bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altering expression of a vacuolar iron transporter doubles iron content in white wheat flour
Authors: Connorton James M. , Jones Eleanor R. , Rodríguez-Ramiro Ildefonso , Fairweather-Tait Susan , Uauy Cristobal , Balk Janneke 
Published: April 2017

SummaryIron deficiency anaemia is a major global health issue, which has prompted mandatory fortification of cereal products with iron salts or elemental iron in many countries around the world. Rather than post-harvest fortification, biofortification - increasing the intrinsic nutritional quality of crops - is a more sustainable way of alleviating nutrient deficiencies. To identify target genes for biofortification of wheat (Triticum aestivum), we functionally characterized homologues of theVacuolar Iron Transporter(VIT). The wheat genome contains twoVITparalogues,TaVIT1andTaVIT2, which have different expression patterns, but are both low in the endosperm. TaVIT2, but not TaVIT1, was able to transport iron in a yeast complementation assay. TaVIT2 also transported manganese but not zinc. By over-expressingTaVIT2under the control of an endosperm-specific promoter, we achieved a 2-fold increase in iron in white flour fractions, exceeding minimum UK legal fortification levels. The highiron trait was consistent across independent lines and was stable in the next generation and in two different growth conditions. The single-gene approach impacted minimally on plant growth and was also effective in barley. The anti-nutrient phytate was not increased in white flour from the cisgenic wheat lines, suggesting that food products made from it could contribute to improved iron nutrition.
Variation in the modality of a yeast signaling pathway is mediated by a single regulator
Authors: Palme Julius , Wang Jue , Springer Michael 
Published: April 2017

AbstractBimodal gene expression by genetically identical cells is a pervasive feature of signaling networks. In the galactose-utilization (GAL) pathway ofSaccharomyces cerevisiae, induction can be unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation of modality is regulated by an interplay between two features of the pathway response, the fraction of cells that are in the induced subpopulation and their expression level. Combined, the variations in these features are sufficient to explain the observed effects of natural variation and pre-induction conditions on the modality of induction in both mechanistic and phenomenological models. Both natural variation and pre-induction conditions act by modulating the expression and function of the galactose sensorGAL3. The ability to alter modality may allow organisms to adapt their level of “bet hedging” to the conditions they experience, and thus help optimize fitness in complex, fluctuating natural environments.
NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma
Authors: Xiao Zhi-Jie , Liu Jing , Wang Si-Qi , Zhu Yun , Gao Xu-Yuan , Tin Vicky Pui-Chi , Qin Jing , Wang Jun-Wen , Wong Maria Pik 
Published: April 2017

AbstractCancers display intratumoral genetic and molecular heterogeneity with tumor initiating cells (TIC) showing enhanced tumor phenotypes. In this study, we show the calcium pathway transcription factor NFATc2 is a novel regulator of lung TIC through the NFATc2/SOX2/ALDH1A1 regulatory axis.In vitroandin vivocancer cell modeling demonstrated supportive evidences including cell renewal, tumorigenicity at limiting dose, cell motility, resistance to cytotoxic chemotherapy and EGFR targeted therapy. In human lung cancers, high NFATc2 expression predicts poor tumor differentiation, adverse recurrence-free and overall patient survivals. Mechanistic investigations identified NFATc2 response elements in the SOX2 3’ enhancer region, and NFATc2/SOX2 coupling upregulates ALDH1A1 by binding to its 5’ enhancer. Through this axis, oxidative stresses and reactive oxygen species induced by cancer drug treatment are attenuated, accounting for a mutation-independent mechanism of drug resistance. Targeting this axis provides a novel approach for the long term treatment of lung cancer through TIC elimination.
Comprehensive characterization of the complexlolalocus reveals a novel role in the octopaminergic pathway via Tyramine beta-hydroxylase activation
Authors: Dinges Nadja , Morin Violeta , Kreim Nastasja , Southall Tony D. , Roignant Jean-Yves 
Published: April 2017

Summarylongitudinals lacking (lola)is among the most complex genes inDrosophila melanogaster, encoding up to twenty protein isoforms and acting as a key transcription factor in axonal pathfinding and neural reprogramming. Most of previous studies employed loss-of-function alleles disrupting common exons oflola, making it difficult to delineate its functions. To address this issue we have generated specific mutations in each isoform using the CRISPR/Cas9 system. Our targeted screen allows us to revisit the previously demonstrated roles for few isoforms and to demonstrate a specific function for one variant in axon guidance via activation of the microtubule-associated factor Futsch. Importantly, we also reveal a critical role for a second variant in preventing neurodegeneration via the control of the octopaminergic pathway. This variant is expressed almost exclusively in the octopaminergic cells and is involved in the transcriptional activation of a key enzyme of the pathway. Thus, our comprehensive study greatly expands the functional repertoire of Lola functions, and adds novel insights into the transcriptional regulatory control of neurotransmitter expressionin vivo.
Exploring the Diversity ofBacilluswhole genome sequencing projects using Peasant, the Prokaryotic Assembly and Annotation Tool
Authors: Brenner Jonathon , Kalesinskas Laurynas , Putonti Catherine 
Published: April 2017

ABSTRACTBackgroundThe persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects.ResultsThe Prokaryotic Assembly and Annotation Tool, Peasant, automates the processes of read quality control, genome assembly, and annotation for microbial sequencing projects. High-quality assemblies and annotations can be generated by Peasant without the need of programming expertise or high-performance computing resources. Furthermore, statistics are calculated so that users can evaluate their sequencing project. To illustrate the computational speed and accuracy of Peasant, the SRA records of 322 Illumina platform whole genome sequencing assays forBacillusspecies were retrieved from NCBI, assembled and annotated on a single desktop computer. From the assemblies and annotations produced, a comprehensive analysis of the diversity of over 200 high-quality samples was conducted, looking at both the 16S rRNA phylogenetic marker as well as theBacilluscore genome.ConclusionsPeasant provides an intuitive solution for high-quality whole genome sequence assembly and annotation for users with limited programing experience and/or computational resources. The analysis of theBacilluswhole genome sequencing projects exemplifies the utility of this tool. Furthermore, the study conducted here provides insight into the diversity of the species, the largest such comparison conducted to date.
Mode of sucrose delivery alters reward-related phasic dopamine signals in nucleus accumbens
Authors: McCutcheon James E , Roitman Mitchell F 
Published: April 2017

AbstractIn studies of appetitive Pavlovian conditioning, rewards are often delivered to subjects in a manner that confounds several processes. For example, delivery of a sugar pellet to a rodent requires movement to collect the pellet and is associated with sensory stimuli such as the sight and sound of the pellet arrival. Thus, any neurochemical events occurring in proximity to the reward may be related to multiple coincident phenomena. We used fast-scan cyclic voltammetry in rats to compare nucleus accumbens dopamine responses to two different modes of delivery: sucrose pellets, which require goal-directed action for their collection and are associated with sensory stimuli, and intraoral infusions of sucrose, which are passively received and not associated with external stimuli. We found that when rewards were unpredicted both pellets and infusions evoked similar dopamine release. However, when rewards were predicted by distinct cues, greater dopamine release was evoked by pellet cues than infusion cues. Thus, dopamine responses to pellets, infusions as well as predictive cues suggest a nuanced role for dopamine in both reward seeking and reward evaluation.
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
Authors: Ramazzotti Daniele , Graudenzi Alex , De Sano Luca , Antoniotti Marco , Caravagna Giulio 
Published: April 2017

AbstractBackgroundA large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types.ResultsWe introduceTRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools,TRaITsupports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena.TRaITimproves accuracy, robustness to data-specific errors and computational complexity compared to competing methods.ConclusionsWe show that the application ofTRaITto single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses.
A theoretical model of jump diffusion-mean reversion
Authors: Chakrabarty Anindya , Luo Zongwei , Dubey Rameshwar , Jiang Shan 
Published: April 2017

Purpose
The purpose of this paper is to develop a theoretical model of a jump diffusion-mean reversion constant proportion portfolio insurance strategy under the presence of transaction cost and stochastic floor as opposed to the deterministic floor used in the previous literatures.

Design/methodology/approach
The paper adopts Merton’s jump diffusion (JD) model to simulate the price path followed by risky assets and the CIR mean reversion model to simulate the path followed by the short-term interest rate. The floor of the CPPI strategy is linked to the stochastic process driving the value of a fixed income instrument whose yield follows the CIR mean reversion model. The developed model is benchmarked against CNX-NIFTY 50 and is back tested during the extreme regimes in the Indian market using the scenario-based Monte Carlo simulation technique.

Findings
Back testing the algorithm using Monte Carlo simulation across the crisis and recovery phases of the 2008 recession regime revealed that the portfolio performs better than the risky markets during the crisis by hedging the downside risk effectively and performs better than the fixed income instruments during the growth phase by leveraging on the upside potential. This makes it a value-enhancing proposition for the risk-averse investors.

Originality/value
The study modifies the CPPI algorithm by re-defining the floor of the algorithm to be a stochastic mean reverting process which is guided by the movement of the short-term interest rate in the economy. This development is more relevant for two reasons: first, the short-term interest rate changes with time, and hence the constant yield during each rebalancing steps is not practically feasible; second, the historical literatures have revealed that the short-term interest rate tends to move opposite to that of the equity market. Thereby, during the bear run the floor will increase at a higher rate, whereas the growth of the floor will stagnate during the bull phase which aids the model to capitalize on the upward potential during the growth phase and to cut down on the exposure during the crisis phase.
A bibliographic study on big data: concepts, trends and challenges
Authors: Mishra Deepa , Luo Zongwei , Jiang Shan , Papadopoulos Thanos , Dubey Rameshwar 
Published: April 2017

Purpose
The purpose of paper is twofold. First, it provides a consolidated overview of the existing literature on “big data” and second, it presents the current trends and opens up various future directions for researchers who wish to explore and contribute in this rapidly evolving field.

Design/methodology/approach
To achieve the objective of this study, the bibliographic and network techniques of citation and co-citation analysis was adopted. This analysis involved an assessment of 57 articles published over a period of five years (2011-2015) in ten selected journals.

Findings
The findings reveal that the number of articles devoted to the study of “big data” has increased rapidly in recent years. Moreover, the study identifies some of the most influential articles of this area. Finally, the paper highlights the new trends and discusses the challenges associated with big data.

Research limitations/implications
This study focusses only on big data concepts, trends, and challenges and excludes research on its analytics. Thus, researchers may explore and extend this area of research.

Originality/value
To the knowledge of the authors, this is the first study to review the literature on big data by using citation and co-citation analysis.
Fabric defect detection based on sparse representation of main local binary pattern
Authors: Liu Zhoufeng , Yan Lei , Li Chunlei , Dong Yan , Gao Guangshuai 
Published: April 2017

Purpose
The purpose of this paper is to find an efficient fabric defect detection algorithm by means of exploring the sparsity characteristics of main local binary pattern (MLBP) extracted from the original fabric texture.

Design/methodology/approach
In the proposed algorithm, original LBP features are extracted from the fabric texture to be detected, and MLBP are selected by occurrence probability. Second, a dictionary is established with MLBP atoms which can sparsely represent all the LBP. Then, the value of the gray-scale difference between gray level of neighborhood pixels and the central pixel, and the mean of the difference which has the same MLBP feature are calculated. And then, the defect-contained image is reconstructed as normal texture image. Finally, the residual is calculated between reconstructed and original images, and a simple threshold segmentation method can divide the residual image, and the defective region is detected.

Findings
The experiment result shows that the fabric texture can be more efficiently reconstructed, and the proposed method achieves better defect detection performance. Moreover, it offers empirical insights about how to exploit the sparsity of one certain feature, e.g. LBP.

Research limitations/implications
Because of the selected research approach, the results may lack generalizability in chambray. Therefore, researchers are encouraged to test the proposed propositions further.

Originality/value
In this paper, a novel fabric defect detection method which extracts the sparsity of MLBP features is proposed.
Experimental study on cutting flexible sheet materials using an oscillating knife
Authors: Cosson-Coche Quentin , Cahuc Olivier , Darnis Philippe , Laheurte Raynald , Teissandier Denis , Chabirand Didier 
Published: April 2017

Purpose
The purpose of this paper is to understand the impact of the cutting forces on the quality of pieces in industrial cutting of multi-ply textile material. It also tries to establish a cutting model that can simulate the cutting forces in order to understand the behaviour of the blade.

Design/methodology/approach
Working on an industrial machine, a cutting head with an oscillating knife is instrumented with different sensors. Using this equipment, cutting forces can be analysed experimentally while the fabric is being cut along a straight line.

Findings
A model of the physical phenomena of the cutting forces is proposed, taking different parameters into account such as the geometry of the blade, the properties of the material being cut and the parameters of the cut. The simulated forces and the monitored forces are compared and parameters for minimising the cutting forces of fabrics are deduced.

Research limitations/implications
Due to the wide diversity of fabrics, all with different mechanical characteristics, this research only began with the study of denim in a straight cut.

Originality/value
This paper describes an instrumentation of automatic cutting head for textile. It manages to simulate the action of the fabrics on the blade through effort monitoring and help in the understanding of the multi-ply cutting process.
Assessment of the non-woven, goose down and duck down as thermally insulating materials for the clothing protecting against cold
Authors: Dabrowska Anna Katarzyna , Bartkowiak Grazyna , Karcz Jagna , Frydrych Iwona 
Published: April 2017

Purpose
The purpose of this paper is to compare morphological and physical features of three kinds of materials intended for the insulating layer in the clothing protecting against cold – high-bulk non-woven, goose down (GD) and duck down (DD).

Design/methodology/approach
Comparison of thermal performance of developed textile systems with the non-woven, GD and DD content was based on basic biophysical properties related to comfort sensations of the user such as thermal resistance, water vapor resistance and air permeability. In this study, light microscopy and scanning electron microscopy methods were employed to visualize the surface and internal structure of non-woven, GD and DD samples.

Findings
The paper indicates the advantages and disadvantages of each of selected insulating material. For the down samples, significantly higher thermal resistance in a dry state than for the non-woven samples can be achieved. Meanwhile, textile systems with the non-woven provide lower value of water vapor resistance. The selected textile systems for the research were characterized by a comparable air permeability.

Originality/value
This paper allows for an evaluation of high-bulk non-woven, DD and GD samples in terms of providing optimal thermal performance in clothing protecting against cold.
The migration and institutional sheltering of children and adolescents in the Federal District, Brazil
Authors: Penso Maria Aparecida , Fukuda Cláudia Cristina , Costa Liana Fortunato , Villela Luisa 
Published: April 2017

Purpose
The purpose of this paper is to relate the phenomenon of migration to the Federal District (DF, Brazil), with the figures for institutional shelter of children and adolescents.

Design/methodology/approach
The method chosen was the documental analysis of special folders that were processed in the Defense Office for Children and Adolescents of the DF from January 2007 to August 2009. The sample consisted of 545 special folders, referring to a total of 1,007 children and adolescents.

Findings
The results indicate that most children and adolescents received at the shelters were from families living in the satellite cities of the DF (53.4 percent) and surroundings (8.3 percent), and were mainly from rural areas of the Northeast region of the country and also from the deprived areas of the states of Goiás and Minas Gerais, near the DF. Among the main reasons for institutional shelter, is violence, abandonment by family, poverty and living on the streets.

Research limitations/implications
It can be inferred that the policies of “population clusters” in the DF were responsible for this migratory process and population growth of satellite cities and surrounding areas. It is understood in this way that the migration processes resulted in the rupture of the bond with the family of origin and an insertion into a reality, which again challenge these families in a situation of poverty and violence.

Social implications
The reality of vulnerability and social exclusion of migrant families who leave their support networks in their home states need urgent attention of local public policies, especially with regard to encouraging the construction of other support networks and creating contexts of cultural identification in the communities, especially the neediest. The support and presence of quality public services in these communities and the preventive action of social policies are also considered essential to ensure quality of life and adequate subsistence to the people who migrate to the DF.

Originality/value
Brasília became the symbol of hope for unemployed people or for those suffering from their income being below the poverty level. Faced with this migratory reality, this paper discusses the situation of families of children and adolescents institutionally sheltered in the DF, given their social situation regarding poverty, unemployment, lack of support from their family of origin and lack of access of distribution of public policies and income generation.
The journey from first inspection to quality standards (1857-2016): are we there yet?
Authors: Campbell Martin 
Published: April 2017

Purpose
The purpose of this paper is to qualitatively analyse the inspection and regulation of care for people with learning disabilities and mental health problems in Scotland, in two time periods.

Design/methodology/approach
The paper uses comparative historical research drawing on primary sources from 1857 to 1862 in the form of Annual Reports of the General Board of Commissioners in Lunacy for Scotland and associated papers, to compare inspection methods, quality standards and to identify persistent challenges to effective inspection.

Findings
Political, clinical and public awareness led initially to criticisms of existing care and eventually to the development of the “The Lunacy Act” of 1857. This Act resulted in the first attempts to set minimum standards of care for individuals at risk, with enforceable regulation. Some factors recur as challenges to effective practice in the inspection and regulation of care today.

Practical implications
There are problems of definition, reliable monitoring of quality standards and adequate, independent inspection of services that respond to unacceptable standards of care. There is a growing evidence base about best methods of inspection of services for people in care who are most at risk. These methods attempt to strike a balance between evidence- and value-based judgments. Perspectives from history may help focus resources.

Originality/value
This paper compares common and common challenges in two time periods to investigate what can be learned about the development of policy and practice in inspection and regulation of care.