bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial Characterization of the Two ClpP Paralogs ofChlamydia trachomatisSuggests Unique Functionality for Each
Authors: Wood Nicholas A. , Chung Krystal , Blocker Amanda , de Almeida Nathalia Rodrigues , Conda-Sheridan Martin , Fisher Derek J. , Ouellette Scot P. 
Published: July 2018

AbstractChlamydiais an obligate intracellular bacterium that differentiates between two distinct functional and morphological forms during its developmental cycle: elementary bodies (EBs) and reticulate bodies (RBs). EBs are non-dividing, small electron dense forms that infect host cells. RBs are larger, non-infectious replicative forms that develop within a membrane-bound vesicle, termed an inclusion. Given the unique properties of each developmental form of this bacterium, we hypothesized that the Clp protease system plays an integral role in proteomic turnover by degrading specific proteins from one developmental form or the other.Chlamydiahas five uncharacterizedclpgenes:clpX,clpC, twoclpPparalogs, andclpB. In other bacteria, ClpC and ClpX are ATPases that unfold and feed proteins into the ClpP protease to be degraded, and ClpB is a deaggregase. Here, we focused on characterizing the ClpP paralogs. Transcriptional analyses and immunoblotting determined these genes are expressed mid-cycle. Bioinformatic analyses of these proteins identified key residues important for activity. Over-expression of inactiveclpPmutants inChlamydiasuggested independent function of each ClpP paralog. To further probe these differences, we determined interactions between the ClpP proteins using bacterial two-hybrid assays and native gel analysis of recombinant proteins. Homotypic interactions of the ClpP proteins, but not heterotypic interactions between the ClpP paralogs, were detected. Interestingly, ClpP2, but not ClpP1, protease activity was detectedin vitro. This activity was stimulated by antibiotics known to activate ClpP, which also blocked chlamydial growth. Our data suggest the chlamydial ClpP paralogs likely serve distinct and critical roles in this important pathogen.ImportanceChlamydia trachomatisis the leading cause of preventable infectious blindness and of bacterial sexually transmitted infections worldwide. Chlamydiae are developmentally regulated, obligate intracellular pathogens that alternate between two functional and morphologic forms with distinct repertoires of proteins. We hypothesize that protein degradation is a critical aspect to the developmental cycle. A key system involved in protein turnover in bacteria is the Clp protease system. Here, we characterized the two chlamydial ClpP paralogs by examining their expression inChlamydia, their ability to oligomerize, and their proteolytic activity. This work will help understand the evolutionarily diverse Clp proteases in the context of intracellular organisms, which may aid in the study of other clinically relevant intracellular bacteria.
Functional Testing of Thousands of Osteoarthritis-Associated Variants for Regulatory Activity
Authors: Klein Jason Chesler , Keith Aidan , Rice Sarah J. , Shepherd Colin , Agarwal Vikram , Loughlin John , Shendure Jay 
Published: July 2018

AbstractTo date, genome-wide association studies have implicated at least 35 loci in osteoarthritis, but due to linkage disequilibrium, we have yet to pinpoint the specific variants that underlie these associations, nor the mechanisms by which they contribute to disease risk. Here we functionally tested 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identified six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that our most significant hit, rs4730222, drives increased expression of an alternative isoform ofHBP1in a heterozygote chondrosarcoma cell line, a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients.
Lemon: a framework for rapidly mining structural information from the Protein Data Bank
Authors: Fine Jonathan , Chopra Gaurav 
Published: July 2018

AbstractMotivationThe protein data bank (PDB) currently holds over 140,000 biomolecular structures and continues to release new structures on a weekly basis. The PDB is an essential resource to the structural bioinformatics community to develop software that mine, use, categorize, and analyze such data. New computational biology methods are evaluated using custom benchmarking sets derived as subsets of 3D experimentally determined structures and structural features from the PDB. Currently, such benchmarking features are manually curated with custom scripts in a non-standardized manner that results in slow distribution and updates with new experimental structures. Finally, there is a scarcity of standardized tools to rapidly query 3D descriptors of the entire PDB.ApproachOur solution is the Lemon framework, a C++11 library with Python bindings, which provides a consistent workflow methodology for selecting biomolecular interactions based on user criterion and computing desired 3D structural features. This framework can parse and characterize the entire PDB in less than ten minutes on modern, multithreaded hardware. The speed in parsing is obtained by using the recently developed MacroMolecule Transmission Format (MMTF) to reduce the computational cost of reading text-based PDB files. The use of C++ lambda functions and Python binds provide extensive flexibility for analysis and categorization of the PDB by allowing the user to write custom functions to suite their objective. We think Lemon will become a one-stop-shop to quickly mine the entire PDB to generate desired structural biology features. The Lemon software is available as a C++ header library along with example functions at https://github.com/chopralab/lemon.
Molecular interaction and transport limitation in macromolecular binding to surfaces
Authors: Hemker Pieter Wilhelm , Miszta Adam , Bierbower Sonya M. , Hemker Hendrik Coenraad , Hermens Wim 
Published: July 2018

AbstractBinding of macromolecules to surfaces, or to surface-attached binding partners, is usually described by the classical Langmuir model, which does not include interaction between incoming and adsorbed molecules or between adsorbed molecules.The present study introduces the “Surfint” model, including such interactions. Instead of the exponential binding behaviour of the Langmuir model, the Surfint model has tanh binding equations, as confirmed by a random sequential adsorption (RSA) computer simulation.For high binding affinity, sorption kinetics become diffusion-limited as described by the existing unstirred-layer model “Unstir”, for which we present the exact analytical solution of its binding equations expressed in Lambert W-functions.Low-affinity binding of thrombin on heparin, and high-affinity binding of prothrombin on phospholipid vesicles, were measured by ellipsometry and were best described by the Surfint and Unstir models, respectively.
Drosophila insulin-like peptide dilp1 increases lifespan and glucagon-like Akh expression epistatic to dilp2
Authors: Post Stephanie , Liao Sifang , Yamamoto Rochele , Veenstra Jan A. , Nässel Dick R. , Tatar Marc 
Published: July 2018

SummaryInsulin/IGF signaling (IIS) regulates essential processes including development, metabolism, and aging. The Drosophila genome encodes eight insulin/IGF-like peptide (dilp) paralogs, including tandem-encoded dilp1 and dilp2. Many reports show that longevity is increased by manipulations that decrease DILP2 in adults. In contrast, dilp1 is expressed primarily in pupal stages, but also during adult reproductive diapause, although we find that dilp1 is also highly expressed in adult dilp2 mutants under non-diapause conditions. The inverse expression of dilp1 and dilp2 suggests these genes interact to regulate aging. Here, we study dilp1 and dilp2 single and double mutants to describe epistatic and synergistic interactions affecting longevity, metabolism and adipokinetic hormone (AKH), a functional homolog of glucagon. Mutants of dilp2 extend lifespan and increase Akh mRNA and protein in a dilp1-dependent manner. Loss of dilp1 alone has no impact on these traits, whereas transgene expression of dilp1 increases lifespan in dilp1-dilp2 double mutants. On the other hand, dilp1 and dilp2 redundantly interact to control circulating sugar, starvation resistance and compensatory dilp5 expression. These later interactions do not correlate with patterns for how dilp1 and dilp2 affect longevity and AKH. Thus, repression or loss of dilp2 slows aging because its depletion induces dilp1, which acts as a pro-longevity factor. Likewise, dilp2 regulates Akh through epistatic interaction with dilp1. Akh and glycogen affect aging in C. elegans and Drosophila, suggesting that dilp2 modulates lifespan via dilp1 and in part by regulating Akh. Whether DILP1 acts as an insulin receptor agonist or inhibitor remains to be resolved.
Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data
Authors: Mignogna Kristin M. , Bacanu Silviu A. , Riley Brien P. , Wolen Aaron R. , Miles Michael F. 
Published: July 2018

AbstractGenome-wide association studies on alcohol dependence, by themselves, have yet to account for the estimated heritability of the disorder and provide incomplete mechanistic understanding of this complex trait. Integrating brain ethanol-responsive gene expression networks from model organisms with human genetic data on alcohol dependence could aid in identifying dependence-associated genes and functional networks in which they are involved. This study used a modification of the Edge-Weighted Dense Module Searching for genome-wide association studies (EW-dmGWAS) approach to co-analyze whole-genome gene expression data from ethanol-exposed mouse brain tissue, human protein-protein interaction databases and alcohol dependence-related genome-wide association studies. Results revealed novel ethanol-regulated and alcohol dependence-associated gene networks in prefrontal cortex, nucleus accumbens, and ventral tegmental area. Three of these networks were overrepresented with genome-wide association signals from an independent dataset. These networks were significantly overrepresented for gene ontology categories involving several mechanisms, including actin filament-based activity, transcript regulation, Wnt and Syndecan-mediated signaling, and ubiquitination. Together, these studies provide novel insight for brain mechanisms contributing to alcohol dependence.
Making use of an enduring public administration myth
Authors: Marshall Gary 
Published: July 2018

Purpose
The purpose of this paper is to examine the concept of the public interest. The central question is whether the public interest is a usable concept in a time of social and political change. A historical overview of the public interest is provided. Two researchers are highlighted: David John Farmer and O.C. McSwite. The paper concludes by proposing the refusal of subjective identification with the public interest.

Design/methodology/approach
Discourse theory and Lacanian psychoanalysis are discussed in this paper. The emphasis in both approaches is to examine ethical challenges in politics and administration through new epistemological lenses. A further use of these research strategies is to identify existing institutional practices and situate administrative decision-making within those practices.

Findings
The findings in this paper indicate that while institutional resistance is useful, it can also be co-opted or result in retribution. In both cases, power is asserted and maintained by those who hold institutional power. David John Farmer’s work on anti-administration and O.C. McSwite’s work on administrative refusal are effective strategies to address the abuse of institutional power.

Originality/value
This paper introduces the concept of subjective identification to the literature of public administration. Subjective identification offers administrators a new approach to the ethical dilemmas they face in the workplace.
Using situational crisis communication theory to understand Orlando hotels’ Twitter response to three crises in the summer of 2016
Authors: Barbe Danielle , Pennington-Gray Lori 
Published: July 2018

PurposeThe purpose of this paper is to assess the crisis communication strategies implemented by hotel and lodging organizations via social media. Specifically, this study analyzed Twitter content by hotels in Orlando, Florida during the summer of 2016 when several crises occurred that made global media coverage, including the alligator snatching on Disney property, the mass shooting at Pulse nightclub and growing concerns of Zika virus.Design/methodology/approachTo understand crisis communication in the hotel industry, this study was guided by the technology-environment-organization framework and situational crisis communication theory (SCCT). Twitter content between June 1 and August 31, 2016 from Orlando hotels was collected and content analyzed to determine: was the message related to the crisis event, the SCCT strategy used and the influence of hotel organizational factors (ownership, size, classification) on the use of social media for crisis communication.FindingsResults indicate that most hotels are not currently using Twitter as a form of crisis communication. Only the shooting at Pulse Nightclub was communicated and the SCCT bolster strategy was used throughout each of the crisis-related message, reminding stakeholders that they too are a victim.Originality/valueThis study provides insight into the ways hotels are using social media for crisis communication. Each crisis explored was different, and while the hotels were not responsible for creating the crises, they are responsible for the safety of guests. These results inform hoteliers that there is a responsibility to communicate during a crisis, particularly for informative purposes.
Organizational characteristics of cross-border mergers and acquisitions
Authors: Li Yu , Redding K.S. , Xie En 
Published: July 2018

PurposeGiven that several publicly announced international merger and acquisition deals have been abandoned in recent years, the purpose of this paper is to present a synthesis of influential articles that examine organizational characteristics of cross-border acquisition transactions. The synthesis is framed through general traits and resources, learning and prior acquisition experience, and top-level management and governance attributes. Specifically, the paper conceptualizes key organizational attributes influencing the propensity of cross-border negotiations, and the most common characteristics and post-deal effects by illustrating several case examples from around the world.Design/methodology/approachOwing to fairness and integrity principles of the literature survey studies, the paper adopts an exploratory review design to present a synthesis of several influential articles published in strategy, international business and corporate finance journals. Since case method and storytelling are the best qualitative approaches to conceptualizing extant theoretical contributions, a number of case examples—successful, delayed and abandoned—from around the world have been discussed by leveraging the case information from archival sources.FindingsDrawing on resource-based view, organizational learning, upper echelons and agency theory perspectives, the paper underscores three observations. First, organizational characteristics such as firm age, firm size, ownership structure, slack resources, marketing resources, technological intensity, export intensity and business group affiliation have different impacts on the propensity of publicly announced cross-border deals. Second, firm’s prior acquisition experience and firm’s acquisition experience in the target country have positive or moderating effects on the success of a cross-border merger. Third, top-level management characteristics such as CEO foreign nationality and CEO international career experience, and governance characteristics such as board size, the number of independent directors and directors with overseas experience, have mixed effects on the incidence of cross-border acquisitions.Practical implicationsThe paper puts forth several recommendations for top-level managers participating in cross-border acquisition negotiations, such as learning from peers in the same industry, learning from predecessors in the target country and learning from failure negotiations in the same industry and other industries.Originality/valueNested within the organizational, international business strategy and corporate finance literature, the paper presents a synthesis of influential publications that study organizational characteristics affecting the propensity of cross-border acquisitions. The cases discussed in this paper are unique examples from around the world.
Beyond eventification: capacity building in post-disaster temporariness
Authors: Pasquinelli Cecilia , Koukoufikis Georgios , Gogishvili David 
Published: July 2018

PurposeThe paper aims to explore cultural events in a post-disaster town cultural events in a post-disaster town, L’Aquila, Italy, facing a long-term process of adaptation and recovery after the 2009 earthquake.Design/methodology/approachA time-based conceptual framework is applied in a case analysis relying on primary and secondary data. In-depth semi-structured interviews with local actors, direct observations and participation in local events and public debates enriched the analysis.FindingsIn the absence of a clear-cut urban policy framework, an urban heritage of cultural events emerged from local actors’ initiatives, with some evidence of local capacity building. Elements of events’ institutionalisation and signals of a serious risk of vanishing in the post-disaster transitioning context are discussed.Originality/valueThe study involves development of a theoretical framework for analysing the temporal process of evolution of a local system of cultural events as instruments for place-making and capacity building in a post-disaster town. New light is cast on the meaning of “eventification.”
Bringing active learning into the accounting classroom
Authors: Sugahara Satoshi , Dellaportas Steven 
Published: July 2018

Purpose
The purpose of this study is to investigate the effect of an accounting education pedagogy incorporating active learning approaches designed to engage first-year undergraduate business students and to aspire them to continue accounting as their academic major and entry into the accounting profession.

Design/methodology/approach
Data were collected from a questionnaire with a pre-/post-test design of 24 undergraduate business students enrolled in a course titled Accounting Active Learning Seminar (AALS) (test group) and 33 students who did not participate in the AALS (control group). The AALS incorporates various types of active learning methods designed by the authors to inspire students to continue with accounting as a career choice.

Findings
The findings show that participation in the AALS improved student’s motivation in accounting education and the likelihood of choosing accounting as their academic major. The active learning methods implemented in the AALS were effective in improving students’ confidence, of which degree contributed to students’ stronger works aspiration towards accounting professions. Further it was found that students who did not participate in the AALS tended to have lower attention dimensions of motivation, which was also significantly associated with lower percentage of students’ choice of academic major in accounting.

Originality/value
This is one of the few studies to empirically examine active learning on student engagement and performance with a focus on accounting. While the evidence shows that active learning has pedagogical benefits, the full potential of active learning is more likely to be realized when accounting educators design active learning carefully to address the “attention” and “confidence” attributes.
The role of emotional aspects in the information retrieval from the web
Authors: Yari Zanganeh Marzieh , Hariri Nadjla 
Published: July 2018

Purpose
The purpose of this paper is to identify the role of emotional aspects in information retrieval of PhD students from the web.

Design/methodology/approach
From the methodological perspective, the present study is experimental and the type of study is practical. The study population is PhD students of various fields of science. The study sample consists of 50 students as selected by the stratified purposive sampling method. The information aggregation is performed by observing the records of user’s facial expressions, log file by Morae software, as well as pre-search and post-search questionnaire. The data analysis is performed by canonical correlation analysis.

Findings
The findings showed that there was a significant relationship between emotional expressions and searchers’ individual characteristics. Searchers satisfaction of results, frequency internet search, experience of search, interest in the search task and familiarity with similar searches were correlated with the increased happy emotion. The examination of user’s emotions during searching performance showed that users with happiness emotion dedicated much time in searching and viewing of search solutions. More internet addresses with more queries were used by happy participants; on the other hand, users with anger and disgust emotions had the lowest attempt in search performance to complete search process.

Practical implications
The results imply that the information retrieval systems in the web should identify emotional expressions in a set of perceiving signs in human interaction with computer, similarity, face emotional states, searching and information retrieval from the web.

Originality/value
The results explicit in the automatic identification of users’ emotional expressions can enter new dimensions into their moderator and information retrieval systems on the web and can pave the way of design of emotional information retrieval systems for the successful retrieval of users of the network.
Investor sentiment and timely loss recognition
Authors: Duong Hong Kim , Schuldt Michael , Gotti Giorgio 
Published: July 2018

PurposeThe purpose of this paper is to investigate the impact of investor sentiment on timely loss recognition by examining a sample of firms for the period 1988-2015.Design/methodology/approachThe authors use the accruals-based model of Ball and Shivakumar (2005) and a sentiment measure in their primary analysis. Supporting analyses include an extension of Simpson (2013) using an abnormal accruals analysis with subsamples of firms with bad news, the use of a Khan and Watts (2009) quarter firm-level measure of conservatism and an investigation of the monitoring role played by financial analysts.FindingsThe study finds that managers strategically report more losses in high sentiment periods than in low sentiment periods. This loss timing behavior results in an average 37.8 per cent increase in the acceleration of loss recognition. This study additionally finds a negative correlation between investor sentiment and abnormal accruals when managers are reporting bad news, and that a greater number of financial analysts following a firm curtails managers’ acceleration of loss recognition in high sentiment periods.Originality/valueThis study contributes to the corporate disclosure literature by showing that managers strategically recognize losses, and such behavior is more prevalent in high sentiment periods. Managers take advantage of prevailing investor sentiment to accelerate losses in high sentiment periods to mitigate market penalties from reporting bad news.