bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunomodulatory spherical nucleic acids
Authors: Radovic-Moreno Aleksandar F. , Chernyak Natalia , Mader Christopher C. , Nallagatla Subbarao , Kang Richard S. , Hao Liangliang , Walker David A. , Halo Tiffany L. , Merkel Timothy J. , Rische Clayton H. , Anantatmula Sagar , Burkhart Merideth , Mirkin Chad A. , Gryaznov Sergei M. 
Published: March 2015

Significance
We show that by organizing immunomodulatory nucleic acids into spherical nucleic acid (SNA) form, significant increases in activity are observed. Treatment of mice with cancer using immunostimulatory SNAs and nonalcoholic steatohepatitis (NASH) using immunoregulatory SNAs leads to improved disease outcomes vs. their unstructured counterparts. These improvements derive from several key SNA properties, including rapid cellular uptake, endosomal delivery, and multivalent binding. Overall, this work underscores the importance of the spatial orientation and presentation of oligonucleotides in the design of novel immunomodulators.
The CDX1–microRNA-215 axis regulates colorectal cancer stem cell differentiation
Authors: Jones Matthew F. , Hara Toshifumi , Francis Princy , Li Xiao Ling , Bilke Sven , Zhu Yuelin , Pineda Marbin , Subramanian Murugan , Bodmer Walter F. , Lal Ashish 
Published: March 2015

Significance
In the colon, stem cell self-renewal and multipotency is regulated by the polycomb complex protein BMI1, among other genes. Differentiation is regulated by the transcription factor caudal-type homeobox 1 (CDX1), expression of which coincides with repression of BMI1. Colorectal cancer stem cells (CSCs) express BMI1 but not CDX1. Tumors that silence CDX1 have a higher proportion of CSCs and an undifferentiated histology, whereas aberrant CDX1 expression is associated with intestinal metaplasias such as Barrett's esophagus. We have identified microRNA-215 (miR-215) as a target of CDX1 in colon cancer that mediates repression of BMI1. MiR-215 operates downstream of CDX1 to promote differentiation and inhibit stemness. In combination with recent advances in the therapeutic uses of small RNAs, miR-215 could offer a novel method to specifically target CSCs.
Frontier studies on highly selective bio-regulators useful for environmentally benign agricultural production
Authors: Hayashi Hideo 
Published: March 2015

Abstract
Fungal metabolites active for insects were obtained from fermentation products using okara media. The mechanisms of action of these compounds against insects were clarified using voltage clamp electrophysiology. The branching factor inducing hyphal branching in arbuscular mycorrhizal (AM) fungi was isolated from the root exudates of Lotus japonicus and identified as 5-deoxystrigol. Strigolactones were originally identified as seed germination stimulants of parasitic weeds; therefore, synthetic strigolactones were developed to exhibit the inducing activity of hyphal branching in AM fungi and diminish the stimulating activity of seed germination of parasitic weeds. Signaling molecules, acylhomoserine lactones (AHLs), in quorum sensing were identified in the fungal strain Mortierella alpina A-178, and the true producer of AHLs was clarified as symbiotic bacteria in the fungus. Since acyl-(S)-adenosylmethionine analogs may be good candidates for competitive inhibitors of AHL synthases, intermediate mimics in the biosynthesis of AHLs have been synthesized.
Thermostability and reactivity in organic solvent of O-phospho-l-serine sulfhydrylase from hyperthermophilic archaeon Aeropyrum pernix K1
Authors: Nakamura Takashi , Asai Shinji , Nakata Kaori , Kunimoto Kohei , Oguri Masateru , Ishikawa Kazuhiko 
Published: March 2015

Abstract
O-phospho-l-serine sulfhydrylase (OPSS) from archaeon Aeropyrum pernix K1 is able to synthesize l-cysteine even at 80 °C. In this article, we compared thermal stability and reactivity in organic solvent of OPSS with those of O-acetyl-l-serine sulfhydrylase B (OASS-B) from Escherichia coli. As a result, the thermostability of OPSS was much higher than that of OASS-B. Moreover, the activity of OPSS increased in the reaction mixture containing the organic solvent, such as N, N′-dimethyl formamide and 1,4-dioxane, whereas that of OASS-B gradually decreased as the content of organic solvent increased. From the crystal structural analysis, the intramolecular electrostatic interactions of N-terminal domain in OPSS seemed to be correlated with the tolerance of OPSS to high temperature and organic solvent. These results indicate that OPSS is more superior to OASS-B for the industrial production of l-cysteine and unnatural amino acids that are useful pharmaceuticals in the presence of organic solvent.
Accumulation of lipid in rat liver was induced by vitamin B6 deficiency and was ameliorated by supplemental phosphatidylcholine in the diet
Authors: Kitagawa Erina , Yamamoto Tatsuya , Yamamoto Kohei , Nakagawa Tomoyuki , Hayakawa Takashi 
Published: March 2015

Abstract
We investigated the efficacy of supplementing the diet with pteroylmonoglutamic acid (PGA), choline, or phosphatidylcholine (PC) in ameliorating the lipid accumulation in rat liver that is induced by vitamin B6 (B6) deficiency. In Experiment 1, male Wistar rats were fed a control, B6-deficient, or PGA-, choline-, or PC-supplemented (10 mg, 4 g, and 6.3 g/kg of diet, respectively) B6-deficient diet containing l-methionine at 9 g/kg of diet for 35 days. In Experiment 2, rats were fed a control, B6-deficient, or PC-supplemented (at 3.15, 6.3, or 12.6 g PC/kg of diet) B6-deficient diet for 35 days. Choline or PC supplementation ameliorated liver lipid deposition and returned plasma lipids to normal. Judging from these results, it appeared that B6 deficiency decreased the synthesis of PC in the liver, thereby decreasing the secretion of very low-density lipoproteins, and in consequence producing lipid accumulation in the liver and reductions of plasma lipids.
Inhibitors for cholesterol ester accumulation in macrophages from Chinese cabbage
Authors: Takamoto Haruka , Eguchi Keisuke , Kawabata Tetsuro , Fujiwara Yukio , Takeya Motohiro , Tsukamoto Sachiko 
Published: March 2015

AbstractThe cholesterol ester accumulates in macrophages in the early stage of atherosclerotic lesions, leading to the formation of foam cells. We examined the inhibitory effects of the crude extracts of 22 edible plants on foam cell formation and isolated nine chlorophyll derivatives as potent inhibitors from Chinese cabbage. The results of the present study suggest that the chlorophyll derivatives contained in edible plants may be useful for the prevention and treatment of atherosclerosis.
Cell biology of the Koji mold Aspergillus oryzae
Authors: Kitamoto Katsuhiko 
Published: March 2015

Abstract
Koji mold, Aspergillus oryzae, has been used for the production of sake, miso, and soy sauce for more than one thousand years in Japan. Due to the importance, A. oryzae has been designated as the national micro-organism of Japan (Koku-kin). A. oryzae has been intensively studied in the past century, with most investigations focusing on breeding techniques and developing methods for Koji making for sake brewing. However, the understanding of fundamental biology of A. oryzae remains relatively limited compared with the yeast Saccharomyces cerevisiae. Therefore, we have focused on studying the cell biology including live cell imaging of organelles, protein vesicular trafficking, autophagy, and Woronin body functions using the available genomic information. In this review, I describe essential findings of cell biology of A. oryzae obtained in our study for a quarter of century. Understanding of the basic biology will be critical for not its biotechnological application, but also for an understanding of the fundamental biology of other filamentous fungi.
WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
Authors: Rackham Owen J. L. , Dellaportas Petros , Petretto Enrico , Bottolo Leonardo 
Published: March 2015

Abstract
Motivation: As the number of studies looking at differences between DNA methylation increases, there is a growing demand to develop and benchmark statistical methods to analyse these data. To date no objective approach for the comparison of these methods has been developed and as such it remains difficult to assess which analysis tool is most appropriate for a given experiment. As a result, there is an unmet need for a DNA methylation data simulator that can accurately reproduce a wide range of experimental setups, and can be routinely used to compare the performance of different statistical models.
Results: We have developed WGBSSuite, a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide. Several simulator parameters can be derived directly from real datasets provided by the user in order to mimic real case scenarios. Thus, it is possible to choose the most appropriate statistical analysis tool for a given simulated design. To show the usefulness of our simulator, we also report a benchmark of commonly used methods for differential methylation analysis.
Availability and implementation: WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/
Contact: owen.rackham@imperial.ac.uk or l.bottolo@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes
Authors: Smaoui Mohamed Raef , Orland Henri , Waldispühl Jérôme 
Published: March 2015

Abstract
Motivation: Amyloids play a role in the degradation of β-cells in diabetes patients. In particular, short amyloid oligomers inject themselves into the membranes of these cells and create pores that disrupt the strictly controlled flow of ions through the membranes. This leads to cell death. Getting rid of the short oligomers either by a deconstruction process or by elongating them into longer fibrils will reduce this toxicity and allow the β-cells to live longer.
Results: We develop a computational method to probe the binding affinity of amyloid structures and produce an amylin analog that binds to oligomers and extends their length. The binding and extension lower toxicity and β-cell death. The amylin analog is designed through a parsimonious selection of mutations and is to be administered with the pramlintide drug, but not to interact with it. The mutations (T9K L12K S28H T30K) produce a stable native structure, strong binding affinity to oligomers, and long fibrils. We present an extended mathematical model for the insulin–glucose relationship and demonstrate how affecting the concentration of oligomers with such analog is strictly coupled with insulin release and β-cell fitness.
Availability and implementation: SEMBA, the tool to probe the binding affinity of amyloid proteins and generate the binding affinity scoring matrices and R-scores is available at: http://amyloid.cs.mcgill.ca
Contact: jeromew@cs.mcgill.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Computational approaches towards understanding human long non-coding RNA biology
Authors: Jalali Saakshi , Kapoor Shruti , Sivadas Ambily , Bhartiya Deeksha , Scaria Vinod 
Published: March 2015

Abstract
Long non-coding RNAs (lncRNAs) form the largest class of non-protein coding genes in the human genome. While a small subset of well-characterized lncRNAs has demonstrated their significant role in diverse biological functions like chromatin modifications, post-transcriptional regulation, imprinting etc., the functional significance of a vast majority of them still remains an enigma. Increasing evidence of the implications of lncRNAs in various diseases including cancer and major developmental processes has further enhanced the need to gain mechanistic insights into the lncRNA functions. Here, we present a comprehensive review of the various computational approaches and tools available for the identification and annotation of long non-coding RNAs. We also discuss a conceptual roadmap to systematically explore the functional properties of the lncRNAs using computational approaches.
Contact: vinods@igib.in
Evaluating the performance of otolith morphometrics in deriving age compositions and mortality rates for assessment of data-poor tropical fisheries
Authors: Williams Ashley J. , Newman Stephen J. , Wakefield Corey B. , Bunel Melanie , Halafihi Tuikolongahau , Kaltavara Jeremie , Nicol Simon J. 
Published: March 2015

Abstract
Deepwater snappers (Family Lutjanidae) are important to artisanal and subsistence fisheries in Pacific Island countries. Most species of deepwater snapper are considered vulnerable to exploitation due to their extended longevity and low natural mortality rates. However, the sustainability of deepwater snapper fisheries in Pacific Island countries remains uncertain because there are limited resources available to collect the required data for comprehensive stock assessments. Reliable estimates of the age composition for exploited deepwater snapper populations are limited primarily because of the lack of skills and resources required for routine age estimation from sectioned otoliths. The development of alternative low-cost approaches to derive estimates of age for deepwater snappers is required. We evaluated the performance of using otolith morphometrics (weight, length, width, and thickness) to obtain estimates of age for the most important target species in these fisheries: Etelis carbunculus, E. marshi, E. coruscans, and Pristipomoides filamentosus. We compared age compositions and fishing mortality rates (F) derived from otolith morphometrics with those derived from counts of annual increments in otoliths. We then used the ratio of F to natural mortality (M) as a biological indicator to evaluate the potential effects on management responses by comparing estimates of F/M derived from otolith morphometrics with those derived from annual increment counts. Age compositions and estimates of F and F/M did not differ significantly between those derived from otolith morphometrics and those derived from annual increment counts for all species. These results demonstrate that management responses would likely be similar whether based on age estimates derived from sectioned otoliths, or predicted from otolith morphometrics. In the absence of sufficient resources to section otoliths for age estimation, we recommend that otolith morphometrics be used as a proxy for age in assessments of deepwater snapper fisheries in Pacific Island countries, and potentially for other similar data-limited fisheries.
Urinary tract infection caused by Actinobaculum schaalii: a urosepsis pathogen that should not be underestimated
Authors: Le Brun Cécile , Robert Sylvie , Tanchoux Colas , Bruyere Franck , Lanotte Philippe 
Published: March 2015

Introduction:

Actinobaculum schaalii is a Gram‐positive facultative anaerobic coccoid rod bacterium that grows slowly in culture. This bacterium was classified as a new genus in 1997 but is often overlooked or considered a contaminant because of both its resemblance to the normal bacterial flora on skin and mucosa and the overgrowth of other bacteria. During the past decade, A. schaalii has emerged as a more common urinary tract pathogen than previously thought.

Case presentation:
Here, we describe the case of a patient with an untreated A. schaalii urinary tract infection that turned into urosepsis.

Conclusion:
This case shows that the invasive potential of this bacterium should not always be ruled out.
Using factor-cluster analysis to segment patrons of casual dining establishments in the United States
Authors: Duncan Jennifer L. , Josiam Bharath M. , Kim Young  Hoon , Kalldin Alexandria C. 
Published: March 2015

Purpose
– Focussing on behaviors and attitudes of casual dining patrons, the purpose of this paper is to use a factor-cluster approach to segment patrons into market groups and attempts to determine if differences exist in motivational factors among segments.

Design/methodology/approach
– Factor-cluster analysis is an alternative segmentation method to more traditionally used methods based on consumer demographics. Push and pull motivators were analyzed through factor analysis to determine important groupings. Then, to identify homogenous subgroups, k-means cluster analysis was conducted to segment 559 survey respondents based on factor importance.

Findings
– Three diverse groups were identified: Fraternizing Kitchen Fearfuls, Functional Feasters, and Foodie Fanatics. The various push and pull factors appeared to affect segments differently, with each cluster ascribing various importance levels to each of the factors used in the clustering approach.

Research limitations/implications
– Limitations include the use of a convenience sample and on-campus sampling. Future research should use random sampling methods and obtain surveys from sites not associated with a college campus.

Practical implications
– Though not often used in hospitality research, factor-cluster analysis can be useful to segment diners based on behavioral intentions and attributes, allowing marketers to more accurately target these diverse consumer segments. Marketing implications for casual dining restaurants are suggested.

Originality/value
– Using the involvement construct with push/pull motivators, this study groups respondents though factor-cluster analysis. Though used in tourism studies, factor-cluster analysis has yet to be studied in the context of casual dining restaurant patrons.
What determines British consumers’ motivation to buy sustainable seafood?
Authors: Honkanen Pirjo , Young James A. 
Published: March 2015

Purpose
– The purpose of this paper is to explore the role of determinants of consumers’ buying intentions for sustainable seafood.

Design/methodology/approach
– Survey data from 755 representative respondents in the UK were collected. Structural equation modelling was used to analyse the data. The theory of planned behaviour was used as a framework for the analysis, with an additional variable, personal norm, which seems to be especially relevant for environmental behaviour.

Findings
– The results confirmed the expected relationships: the motivation to buy sustainable seafood is increased by a positive attitude towards buying sustainable seafood, perceived pressure from important others such as family, friends and colleagues, and by a strong moral obligation. Attitude towards buying sustainable seafood was the strongest predictor of intention found in the study. To reach a goal of consumers placing greater emphasis upon purchasing more sustainable seafood, both attitudinal and normative messages could be used. Further implications of the findings and the scope for further research are discussed.

Research limitations/implications
– The study is correlational in nature, thus limiting the causal inferences that can be made from the results. It does, however, help to explain the relationships in explored in the model.

Originality/value
– This paper addresses the issue of motivation to buy sustainable seafood which has not received much attention in literature, but is an important issue for anyone trying to increase consumer sustainable behaviour.
How differing demographic factors impact consumers’ loyalty towards national or international fast food chains
Authors: Srivastava R.K. 
Published: March 2015

Purpose
– The purpose of this paper is to study differing demographic factors affecting fast-food customers loyalty towards national or international fast food chains. It also compares the variation between global and local fast food chains as the products offered are culturally different.

Design/methodology/approach
– A variety of variables used to gain a holistic view, which includes factors such as quality, price, food and demographic profile of consumers affecting loyalty of fast food chains. The study adopts the theory and method of the trust-commitment-loyalty explanation chain and examines the consumer survey adapted from Fast food by Sahagun et al. (2014). The present analyses 542 filled questionnaires in which systematic sampling is used. Systematic sampling procedure is adopted.

Findings
– Indians prefer global fast food chains compared to Indian fast food chains. Loyalty towards global brands is higher than that for Indian brands because they are found to be of better quality which leads to higher frequency of visit and recommendation of the brands to their friends and colleagues. There are ethnic variations towards global and Indian fast food chains. Global brand of food chains generated more good word of mouth publicity compared to Indian food chains. Demographic factors play a role in the patronage of fast food chains.

Research limitations/implications
– One of the limitations of this research is the study adapts the theory and method of the trust-commitment-loyalty explanation chain and examines the consumer survey adapted from a study of Sahagun et al. (2014) on fast food for emerging markets. Only India is studied, but the addition of other countries like Brazil, China, Russia and South Africa can add value.

Practical implications
– Fast food managers had to illustrate the satisfaction on affective response, such as quality of food, convenient location, variety, service and value for money. Demographic variables like gender, age, education, income and ethnicity, global and local Brand will affect the perceptions.

Originality/value
– This is the first attempt to study the loyalty of consumers in emerging markets, which is witnessing the entry of many fast food global chains. It studies the demographic variables effect on the loyalty and the behaviour of consumers and compares to local and global brand fast food chains. The research will be use to global managers who are planning to expand in emerging markets like India.
Implementing National Food Security Act in India: issues and challenges
Authors: Tanksale Ajinkya , Jha J.K. 
Published: March 2015

Purpose
– National Food Security Act 2013 (NFSA) is a unique step taken by Indian government to fight against hunger and protect right of the people for food. With its peculiarities like the life cycle approach, women empowerment, consideration of vulnerable sections in society and proposed reforms in public distribution system (PDS), NFSA is a promising effort for food security in India. The purpose of this paper is to put forth various aspects of NFSA and to identify issues and challenges for its implementation in the light of Indian PDS.

Design/methodology/approach
– Understanding the implications of NFSA, mapping the existing system of foodgrains distribution in India and analysing existing literature and secondary data available from assorted sources are the steps followed in this endeavour.

Findings
– Limited resources and exponentially increasing population, lack of infrastructure, operational inefficiencies and poor performance of the PDS are the major hurdles in successful implementation of the proposed act. This study gives emphasis on the need of major reforms in procurement, storage, movement and distribution of foodgrains strategies.

Research limitations/implications
– This paper focusses mainly on the operational and strategic aspects of PDS and its implications on NFSA. There is a wide scope for future research on sustainability of the act through agricultural and biotechnological innovations, financial analysis and strategic aspects.

Originality/value
– This study is an unique attempt of mapping and auditing of the entire complex value chain of the Indian PDS for implementation of NFSA. As NFSA is going to redefine the food security aspects, this pioneering work will be useful for researchers and policy makers working in this field in India and other developing countries.