to see ourselves as partners in dynamic co-creative processes reaching beyond dualities. To live by such a life requires courage. This paper concentrates on how cybernetics principles may be applied on an individual basis to provide a more holistic way of coping with the challenges of everyday life in the early twenty-first century. The author sees how he can live a balanced life, cope with uncertainty, live with courage, move beyond dualities and develop a breadth of knowledge to help us navigate the events of the lives.

Design/methodology/approach
– This paper provides a brief outline of some cybernetic principles and how they might be transferred to a cybernetic lifestyle. The focus is on how the author might integrate cybernetic principles into the individual life on a day-to-day basis.

Findings
– Breadth of knowledge, moving beyond dualities, the observer, living with courage, uncertainty and living a balanced life are discussed from a cybernetic viewpoint.

Practical implications
– It gives cyberneticians cause to consider their lives and how cybernetic principles help them in everyday life.

Social implications
– The more cyberneticians exhibit cybernetics principles in their life, the more it will be noticed by those around them.

Originality/value
– The approach of this paper is about cybernetics as an individual lifestyle rather than a more generalised examination of the role of cybernetics.
Dissipation of the solar-energetic gradient as the origin of binarism in human meaning systems
Authors: Elio Porto Lito 
Published: December 2013

Purpose
– This paper aims to formulate a hypothesis for the origin and position of binarism within human meaning systems. Specifically, binarism exists ineluctably as a living system's impetus toward life over death, and then – at the symbolic level within human meaning systems – as a device by which humans more efficiently dissipate the solar-energetic gradient.

Design/methodology/approach
– Organisms composing terrestrial ecosystems acquire and degrade solar energy or its derivatives, thereby reducing the thermal gradient impressed on Earth by the Sun. Kay and Schneider call this “the thermodynamic imperative of the restated second law for open systems.” This paper connects the “thermodynamic imperative” to aspects of human meaning systems and pushes Serres' notion regarding homeostasis and the origin of communication one step further to consider such an origin in terms of a binarism born of solar-energetic gradient dissipation.

Findings
– It is hypothesized that the human homoiotherm extends the ineluctable binarism of life over death for all living systems to a symbolic level – as a first, or local, “energetic order” – which serves as a foundational device of human meaning systems; humans efficiently use this binary device to produce entropy and maintain homeostasis within individual organisms and comprehensive ecosystems; and human language, and ultimately the entirety of human meaning systems, emerges from the dissipation of the solar-energetic gradient.

Originality/value
– Modern Western philosophical concepts related to binarism – i.e. Kantian and Hegelian dialectics – are not associated with ecological imperatives. The present hypothesis proposes the co-existence of both a fundamental binarism (i.e. impetus of life over death) and more complex symbolic differentials (in a Leibnizian/Deleuzian sense) as necessary for the emergence of complex human meaning systems in consonance with thermodynamic and ecological imperatives.
Huffman coding as metaphor
Authors: Mohr August 
Published: December 2013

Purpose
– David Huffman, as a graduate student, earned his immortality by solving a problem that had stumped Claude Shannon, the creator of the field of information theory. How he saw the problem differently and the nature of his discovery have implications for how we get stuck, how we get unstuck, and how the internal models limit the ability to see patterns in the world. The paper aims to discuss these issues.

Design/methodology/approach
– This paper describes how Huffman discovered his elegant algorithm, why it had not been discovered previously, how the algorithm may relate to the attempt to find meaning in decision making, and generalises implications for problem solving and daily lives.

Findings
– Huffman was only able to see the problem anew in the cathartic moment of abandoning it. The algorithm he discovered suggests that the concept of “meaning” was an obstacle in his process.

Practical implications
– Huffman coding is one of the underpinnings of computer science. While it should be widely understood for that alone, the process of its discovery and its fundamental methodology are deeply instructional.

Originality/value
– Alexander Pope said “As the twig is bent, so grows the tree”, a classic statement about conscious purpose and man's controlling nature. Huffman's algorithm suggests the real world works the other way around: “As the leaves are lit, so grows the tree”.