bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida albicansdispersed cells signify a developmental state distinct from biofilm and planktonic phases
Authors: Uppuluri Priya , Zaldivar Maikel Acosta , Anderson Matthew Z , Dunn Matthew J. , Berman Judith , Lopez Ribot Jose Luis , Koehler Julia 
Published: February 2018

AbstractCandida albicanssurface-attached biofilms are sites of amplification of an infection through continuous discharge of cells capable of initiating new infectious foci. Yeast cells released from biofilms on intravenous catheters have direct access to the bloodstream. We previously reported that dispersed cells are largely lateral yeast cells that originate from the hyphal layers of the biofilm. Compared to their planktonic counterparts, these biofilm-dispersed yeast cells displayed enhanced virulence-associated gene expression and drug resistance. Little is known about the molecular properties of dispersed cells. We found that the inducer of dispersal,PES1, genetically interacts with the repressor of filamentation,NRG1, in a manner that supports a genetic definition of dispersed cells as yeast. We combined a flow biofilm model with RNA sequencing technology, to identify transcriptomic characteristics of freshly dispersed yeast cells versus biofilms or age-matched planktonic yeast cells growing in glucose-rich medium. Dispersed cells largely inherited a biofilm-like mRNA profile but with one stark difference: dispersed cells were transcriptionally reprogrammed to metabolize alternative carbon sources, while their sessile parents expressed glycolytic genes, despite exposure to the same nutritional signals. Our studies hence define dispersal cell production as an intrinsic step of biofilm development which generates propagules capable of colonizing distant host sites. This developmental step anticipates the need for virulence-associated gene expression before experiencing the associated external signals.
Random forest based similarity learning for single cell RNA sequencing data
Authors: Pouyan Maziyar Baran , Kostka Dennis 
Published: February 2018

AbstractMotivationGenome-wide transcriptome sequencing applied to single cells (scRNA-seq) is rapidly becoming an assay of choice across many fields of biological and biomedical research. Scientific objectives often revolve around discovery or characterization of types or sub-types of cells, and therefore obtaining accurate cell–cell similarities from scRNA-seq data is critical step in many studies. While rapid advances are being made in the development of tools for scRNA-seq data analysis, few approaches exist that explicitly address this task. Furthermore, abundance and type of noise present in scRNA-seq datasets suggest that application of generic methods, or of methods developed for bulk RNA-seq data, is likely suboptimal.ResultsHere we present RAFSIL, a random forest based approach to learn cell–cell similarities from scRNA-seq data. RAFSIL implements a two-step procedure, where feature construction geared towards scRNA-seq data is followed by similarity learning. It is designed to be adaptable and expandable, and RAFSIL similarities can be used for typical exploratory data analysis tasks like dimension reduction, visualization, and clustering. We show that our approach compares favorably with current methods across a diverse collection of datasets, and that it can be used to detect and highlight unwanted technical variation in scRNA-seq datasets in situations where other methods fail. Overall, RAFSIL implements a flexible approach yielding a useful tool that improves the analysis of scRNA-seq data.Availability and ImplementationThe RAFSIL R package is available online atwww.kostkalab.net/software.html
Structural model of Cyc2, the primary electron acceptor of Acidithiobacillus ferrooxidans’ respiratory chain, as a modular cytochrome - β-barrel fusion protein, and mechanistic proposals based on this model
Authors: Abriata Luciano A. 
Published: February 2018

AbstractAcidithiobacillus ferrooxidans oxidizes Fe(II) to Fe(III) to feed electrons into its respiratory chain. The primary electron acceptor of this complex system is Cyc2, an outer membrane protein of unknown structure. This work proposes a feasible model of Cyc2’s global structure, based on homology modeling, residue-residue coevolution data, bioinformatics predictions and limited knowledge about Cyc2’s function. The proposal is that the sequence segment spanning residues ~30 to ~90 folds as a cytochrome-like domain that contains a heme group which would presumably bind and oxidize external Fe(II), whereas the remaining segment from residue ~90 until the end adopts a β-barrel fold similar to that of most outer membrane proteins. Such model differs strongly from a published model, but is backed up by more data and is more compatible with the known topology of outer membrane proteins and with Cyc2’s function of internalizing reducing equivalents. The small size of the cytochrome-like domain would allow it to reside inside, and/or slide through, the β-barrel domain, thus communicating in a controlled fashion the extracellular medium with the periplasm to import electrons through the outer membrane. All the models discussed are provided as PyMOL session files in the Supporting Information and can be visualized online at http://lucianoabriata.altervista.org/modelshome.html
Long term context dependent genetic adaptation of the viral genetic cloud
Authors: Klein Tzipi , Bordería Antonio V. , Barbezange Cyril , Vignuzzi Marco , Louzoun Yoram 
Published: February 2018

ABSTRACTRNA viruses generate a cloud of genetic variants within each host. This cloud contains high frequency genotypes, and a very large number of rare variants. While the dynamics of frequent variants are affected by the fitness of each variant, the rare variants cloud is affected by more complex genetic factors, including context dependent mutations. It serves as a spearhead for the viral population’s movement within the adaptive landscape. We here use an experimental evolution system to show that the genetic cloud surrounding the Coxsackie virus master sequence slowly, but steadily, evolves over hundreds of generations. The evolution of the rare variants cloud often precedes the appearance of high frequency variants. The rare variants cloud’s evolution is driven by a combination of a context-dependent mutation pattern and selection for and against specific nucleotide compositions.This combination affects the mutated dinucleotide distribution, and eventually leads to a non-uniform dinucleotide distribution in the main viral sequence. We then tested these conclusions on other RNA viruses with similar conclusions.
revtools: An R package to support article screening for evidence synthesis
Authors: Westgate Martin J. 
Published: February 2018

AbstractThe field of evidence synthesis is growing rapidly, with a corresponding increase in the number of software tools and workflows to support the construction of systematic reviews, systematic maps, and meta-analyses. Despite much progress, however, a number of problems remain including slow integration of new statistical or methodological approaches into user-friendly software, low prevalence of open-source software, and poor integration among distinct software tools. These issues hinder the utility and transparency of new methods to the research community. Here I present revtools, an R package to support article screening during evidence synthesis projects. It provides tools for the import and de-duplication of bibliographic data, screening of articles by title or abstract, and visualization of article content using topic models. The software is entirely open-source and combines command-line scripting for experienced programmers with custom-built user interfaces for casual users, with further methods to support article screening to be added over time. Revtools provides free access to novel methods in an open-source environment, and represents a valuable step in expanding the capacity of R to support evidence synthesis projects.
Aggregation recovers developmental plasticity in mouse polyploid embryos
Authors: Imai Hiroyuki , Fujii Wataru , Kusakabe Ken Takeshi , Kiso Yasuo , Kano Kiyoshi 
Published: February 2018

ABSTRACTPolyploidy is comparatively prevalent in amphibians and fishes, but is infrequent in animals because of lethality after implantation. On the contrary, tetraploid embryos normally develop into blastocysts, and embryonic stem cells can be established from tetraploid blastocysts in mice. Thus, polyploidization does not seem to be so harmful during preimplantation development. However, the mechanisms by which early mammalian development accepts polyploidization are still poorly understood. In this study, we aimed to elucidate the effect of polyploidization on early mammalian development and to further comprehend its tolerability using hyperpolyploid embryos produced by artificial, repetitive whole genome duplication. Therefore, we successfully established several types of polyploid embryos (tetraploid, octaploid, and hexadecaploid), produced using repeated electrofusion of two-cell embryos in mice, and studied their developmental potentialin vitro. We demonstrated that all types of these polyploid embryos maintained the ability to develop to the blastocyst stage, which implies that mammalian cells might have basic cellular functions in implanted embryos, despite polyploidization. However, the inner cell mass was absent in the hexadecaploid blastocysts. To complement the total cells in blastocysts, a fused hexadecaploid embryo was produced by aggregating a number of hexadecaploid embryos. The results indicated that the fused hexadecaploid embryo finally recovered pluripotent cells in blastocysts. Thus, our findings suggested that early mammalian embryos may have the tolerability and higher plasticity to adapt to hyperpolyploidization for blastocyst formation, despite intense alteration of the genome volume.
Kmer-db: instant evolutionary distance estimation
Authors: Deorowicz Sebastian , Gudys Adam , Dlugosz Maciej , Kokot Marek , Danek Agnieszka 
Published: February 2018

AbstractSummaryKmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40,715 pathogens in less than 4 minutes (on a modern workstation), 44 times faster than Mash, its main competitor.Availability and Implementationhttps://github.com/refresh-bio/kmer-dbContactsebastian.deorowicz@polsl.plSupplementary informationSupplementary data are available at publisher’s Web site
Multivariate directed connectivity analysis (MDCA) enables decoding of directed interactions in neural and social networks
Authors: Schlegel Alexander , Vance Bennet , Alexander Prescott , Tse Peter U. 
Published: February 2018

AbstractMany scientific fields currently face the daunting task of studying the dynamics of complex networks. For example, while we know that the rich mental phenomena of humans and other animals are mediated by complex systems of neural circuits in the brain, the mechanistic links between these biological networks and the functions that they mediate are poorly understood. Here we present a novel class of methods, termed multivariate directed connectivity analysis, to investigate network dynamics via patterns of directed interactions between network nodes. We validate these methods using simulated data and apply them to three real-world datasets, two neuroscientific and one investigating the 2016 US presidential candidates’ influence on the social media service Twitter. We find that these methods enable novel understanding of how information processing is distributed across networks. The methods are generally applicable to the study of dynamic information networks in biological, computational, and other fields of research.
Structure of a novel dimeric SET domain methyltransferase that regulates cell motility
Authors: Pivovarova Yulia , Liu Jun , Lesigang Johannes , Koldyka Oliver , Rauschmeier Rene , Hu Ke , Dong Gang 
Published: February 2018

AbstractLysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii was recently shown to play a critical role in regulating cellular motility. Here we report a 2.1-Å resolution crystal structure of the conserved and functional C-terminal portion (aa289-709) of T. gondii AKMT. AKMT dimerizes via a unique intermolecular interface mediated by the C-terminal TPR (tetratricopeptide repeat)-like domain together with a specific zinc-binding motif that is absent from all other KMTs. Disruption of AKMT dimerization impaired both its enzyme activity and parasite egress from infected host cells in vivo. Structural comparisons reveal that AKMT is related to the KMTs in the SMYD family, with, however, a number of distinct structural features in addition to the unusual dimerization interface. These features are conserved among the apicomplexan parasites and their free-living relatives, but not found in any known KMTs in animals. AKMT therefore is the founding member of a new subclass of KMT that has important implications for the evolution of the apicomplexans.
The communicative constitution of adaptive capacity during Sweden’s Västmanland wildfire
Authors: Jahn Jody L.S. , Johansson Catrin 
Published: February 2018

Purpose
The purpose of this paper is to explain how adaptive capacity is accomplished through communication processes and can contribute to enhancing disaster resilience. The authors adopt a structurational “four flows” explanation of communication processes.

Design/methodology/approach
The authors observed and analyzed discourse in meetings of a crisis communication network consisting of representatives of municipalities and public authorities involved in crisis communication management during the Västmanland wildfire in Sweden.

Findings
Adaptive capacity during the wildfire was principally accomplished through the structurational communication processes or “flows” of self-structuring, activity coordination, and institutional positioning. These flows intersected demonstrating how communication accomplishes the development of a responsive affiliation, organizes stabilizing structuring practices, and enables adaptive structuring practices.

Research limitations/implications
The main contribution of this study is a communicative explanation for adaptive capacity, which draws from a structurational model of constitutive communication, and lends further understanding to improvisation during disasters.

Practical implications
The authors discuss the findings in relation to improvisation, suggesting how the findings can inform future coordinated crisis communication for the public and news media. The recommendations address how practitioners might build a responsive affiliation, use minimal structures (e.g. communication practices), and maintain flexibility by introducing group reflexivity behaviors.

Originality/value
The authors provide new theoretical and empirical knowledge of the communicative constitution of adaptive capacity during a disaster.
Corporate governance practices and comprehensive income
Authors: López-Quesada Erika , Camacho-Miñano María-del-Mar , O. Idowu Samuel 
Published: February 2018

PurposeThe purpose of this paper is to analyze the effect of corporate governance practices on firms’ financial performance, as measured by comprehensive income (CI).Design/methodology/approachUsing a sample of 237 firms from the Standards & Poor (S&P) 500 index during the years 2004-2009, multivariate statistical analyses are conducted to confirm the authors’ main hypothesis.FindingsThe results indicate that having high levels of corporate governance culture has a positive impact on a measure of firms’ financial performance, namely, CI. Furthermore, they indicate a positive correlation between a higher percentage of external directors and financial performance, and a negative relationship between number of board meetings and financial performance.Originality/valueThe main contribution of this research is that good corporate governance strategies deliver superior financial performance for businesses in terms of CI. This serves as a method of value creation, which is the ultimate goal of a business. In addition to the use of CI as an indicator of financial performance, a unique measure of corporate governance level is tested.
Indian PharmaChem: a resource allocation peccadillo
Authors: Nath Roy Sudipendra , Sengupta Tuhin 
Published: February 2018

Subject area
Operations Management

Study level/applicability
MBA/Post Graduate

Case overview
This case attempts to highlight a very common resource allocation dilemma in a real-life scenario. The majority of today’s problems are solved by the methodology of trial and error. This case shows how a generic trial-and-error solution, if buttressed by a proper quantitative methodology, can have substantial impact on the bottom-line of an organization. The case concentrates on three disparate focus areas in a didactic fashion, namely, the ability to retrieve raw data and convert it into a utilizable form if a quantitative method is to be applied; the ability to comprehend the resource constraints of a typical real-life situation; and the skill required to develop and solve an optimization problem in Excel Solver, a product which can easily be accessed by any practitioner.

Expected learning outcomes
Expected learning outcomes are as follows: students learn to formulate a Mixed-Integer programming model; to interpret optimal solutions and appreciate the application of “Optimization”; to recommend a resource allocation strategy; and to understand the importance of cost minimization in organizations.

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: 9: Operations and Logistics
Impact of regulation on advertising and promotion of traditional herbal medicines and food supplements
Authors: Dzeparoski Marjan , Trajkovic-Jolevska Suzana 
Published: February 2018

Purpose
The purpose of this paper is to show that advertising as part of product promotion is in strict correlation with the specific regulation of each product category, food supplements and herbal/over-the-counter medicines. Main contributions of the paper are two-fold. First, it demonstrates that there are products when certain botanical is registered according to legislation as herbal medicine, but at the same time it can be found in sales as food supplement. This can happen within the same country, but it is more frequent within different countries. Second, the possibility for regulation harmonization is discussed.

Design/methodology/approach
In this paper, a comparative analysis of regulation for concerned products in European Union and countries of interest is made. In two case studies, a comparative analysis of marketing of the products in Macedonia and Serbia is made.

Findings
Food supplements are subject to more liberal regulation in comparison with herbal/over-the-counter medicines, but should not be attributed indications and properties that they do not possess. Regulation is stricter and more complex for over-the-counter medicines as a separate class of medicines, these must be correlated with registered properties and indications and are subject to approval by regulatory bodies (print media: advertisement in newspaper/magazine, poster, brochure, flyer, banner and billboard and electronic media: TV spot, radio advertising and internet advertisement).

Research limitations/implications
Countries of interest: EU, Macedonia, Serbia, Montenegro, Albania, Kosovo, Bosnia and Herzegovina.

Practical implications
The paper will contribute toward the creation of promotional and marketing steps in placement of these products on the market in countries of interest, based on regulation of the product category.

Social implications
The discussed opportunities for harmonization are applicable and realistic and can positively contribute for better flow and placement of food supplements and herbal/over-the-counter medicines in different countries. The results of the case studies can also be used for regulatory activities and preparation of marketing materials for other products on other markets of interest with same or similar regulation.

Originality/value
For the first time, a comparative analysis of regulation is made for concerned products in countries of interest. Possibility for regulation harmonization is discussed.
Medical errors: extreme service failures and recoveries
Authors: Black Hulda G. , Goad Emily A. , Attaway Jill S. 
Published: February 2018

Purpose
The purpose of this research is to investigate the relationship among jurors’ attribution of responsibility of the error, patient styles and juror decisions (e.g. acquittal of the physician). Specifically, this research examines the influence of an individual’s approach to their healthcare (active vs. passive), and decisions to acquit in malpractice cases.

Design/methodology/approach
In total, 459 individuals were surveyed using a commercial call center for participation in a corresponding mail survey. Surveys were also distributed to undergraduate business students at a Midwestern university.

Findings
Cluster analysis revealed two categories of patient styles: “active patients” (39.4 per cent) and “passive patients” (60.6 per cent). Regardless of patient style, this research found all respondents viewed medical error disclosure as important. However, respondents in the passive group were more likely to acquit the physician and the hospital nursing staff as compared with those classified as active.

Practical implications
The safety of patients in the healthcare system and prevention of errors is a critical issue. However, when errors occur, medical providers should disclose information to the patient and take responsibility to attenuate their negative impact. Further, this research reveals that patients who rely more on their physicians, trust their recommendations and question physicians less are more likely to acquit. Medical providers can use this information as motivation to continue to build this type of trust with their patients.

Originality/value
Medical errors are costly for all parties involved. This research provides insight for not only members of the legal profession involved in medical malpractice cases, but also risk managers and hospital administrators and healthcare providers regarding the decision-making process used by individuals serving on a jury.