bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal genomic surveillance ofPlasmodium falciparummalaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand
Authors: Cerqueira Gustavo C. , Cheeseman Ian H. , Schaffner Steve F. , Nair Shalini , McDew-White Marina , Phyo Aung Pyae , Ashley Elizabeth A. , Melnikov Alexandre , Rogov Peter , Birren Bruce W. , Nosten François , Anderson Timothy J.C. , Neafsey Daniel E. 
Published: November 2016

AbstractBackgroundArtemisinin-based combination therapies are the first line of treatment forPlasmodium falciparuminfections worldwide, but artemisinin resistance (ART-R) has risen rapidly in in Southeast Asia over the last decade. Mutations inkelch13have been associated with artemisinin (ART) resistance in this region. To explore the power of longitudinal genomic surveillance to detect signals inkelch13and other loci that contribute to ART or partner drug resistance, we retrospectively sequenced the genomes of 194P. falciparumisolates from five sites in Northwest Thailand, bracketing the era in which there was a rapid increase in ART-R in this region (2001–2014).ResultsWe evaluated statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance should increase frequency over this period. AfterKelch13-C580Y, the strongest temporal change was seen at a SNP in phosphatidylinositol 4-kinase (PI4K), situated in a pathway recently implicated in the ART-R mechanism. However, other loci exhibit temporal signatures nearly as strong, and warrant further investigation for involvement in ART-R evolution. Through genome–wide association analysis we also identified a variant in a kelch-domain–containing gene on chromosome 10 that may epistatically modulate ART-R.ConclusionsThis analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated loci and improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of thekelch13locus associated with ART-R parasites may yield new molecular markers for resistance surveillance and may retard the emergence or spread of ART-R in African parasite populations.
The Tension-sensitive Ion Transport Activity of MSL8 is Critical for its Function in Pollen Hydration and Germination
Authors: Hamilton Eric S. , Haswell Elizabeth S. 
Published: November 2016

AbstractAll cells respond to osmotic challenges, including those imposed during normal growth and development. Mechanosensitive (MS) ion channels provide a conserved mechanism for regulating osmotic forces by conducting ions in response to increased membrane tension. We previously demonstrated that the MS ion channel MscS-Like 8 (MSL8) is required for pollen to survive multiple osmotic challenges that occur during the normal process of fertilization, and that it can inhibit pollen germination. However, it remained unclear whether these physiological functions required ion flux through a mechanically gated channel provided by MSL8. We introduced two point mutations into the predicted pore-lining domain of MSL8 that disrupted normal channel function in different ways. The Ile711Ser mutation increased the tension threshold of the MSL8 channel while leaving conductance unchanged, and the Phe720Leu mutation severely disrupted the MSL8 channel. Both of these mutations impaired the ability of MSL8 to preserve pollen viability during hydration and to maintain the integrity of the pollen tube when expressed at endogenous levels. When overexpressed in amsl8-4null background, MSL8I711Scould partially rescue loss-of-function phenotypes, while MSL8F720Lcould not. When overexpressed in the wild type Lerbackground, MSL8I711Ssuppressed pollen germination, similar to wild type MSL8. In contrast, MSL8F720Lfailed to suppress pollen germination and increased pollen bursting, thereby phenocopying themsl8-4mutant. Thus, an intact MSL8 channel is required to for normal pollen function during hydration and germination. These data establish MSL8 as the first plant MS channel to fulfill previously established criteria for assignment as a mechanotransducer.
tRNA-derived small RNAs target transposable element transcripts
Authors: Choudury Sarah , Slotkin R. Keith , Martinez German 
Published: November 2016

ABSTRACTtRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plantArabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs arebona-fideregulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.
A positive association between population genetic differentiation and speciation rates in New World birds
Authors: Harvey Michael G. , Seeholzer Glenn F. , Smith Brian Tilston , Rabosky Daniel L. , Cuervo Andrés M. , Klicka John T. , Brumfield Robb T. 
Published: November 2016

AbstractAlthough an implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, its true significance remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. Combining population genetics datasets including 17,746 individuals from 176 New World bird species with speciation rates estimated from phylogenetic data, we show that the population differentiation rates within species predict their speciation rates over long timescales. Although relatively little variance in speciation rate is explained by population differentiation rate, the relationship between the two is robust to diverse strategies of sampling and analyzing both population-level and species-level datasets. Population differentiation occurs at least three to five times faster than speciation, suggesting that most populations are ephemeral. Population differentiation and speciation rates are more tightly linked in tropical species than temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest investigations into the processes responsible for population differentiation can reveal factors that contribute to broad-scale patterns of diversity.
Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution
Authors: Liu Xueliang , Lopez Paola A. , Giessen Tobias W. , Giles Michael , Way Jeffrey C. , Silver Pamela A. 
Published: November 2016

AbstractGenetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ferritin protein, we discovered key mutations that lead to significantly enhanced cellular magnetism, resulting in increased physical attraction of ferritin-expressing cells to magnets and increased contrast for cellular magnetic resonance imaging (MRI). The magnetic mutants further demonstrate increased iron biomineralization measured by a novel fluorescent genetic sensor for intracellular free iron. In addition, we engineeredEscherichia colicells with multiple genomic knockouts to increase cellular accumulation of various metals. Lastly to explore further protein candidates for biomagnetism, we characterized members of the DUF892 family using the iron sensor and magnetic columns, confirming their intracellular iron sequestration that results in increased cellular magnetization.
Convergence or divergence? Corporate climate-change reporting in China
Authors: Yang Helen Hong , Farley Alan 
Published: November 2016

PurposeThis paper aims to investigate the extent international and domestic guidelines have influenced the content of corporate environmental reporting (CER) in the context of China’s radical institutional transition from bureaucratic secrecy to openness, marked by the first nationwide guidelines on Open Government Information (OGI) and Open Environment Information (OEI), effective in 2008.Design/methodology/approachThe study develops a research instrument that captures international and Chinese national guidelines pertaining to environmental information disclosure. This instrument is used to analyse 471 reports of leading 100 listed Chinese companies for the critical period between 2006 and 2010. Chi-square test statistics are used to analyse the significance of differences in reporting items supported by Chinese guidelines versus those supported by international reporting guidelines only.FindingsPartial convergence in climate-change reporting co-exists with divergent China specific interpretation of climate change. The coercive institutional influences of the Chinese government’s guidance in OGI and OEI led to the rapid growth of CER in 2008 compared to 2006, despite compliance being voluntary.Originality/valueThe study is innovative in explicitly measuring any changes in reporting relative to the potential for additional reporting. Such a method more accurately evaluates the effect of institutional influences on reporting. The study provides a fresh profile of the content and the reporting medium of CER, with a particular focus on climate change in the Chinese context. The findings highlight research into CER based on annual reports risks results being incomplete and misleading. Findings have practical implications for policy makers in other emerging economies.
Voluntary disclosure of intangibles and analysts’ earnings forecasts and recommendations
Authors: Maaloul Anis , Ben Amar Walid , Zeghal Daniel 
Published: November 2016

Purpose
The purpose of this paper is to investigate the relationship between voluntary disclosure of intangibles and financial analysts’ earnings forecasts properties.

Design/methodology/approach
Disclosures about intangible assets were hand-collected through content analysis of annual reports of a sample of US non-financial firms, while analysts’ earnings forecasts properties were collected from Bloomberg Professional database. The authors relied on correlation and multivariate regression analyses to test the research hypotheses.

Findings
The results show that increased intangible disclosures affect analysts’ earnings forecasts accuracy, dispersion, and favourable consensus recommendations. However, this effect varies according to the nature of intangible assets.

Practical implications
The results may be of interest to different market participants such as corporate managers, financial analysts, and standards setting bodies that recently published guidelines on voluntary disclosure of intangibles.

Originality/value
This study develops a new comprehensive index to measure the content of narrative disclosures about a large number of intangibles, such as human, structural, and relational assets. The findings contribute to the current debate on the value-relevance of narrative disclosures on intangibles to investors and financial analysts.
The use of generalized audit software by Egyptian external auditors
Authors: Kim Hyo-Jeong , Kotb Amr , Eldaly Mohamed Khaled 
Published: November 2016

Purpose
The purpose of this paper is to explore: the actual usage of generalized audit software (GAS) features among Egyptian external auditors, through the technology acceptance model (TAM); how the conceptual complexity of GAS features impact its actual usage; and what factors influencing the GAS use by Egyptian external auditors.

Design/methodology/approach
External audit professionals at 12 international audit firms, including the Big 4 and eight medium-sized firms, in Egypt were surveyed.

Findings
The results show that the basic features including database queries, ratio analysis, and audit sampling were higher in GAS use, perceived usefulness, and perceived ease of use among Egyptian external auditors than the advanced features: digital analysis, regression/ANOVA, and data mining classification. The structural equation modelling analysis by GAS features suggests that perceived ease of use has a stronger effect on GAS use when the conceptual complexity of GAS features is high. The analysis also support that the use of GAS by Egyptian external auditors is more affected by co-worker, supervisor, or organization through perceived usefulness, but not by job relevance, output quality, and result demonstration.

Research limitations/implications
Although Egyptian external auditors participated in this study may limit the extent to which the findings may be generalized, the responses provide an insight into the actual usage of GAS features by external auditors and the impact of conceptual complexity of GAS features, which is consistent with the literature concerning the relatively low level of utilizing the advanced features of GAS by internal auditors, suggesting that the issues revealed should be of concern.

Practical implications
The results reported in this paper are useful to audit software developers and audit firms in their understanding of factors influencing GAS usage in a different audit context.

Originality/value
The study adds value to prior research by providing context-contingent insight into the application of TAM in an unexplored audit context.
Service flexibility: conceptualizing value creation in service
Authors: Brozovic Danilo , Nordin Fredrik , Kindström Daniel 
Published: November 2016

Purpose
The purpose of this paper is to analyze the subject-specific literature on service and flexibility and derive a conceptualization of the linkages between provider flexibility and customers’ value creation.

Design/methodology/approach
The authors analyze existing perspectives on service and flexibility and propose linkages between provider flexibility and customer value creation.

Findings
Drawing on the service logic literature, and utilizing real-world examples, this paper advances propositions and a conceptual model of how flexibility can contribute to value creation.

Research limitations/implications
This paper establishes the basis for a practical and applicable flexibility perspective on value creation. It is particularly important for service-oriented providers and other firms operating in dynamic contexts.

Practical implications
The propositions and conceptual model offer suggestions on the manner in which provider flexibility contributes to customer value creation. Contextual influences that moderate provider flexibility in value creation are also included.

Originality/value
This paper contributes a novel perspective on service, which may serve as the starting point for the development of a more formal flexibility perspective on value creation.
Renal function in HIV/HBV co‐infected and HBV mono‐infected patients on a long‐term treatment with tenofovir in real life setting
Authors: Milazzo Laura , Gervasoni Cristina , Falvella Felicia Stefania , Cattaneo Dario , Mazzali Cristina , Ronzi Paola , Binda Francesca , Cheli Stefania , Sollima Salvatore , Antinori Spinello 
Published: November 2016

SummaryThe human immunodeficiency virus (HIV)/hepatitis B virus (HBV) co‐infection is likely to be associated with an increased risk of kidney disease, due to the additional factors that may affect renal function in the HIV population. We aimed to evaluate renal toxicity in HIV/HBV and HBV mono‐infected patients on long‐term therapy with tenofovir (TDF) and to explore the association of polymorphisms in ATP‐binding cassette (ABCC)2, ABCC4, ABCC10 with the development of renal dysfunction. From September 2006 to November 2014, 44 HIV/HBV co‐infected and 34 HBV mono‐infected patients were commenced on TDF. Data of renal safety were retrospectively collected and analyzed. ABCC2, ABCC4 and ABCC10 genotypes were identified by real‐time PCR. Over 60 months of observation, there was a significant increase in mean creatinine levels from baseline (P<.01) that was not significantly different between the two study groups. Moreover, a significant decline in estimated glomerular filtration rate (eGFR) was observed from baseline (P<.01), and it was significantly greater in HBV mono‐infected than co‐infected patients (P=.03). The distribution of ABCC2, ABCC4 and ABCC10 genotypes among a subgroup of 34 patients did not show significant association with eGFR decline <90 mL/min per 1.73 m2. Although our findings showed a statistically significant decrease in eGFR with long‐term use of TDF, its clinical impact seems to be modest. The role of genetic factors to identify patients at greater risk for developing tenofovir‐induced renal toxicity needs to be further investigated.
Challenges of Implementing a Communication‐and‐Resolution Program Where Multiple Organizations Must Cooperate
Authors: Mello Michelle M. , Armstrong Sarah J. , Greenberg Yelena , McCotter Patricia I. , Gallagher Thomas H. 
Published: November 2016

ObjectiveTo implement a communication‐and‐resolution program (CRP) in a setting in which liability insurers and health care facilities must collaborate to resolve incidents involving a facility and separately insured clinicians.Study SettingSix hospitals and clinics and a liability insurer in Washington State.Study DesignSites designed and implemented CRPs and contributed information about cases and operational challenges over 20 months. Data were qualitatively analyzed.Data Collection MethodsData from interviews with personnel responsible for CRP implementation were triangulated with data on program cases collected by sites and notes recorded during meetings with sites and among project team members.Principal FindingsSites experienced small victories in resolving particular cases and streamlining some working relationships, but they were unable to successfully implement a collaborative CRP. Barriers included the insurer's distance from the point of care, passive rather than active support from top leaders, coordinating across departments and organizations, workload, nonparticipation by some physicians, and overcoming distrust.ConclusionsOperating CRPs where multiple organizations must collaborate can be highly challenging. Success likely requires several preconditions, including preexisting trust among organizations, active leadership engagement, physicians' commitment to participate, mechanisms for quickly transmitting information to insurers, tolerance for missteps, and clear protocols for joint investigations and resolutions.
Integrated Approach to Reduce Perinatal Adverse Events: Standardized Processes, Interdisciplinary Teamwork Training, and Performance Feedback
Authors: Riley William , Begun James W. , Meredith Les , Miller Kristi K. , Connolly Kathy , Price Rebecca , Muri Janet H. , McCullough Mac , Davis Stanley 
Published: November 2016

ObjectiveTo improve safety practices and reduce adverse events in perinatal units of acute care hospitals.Data SourcesPrimary data collected from perinatal units of 14 hospitals participating in the intervention between 2008 and 2012. Baseline secondary data collected from the same hospitals between 2006 and 2007.Study DesignA prospective study involving 342,754 deliveries was conducted using a quality improvement collaborative that supported three primary interventions. Primary measures include adoption of three standardized care processes and four measures of outcomes.Data Collection MethodsChart audits were conducted to measure the implementation of standardized care processes. Outcome measures were collected and validated by the National Perinatal Information Center.Principal FindingsThe hospital perinatal units increased use of all three care processes, raising consolidated overall use from 38 to 81 percent between 2008 and 2012. The harms measured by the Adverse Outcome Index decreased 14 percent, and a run chart analysis revealed two special causes associated with the interventions.ConclusionsThis study demonstrates the ability of hospital perinatal staff to implement efforts to reduce perinatal harm using a quality improvement collaborative. Findings help inform the relationship between the use of standardized care processes, teamwork training, and improved perinatal outcomes, and suggest that a multiplicity of integrated strategies, rather than a single intervention, may be essential to achieve high reliability.
Evaluation of Cross‐contamination of Nylon Bags with Heavy‐loaded Gasoline Fire Debris and with Automotive Paint Thinner
Authors: Belchior Filipa , Andrews Stephen P. 
Published: November 2016

AbstractNylon bags are used for packaging fire debris in several countries, particularly in Europe. The possibility of cross‐contamination during transport from the fire scene to the laboratory, in normal casework conditions in the U.K., was studied for two brands of nylon bags, using simulated heavy‐loaded fire debris. Three experiments were carried out with each brand, using as sample a piece of cotton fabric soaked with gasoline. One experiment was carried out using automotive paint thinner (oxygenated solvent). Each sample was sealed in a nylon bag and stored in contact with eight empty bags. The empty bags were analysed at regular intervals for a period of time up to 8 weeks, using SPME and GC/MS. Cross‐contamination was found for components of gasoline (toluene and C2‐alkylbenzenes) in the two brands of nylon bags used, after 4 days and 2 weeks. Cross‐contamination using automotive topcoat thinner was detected after 2 days.
Effect of Surface Properties on Colloid Retention on Natural and Surrogate Produce Surfaces
Authors: Lazouskaya Volha , Sun Taozhu , Liu Li , Wang Gang , Jin Yan 
Published: November 2016

AbstractBacterial contamination of fresh produce is a growing concern in food industry. Pathogenic bacteria can attach to and colonize the surfaces of fresh produce and cause disease outbreaks among consumers. Surface properties of both bacteria and produce affect bacterial contamination; however, the effects of produce roughness, topography, and hydrophobicity on bacterial retention are still poorly understood. In this work, we used spherical polystyrene colloids as bacterial surrogates to investigate colloid retention on and removal (by rinsing) from fresh produce surfaces including tomato, orange, apple, lettuce, spinach, and cantaloupe, and from surrogate produce surface Sharklet (a micro‐patterned polymer). All investigated surfaces were characterized in terms of surface roughness and hydrophobicity (including contact angle and water retention area measurements). The results showed that there was no single parameter that dominated colloid retention on fresh produce, yet strong connection was found between colloid retention and water retention and distribution on all the surfaces investigated except apple. Rinsing was generally not efficient in removing colloids from produce surfaces, which suggests the need to modify current cleaning procedures and to develop novel contamination prevention strategies. This work offers a physicochemical approach to a food safety problem and improves understanding of mechanisms leading to produce contamination.