bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustically Detonated Biomolecules for Genetically Encodable Inertial Cavitation
Authors: Bar-Zion Avinoam , Nourmahnad Atousa , Mittelstein David R. , Yoo Sangjin , Malounda Dina , Abedi Mohamad , Lee-Gosselin Audrey , Maresca David , Shapiro Mikhail G. 
Published: April 2019

ABSTRACTRecent advances in molecular engineering and synthetic biology have made it possible for biomolecular and cell-based therapies to provide highly specific disease treatment. However, both the ability to spatially target the action of such therapies, and their range of effects on the target tissue remain limited. Here we show that biomolecules and cells can be engineered to deliver potent mechanical effects at specific locations inside the body under the direction of focused ultrasound. This capability is based on gas vesicles, a unique class of air-filled protein nanostructures derived from buoyant photosynthetic microbes. We show that low-frequency ultrasound can convert these nanoscale biomolecules into micron-scale cavitating bubbles, as demonstrated with acoustic measurements and ultrafast optical microscopy. This allows gas vesicles targeted to cell-surface receptors to serve as remotely detonated cell-killing agents. In addition, it allows cells genetically engineered to express gas vesicles to be triggered with ultrasound to lyse and release therapeutic payloads. We demonstrate these capabilitiesin vitro,in cellulo, andin vivo. This technology equips biomolecular and cellular therapeutics with unique capabilities for spatiotemporal control and mechanical action.
RNAsamba: coding potential assessment using ORF and whole transcript sequence information
Authors: Camargo Antonio P. , Sourkov Vsevolod , Carazzolle Marcelo F. 
Published: April 2019

AbstractMotivationThe advent of high-throughput sequencing technologies made it possible to obtain large volumes of genetic information, quickly and inexpensively. Thus, many efforts are devoted to unveil the biological roles of genomic elements, being one of the main tasks the identification of protein-coding and long non-coding RNAs.ResultsWe describe RNAsamba, a tool to predict the coding potential of RNA molecules from sequence information using a deep-learning model that processes both the whole sequence and the ORF to look for patterns that distinguish coding and non-coding RNAs. We evaluated the model in the classification of coding and non-coding transcripts of humans and five other model organisms and show that RNAsamba mostly outperforms other state-of-the-art methods. We also show that RNAsamba can identify coding signals in partial-length ORFs and UTR sequences, evidencing that its model is not dependent on the presence of complete coding regions. RNAsamba is a fast and easy tool that can provide valuable contributions to genome annotation pipelines.Availability and implementationThe source code of RNAsamba is freely available at:https://github.com/apcamargo/RNAsamba.
Crystal structures of the outer membrane transporter FoxA provide novel insights into TonB-mediated siderophore uptake and signalling
Authors: Josts Inokentijs , Veith Katharina , Tidow Henning 
Published: April 2019

AbstractMany microbes and fungi acquire the essential ion Fe3+through the synthesis and secretion of high-affinity chelators termed siderophores. In Gram-negative bacteria, these ferric-siderophore complexes are actively taken up using highly specific TonB-dependent transporters (TBDTs) located in the outer bacterial membrane (OM). However, the detailed mechanism of how the inner-membrane protein TonB connects to the transporters in the OM as well as the interplay between siderophore- and TonB-binding to the transporter is still poorly understood. Here, we present three crystal structures of the TBDT FoxA fromPseudomonas aeruginosa(containing a signalling domain) in complex with the siderophore ferrioxamine B and TonB and combine them with a detailed analysis of binding constants. The structures show that both siderophore and TonB-binding is required to form a translocation-competent state of the FoxA transporter in a two-step TonB-binding mechanism. The complex structure also indicates how TonB-binding influences the orientation of the signalling domain.
Evaluation of the Accelerate Pheno™ system to identify bacteria and determine antimicrobial susceptibility in positive blood cultures
Authors: Fernandez-Pittol Mariana J. , Morales Javier , Rubio Elisa , Fasanella Assumpta , Alejo-Cancho Izaskun , Almela Manel , Marco Francesc , Vila Jordi , Casals-Pascual Climent 
Published: April 2019

AbstractIntroductionNew platforms have recently been developed to reduce response time of identification and antimicrobial susceptibility of bacterial isolates in positive blood cultures from patients with bloodstream infections. The Accelerate Pheno™ system (Accelerate Diagnostics, Inc.) provides information on pathogen identification and antibiotic susceptibility in approximately 1.5 and 7 hours, respectively.MethodsIn this study we compared the Accelerate Pheno™ system with the standard procedure used in our laboratory. A total of 41 blood cultures were prospectively analysed with the Accelerate Pheno™ system and our standard methods, which include identification by MALDI-TOF mass spectrometry and antibiotic susceptibility testing (AST) by BD Phoenix system and E-test.ResultsThe correlation between the two methods using Cohen’s kappa coefficient was 0.82; mean (sd) time of identification for MALDI-TOF MS was 0.7 (0.22) hours and 1.43 (0.14) hours for the Accelerate Pheno™ system. The mean (sd) time of AST with the BD Phoenix system was 15.85 (2.57) hours and with the Accelerate Pheno™ system 6.7 (0.12) hours. AST results showed an overall essential agreement of 92% for the minimal inhibitory concentrations (MIC) and an overall category agreement of 96%. Among Gram positive isolates, essential and category agreements of 100% were observed. In Gram negative isolates 10 discrepancies were detected, which were classified as 7 major and 3 minor errors. Discrepancies in the Accelerate Pheno™ system were observed particularly for P. aeruginosa.ConclusionThe Accelerate Pheno™ system can improve turn-around time in the management of patients with bloodstream infections.
Distinct evolutionary trajectories of neuronal and hair cell nicotinic acetylcholine receptors
Authors: Marcovich Irina , Moglie Marcelo J. , Freixas Agustín E. Carpaneto , Trigila Anabella P. , Franchini Lucia F. , Plazas Paola V. , Lipovsek Marcela , Elgoyhen Ana Belén 
Published: April 2019

ABSTRACTThe expansion and pruning of ion channel families has played a crucial role in the evolution of nervous systems. Remarkably, with a highly conserved vertebrate complement, nicotinic acetylcholine receptors (nAChRs) are unique among ligand-gated ion channels in that members of the family have distinct roles in synaptic transmission in non-overlapping domains, either in the nervous system, the inner ear hair cells or the neuromuscular junction. Here, we performed a comprehensive analysis of vertebrate nAChRs sequences, single cell expression patterns and comparative functional properties of receptors from three representative tetrapod species. We show that hair cell nAChRs underwent a distinct evolutionary trajectory to that of neuronal receptors. These were most likely shaped by different co-expression patterns and co-assembly rules of component subunits. Thus, neuronal nAChRs showed high degree of coding sequence conservation, coupled to greater co-expression variance and conservation of functional properties across tetrapod clades. In contrast, hair cell α9α10 nAChRs exhibited greater sequence divergence, narrow co-expression pattern and great variability of functional properties across species. These results point to differential substrates for random change within the family of gene paralogs that relate to the segregated roles of nAChRs in synaptic transmission.Significance statementOur work exploits several peculiarities of the family of vertebrate nicotinic acetylcholine receptors (nAChRs) to explore the evolutionary trajectories of a ligand-gated ion channel family. By performing a comprehensive comparative analysis of nAChR subunits coding sequences, single cell expression patterns and functional properties we found a contrasting evolutionary history between nAChRs with widespread expression in the nervous system compared to those with isolated expression in the inner ear. Evolutionary changes were focused on differences in co-expression and co-assembly patterns for the former and coding sequences in the latter. This multidisciplinary approach provides further insight into the evolutionary processes that shaped the nervous and sensory systems of extant animals.
Sex Discordance and Risk of Breast Cancer, A Twin Study
Authors: Aduse-Poku Livingstone , Jahanfar Shayesteh 
Published: April 2019

AbstractObjectiveThe purpose of the study is to perform an analysis of the relationship between sex discordance and risk of breast cancer in female twins in the United States.MethodsA cross-sectional study of 14,462 female twins was conducted using data from Washington State Twin Registry (WSTR) in the USA. The variables collected included, BMI, age, race and zygosity. This study used Generalized Estimating Equation (GEE) modeling to determine the relationships between twin pairs and variables of interest such as breast cancer and sex concordance. Zygosity, BMI, age and race were used for adjustment. Proband wise concordance was done to ascertain the heritability of breast cancer in twins.ResultsBeing a female-female twin pair increased the odds of breast cancer by 34% (95%CI: 1.18-1.53). After adjusting for zygosity, age, BMI, race, and childbirth, the odds of breast decreased by 31% in female-female twin pairs [AOR (95%CI):0.69 (0.53-0.90)]. The proband wise concordance was higher in monozygotic twins as compared to dizygotic twins. The values for dizygotic and monozygotic twins were 4 and 17 respectively.ConclusionThe findings of the study show that there is a positive association between sex concordance and breast cancer in female twins though other factors such as zygosity, BMI and age can influence breast cancer diagnosis. From our study, the proband wise concordance for monozygotic twins was higher than that of dizygotic twins. Breast cancer is therefore considered heritable.
Artificial light is the main driver of nocturnal feeding by the Rock dove (Columba livia) in urban areas
Authors: Leveau Lucas M. 
Published: April 2019

AbstractArtificial light at night (ALAN) is one of the most extreme alterations of urban areas, which drives nocturnal activity by diurnal species. Although the Rock Dove (Columba livia) is a common species in urban centers worldwide known to have nocturnal activity in urban areas, it is unknown what is the role of ALAN in its nocturnal activity. Moreover, studies that address the relationship between ALAN and nocturnal activity of diurnal birds are scarce in the Southern hemisphere. The objectives of this study were: 1) to evaluate the extent of nocturnal activity in the Rock Dove in large cities of Argentina; and 2) to analyze the influence of ALAN, pedestrian traffic and car traffic on the nocturnal activity in two cities, Buenos Aires and Salta. I visited the most urbanized areas of five large cities in Argentina, and surveyed lighted streets once after 30 minutes after sunset. In Buenos Aires and Salta, I compared environmental conditions between sites were doves were seen feeding with random sites were doves were not recorded feeding. Nocturnal feeding of the Rock Dove was recorded in three of five cities surveyed. ALAN was positively related to nocturnal feeding activity in Salta and Buenos Aires. The results obtained suggest that urbanization promotes a nocturnal activity of the Rock Dove, which occurs in cities located in a vast range of altitudes and biogeographic contexts. Moreover, the nocturnal activity is mainly driven by ALAN, which probably alters the circadian rhythm of doves.
Trait-specific trade-offs prevent niche expansion in two parasites
Authors: Lievens Eva J. P. , Michalakis Yannis , Lenormand Thomas 
Published: April 2019

AbstractThe evolution of host specialization has been studied intensively, yet it is still often difficult to determine why parasites do not evolve broader niches – in particular when the available hosts are closely related and ecologically similar. Here, we used an experimental evolution approach to study the evolution of host specialization, and its underlying traits, in two sympatric parasites:Anostracospora rigaudiandEnterocytospora artemiae, microsporidians infecting the brine shrimpArtemia franciscanaandArtemia parthenogenetica. In the field, both parasites regularly infect both hosts, yet experimental work has revealed that they are each partially specialized. We serially passaged the parasites on one, the other, or an alternation of the two hosts; after ten passages, we assayed the infectivity, virulence, and spore production rate of the evolved lines. In accordance with previous studies,A. rigaudimaintained a higher fitness onA. parthenogenetica, andE. artemiaeonA. franciscana, in all treatments. The origin of this specialization was not infectivity, which readily evolved and traded off weakly between the host species for both parasites. Instead, the overall specialization was caused by spore production, which did not evolve in any treatment. This suggests the existence of a strong trade-off between spore production inA. franciscanaand spore production inA. parthenogenetica, making this trait a barrier to the evolution of generalism in this system. This study highlights that the shape of between-host trade-offs can be very heterogeneous across parasite traits, so that only some traits are pivotal to specialization.
Identification of a dominant chlorosis phenotype through a forward screen of theTriticum turgidumcv. Kronos TILLING population
Authors: Harrington Sophie A. , Cobo Nicolas , Karafiátová Miroslava , Doležel Jaroslav , Borrill Philippa , Uauy Cristobal 
Published: April 2019

AbstractDurum wheat(Triticum turgidum)derives from a hybridization event approximately 400,000 years ago which led to the creation of an allotetraploid genome. Unlike with more ancient whole genome duplications, the evolutionary recent origin of durum wheat means that its genome has not yet been fully diploidised. As a result, many of the genes present in the durum genome act in a redundant fashion, meaning that, in many cases, loss-of-function mutations must be present in both gene copies to observe a phenotypic effect. This redundancy has hindered the use of forward genetic screens in durum wheat. Here we use a novel set of induced variation within the cv. Kronos TILLING population to identify a locus controlling a dominant, environmentally-dependent chlorosis phenotype. We carried out a forward screen of the sequenced cv. Kronos TILLING lines for senescence phenotypes and identified a single line with a dominant early senescence and chlorosis phenotype. Mutant plants contained overall less chlorophyll throughout their development and displayed premature flag leaf senescence. A segregating population was classified into discrete phenotypic groups and subjected to bulked-segregant analysis using exome capture followed by next-generation sequencing. This allowed the identification of a single region on chromosome 3A,Yellow Early Senescence 1 (YES-1),which was associated with the mutant phenotype. To obtain further SNPs for fine-mapping, we isolated chromosome 3A using flow sorting and sequenced the entire chromosome. By mapping these reads against both the cv. Chinese Spring reference sequence and the cv. Kronos assembly, we could identify high-quality, novel EMS-induced SNPs in non-coding regions withinYES-1that were previously missed in the exome capture data. This allowed us to fine-mapYES-1to 4.3 Mb, containing 59 genes. Our study shows that populations containing induced variation can be sources of novel dominant variation in polyploid crop species, highlighting their importance in future genetic screens. We also demonstrate the value of using cultivar-specific genome assemblies alongside the gold-standard reference genomes particularly when working with non-coding regions of the genome. Further fine-mapping of theYES-1locus will be needed to identify the causal SNP underpinning this dominant, environmentally dependent phenotype.
Purposeful Design of a Survey Tool to Evaluate the Adequacy of Hospitals’ Water Sanitation and Hygiene and Allocate Responsibility for Action – from Wash FIT to Wash Fast
Authors: Maina Michuki , Zosi Mathias , Kimemia Grace , Mwaniki Paul , Hayter Arabella , Montgomery Margaret , McKnight Jacob , Tosas-Auguet Olga , Schultsz Constance , English Mike 
Published: April 2019

ABSTRACTBackgroundPoor water sanitation and hygiene (WASH) in health care facilities increases hospital associated infections and results in greater use of second line antibiotics, which drives antimicrobial resistance. The existing assessment tool, Water and Sanitation for Health Facility Improvement Tool (WASH FIT), is designed for self-assessment in smaller primary facilities. A tool is needed for larger facilities with multiple inpatient units, that supports comparison of multiple facilities and identifies who is responsible for action at different levels of the health system.MethodsWe adapted the WASH FIT tool to: 1) create a simple numeric scoring approach to enable comparison of hospitals and facilitate tracking of WASH performance over time; (2) identify indicators that can be assessed and scored for each hospital ward to help identify variation within facilities and; (3) identify those responsible to effect positive change at different levels of the health system. We used a pilot, analysis of interview data and consultative stakeholder meetings to establish the feasibility and face validity of the WASH Facility Survey Tool (WASH FAST).ResultsWASH FAST can be used to produce an aggregate percentage score at facility level to summarise hospitals’ overall WASH status and illustrate variation across hospitals. Thirty-four of the 65 indicators spanning four WASH domains can be assessed at ward level enabling between ward variations to be highlighted. Three levels of responsibility for WASH service monitoring and improvement were identified that were supported by qualitative data and multiple stakeholders: the county/regional level, hospital senior management and the infection prevention and control committee within the healthcare facility.ConclusionWe propose WASH FAST can be used as a survey tool to assess, improve and monitor progress of WASH and IPC in hospitals in resource-limited settings, providing useful data for decision making and contributing to wider quality improvement efforts.
Understanding the impact of financial incentives on NFC mobile payment adoption
Authors: Zhao Haidong , Anong Sophia T. , Zhang Lini 
Published: April 2019

PurposeThe purpose of this paper is to investigate the effects of financial incentives on consumers’ intention to adopt near field communication (NFC) mobile payment.Design/methodology/approachAn online experiment was conducted crossing two levels of incentive types (cash back and discount), two levels of incentive amounts (5 and 10 percent), and two levels of incentive promotion periods (one and three months). A total of eight treatment conditions plus one control group comprised the 2×2×2 factorial design. A sample of 463 subjects with no prior experience with NFC mobile payment was recruited using a Qualtrics panel.FindingsThis study found that: the availability of financial incentives had a positive effect on intention to adopt NFC mobile payment; financial incentives indirectly affected intention through perceived risk; and while different types, amounts or promotion periods did not seem to matter for those in the low perceived risk group, the main effect of promotion period and the interaction effect between amount and promotion period were significant for those in the high perceived risk group.Research limitations/implicationsThe study sample was limited from 18 to 35 age group, which could have affected the varied effect of the different attributes of incentives that were examined.Originality/valueThis study is the first to give some empirical evidence about the impact of financial incentives on NFC mobile payment adoption. The results provide insight to providers as well as retailers offering the incentive payment option.
The effects of risk appraisal and coping appraisal on the adoption intention of m-payment
Authors: Wang Shih-Tse 
Published: April 2019

Purpose
Although debit and credit cards are widely accepted, consumers still have significant concerns pertaining to the risk of the cards’ usage. Mobile payment (m-payment) acts as identification and a virtual card for consumers, and is viewed as more secure than card payments. However, the influence of consumers’ appraisal of debit and credit cards usage and using m-payment on the adoption intention of m-payment is unclear. Using the protection motivation theory, the purpose of this paper is to explore the effect of risk appraisal of using debit or credit cards and coping appraisal of using m-payment on the adoption intention of m-payment.

Design/methodology/approach
A total of 418 volunteers participated in this study, and structural equation modeling was employed to test the employed conceptual model.

Findings
The results revealed that risk appraisal (i.e. vulnerability, severity and benefit) of using debit or credit cards did not affect m-payment adoption intention. Moreover, self-efficacy and response efficacy positively affected m-payment adoption intention, whereas response cost negatively influenced m-payment adoption intention.

Originality/value
Both theoretical and practical implications are presented in this paper for m-payment marketers to develop effective communication strategies for promoting m-payment adoption.
The intellectual capital of higher education institutions
Authors: Pedro Eugénia , Leitão João , Alves Helena 
Published: April 2019

PurposeThe purpose of this paper is to present an innovative operational proposal for measuring the intellectual capital (IC) of higher education institutions (HEIs) through a strategic prospective lens of analysis.Design/methodology/approachAfter providing a literature review on the methods for measuring IC that focuses on the organisational IC of HEIs, four case studies applied to Portuguese HEIs are presented, using a matrix of cross-referenced impacts – multiplications applied to a classification (MICMAC) approach.FindingsThe empirical findings reveal how human capital, structural capital and relational capital make up the core components and provide a fairly diversified list of the measurement indicators for the operational evaluation of the IC of HEIs.Practical implicationsIt contributes into the literature of strategic prospective analysis of HEIs by: analysing the measurement systems for the organisational IC interrelated with HEIs; identifying the key components to the organisational IC of HEIs and their respective measurement indicators; and draufting a new method for operationally implementing organisational IC through the systematic application of the components and indicators identified.Originality/valueThrough an innovative vision, the present study reconciles and systematically structures the methods already proposed by other authors before presenting an innovative operational approach and an alternative to the already existing methods. In addition, the structure of this proposal itself enables HEIs to choose from among the various indicators proposed for IC, correspondingly those that best align with the type of institution under evaluation.