bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of techniques for differential expression analysis on RNA-Seq data
Authors: Zhang Zong Hong , Jhaveri Dhanisha J. , Marshall Vikki M. , Bauer Denis C. , Edson Janette , Narayanan Ramesh K. , Robinson Gregory J. , Lundberg Andreas E. , Bartlett Perry F. , Wray Naomi R. , Zhao Qiong-Yi 
Published: May 2014

AbstractRecent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balancedvs.unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
Extensive Regulation of Metabolism and Growth during the Cell Division Cycle
Authors: Slavov Nikolai , Botstein David , Caudy Amy 
Published: May 2014

AbstractYeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between the oscillations in single cells and synchronized cultures is poorly understood. To understand this relationship and the coordination between metabolism and cell division, we collected and analyzed DNA-content, gene-expression and physiological data, at hundreds of time-points, from cultures metabolically-synchronized at different growth rates, carbon sources and biomass densities. The data enabled us to extend and generalize our mechanistic model, based on ensemble average over phases (EAP), connecting the population-average geneexpression of asynchronous cultures to the gene-expression dynamics in the single-cells comprising the cultures. The extended model explains the carbon-source specific growth-rate responses of hundreds of genes. Our physiological data demonstrate that the frequency of metabolic cycling in synchronized cultures increases with the biomass density, suggesting that this cycling is an emergent behavior, resulting from the entraining of the single-cell metabolic cycle by a quorum-sensing mechanism, and thus underscoring the difference between metabolic cycling in single cells and in synchronized cultures. Measurements of constant levels of residual glucose across metabolically synchronized cultures indicate that storage carbohydrates are required to fuel not only the G1/S transition of the division cycle but also the metabolic cycle. Despite the large variation in profiled conditions and in the scale of their dynamics, most genes preserve invariant dynamics of coordination with each other and with the rate of oxygen consumption. Similarly, the G1/S transition always occurs at the beginning, middle or end of the high oxygen consumption phases, analogous to observations in human and drosophila cells. These results highlight evolutionary conserved coordination among metabolism, cell growth and division.
Artificially Inducing Close Apposition of Endoplasmic Reticulum and Mitochondria Induces Mitochondrial Fragmentation
Authors: Miller Victoria J. , Stephens David J. 
Published: May 2014

SummaryCycles of mitochondrial fission and fission are essential for normal cell physiology. Defects in the machinery controlling these processes lead to neurodegenerative disease. While we are beginning to understand the machinery that drives fission, our knowledge of the spatial and temporal control of this event is lacking. Here we use a rapamycin-inducible heterodimerization system comprising both ER and mitochondrial transmembrane components to bring the ER membrane into close physical proximity with mitochondria. We show that this artificial apposition of membranes is sufficient to cause rapid mitochondrial fragmentation. Resulting mitochondrial fragments are shown to be distinct entities using fluorescence recovery after photobleaching. We also show that these fragments retain a mitochondrial membrane potential. In contrast, inducible tethering of the peripheral ER exit site protein TFG does not cause mitochondrial fragmentation suggesting that very close apposition of the two membranes is required.
Cis-regulatory Elements and Human Evolution
Authors: Siepel Adam , Arbiza Leonardo 
Published: May 2014

AbstractModification of gene regulation has long been considered an important force in human evolution, particularly through changes tocis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study ofcis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider “new frontiers” in this field stemming from recent research on transcriptional regulation.
Lipoate-Protein Ligase and Octanoyltransferase Are Essential for Protein Lipoylation in Mitochondria of Arabidopsis
Authors: Ewald Ralph , Hoffmann Christiane , Florian Alexandra , Neuhaus Ekkehard , Fernie Alisdair R. , Bauwe Hermann 
Published: May 2014

AbstractProsthetic lipoyl groups are required for the function of several essential multienzyme complexes, such as pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase (KGDH), and the glycine cleavage system (glycine decarboxylase [GDC]). How these proteins are lipoylated has been extensively studied in prokaryotes and yeast (Saccharomyces cerevisiae), but little is known for plants. We earlier reported that mitochondrial fatty acid synthesis by ketoacyl-acyl carrier protein synthase is not vital for protein lipoylation in Arabidopsis (Arabidopsis thaliana) and does not play a significant role in roots. Here, we identify Arabidopsis lipoate-protein ligase (AtLPLA) as an essential mitochondrial enzyme that uses octanoyl-nucleoside monophosphate and possibly other donor substrates for the octanoylation of mitochondrial PDH-E2 and GDC H-protein; it shows no reactivity with bacterial and possibly plant KGDH-E2. The octanoate-activating enzyme is unknown, but we assume that it uses octanoyl moieties provided by mitochondrial β-oxidation. AtLPLA is essential for the octanoylation of PDH-E2, whereas GDC H-protein can optionally also be octanoylated by octanoyltransferase (LIP2) using octanoyl chains provided by mitochondrial ketoacyl-acyl carrier protein synthase to meet the high lipoate requirement of leaf mesophyll mitochondria. Similar to protein lipoylation in yeast, LIP2 likely also transfers octanoyl groups attached to the H-protein to KGDH-E2 but not to PDH-E2, which is exclusively octanoylated by LPLA. We suggest that LPLA and LIP2 together provide a basal protein lipoylation network to plants that is similar to that in other eukaryotes.
Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner
Authors: Zsögön Agustin , Szakonyi Dóra , Shi Xiuling , Byrne Mary E. 
Published: May 2014

AbstractRibosomal protein mutations in Arabidopsis (Arabidopsis thaliana) result in a range of specific developmental phenotypes. Why ribosomal protein mutants have specific phenotypes is not fully known, but such defects potentially result from ribosome insufficiency, ribosome heterogeneity, or extraribosomal functions of ribosomal proteins. Here, we report that ovule development is sensitive to the level of Ribosomal Protein L27a (RPL27a) and is disrupted by mutations in the two paralogs RPL27aC and RPL27aB. Mutations in RPL27aC result in high levels of female sterility, whereas mutations in RPL27aB have a significant but lesser effect on fertility. Progressive reduction in RPL27a function results in increasing sterility, indicating a dose-dependent relationship between RPL27a and female fertility. RPL27a levels in both the sporophyte and gametophyte affect female gametogenesis, with different developmental outcomes determined by the dose of RPL27a. These results demonstrate that RPL27aC and RPL27aB act redundantly and reveal a function for RPL27a in coordinating complex interactions between sporophyte and gametophyte during ovule development.
Effect of inhibitors on preferential weld corrosion under sweet conditions
Authors: Alawadhi Khaled , Martinez Mylène , Aloraier Abdulkareem , Alsarraf Jalal 
Published: May 2014

Purpose
– The aim of this investigation was to compare the performance of three typical oil field carbon dioxide corrosion inhibitors in controlling preferential weld corrosion (PWC) of X65 pipeline steel in artificial seawater (3.5 weight per cent) saturated with carbon dioxide at one bar pressure.

Design/methodology/approach
– A novel rotating cylinder electrode (RCE) apparatus was used to evaluate the effect of flow on the inhibition for the weld metal (WM), heat-affected zone (HAZ) and parent material. To fulfill this objective, the galvanic currents flowing between the weld regions were recorded using parallel zero-resistance ammeters, and the self-corrosion rates of the couples were obtained by linear polarization resistance measurements.

Findings
– The results showed that when 30 ppm of green oil field inhibitors were present in the service environment, a current reversal took place, resulting in accelerated weld corrosion. At high shear stress, the currents increased and further reversals occurred. The inhibitors were more effective in controlling the self-corrosion rates of the parent material than of the WM and HAZ material. It was concluded that PWC was caused by unstable conditions in which the inhibitor film was selectively disrupted from the WM and HAZ, but remained effective on the parent material.

Originality/value
– Electrochemical corrosion rate measurements were carried out using an RCE produced from the different regions of the weld. An advantage of using the RCE is that the hydrodynamic conditions are very well defined, and it is feasible to translate the conditions that are known to exist in a production pipeline to those used in laboratory tests.
The corrosion inhibition of carbon steel in 5 per cent HCl by Momordica charantia extract
Authors: Xuejun* Xie , Peng* Xiao , Jie He , Wen Xiao , Qiang Fu , Pinguo Zou 
Published: May 2014

Purpose
– To study the inhibition effect and mechanism of the Momordica charantia extract (BM) to 20 A carbon steel in 5 per cent HCl.

Design/methodology/approach
– The weight loss, polarization curve, infrared spectrum (IR) analysis and X-ray photoelectron spectrum (XPS) analysis were carefully investigated to indicate the inhibition effect and mechanism of the BM to 20 A carbon steel in 5 per cent HCl.

Findings
– BM was composed of C, N and O. Functional groups such as N–H and C=O were found in BM. The inhibition efficiency increased with the increasing concentration of BM. BM behaved as a mixed-type inhibitor, and the inhibition of BM to 20 A carbon steel might be its adsorption through the coordinate covalent bonding among the lone pair electrons of N and O and the empty 3d orbits of Fe, and the adsorption on the surface of 20 A carbon steel obeyed the Langmuir isotherm equation.

Research limitations/implications
– The inhibition of the BM to 20 A carbon steel in 5 per cent HCl.

Practical implications
– BM could be used in 5 per cent HCl to prevent 20 A carbon steel from corrosion.

Social implications
– BM could be used in the chemical cleaning of the boilers to prevent the thermal equipments from corrosion.

Originality/value
– The inhibition effect and mechanism of the BM to 20 A carbon steel were studied by the weight loss, polarization curve, IR analysis and XPS analysis. BM was composed of C, N and O. Functional groups such as N–H and C=O were found in BM. BM behaved as a mixed-type inhibitor. The inhibition efficiency increased with the increasing concentration of BM, and the adsorption on the surface of 20 A carbon steel obeyed the Langmuir isotherm equation.
Electromagnetic corrosion control in water cooling systems
Authors: Alencar de Souza Eduardo , Antônio da Cunha Ponciano Gomes José 
Published: May 2014

Purpose
– The aim was to study the effect of an electromagnetic treatment used on corrosion control of carbon steel in cooling systems.

Design/methodology/approach
– The aim was to assess the performance of an electromagnetic treatment used on corrosion control of carbon steel in cooling water systems.

Findings
– The main conclusion is that the electromagnetic system cannot induce a direct effect on the corrosion rates. The use of chemical corrosion inhibitors cannot be suggested.

Social implications
– The optimized industrial use of water is an objective of unquestionable importance, as water is a finite resource. The use of efficient corrosion control on water cooling systems permits the reduction of the water volume required. Consequently, a social benefit can be associated with the improvement of corrosion control technologies.

Originality/value
– The development of alternative corrosion control technologies, such as the use of physical treatments, has been considered as a promising tool. In this work, a consistent assessment of the results achieved on a full-scale system, without using chemical corrosion inhibitors, is presented.
An experimental study on correlation between concrete resistivity and reinforcement corrosion rate
Authors: Ahmad Shamsad 
Published: May 2014

Purpose– The purpose of this paper was to explore the possibility of establishing an empirical correlation between concrete resistivity and reinforcement corrosion rate utilizing the experimental data generated by measuring corrosion current density of reinforced concrete specimens subjected to chloride-induced corrosion at different levels of concrete resistivity.Design/methodology/approach– To generate concrete resistivity vs corrosion current density data in a wide range, ten reinforced concrete specimens were prepared and allowed to corrode under severe chloride exposure. After significantly corroding the specimens, they were removed from the chloride exposure and were subjected to different moisture levels for achieving variation in the resistivity of concrete so that reasonably good number of resistivity vs corrosion rate data can be obtained. Resistivity and corrosion current density tests were conducted for all the ten specimens and their values were measured in wide ranges of 0.8-65 kΩ·cm and 0.08-11 μA/cm2, respectively.Findings– Data generated through this study were utilized to obtain an empirical relationship between concrete resistivity and corrosion current density. The trend of results obtained using the empirical correlation model developed in the present study was in close agreement with that obtained using a theoretical model reported in literature.Originality/value– The empirical correlation between concrete resistivity and reinforcement corrosion rate obtained under this work can be used for evaluation of reinforcement corrosion utilizing the resistivity values measured non-destructively.
Studies on synthesized nontoxic corrosion inhibitors for N80 steel in hydrochloric acid
Authors: Yadav Mahendra , Kumar Sumit , Sharma Dipti 
Published: May 2014

Purpose
– The purpose of this investigation was to evaluate the protective ability of 2-amino-N-octadecylacetamide (AOA) and 2-amino-N-octadecyl-3-(4-hydroxyphenyl) propionamide (AOHP) as corrosion inhibitors for N80 steel in 15 per cent hydrochloric acid (HCl), which may find application as eco-friendly corrosion inhibitors in acidizing processes in the petroleum industry. Due to scale plugging in the well bore, there can be a decline in the crude production rate, and an acidization operation has to be carried out, normally by using 15 per cent HCl to remove the scale plugging. To reduce the aggressive attack of HCl on tubing and casing materials (N80 steel), inhibitors are added to the acid solution during the acidifying process.

Design/methodology/approach
– Different concentrations of the synthesized inhibitors AOA and AOHP were added to the test solution (15 per cent HCl), and the corrosion inhibition efficiencies of these inhibitors for N80 steel were calculated from weight loss determinations, potentiodynamic polarization scans and alternating current (AC) impedance measurements. The influence of temperature (298-323 K) on the inhibition behavior was studied. Surface examinations were performed by means of Fourier transform infrared spectra and scanning electron microscope.

Findings
– AOA and AOHP at 150-ppm concentration showed a maximum efficiency of 90.04 and 94.97 per cent, respectively, at 298 K in 15 per cent HCl solution. Both the inhibitors acted as mixed corrosion inhibitors. The adsorption of the corrosion inhibitors at the surface of the N80 steel was the underlying mechanism of corrosion inhibition.

Originality/value
– This paper reports the preliminary laboratory results of inhibitors AOA and AOHP for the corrosion prevention of N80 steel casings and tubulars exposed to HCl and may be of practical help to petroleum engineers for carrying out acidization in oil wells after further investigation of the compound at higher temperature.
Chinese consumer attitude and purchase intent towards green products
Authors: Tang Yiming , Wang Xiucun , Lu Pingping 
Published: May 2014

Purpose
– The purpose of this paper is to examine how Chinese consumer attitude mediates factors that influence their purchase intention toward low-displacement vehicles.

Design/methodology/approach
– This study utilizes online survey data in China, multiple regression and recursive regression models.

Findings
– Consumers’ environmental concern, perceived effectiveness belief and functional value positively affect their attitude toward such products. Consumer attitude positively affects purchase intention. Consumer attitude fully mediates the influence of environmental concern, and partly mediates the effect of perceived effectiveness belief, and functional value on purchase intention. Consumers’ awareness of government policy is not associated with attitude or purchase intention.

Originality/value
– This is a first empirical study to systematically examine Chinese consumer attitude's mediation effect on factors influencing their purchase intent toward low-displacement vehicles in China.
Psychological and behavioural drivers of male fashion leadership
Authors: Haluk Koksal Mehmet 
Published: May 2014

Purpose
– The purpose of this paper is to identify the factors affecting male fashion leadership behaviour. The study examined the effect of fashion consciousness, fashion knowledge, mood enhancement, decision-making confidence and brand switching as the psychological factors. It also included the influence of behavioural factors such as the information sources, attributes of purchasing fashion clothing and type of retailers on male fashion leadership.

Design/methodology/approach
– The data were collected through a structured questionnaire distributed in the main shopping districts of Beirut, Lebanon, during March 2012.

Findings
– The study uncovered that fashion consciousness, fashion knowledge, confidence in decision making and mood enhancement are to be the most important psychological factors influencing male fashion leadership behaviour. The study also found that frequency of reading fashion magazines is negatively and significantly affecting fashion leadership. Male fashion leaders use colleagues and friends as the main information sources for fashion. The effect of attractiveness, brand name, store image and quality of clothing is positive and significant whilst value for money negatively and significantly influences male fashion leadership. Male fashion leaders mainly shop from specialty shops, chain stores, department stores and the internet.

Originality/value
– Although there are a handful of studies which examined female fashion leadership, the male fashion leadership concept has not been extensively addressed in the literature. In an attempt to at least partially address this, the study attempts to identify the factors affecting male fashion leadership behaviour in Lebanon.
The interaction effect on customer purchase intention in e-commerce
Authors: Yen Yung-Shen 
Published: May 2014

Purpose
– The purpose of this paper is to explore the interaction effect of information richness, retailer brand, and extended offers on customer purchase intention in e-commerce.

Design/methodology/approach
– Hierarchical moderator regression analysis and simple slope analysis were used to test the hypotheses, also 356 savvy internet consumers in Taiwan were investigated.

Findings
– The findings revealed that information richness, retailer brand, and extended offers are positively related to customer purchase intention. However, the interaction effects may differ in these relationships. While information richness complements both retailer brand and extended offers on customer purchase intention, extended offers may substitute retailer brand for increase in purchase intention.

Research limitations/implications
– A bias may exist because of the sample from an online survey. The findings suggest that complements are actually synergistic strategies of factors, while substitution is a switching of the alternative.

Practical implications
– Practitioners shall utilize information richness to the complements, such as retailer brand and extended offers, to strengthen customer purchase intention. In contrast, they may provide extended offers for acquiring customers in the short-term period, when retailer brand is relatively low or unknown.

Originality/value
– The findings of the study provide a new marketing strategy: managing substitutes and complements in adequate factors can give rise to better results for purchase intention increases in e-commerce.