bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Sensitive Detection of Vibrio alginolyticus by Loop-Mediated Isothermal Amplification Combined with a Lateral Flow Dipstick Targeted to the rpoX Gene
Authors: Plaon Saranya , Longyant Siwaporn , Sithigorngul Paisarn , Chaivisuthangkura Parin 
Published: July 2015

Abstract
Vibrio alginolyticus is a major bacterial pathogen causing disease in marine animals. The present study aimed to develop a loop-mediated isothermal amplification (LAMP) coupled with a lateral flow dipstick (LFD) for rapid and simple visual detection of V. alginolyticus–specific amplicons. The biotin-labeled LAMP amplicons from the targeted portion of a gene encoding rpoS-like sigma factor (rpoX) were generated at 60°C for 1 h and then hybridized with a fluorescein isothiocyanate–labeled probe for 5 min for visual detection with LFD. In pure cultures, the detection limit of the LAMP–LFD technique for V. alginolyticus was 1.8 × 102 CFU/mL while that of PCR was 1.8 × 103 CFU/mL. In spiked whiteleg shrimp samples Penaeus vannamei, the sensitivity for V. alginolyticus detection was 2 × 103 CFU/g (equivalent to 4 CFU per reaction) while PCR was 10 times less sensitive. The LAMP–LFD method for V. alginolyticus correctly identified 21 isolates of V. alginolyticus but did not recognize 23 non-V. alginolyticus Vibrio isolates and 15 non-Vibrio isolates. In summary, this LAMP–LFD method targeted to the rpoX gene is a convenient assay for specific identification of V. alginolyticus with high sensitivity.
Received November 11, 2014; accepted March 29, 2015
Kinetic study of the quenching reaction of singlet oxygen by seven rice bran extracts in ethanol solution. Development of a singlet oxygen absorption capacity (SOAC) assay method
Authors: Mukai Kazuo , Ishikawa Eri , Abe Takumi , Ouchi Aya , Nagaoka Shin-ichi , Murata Kazumasa , Miyazawa Teruo , Nakagawa Kiyotaka 
Published: July 2015

Abstract
Measurements of singlet oxygen (1O2) quenching rates (kQ (S)) and the relative singlet oxygen absorption capacity (SOAC) values were performed for seven rice bran extracts 1–7, which contained different concentrations of antioxidants (AOs) (such as α-, β-, γ-, and δ-tocopherols and -tocotrienols, three carotenoids (lutein, β-carotene, and zeaxanthin), and γ-oryzanol), in ethanol at 35 °C using UV–vis spectrophotometry. The concentrations of four tocopherols and four tocotrienols, three carotenoids, and γ-oryzanol contained in the extracts were determined using HPLC-MS/MS, UV-HPLC, and UV–vis absorption spectroscopy, respectively. Furthermore, comparisons of kQ (S) (Obsd.) values observed for the above extracts 1–7 with the sum of the product { [AO-i]} of the values obtained for each AO-i and the concentration ([AO-i]) of AO-i contained in extracts 1–7 were performed. From the results, it has been ascertained that the SOAC method is applicable to general food extracts to evaluate their 1O2-quenching activity.
MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics
Authors: Chen Gengbo , Cui Liang , Teo Guo Shou , Ong Choon Nam , Tan Chuen Seng , Choi Hyungwon 
Published: July 2015

Abstract
Motivation: Accurate cross-sample peak alignment and reliable intensity normalization is a critical step for robust quantitative analysis in untargetted metabolomics since tandem mass spectrometry (MS/MS) is rarely used for compound identification. Therefore shortcomings in the data processing steps can easily introduce false positives due to misalignments and erroneous normalization adjustments in large sample studies.
Results: In this work, we developed a software package MetTailor featuring two novel data preprocessing steps to remedy drawbacks in the existing processing tools. First, we propose a novel dynamic block summarization (DBS) method for correcting misalignments from peak alignment algorithms, which alleviates missing data problem due to misalignments. For the purpose of verifying correct re-alignments, we propose to use the cross-sample consistency in isotopic intensity ratios as a quality metric. Second, we developed a flexible intensity normalization procedure that adjusts normalizing factors against the temporal variations in total ion chromatogram (TIC) along the chromatographic retention time (RT). We first evaluated the DBS algorithm using a curated metabolomics dataset, illustrating that the algorithm identifies misaligned peaks and correctly realigns them with good sensitivity. We next demonstrated the DBS algorithm and the RT-based normalization procedure in a large-scale dataset featuring &gt;100 sera samples in primary Dengue infection study. Although the initial alignment was successful for the majority of peaks, the DBS algorithm still corrected ∼7000 misaligned peaks in this data and many recovered peaks showed consistent isotopic patterns with the peaks they were realigned to. In addition, the RT-based normalization algorithm efficiently removed visible local variations in TIC along the RT, without sacrificing the sensitivity of detecting differentially expressed metabolites.
Availability and implementation: The R package MetTailor is freely available at the SourceForge website http://mettailor.sourceforge.net/.
Contact: hyung_won_choi@nuhs.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
FermiKit: assembly-based variant calling for Illumina resequencing data
Authors: Li Heng 
Published: July 2015

Abstract
Summary: FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.
Availability and implementation: https://github.com/lh3/fermikit
Contact: hengli@broadinstitute.org
Association of Immune Response to Endothelial Cell Growth Factor With Early Disseminated and Late Manifestations of Lyme Disease but Not Posttreatment Lyme Disease Syndrome
Authors: Tang Kevin S. , Klempner Mark S. , Wormser Gary P. , Marques Adriana R. , Alaedini Armin 
Published: July 2015

Abstract
Endothelial cell growth factor has been recently proposed as a potential autoantigen in manifestations of Lyme disease that are thought to involve immune-mediated mechanisms. Our findings indicate that a humoral immune response to this protein is not associated with posttreatment Lyme disease syndrome.
On bounded continuous solutions of the archetypal equation with rescaling
Authors: Bogachev Leonid V. , Derfel Gregory , Molchanov Stanislav A. 
Published: July 2015

The ‘archetypal’ equation with rescaling is given by

y
(
x
)
=

∬

R

2

y
(
a
(
x
−
b
)
)
μ
(

d

a

,

d

b

)

(

x
∈

R

), where
μ
is a probability measure; equivalently,

y
(
x
)
=

E

{
y
(
α
(
x
−
β
)
)
}

, with random
α
,
β
and

E

denoting expectation. Examples include (i) functional equation

y
(
x
)
=

∑

i

p

i

y
(

a
i

(
x
−

b
i

)
)

; (ii) functional–differential (‘pantograph’) equation

y
′

(
x
)
+
y
(
x
)
=

∑

i

p

i

y
(

a
i

(
x
−

c
i

)
)

(
p

i

>0,

∑

i

p

i

=
1

). Interpreting solutions
y
(
x
) as harmonic functions of the associated Markov chain (
X

n

), we obtain Liouville-type results asserting that any bounded continuous solution is constant. In particular, in the ‘critical’ case

E

{
ln
⁡

|

α

|

}
=
0

such a theorem holds subject to uniform continuity of
y
(
x
); the latter is guaranteed under mild regularity assumptions on
β
, satisfied e.g. for the pantograph equation (ii). For equation (i) with
a

i

=
q

m

i

(

m
i

∈

Z

,

∑
i

p
i

m
i

=
0

), the result can be proved without the uniform continuity assumption. The proofs exploit the iterated equation

y
(
x
)
=

E

{
y
(

X
τ

)

|

X
0

=
x
}

(with a suitable stopping time
τ
) due to Doob's optional stopping theorem applied to the martingale
y
(
X

n

).
Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
Authors: Ni Xumin , Yang Xiong , Guo Wei , Yuan Kai , Zhou Ying , Ma Zhiming , Xu Shuhua 
Published: July 2015

ABSTRACTAs a chromosome is sliced into pieces by recombination after entering an admixed population, ancestral tracks of chromosomes are shortened with the pasting of generations. The length distribution of ancestral tracks reflects information of recombination and thus can be used to infer the histories of admixed populations. Previous studies have shown that inference based on ancestral tracks is powerful in recovering the histories of admixed populations. However, population histories are always complex, and previous studies only deduced the length distribution of ancestral tracks under very simple admixture models. The deduction of length distribution of ancestral tracks under a more general model will greatly elevate the power in inferring population histories. Here we first deduced the length distribution of ancestral tracks under a general model in an admixed population, and proposed general principles in parameter estimation and model selection with the length distribution. Next, we focused on studying the length distribution of ancestral tracks and its applications under three typical admixture models, which were all special cases of our general model. Extensive simulations showed that the length distribution of ancestral tracks was well predicted by our theoretical models. We further developed a new method based on the length distribution of ancestral tracks and good performance was observed when it was applied in inferring population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, we applied our method in African Americans and Mexicans from the HapMap dataset, and several South Asian populations from the Human Genome Diversity Project dataset. The results showed that the histories of African Americans and Mexicans matched the historical records well, and the population admixture history of South Asians was very complex and could be traced back to around 100 generations ago.
Electric power market reform in Japan after Fukushima Daiichi nuclear plant disaster
Authors: Goto Mika , Sueyoshi Toshiyuki 
Published: July 2015

Purpose
The purpose of this study is to review the current status and related issues on the market reform of Japanese electric power industry after Fukushima Daiichi nuclear plant disaster. We also discuss the future policy direction for the market reform.

Design/methodology/approach
This research compares the reform process of Japanese electric power industry with that of European Union (EU) nations. Then, this study discusses policy issues on the Japanese market reform based upon our comparative analysis.

Findings
Japan may learn many things from the market liberalization process and institution of EU nations. In the learning process, it is necessary to pay attention to industrial differences between Japan and the EU nations. Each country has its own unique features on fuel mix, business environment as well as supply and demand relationship. Such differences may influence a desirable policy direction for each nation’s market reform. The international comparison discussed in this study indicates the importance of a step-by-step approach in which Japan can gradually incorporate European experiences into the Japanese market reform.

Research limitations/implications
Since this study focuses upon the Japanese market reform, the empirical findings may have limited policy implications. The implications obtained from Japanese experience need additional thought in shifting them to other nations. Such an extension will be an important future task of this study.

Originality/value
This study discusses the current policy issues and future direction on the Japanese electricity market reform. This study also suggests its future direction. Previous research has never discussed the Japanese experience. Policy makers, corporate leaders, and individuals in the world, who are involved in the energy industry, have been paying attention to the Japanese future energy direction after Fukushima Daiichi nuclear plant disaster. This study provides such a future energy direction on Japanese market reform from European experience.
Fresh driver for economic growth: fracking the UK nation
Authors: Ochieng Edward G. , Price Andrew D.F. , Egbu Charles O. , Ruan Ximing , Zuofa Tarila 
Published: July 2015

Purpose
The purpose of this paper was to examine UK shale gas viability. The recent commitment to shale gas exploration in the UK through fracking has given rise to well-publicised economic benefits and environmental concerns. There is potential for shale gas exploration in different parts of the UK over the next couple of decades. As argued in this study, if it does, it would transform the energy market and provide long-term energy security at affordable cost.

Design/methodology/approach
Interviews with senior practitioners and local communities were recorded, transcribed and entered into qualitative research software Nvivo. Validity and reliability were achieved by first assessing the plausibility in terms of already existing knowledge on some of the economic and environmental issues raised by participants.

Findings
Findings from this study suggest that environmental, health and safety risks can be managed effectively provided operational best practices are implemented and monitored by the Health and Safety Executive; Department of Energy, Climate Change; and the Mineral Planning Authorities. Participants further suggested that the integration of shale gas technology will protect consumers against rising energy prices and ensure that government does not get exposed to long-term geopolitical risks.

Practical implications
The present study corroborates the position that environmental, health and safety risks can be managed effectively provided operational best practices are implemented and monitored by the Health and Safety Executive; Department of Energy, Climate Change; and the Mineral Planning Authorities.

Social implications
The present study confirms that the government is committed to ensuring that the nation maximises the opportunity that cost-effective shale gas technology presents, not just investment, cheap energy bills and jobs but providing an energy mix that will underpin the UK long-term economic prosperity.

Originality/value
The present study corroborates the position that environmental, health and safety risks can be managed effectively provided operational best practices are implemented and monitored by the Health and Safety Executive; Department of Energy, Climate Change; and the Mineral Planning Authorities. As shown in this study, the UK has a very strong regulatory regime compared to USA; therefore, environmental, health and safety risks will be very well managed and unlikely to escalate into the crisis being envisioned.
User involvement in assisted reproductive technologies: England and Portugal
Authors: Samorinha Catarina , Lichon Mateusz , Silva Susana , Dent Mike 
Published: July 2015

Purpose
– The purpose of this paper is to compare user involvement in the case of assisted reproductive technologies in England and Portugal through the concepts of voice, choice and co-production, assessing the implications for user empowerment.

Design/methodology/approach
– This qualitative study draws primarily on policy review and uses exploratory semi-structured interviews with key informants as a way of illustrating points. Data on the following themes was compared: voice (users’ representativeness on licensing bodies and channels of communication between users and doctors); choice (funding and accessibility criteria; choice of fertility centres, doctors and level of care); and co-production (criteria through which users actively engage with health professionals in planning the treatment).

Findings
– Inter- and intra-healthcare systems variations between the two countries on choice and co-production were identified. Differences between funding and accessibility, regions, public and private sectors and attitudes towards doctor-patient relationship (paternalistic/partnership) were the key issues. Although consumer choice and indicators of co-production are evident in treatment pathways in both countries, user empowerment is not. This is limited by inequalities in accessibility criteria, dependence on doctors’ individual perspectives and lack of genuine and formal hearing of citizens’ voice.

Originality/value
– Enhancing users’ involvement claims for individual and organizational cultures reflecting user-centred values. Effective ways to incorporate users’ knowledge in shared decision making and co-design are needed to empower patients and to improve the delivery of care.
Customer heterogenity in the development of e-loyalty
Authors: Chocarro Raquel , Cortiñas Monica , Villanueva Maria Luisa 
Published: July 2015

Purpose
– The purpose of this study is to identify customer-specific differences in a general model of e-loyalty taking into account the existence of unobserved heterogeneity. Specifically, this paper aims to test for the presence of customer heterogeneity; assess the impact of potential bias when there is no control for heterogeneity; analyse the distinct customer segments that emerge from the empirical estimation of the model; and describe the segments by their demographic and psychological characteristics.

Design/methodology/approach
– Panel data from a survey of online shoppers are used in a post hoc segmentation method, which will enable us to identify segments, while estimating the parameters by means of structural equation models.

Findings
– Three distinct consumer segments emerge. The relative importance of e-loyalty and e-satisfaction is significantly determined by consumers’ shopping styles.

Originality/value
– This study highlights the need to consider unobserved customer heterogeneity when attempting to explain satisfaction and loyalty development processes in the retail context in general and e-commerce in particular. To the authors’ knowledge, this is the first time this approach has been used to analyse the impact of customer heterogeneity on e-satisfaction and e-loyalty.
Endangers culture heritage
Authors: Hussein Moustafa Laila 
Published: July 2015

Purpose
– The purpose of this paper is to present the results of a survey sent to librarians and archivists in national and academic libraries in the Middle East and North Africa and the results of eight in-person interviews about the status and content of wartime disaster management plans in their institutions. Based on the research and analysis it presents, the paper concludes that the majority of the region’s libraries and archives either lack or have insufficient plans in place and stresses the need to establish and implement protocols for the protection and preservation of their priceless holdings. In addition to analysis the paper offers some recommendations for overcoming the impact of future disasters on the holdings of these libraries.

Design/methodology/approach
– The research is based on survey and interviews that was done with librarians, archives, managers from the Middle East.

Findings
– The paper presented the result of trying to find if libraries, and archives has disaster planning or no. Most of the libraries do not have a disaster plan and maybe do not even know what it means.

Research limitations/implications
– The research is covering some of the libraries in the Middle East and it was meant to be send to every library and archive but at least to the national libraries of each country in the Middle East.

Social implications
– Disaster planning is very needed to protect any people culture heritage and not having one in spite all the wars and damaged of libraries is something the author’s research addressed.

Originality/value
– No one has written about this topic, and the author’s first paper was the scan of literature review of all what was written about disaster planning in a time of war. As a result of not finding anyone who wrote about that topic, the author decided to conduct the survey and the interview to find out if there is a plan or no. The author’s work is original and very important to help in preserving the world heritage in the Middle East.
Knowledge transferred through organizational stories: a typology
Authors: Colon-Aguirre Monica 
Published: July 2015

Purpose– The purpose of this study is to look at organizational stories shared among academic librarians who work at the reference desk, and create a typology of the stories based on the knowledge transferred in these. Previous research suggests that stories are the main way in which organizations communicate common values, organizational rules and promote organizational learning. The main question researched here will be: what kind of knowledge is transferred through the stories shared among librarians? This is an important consideration since the meaning carried through the story can shape the employee’s perception of the organization.Design/methodology/approach– This research employed long interviews using a semi-structured questionnaire based on the works of Yiannis Gabriel (2000) as a guide. A total of 20 reference librarians working at four different academic institutions in the southern USA participated in this study.Findings– The analysis of the data reveals a typology of organizational stories shared. The main topics covered by the stories all deal with cultural knowledge exchanges, while also serve as coping mechanisms and present important organizational culture aspects. The stories shared also reflect negative aspects related to the lack of proper communication within the organizations, with the presence of rumors among the narratives shared.Originality/value– These findings can serve as a first step for the development of healthier organizational cultures in libraries and may have implications for training and development, change management, motivation and collective memory.
Succession planning process that includes visible minority librarians
Authors: Kumaran Maha 
Published: July 2015

Purpose– The purpose of this paper is to stress the importance of including visible minority librarians in the process of succession planning in academic libraries. In Canada visible minorities is the accepted term used for librarians of color. This paper identifies the challenges faced by these librarians in putting their names forward for administrative/leadership positions and proposes ideas on how to include these librarians in the succession planning processes so the leadership/administrative pool can also reflect the multicultural student demographics.Design/methodology/approach– This paper is an extensive study of the literature on succession planning and visible minority or ethnic librarians in the academic libraries. Literature shows that the senior administration of academic libraries does not reflect the population demographic it serves.Findings– This paper shows that visible minority librarians are not proactively found, recruited, retained. They are certainly not being included in succession planning processes. It suggests that academic libraries follow certain processes and strategies to include these librarians in their succession planning.Research limitations/implications– The paper focusses widely on North American visible minorities, but this information is applicable to any community with visible minorities.Practical implications– Libraries can start thinking about creating strategies for including visible minority libraries in their succession planning processes.Originality/value– This paper addresses a gap in the literature. Literature review showed that there are no papers that speak to the importance of including minority librarians in the succession planning processes.