bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating time of HIV-1 infection from next-generation sequence diversity
Authors: Puller Vadim , Neher Richard , Albert Jan 
Published: April 2017

AbstractEstimating the time since infection (TI) in newly diagnosed HIV-1 patients is challenging, but important to understand the epidemiology of the infection. Here we explore the utility of virus diversity estimated by next-generation sequencing (NGS) as novel biomarker by using a recent genome-wide longitudinal dataset obtained from 11 untreated HIV-1-infected patients with known dates of infection. The results were validated on a second dataset from 31 patients.Virus diversity increased linearly with time, particularly at 3rd codon positions, with little inter-patient variation. The precision of the TI estimate improved with increasing sequencing depth, showing that diversity in NGS data yields superior estimates to the number of ambiguous sites in Sanger sequences, which is one of the alternative biomarkers. The full advantage of deep NGS was utilized with continuous diversity measures such as average pairwise distance or site entropy, rather than the fraction of polymorphic sites. The precision depended on the genomic region and codon position and was highest when 3rd codon positions in the entirepolgene were used. For these data, TI estimates had a mean absolute error of around 1 year. The error increased only slightly from around 0.6 years at a TI of 6 months to around 1.1 years at 6 years.Our results show that virus diversity determined by NGS can be used to estimate time since HIV-1 infection many years after the infection, in contrast to most alternative biomarkers. We provide the regression coefficients as well as web tool for TI estimation.Author summaryHIV-1 establishes a chronic infection, which may last for many years before the infected person is diagnosed. The resulting uncertainty in the date of infection leads to difficulties in estimating the number of infected but undiagnosed persons as well as the number of new infections, which is necessary for developing appropriate public health policies and interventions. Such estimates would be much easier if the time since HIV-1 infection for newly diagnosed cases could be accurately estimated. Three types of biomarkers have been shown to contain information about the time since HIV-1 infection, but unfortunately, they only distinguish between recent and long-term infections (concentration of HIV-1-specific antibodies) or are imprecise (immune status as measured by levels of CD4+ T-lymphocytes and viral sequence diversity measured by polymorphisms in Sanger sequences).In this paper, we show that recent advances in sequencing technologies, i.e. the development of next generation sequencing, enable significantly more precise determination of the time since HIV-1 infection, even many years after the infection event. This is a significant advance which could translate into more effective HIV-1 prevention.
Boreal river impoundments caused little change in fish diversity but clear community assemblage shifts: A multi-scale analysis
Authors: Turgeon Katrine , Turpin Christian , Gregory-Eaves Irene 
Published: April 2017

AbstractHydroelectricity is often presented as a clean and renewable energy source, but river flow regulation and fragmentation caused by dams are recognized to impact aquatic biodiversity in temperate and tropical ecosystems. However, the effects of boreal river impoundment are not clear as the few studies that exist have not been able to separate the hydrological changes brought about by dams from other factors (e.g.fish stocking, and species introduction).We adopted a multi-scale analysis to examine changes in nearshore fish communities over 20 years (spanning before and after impoundment) using a network of 24 sampling stations spread across from four reservoirs and two hydroelectricity complexes located in the boreal region (Northern Québec, Canada). Given the remote location, confounding factors were minimal.We found no strong temporal trends in alpha- and gamma-diversity in impacted stations (upstream and downstream of the dam) relative to reference sites across the three spatial scales. Using beta-diversity analyses, we also detected a high stability in fish composition over time and space at the complex and reservoir scales.At the scale of the sampling stations, we observed higher rates of species turnover (beta-diversity) coincident with the time of reservoir filling and shortly after. Likewise, we detected species assemblage shifts that correlated with time since impoundment only at the sampling station scale. This pattern was masked at the complex and reservoir scales.Synthesis and applications. Overall, the isolated effect of impoundment in these remote boreal ecosystems caused no loss of species and little change in fish diversity over 20 years, but resulted in substantial species assemblage shifts. Our work shows that examining community data at different scales is key to understand the anthropogenic impacts on fish biodiversity.
A novel role forEts4in axis specification and cell migration in the spiderParasteatoda tepidariorum
Authors: Pechmann Matthias , Benton Matthew A. , Kenny Nathan J. , Posnien Nico , Roth Siegfried 
Published: April 2017

AbstractOrganizers play important roles during the embryonic development of many animals. The most famous example is the Spemann organizer that sets up embryonic axes in amphibian embryos.In spiders, a group of BMP secreting mesenchymal cells (the cumulus) functions as an organizer of the dorsoventral axis. Similar to experiments performed with the Spemann organizer, transplantation of the cumulus is able to induce a secondary axis in spiders.Despite the importance of this structure, it is unknown which factors are needed to activate cumulus specific gene expression.To address this question, we performed a transcriptomic analysis of early embryonic development in the spiderParasteatoda tepidariorum.Through this work, we found that the transcription factorPt-Ets4is needed for cumulus integrity, dorsoventral patterning and for the activation ofPt-hunchbackandPt-twistexpression. Furthermore, ectopic expression ofPt-Ets4is sufficient to induce cell delamination and migration by inducing a mesoderm-like cell fate.
Effects of mestranol on estrogen receptors expression in zebrafish
Authors: Cheng Lianqiang , Wang Xiaowen , Li Shijun , Liu Yongjun , Guo Zhengxin 
Published: April 2017

AbstractThe estrogen receptor (ER) genes, which encode a group of important ligand-activated transcriptional factors, can modulate estrogen-target gene activities. Zebrafish (Danio rerio) have three ER receptor genes,esr1,esr2a, andesr2b. In this study, we examined the mRNA expression levels of these ER receptors after treatment with mestranol (EE3ME). Zebrafish larvae were exposed to 0.01, 0.1, 1, and 10 mg/L from 6 hours post-fertilization (hpf) and the mRNA expression levels of the ER genes were determined at 24, 48, 72 and 96 hpf. Treatment with mestranol led to a significant stimulation ofesr1mRNA expression at lower concentration and reached maximum at 72 hpf, however, the esr1 mRNA levels were reduced at higher mestranol concentration during exposure. The gene expression ofesr2bwas markedly decreased and theesr2aremained unaffected at all concentration in the duration. Altogether, these results suggested mestranol might cause the disruption of endocrine activities in fish by mediating ER genes expression.
Meaning-making through research
Authors: Kulkarni Mukta 
Published: April 2017

Purpose
In outlining the author’s experiences as a researcher and as an individual who engages with persons with a disability, the author wonders what meaningful research means when research subjects are people that society lumps together, largely views as stigmatized, and does not seem to understand. The author also notes how the research journey has impacted the author as an individual in rather unexpected ways. The paper aims to discuss this issues.

Design/methodology/approach
The author notes her personal experiences which can help all of us surface and think through our attempts at meaning-making through research.

Findings
When we do not quite understand our research subjects, the syntax of our thoughts can be dictated by our institutional contexts, and it is likely that we capture and feed the period’s dominant assumptions back into the context.

Originality/value
The author’s journey has been marked with worries, and has taught the author humility and acceptance. It has taught the author how we need to understand the subjects as whole beings, our institutional setting as it predisposes us to organize our research worlds, and our own biases as a researcher. Learning this is especially important for all of us when we study stigmatized subjects because definitions, measurement, and how we showcase a collective have implications for individual human beings.
Working with the divides
Authors: Avery Helen , Nordén Birgitta 
Published: April 2017

PurposeThe paper aims to provide a conceptual map of how to mediate between sustainability theory and practice in higher education and how disciplinary divides can be bridged. It further looks at issues linked to knowledge views and drivers for institutional change that affect opportunities for whole institution development promoting action preparedness.Design/methodology/approachTaking its point of departure in the University Educators for Sustainable Development report UE4SD (2014, 2015), the paper discusses ways that ideas and interaction can be mediated in higher education settings, to connect sustainability research with vocational programmes. Different options are considered and compared.FindingsAlthough the literature stresses both action orientation and the need for holistic transdisciplinary approaches, many institutional drivers limit opportunities for more integrating approaches.Research limitations/implicationsHowever, while conclusions may hold for universities at an overarching level, it is likely that certain research and teaching environments have been able to transcend such barriers.Practical implicationsConceptually mapping the different forms that dialogue, interaction and flows of ideas take within higher education institutions has relevance for whole institution development for sustainability.Social implicationsImportantly, producing sustainability science with relevance to practice in various professions is a fundamental condition to support accelerated transitions to sustainability at societal levels.Originality/valueThe paper makes a significant contribution by focusing on concrete institutional pathways for knowledge exchange and negotiation that can support education for sustainability in higher education.
Determinants of services co-creation with business customers
Authors: Jouny-Rivier Elodie , Reynoso Javier , Edvardsson Bo 
Published: April 2017

PurposeThis paper aims to identify and analyze factors that determine firms’ commitment to co-create new services with business customers.Design/methodology/approachA quantitative study based on a scenario method, involving an online survey of French service companies, reveals the determinants of commitment to service co-creation.FindingsCustomer benefits and organizational sacrifices, as well as firm-related factors (specialization, partners’ involvement and innovativeness) correlate with firms’ commitment to co-create new services. The proposed, empirically grounded model details factors that determine firms’ commitment to co-create new services with business customers, including innovative culture as a key determinant.Practical implicationsThe identified factors that affect firms’ commitment to co-create services can guide managers’ efforts to improve customer relationships and thus their service innovation processes.Originality/valueThis study identifies and analyzes characteristics of committed firms, as well as the benefits and sacrifices they face in co-creating new services, in a novel way. Thus, it helps define the fit between a service offering and business customers’ participation in new service development contexts.
The interplay of customer experience and commitment
Authors: Keiningham Timothy , Ball Joan , Benoit (née Moeller) Sabine , Bruce Helen L. , Buoye Alexander , Dzenkovska Julija , Nasr Linda , Ou Yi-Chun , Zaki Mohamed 
Published: April 2017

PurposeThis research aims to better understand customer experience, as it relates to customer commitment and provides a framework for future research into the intersection of these emerging streams of research.Design/methodology/approachThis research contributes to theoretical and practical perspectives on customer experience and its measurement by integrating extant literature with customer commitment and customer satisfaction literature.FindingsThe breadth of the domains that encompass customer experience – cognitive, emotional, physical, sensorial and social – makes simplistic metrics impossible for gauging the entirety of customers’ experiences. These findings provide strong support of the need for new research into customer experience and customer commitment.Practical implicationsGiven the complexity of customer experience, managers are unlikely to track and manage all relevant elements of the concept. This research provides a framework identifying empirically the most salient attributes of customer experience with particular emphasis on those elements that enhance commitment. This offers insight into service design to correspond with specific commitment and experience dimensions.Originality/valueThis research is the first to examine the customer experience as it relates to customer commitment – a key factor in customer loyalty, positive word of mouth and other desired outcomes for managers and marketers. This paper provides a framework for future research into these emerging topics.
Red: NCSS notable trade book lesson plan
Authors: Sunal Cynthia , Odebiyi Oluseyi Matthew 
Published: April 2017

Purpose
This early grades lesson for ages 4-7 explores the concept of bullying, focusing on its occurrence among students in day-to-day school experiences. The purpose of this paper is to depict typical bullying occurring in school, for example, during peer play using the book Red as a resource.

Design/methodology/approach
The story line describes bullying and how one’s actions can contribute to promoting and to preventing bullying.

Findings
The story line describes bullying and how one’s actions can contribute to promoting and to preventing bullying.

Practical implications
The lesson sequence builds awareness of the consequences of bullying and how to deal with bullying when it occurs. The focus is on non-aggressive, non-provoking, active approaches to responding to bullying.

Originality/value
The aim is to help students develop anti-bullying behaviors and to make school a safe place for every student.
Classroom convention: teaching comparative constitutional design through simulation
Authors: Fisher Sarah , Justwan Florian 
Published: April 2017

Purpose
The purpose of this paper is to detail a simulation exploring the academic and real-world debates surrounding constitutional design.

Design/methodology/approach
The authors deployed this simulation in different contexts: undergraduate courses in comparative politics and middle school classrooms of gifted students in India.

Findings
In conjunction with discussion of institutional setup, such as parliamentary vs presidential systems and judicial review vs parliamentary sovereignty, the students were required to design a new constitution for a fictional country that just overthrew a brutal dictator. Throughout the simulation, the students were assigned to be the representatives of a particular ethnic group, each with distinct interests to be represented during the constitutional convention.

Originality/value
The authors detail the learning objectives and simulation setup for this constitutional convention. Finally, the authors discuss some issues raised by the students during the simulation.
“Women know how to get things done”: narrative of an intersectional movement
Authors: Vickery Amanda Elizabeth 
Published: April 2017

Purpose
The purpose of this paper is to explore how African-American women, both individually and collectively, were subjected to both racism and sexism when participating within civil rights organizations.

Design/methodology/approach
Because of the intersection of their identities as both African and American women, their experiences participating and organizing within multiple movements were shaped by racism and patriarchy that left them outside of the realm of leadership.

Findings
A discussion on the importance of teaching social studies through an intersectional lens that personifies individuals and communities traditionally silenced within the social studies curriculum follows.

Originality/value
The aim is to teach students to adopt a more inclusive and complex view of the world.
Separate is Never Equal: Sylvia Mendez and Her Family’s Fight for Desegregation: written by Duncan Tonatiuh
Authors: Sturm Elizabeth 
Published: April 2017

Purpose
The purpose of this paper is to use Separate is Never Equal: Sylvia Mendez and Her Family’s Fight for Desegregation, by Duncan Tonatiuh, along with other materials on school segregation to address the question, is separate ever equal?

Design/methodology/approach
Students compare and contrast segregated schooling using a Venn diagram, then research other instances of school segregation, paying attention to the time periods, geographic locations, and impact on segregated individuals. In pairs, students identify these locations on a US map and create a class timeline of the instances of segregation they uncover. Using their research, the class then discusses segregation and its impact on the segregated groups and individuals. Afterwards, students compare their school to the schools researched to determine if segregation exists in their school, and form a class position statement on the importance and benefits of school desegregation.

Findings
Students will build an understanding of the importance and benefits of school desegregation and the negative impact of segregation.

Originality/value
This lesson plan brings together multiple texts that illustrate the impact of segregation on various cultures in America.
Serum H‐ficolin levels: Clinical association with interstitial lung disease in patients with systemic sclerosis
Authors: Miyagawa Takuya , Asano Yoshihide , de Mestier Yuka , Saigusa Ryosuke , Taniguchi Takashi , Yamashita Takashi , Nakamura Kouki , Hirabayashi Megumi , Miura Shunsuke , Ichimura Yohei , Takahashi Takehiro , Yoshizaki Ayumi , Miyagaki Tomomitsu , Sugaya Makoto , Sato Shinichi 
Published: April 2017

AbstractFicolins, a group of oligomeric lectins consisting of three isoforms (H‐, L‐ and M‐ficolin), contribute to innate immunity via activating the complement pathway and/or acting directly as opsonins against pathogens and apoptotic cells. Because apoptotic cells likely drive the development of systemic sclerosis (SSc) partly through innate immunity, we assessed the clinical association of serum H‐ficolin levels in SSc patients. Despite no difference in serum H‐ficolin levels between SSc and control subjects, SSc patients with decreased serum H‐ficolin levels tended to have a higher prevalence of interstitial lung disease (ILD). More importantly, serum H‐ficolin levels inversely correlated with ground‐glass opacity score on chest computed tomography in SSc‐ILD patients. Therefore, H‐ficolin‐related innate immunity may be involved in SSc‐ILD development.
Mechanism of the vasorelaxant effect induced by trans‐4‐methyl‐β‐nitrostyrene, a synthetic nitroderivative, in rat thoracic aorta
Authors: Teófilo Taylena Maria , Arruda‐Barbosa Loeste , Rodrigues‐Silva Jussara Mathyelle , Vale Joyce Karen Lima , Borges Rosivaldo Santos , Duarte Gloria Pinto , Magalhães Pedro Jorge Caldas , Lahlou Saad 
Published: April 2017

SummaryMechanisms underlying the vasorelaxant effects of trans‐4‐methyl‐β‐nitrostyrene (T4MeN) were studied in rat aortic rings. In endothelium‐intact preparations, T4MeN fully and similarly relaxed contractions induced by phenylephrine (PHE) (IC50 = 61.41 [35.40‐87.42] μmol/L) and KCl (IC50 = 83.50 [56.63‐110.50] μmol/L). The vasorelaxant effect of T4MeN was unchanged by endothelium removal, pretreatment with L‐NAME, indomethacin, tetraethylammonium, ODQ or MDL‐12,330A. Under Ca2+‐free conditions, T4MeN significantly reduced with a similar potency: (i) phasic contractions induced by PHE, but not by caffeine; (ii) contractions due to CaCl2 in aortic preparations stimulated with PHE (in the presence of verapamil) or high KCl; (iii) contractions evoked by the restoration of external Ca2+ levels after depletion of intracellular Ca2+ stores in the presence of thapsigargin. In contrast, T4MeN was more potent at inhibiting contractions evoked by the tyrosine phosphatase inhibitor, sodium orthovanadate, than those induced by the activator of PKC, phorbol‐12,13‐dibutyrate. These results suggest that T4MeN induces an endothelium‐ independent vasorelaxation that appears to occur intracellularly through the inhibition of contractions that are independent of Ca2+ influx from the extracellular milieu but involve phosphorylation of tyrosine residues.
Contracting on GAAP Changes: Large Sample Evidence
Authors: CHRISTENSEN HANS B. , NIKOLAEV VALERI V. 
Published: April 2017

ABSTRACTWe explore revealed preferences for the contractual treatment of changes to GAAP in a large sample of private credit agreements issued by publicly held U.S. firms. We document a significant time‐trend toward excluding GAAP changes from the determination of covenant compliance over the period from 1994 to 2012. This trend is positively associated with proxies for standard setters’ shift in focus toward relevance and international accounting harmonization. At the firm level, borrowers facing higher uncertainty are more likely to write contracts that include GAAP changes, but these firms also show a more pronounced time‐trend toward excluding GAAP changes. While this evidence is broadly consistent with an efficiency role for GAAP changes in debt contracting, it is also consistent with a shift in standard setters’ focus offering a partial explanation of why fewer contracts rely on GAAP changes in 2012 than in 1994.
Do males choose their mates in the lekking moth Achroia grisella? Influence of female body mass and male reproductive status on male mate choice
Authors: Goubault Marlène , Burlaud Rebecca 
Published: April 2017

AbstractLekking males aggregate to attract females and contribute solely to egg fertilization, without any further parental care. Evolutionary theory therefore predicts them to be nonchoosy toward their mates, because any lost mating opportunities would outweigh the benefits associated with such preferences. Nevertheless, due to time costs, the production of energetically costly sexual displays, and potential sperm limitation, the mating effort of lekking males is often considerable. These factors, combined with the fact that many females of varying quality are likely to visit leks, could favor the evolution of male mate preferences. Here, we show that males of the lekking lesser wax moth, Achroia grisella, were indeed more likely to mate with heavier females in choice experiments, even at their virgin mating (i.e., when their reproductive resources have not yet been depleted by previous matings). This differential female mating success could not be attributed to female behavior as heavy and light females showed similar motivation to mate (i.e., latency to approach the males) and time to copulate. Males seem to benefit from mating with heavier females, as fecundity positively correlated with female mass. This new empirical evidence shows that male mate choice may have been underestimated in lekking species.