bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass spectrometry as a quantitative tool in plant metabolomics
Authors: Jorge Tiago F. , Mata Ana T. , António Carla 
Published: September 2016

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.
This article is part of the themed issue ‘Quantitative mass spectrometry’.
Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response
Authors: Jones Jana , Mirzaei Mehdi , Ravishankar Prathiba , Xavier Dylan , Lim Do Seon , Shin Dong Hoon , Bianucci Raffaella , Haynes Paul A. 
Published: September 2016

We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS–PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography–mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.
This article is part of the themed issue ‘Quantitative mass spectrometry’.
On the preservation of non-covalent protein complexes during electrospray ionization
Authors: Chingin Konstantin , Barylyuk Konstantin , Chen Huanwen 
Published: September 2016

The application range of electrospray ionization mass spectrometry for the quantitative determination of stoichiometries and binding constants for non-covalent protein complexes is broadly discussed. The underlying fundamental question is whether or not the original molecular equilibrium can be preserved during the ionization process and be revealed by subsequent mass spectrometry analysis. Here, we take a new look at this question by discussing recent studies in droplet chemistry.This article is part of the themed issue ‘Quantitative mass spectrometry’.
The significance of petroleum bitumen in ancient Egyptian mummies
Authors: Clark K. A. , Ikram S. , Evershed R. P. 
Published: September 2016

Mummification was practised in ancient Egypt for more than 3000 years, emerging from initial observations of buried bodies preserved by natural desiccation. The use of organic balms (and other funerary practices) was a later introduction necessitated by more humid burial environments, especially tombs. The dark colour of many mummies led to the assumption that petroleum bitumen (or natural asphalt) was ubiquitous in mummification; however, this has been questioned for more than 100 years. We test this by investigating 91 materials comprising balms, tissues and textiles from 39 mummies dating fromca3200 BC to AD 395. Targeted petroleum bitumen biomarker (steranes and hopanes) analyses by gas chromatography-mass spectrometry selected ion monitoring (GC-MS SIM,m/z217 and 191) showed no detectable bitumen use before the New Kingdom (ca1550–1070 BC). However, bitumen was used in 50% of New Kingdom to Late Period mummies, rising to 87% of Ptolemaic/Roman Period mummies. Quantitative determinations using14C analyses reveal that even at peak use balms were never more than 45%w/wbitumen. Critically, the dark colour of balms can be simulated by heating/ageing mixtures of fats, resins and beeswax known to be used in balms. The application of black/dark brown balms to bodies was deliberate after the New Kingdom reflecting changing funerary beliefs and shifts in religious ideology.This article is part of the themed issue ‘Quantitative mass spectrometry’.
Discovery of flavivirus-derived endogenous viral elements in twoAnophelesmosquito genomes supports the existence ofAnopheles-associated insect-specific flaviviruses
Authors: Lequime Sebastian , Lambrechts Louis 
Published: September 2016

AbstractTheFlavivirusgenus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of theAedesandCulexgenera in the Culicinae subfamily, which also includes most arbovirus vectors. Mosquitoes of the Anophelinae subfamily are not considered significant arbovirus vectors, however flaviviruses have occasionally been detected in field-caughtAnophelesspecimens. Whether such observations reflect occasional spillover or laboratory contamination or whetherAnophelesmosquitoes are natural hosts of flaviviruses is unknown. Here, we providein silicoandin vivoevidence of transcriptionally active, flavivirus-derived endogenous viral elements (EVEs) in the genome ofAnopheles minimusandAnopheles sinensis. Such non-retroviral endogenization of RNA viruses is consistent with a shared evolutionary history between flaviviruses andAnophelesmosquitoes. Phylogenetic analyses of the two newly described EVEs support the existence of a distinct clade ofAnopheles-associated ISFs.
Deriving robust biomarkers from multi-site resting-state data: An Autism-based example
Authors: Abraham Alexandre , Milham Michael , Martino Adriana Di , Craddock R. Cameron , Samaras Dimitris , Thirion Bertrand , Varoquaux Gael 
Published: September 2016

AbstractResting-state functional Magnetic Resonance Imaging (R-fMRI) holds the promise to reveal functional biomarkers of neuropsychiatric disorders. However, extracting such biomarkers is challenging for complex multi-faceted neuropathologies, such as autism spectrum disorders. Large multi-site datasets increase sample sizes to compensate for this complexity, at the cost of uncontrolled heterogeneity. This heterogeneity raises new challenges, akin to those face in realistic diagnostic applications. Here, we demonstrate the feasibility of inter-site classification of neuropsychiatric status, with an application to the Autism Brain Imaging Data Exchange (ABIDE) database, a large (N=871) multi-site autism dataset. For this purpose, we investigate pipelines that extract the most predictive biomarkers from the data. These R-fMRI pipelines build participant-specific connectomes from functionally-defined brain areas. Connectomes are then compared across participants to learn patterns of connectivity that differentiate typical controls from individuals with autism. We predict this neuropsychiatric status for participants from the same acquisition sites or different, unseen, ones. Good choices of methods for the various steps of the pipeline lead to 67% prediction accuracy on the full ABIDE data, which is significantly better than previously reported results. We perform extensive validation on multiple subsets of the data defined by different inclusion criteria. These enables detailed analysis of the factors contributing to successful connectome-based prediction. First, prediction accuracy improves as we include more subjects, up to the maximum amount of subjects available. Second, the definition of functional brain areas is of paramount importance for biomarker discovery: brain areas extracted from large R-fMRI datasets outperform reference atlases in the classification tasks.
Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Authors: Humphrey Jack , Emmett Warren , Fratta Pietro , Isaacs Adrian M. , Plagnol Vincent 
Published: September 2016

AbstractReliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those linked to TDP-43 do not originate from a particular family of transposable element. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons.This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. Our quantitative analysis pipeline confirms the presence of cryptic exons during TDP-43 depletion and will aid investigation of their relevance to disease.
Towards an Open Data Framework for Body Sensor Networks Supporting Bluetooth Low Energy
Authors: Singh Ninoshka K. , Ricke Darrell O 
Published: September 2016

AbstractMajor companies, healthcare professionals, the military, and other scientists and innovators are now sensing that fitness and health data from wearable biosensors will likely provide new discoveries and insights into physiological, cognitive, and emotional health status of an individual. Having the ability to collect, process, and correlate data simultaneously from a set of heterogonous biosensor sources may be a key factor in informing the development of new technologies for reducing health risks, improving health status, and possibly preventing and predicting disease. The challenge in achieving this is getting easy access to heterogeneous data from a set of disparate sensors in a single, integrated wearable monitoring system. Often times, the data recorded by commercial biosensing devices are contained within each manufacturer’s proprietary platform. Summary data is available for some devices as free downloads or included only in annual premium memberships. Access to raw measurements is generally unavailable, especially from a custom developed application that may include prototype biosensors. In this paper, we explore key ideas on how to leverage the design features of Bluetooth Low Energy to ease the integration of disparate biosensors at the sensor communication layer. This component is intended to fit into a larger, multi-layered, open data framework that can provide additional data management and analytics capabilities for consumers and scientists alike at all the layers of a data access model which is typically employed in a body sensor network system.
Willingness to pay for innovations
Authors: Sadik-Rozsnyai Orsolya 
Published: September 2016

Purpose
Whereas the impact of national culture on consumer innovativeness is widely discussed in the innovation literature, studies are scarce on consumer value and the related consumer willingness to pay (WTP) for innovations. Yet, innovative high-tech companies compete by enhancing their products with new attributes, and assessing consumer WTP for these innovative attributes in different countries is crucial to adapting the launching price and optimizing profits during the critical launch stage. To fill this gap, the purpose of this paper is to examine the impact of national culture and globalization on consumer value and the related WTP for technological innovations.

Design/methodology/approach
Data were collected in two culturally distinct but economically similar countries (France and Germany), using large representative and comparable consumer samples (n=642). Choice-based conjoint analysis was used as the principal method of data analysis.

Findings
This study reveals the significant impact of national culture on consumer value and the related WTP for technological innovations and the moderating effect of household income on this relationship.

Originality/value
This study is the first to reveal and provide strong empirical evidence of the impact of national culture on WTP for innovations. In addition, this study is the first to reveal the moderating effect of income on this relationship and to highlight an emerging European innovation adoption behavior.
Business model configurations: a five-V framework to map out potential innovation routes
Authors: Taran Yariv , Nielsen Christian , Montemari Marco , Thomsen Peter , Paolone Francesco 
Published: September 2016

Purpose
Despite the common understanding that business model (BM) innovation is of vital importance for securing competitive positioning in the market place, managers still seem to lack appropriate frameworks and tools which can support them in renewing and rejuvenating their company’s existing BM. The purpose of this paper is to develop a structural and comprehensive toolbox of available BM configurations, from which companies can choose, to innovate their BM upon, and to design an appropriate BM innovation framework which can facilitate them in re-designing, selecting, and implementing new BM configuration possibilities.

Design/methodology/approach
A structured literature review is conducted to identify all the relevant BM configurations. Then, a value driver analysis is performed to group these BM configurations into appropriate categories. Finally, an ontological classification scheme and a structural and workable process, i.e. a BM innovation framework, are inductively developed.

Findings
The paper systematically develops a list of 71 BM configurations and groups them into an ontological classification scheme according to five groups: Value Proposition, Value Segment, Value Configuration, Value Network, and Value Capture. The paper illustrates how the BM innovation framework, enabled by this ontological classification scheme, provides a platform for identifying BM innovation routes for companies, allowing managers to envisage radical, disruptive, and new-to-the-world BM configuration ideas, or apply existing configurations from other industrial settings in what may be deemed new-to-the-industry innovation.

Originality/value
The paper enriches the amount of potential BM configurations available for managers to choose from when innovating their BMs, and extends the analysis to five core BM configuration categories. Moreover, the BM innovation framework suggested highlights the strong relationships among the value drivers, thus presenting the opportunity for managers to assess potential conflicts or synergies between various value drivers, and to align the BM management process as a whole.
Transformational leadership in leading young innovators – a subordinate’s perspective
Authors: Uusi-Kakkuri Piia , Brandt Tiina , Kultalahti Susanna 
Published: September 2016

PurposeThe purpose of this paper is to investigate what kind of leadership young innovative people prefer and whether their level of innovativeness has an influence on those leadership preferences. It also asks specifically whether some leadership behaviours are preferred over others by young innovators, by comparing that group’s preferences to those of the majority of young people and an outlier group labelled laggards. Leadership preferences are studied in the context of transformational leadership covering transformational leadership, transactional leadership (including passive and active management by exception), rewarding, laissez-faire and authoritative leadership styles.Design/methodology/approachIn total, 297 Finnish university students completed a voluntary leadership behaviour questionnaire and an innovativeness scale. A non-parametric independent samples median test was run to determine if there were differences in the leadership preference score between the innovativeness level groups.FindingsResults indicate that the level of innovativeness influences leadership preferences. Receiving intellectual stimulation from their leader is more important to young innovators than it is to their peers but the former are also less comfortable with active management by exception.Originality/valueYoung innovators leadership preferences have not been studied. Harnessing the full power of this important talent pool is central to the future competitiveness of organizations and nations. This study intends to prompt discussion and studies on how to lead young innovators given their preferences.
Female entrepreneurs: motivations and constraints. An Italian regional study
Authors: Bianchi Marina , Parisi Valentino , Salvatore Renato 
Published: September 2016

Purpose
This paper aims to identify the specific contextual constraints that women might face in becoming entrepreneurs; to correlate these constraints with the motivations that have determined this choice; and to ascertain how strongly constraints and motivations are correlated with individual rewards in terms of personal satisfaction and economic payoffs.

Design/methodology/approach
The empirical base is a survey that the authors conducted among female entrepreneurs in a Southern province of Italy in 2012. Data are analyzed through a correspondence and cluster analysis. The socio-economic context of the province within which these female-led firms operate is taken into account by means of a correspondence canonical analysis.

Findings
In terms of results: first, two-thirds of female entrepreneurs in the province are positively motivated, and this is a determining factor in their choice to become entrepreneurs. This translates into they also being satisfied with the choice they made. Second, contrary to the expectations, being positively motivated and satisfied holds both for firms operating in more dynamic and demanding sectors and for small firms using little financial or human capital.

Research limitations/implications
The chosen research approach has allowed to identify the most important decisional variables that affect female entrepreneurial choice. However, as most of the variables are categorical, the research’s results remain descriptive.

Practical implications
Positive motivations and personal rewards are clearly relevant for women making an entrepreneurial choice. However, they are not enough to stimulate fully the potential for growth of their enterprises: education and a social environment conducive to female creative expression are also necessary. To this end, the authors suggest that an important function of change could be played in particular by universities by fostering a culture of creativity and entrepreneurship.

Social implications
By stressing the connections between positive motivations and wellbeing, the authors suggest that the promotion of women’s entrepreneurial choices through networks and education generates more than purely economic benefits. It also has positive effects on their quality of life and on social welfare as well.

Originality/value
This paper responds to a need – not yet fulfilled in the literature – to better understand the relations between women’s motivation, satisfaction and the type of business selected.
The role of networks for migration flows: an update
Authors: Beine Michel 
Published: September 2016

PurposeThe purpose of this paper is to cover the literature on the role migrants networks in explaining aggregate migration flows between countries. The author emphasizes the specific role of family immigration policies. To that purpose, the author covers briefly the recent experience of seven receiving countries to highlight the importance of these policies in explaining part of the observed network elasticities.Design/methodology/approachThe author first provides a small review of the literature and the issues at stake. The author then provides an update of the estimates of the network elasticities using the data set on migration stocks and flows from Ozdenet al.(2011). Using micro-founded gravity models, the author estimates the network elasticities and discusses the key driving mechanisms explaining their size as well the variation in the amplitude across categories of destination and over time. The author accounts for the issue of multilateral resistance to migration.FindingsThe author obtains estimates that are in line with the ones documented previously in the literature. The author finds that the role of networks in attracting migrants has increased after the 1970s. The author emphasizes the specific role of family immigration policies. To that purpose, the author covers briefly the recent experience of a set of receiving countries to highlight the importance of these policies in explaining part of the observed network elasticities.Originality/valueThis paper covers the literature on the role migrants networks in explaining aggregate migration flows between countries and obtain new estimates of network elasticities that vary over time and across types of destination countries.
Losing our minds? New research directions on skilled emigration and development
Authors: A. Clemens Michael 
Published: September 2016

PurposeThe purpose of this paper is to critique the last decade of research on the effects of high-skill emigration from developing countries, and proposes six new directions for fruitful research.Design/methodology/approachThe study singles out a core assumption underlying much of the recent literature, calling it the “Lump of Learning model” of human capital and development, and describes five ways that research has come to challenge that assumption. It assesses the usefulness of that model in the face of accumulating evidence.FindingsThe axioms of the Lump of Learning model have shaped research priorities in this literature, but many of those axioms do not have a clear empirical basis. Future research proceeding from established facts would set different priorities, and would devote more attention to measuring the effects of migration on skilled migrant households, rigorously estimating human capital externalities, gathering microdata beyond censuses, and carefully considering optimal policy – among others.Originality/valueThe recent literature has pursued a series of extensions to the Lump of Learning model. This study urges instead discarding that model, pointing toward a new paradigm for research on skilled migration and development.