bluuebunny/crossref_metadata_2025_split huggingface dataset:
chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Authors: Silva Mickael , Machado Miguel , Silva Diogo N. , Rossi Mirko , Moran-Gilad Jacob , Santos Sergio , Ramirez Mario , Carriço João André 
Published: August 2017

ABSTRACTGene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available athttps://github.com/B-UMMI/chewBBACAor as a docker image athttps://hub.docker.com/r/ummidock/chewbbaca/.DATA SUMMARYAssembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted asStreptococcus agalactiaetaxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.Code for the chewBBACA suite is available athttps://github.com/B-UMMI/chewBBACAwhile the tutorial example is found athttps://github.com/B-UMMI/chewBBACA_tutorial.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTThe chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.
Heterogeneities in afferent connectivity dominate local heterogeneities in the emergence of response decorrelation in the dentate gyrus
Authors: Mishra Poonam , Narayanan Rishikesh 
Published: August 2017

ABSTRACTThe ability of a neuronal population to effectuate response decorrelation has been identified as an essential prelude to efficient neural encoding. To what extent are diverse forms of local and afferent heterogeneities essential in accomplishing such response decorrelation in the dentate gyrus (DG)? Here, we incrementally incorporated four distinct forms of biological heterogeneities into conductance-based network models of the DG and systematically delineate their relative contributions to response decorrelation. We incorporated intrinsic heterogeneities by stochastically generating several electrophysiologically-validated basket and granule cell models that exhibited significant parametric variability, and introduced synaptic heterogeneities through randomized local synaptic strengths. In including adult neurogenesis, we subjected the valid model populations to randomized structural plasticity and matched neuronal excitability to electrophysiological data. We assessed networks comprising different combinations of these three local heterogeneities with identical or heterogeneous afferent inputs from the entorhinal cortex. We found that the three forms of local heterogeneities were independently and synergistically capable of mediating significant response decorrelation when the network was driven by identical afferent inputs. Strikingly, however, when we incorporated afferent heterogeneities into the network to account for the unique divergence in DG afferent connectivity, the impact of all three forms of local heterogeneities were significantly suppressed by the dominant role of afferent heterogeneities in mediating response decorrelation. Our results unveil a unique convergence of cellular- and network-scale degeneracy in the emergence of response decorrelation in the DG, and constitute a significant departure from the literature that assigns a critical role for local network heterogeneities in input discriminability.SIGNIFICANCE STATEMENTThe olfactory bulb and the dentate gyrus (DG) networks assimilate new neurons in adult rodents, with adult neurogenesis postulated to subserve efficacious information transfer by reducing correlations in neuronal responses to afferent inputs. Heterogeneities emerging from the lateral dendro-dendritic synapses, mediated by locally-projecting neurogenic inhibitory granule cells, are known to play critical roles in channel decorrelation in the olfactory bulb. However, the contributions of different heterogeneities in mediating response decorrelation in DG, comprising neurogenic excitatory granule cells projecting beyond DG and endowed with uniquely divergent afferent inputs, have not been delineated. Here, we quantitatively demonstrate the dominance of afferent heterogeneities, over multiple local heterogeneities, in the emergence of response decorrelation in DG, together unveiling cross-region degeneracy in accomplishing response decorrelation.
A structural and kinetic link between membrane association and amyloid fibril formation of α-Synuclein
Authors: Viennet Thibault , Wördehoff Michael M. , Uluca Boran , Poojari Chetan , Shaykhalishahi Hamed , Willbold Dieter , Strodel Birgit , Heise Henrike , Buell Alexander K. , Hoyer Wolfgang , Etzkorn Manuel 
Published: August 2017

ABSTRACTThe protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve an interplay between cytosolic and membrane-bound forms of αS. Therefore, better insights into the molecular determinants of membrane association and their implications for protein aggregation may help deciphering the pathogenesis of Parkinson’s disease. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR - spectroscopic and complementary biophysical as well as computational methods we structurally and kinetically characterize αS interaction with defined stable planar membranes in a quantitative and site-resolved way. We probe the role of αS acetylation as well as membrane charge, plasticity and available surface area in modulating αS membrane binding modes and directly link these findings to their consequences for αS amyloid fibril formation.
Application of “R” principles to enhance the efficiency of water usage in construction sites
Authors: Waidyasekara K.G.A.S. , De Silva Lalith , Rameezdeen Raufdeen 
Published: August 2017

Purpose
Water conservationists have been promoting a hierarchy of measures to preserve water resources in the face of decreasing freshwater availability in the world. However, applicability of water hierarchy to the construction industry is yet to be investigated. To fill this knowledge gap, the purpose of this paper is to investigate water usage, water use efficiency, and conservation measures relevant to the construction operations.

Design/methodology/approach
A triangulation-based mixed-methods approach was adopted for the collection and analysis of data. First, four case studies were carried out to explore the current practices and the possibilities of applying the water hierarchy to the construction operations. This was followed by a questionnaire survey, administered among construction professionals to obtain their views and to verify the findings of case studies.

Findings
Strategies such as reuse and recycling were found to be less applicable and least preferred by the construction professionals compared to reduce, replace, and eliminate. Based on the research findings, three enabling measures, namely, regulation, responsibility, and reward, were found to enhance the effectiveness of these conservation strategies.

Practical implications
Knowledge on preferences of different water conservation measures among the construction professionals and their effectiveness on construction site could help the construction companies to device strategies to mitigate water wastage and enhance water use efficiency. It could also help policy-makers to develop guidelines that would have higher probability of acceptance among construction stakeholders.

Originality/value
The study proposes an extended water hierarchy (3R.6R) by integrating three enabling measures discussed above for the construction project sites.
Collapse: the decline and fall of master planned golf course communities
Authors: Mothorpe Chris , Wyman David 
Published: August 2017

PurposeThe purpose of this paper is to examine the pricing of vacant lots in master planned golf course communities (GCCs) over the period of 2000-2016. The authors compare the longitudinal pricing behavior of different lot types during this economic cycle and examine the causes of the property bubble and subsequent deterioration of the business model with the arrival of the Financial Economic Crisis (FEC).Design/methodology/approachThe authors construct spatial hedonic models for three master planned GCCs in Pickens County, South Carolina and use interaction dummies to examine the pricing of different types of vacant lots before and after the FEC.FindingsThe authors find that there is a collapse in value for interior lots in the GCCs compared to interior lots in the county. As interior lots comprise over 50 percent of inventory in a typical master planned GCC, this loss of real estate value threatens the viability of such communities in the aftermath of the FEC.Practical implicationsThe research results inform real estate investors, real estate developers, current homebuyers and potential homebuyers of the impacts of the FEC on master planned GCCs and some of the risks associated with such developments.Originality/valueThis is the first paper the authors are aware of that indicates the financial viability of master planned GCCs is associated with the pricing fragility of interior lots during cyclical markets. While demand for premium quality lots suffers, there is a collapse in demand for interior lots during the crisis.
Development of non-leaching and eco-friendly polyhexamethylene guanidine hydrochloride based antimicrobial waterborne polyacrylates
Authors: Ding Wei , Peng Kaimei , Zou Tao , Wang Ruonan , Guo Jinshan , Tu Wei Ping , Liu Chao , Hu Jianqing 
Published: August 2017

Purpose
The purpose of this paper is to develop non-leaching and eco-friendly antimicrobial waterborne polyacrylates with excellent antibacterial properties by grafting antibacterial vinyl monomer, glycidyl methacrylate (GMA) modified polyhexamethylene guanidine hydrochloride (PHMG).

Design/methodology/approach
PHMG of different molecular weights were modified by GMA to synthesize antibacterial vinyl monomer, GMA-modified PHMG (GPHMG). Different content and molecular weights of GPHMG were used to synthesize antimicrobial waterborne polyacrylates through emulsion polymerization.

Findings
The addition of GPHMG gained by modifying PHMG showed little influence on thermal stability of the films, but decreased the glass transition temperature(Tg). Meanwhile, the tensile strength decreased, while the breaking elongation increased. The antibacterial properties of the antibacterial films with different GPHMG contents were studied, when GPHMG content was around 0.9 Wt.%, antibacterial films showed excellent antibacterial activity (antibacterial rate >= 99.99 per cent). When weight content of GPHMG in the films remained constant, antibacterial property of films increased first and then decreased with the increase of molecular weight of GPHMG. The structural antibacterial polymer film had more perdurable antibacterial activity than the blended one.

Research limitations/implications
The grafting efficiency of GPHMG to antimicrobial waterborne polyacrylates could be further improved.

Practical implications
Antimicrobial waterborne polyacrylates with excellent antibacterial properties can be used to antibacterial coating and adhesive.

Originality/value
The antibacterial properties of films with different molecular weight of GPHMG were studied, and the durability and stability of antibacterial properties between structural antimicrobial films and blended antimicrobial films were also investigated by ring-diffusion method.
Incontinentia pigmenti in a male (XY) infant with long‐term follow up over 8 years
Authors: Matsuzaki Yasushi , Rokunohe Akiko , Minakawa Satoko , Nomura Kazuo , Nakano Hajime , Ito Etsuro , Sawamura Daisuke 
Published: August 2017

AbstractIncontinentia pigmenti (IP) is an X‐linked genodermatosis affecting the skin and other sites, including the teeth, nails, hair, eyes and nervous system defects in female patients. Generally lethal in males, there are only a few known cases of males surviving this condition. Nuclear factor (NF)‐κB essential modulator (NEMO), also known as inhibitor of kappa light polypeptide gene enhancer in B cells, kinase gamma (IKBKG), constitutes an essential activator of NF‐κB. Over 80% of female patients with IP carry a common deletion mutation involving exons 4–10 of the IKBKG/NEMO gene. We present the case of a male infant (XY) with IP with no concomitant complications. Polymerase chain reaction (PCR) assay showed that the exon 4–10 deletion band was significantly stronger in the skin sample than in blood. Subsequently, long‐range PCR was performed periodically to confirm the spontaneous regression of mutant cells from his blood. Over a period of 6 years, the 2.6‐kb mutant band gradually became weaker, but we did not confirm complete regression. Our patient was a healthy, 8‐year‐old male child with no complications despite the presence of a 2.6‐kb mutant band in his blood. Further follow up is necessary to assess for complications that may develop later.
Ants are the major agents of resource removal from tropical rainforests
Authors: Griffiths Hannah M. , Ashton Louise A. , Walker Alice E. , Hasan Fevziye , Evans Theodore A. , Eggleton Paul , Parr Catherine L. 
Published: August 2017

Abstract

Ants are diverse and abundant, especially in tropical ecosystems. They are often cited as the agents of key ecological processes, but their precise contributions compared with other organisms have rarely been quantified. Through the removal of food resources from the forest floor and subsequent transport to nests, ants play an important role in the redistribution of nutrients in rainforests. This is an essential ecosystem process and a key energetic link between higher trophic levels, decomposers and primary producers.

We used the removal of carbohydrate, protein and seed baits as a proxy to quantify the contribution that ants, other invertebrates and vertebrates make to the redistribution of nutrients around the forest floor, and determined to what extent there is functional redundancy across ants, other invertebrate and vertebrate groups.

Using a large‐scale, field‐based manipulation experiment, we suppressed ants from c. 1 ha plots in a lowland tropical rainforest in Sabah, Malaysia. Using a combination of treatment and control plots, and cages to exclude vertebrates, we made food resources available to: (i) the whole foraging community, (ii) only invertebrates and (iii) only non‐ant invertebrates. This allowed us to partition bait removal into that taken by vertebrates, non‐ant invertebrates and ants. Additionally, we examined how the non‐ant invertebrate community responded to ant exclusion.

When the whole foraging community had access to food resources, we found that ants were responsible for 52% of total bait removal whilst vertebrates and non‐ant invertebrates removed the remaining 48%. Where vertebrates were excluded, ants carried out 61% of invertebrate‐mediated bait removal, with all other invertebrates removing the remaining 39%. Vertebrates were responsible for just 24% of bait removal and invertebrates (including ants) collectively removed the remaining 76%. There was no compensation in bait removal rate when ants and vertebrates were excluded, indicating low functional redundancy between these groups.

This study is the first to quantify the contribution of ants to the removal of food resources from rainforest floors and thus nutrient redistribution. We demonstrate that ants are functionally unique in this role because no other organisms compensated to maintain bait removal rate in their absence. As such, we strengthen a growing body of evidence establishing ants as ecosystem engineers, and provide new insights into the role of ants in maintaining key ecosystem processes. In this way, we further our basic understanding of the functioning of tropical rainforest ecosystems.
Above‐ground biomass is driven by mass‐ratio effects and stand structural attributes in a temperate deciduous forest
Authors: Fotis Alexander T. , Murphy Stephen J. , Ricart Raleigh D. , Krishnadas Meghna , Whitacre James , Wenzel John W. , Queenborough Simon A. , Comita Liza S. 
Published: August 2017

AbstractForest ecosystems are critical for the global regulation of carbon (C), a substantial portion of which is stored in above‐ground biomass (AGB). While it is well understood that taxonomic and functional composition, stand structure and environmental gradients influence spatial variation inAGB, the relative strengths of these drivers at landscape scales have not been investigated in temperate forests. Furthermore, when biodiversity enhances C storage, it is unclear whether it is through mass‐ratio effects (i.e. the dominant trait in communities regulatesAGB) or through niche complementarity (i.e. increasedAGBdue to interspecific resource partitioning).To address these mechanisms, we analysed data from a census of 28,262 adult trees sampled across 900 ha of temperate deciduous forest in southwestern Pennsylvania. We used data on four key plant functional traits to determine if (1) there is a positive relationship between species diversity andAGBand (2) whether this is due to mass‐ratio effects or niche complementarity. We also sought to (3) identify the physical stand structural attributes and topographic variables that influenceAGBacross this landscape.We foundAGBwas positively related to species richness and negatively related to species evenness, albeit weakly, while functional diversity indices had neutral effects. Above‐ground biomass was enhanced in communities dominated by traits related to greater maximum tree height, deeper minimum rooting depths and larger seeds. Most importantly, areas with highAGBwere dominated byAcer saccharumandLiriodendron tulipifera. Overall, these results support mass‐ratio effects, with little evidence for niche complementarity.Synthesis. Stand structure, topography, and species and functional composition, but not taxonomic or functional diversity, were found to be key drivers of above‐ground biomass at landscape scales (<900 ha) in this temperate deciduous forest. Our findings suggest that simultaneously managing for both high diversity and for above‐ground carbon storage may prove challenging in some forest systems. Our results further indicate that the impact of tree biodiversity loss on above‐ground carbon stocks will depend greatly on the identity of the species that are lost.
Management of indeterminate pulmonary nodules (<1 cm) newly detected during the follow‐up of nasopharyngeal carcinoma patients
Authors: Du Chengrun , Wan Caifeng , Ding Jianhui , Zhang Guangyuan , Zhang Youwang , Hu Chaosu , Ying Hongmei 
Published: August 2017

AbstractAimTo investigate the management for the indeterminate pulmonary nodules newly detected during the follow‐up for nasopharyngeal carcinoma (NPC) patients.MethodsIndeterminate pulmonary lesions were identified by searching medical records of NPC patients, who were followed‐up with thoracic CT between April 2008 and February 2014. Indeterminate pulmonary nodules were defined as opacities that may be solitary or multiple, which were <1 cm in size and not calcified. Nodules which were followed‐up for at least two years, were included into analysis. The nodules with growth were considered as metastatic lesions and those which remained stable or regressed were defined as benign. The relations between the risk of the nodules to develop into metastatic lesions and clinical features and characteristics of nodules were analyzed.ResultsThrough a median follow‐up of 50 months, the majority (81 of 102, 79.4%) had no change in the size of nodules. The nodules have regressed in 11 patients. There were 10 (9.8%) cases with progression at the follow‐up. The 10 patients were considered to have lung metastases, for whom continuous increases of lesions were revealed. The volume doubling time of the increasing nodules ranged from 34 to 105 days. The nodules emerging within two years after primary therapies were more likely to develop into metastatic lesions (P = 0.043).ConclusionTen percent of the indeterminate pulmonary nodules represent metastatic diseases. A short‐interval follow‐up is recommended and if the nodules remain stable after six months follow‐up, it may be proper to prolong the interval of follow‐up.
Wolf's post‐herpetic isotopic response to tocilizumab for rheumatoid arthritis
Authors: Lin Chia‐Hua , Chen Hsiang‐Cheng , Gao Hong‐Wei , Wu Bai‐Yao 
Published: August 2017

AbstractImmediate and delayed hypersensitivity reactions may occur after the first or many exposures to tocilizumab, and they have varying presentations. Here, we describe a Wolf's isotopic response that manifested in a patient as erythema on the same site of a previous healed herpes zoster infection. This phenomenon has rarely been reported in the literature.
Who Influences the Design of Management Accounting Systems? An Exploratory Study
Authors: Hoozée Sophie , Mitchell Falconer 
Published: August 2017

AbstractThis paper outlines the results of an exploratory, survey‐based study of the relative influence of managers and management accountants on management accounting system (MAS) design. The findings reveal that, on average, corporate management have the stronger influence on MAS design. However, the strength of their influence does vary both across firms and the sub‐areas of management accounting and, in a significant number of cases, the management accountants’ influence is the greater. The results, therefore, suggest that the processes by which MASs evolve differ across firms due to the variation that exists in the influence exerted by these two parties in MAS design. This finding is significant for researchers studying change and difference in management accounting practice.