bluuebunny/crossref_metadata_2025 huggingface dataset:
Reprogramming of human fibroblasts toward a cardiac fate
Authors: Nam Young-Jae , Song Kunhua , Luo Xiang , Daniel Edward , Lambeth Kaleb , West Katherine , Hill Joseph A. , DiMaio J. Michael , Baker Linda A. , Bassel-Duby Rhonda , Olson Eric N.
Published: March 2013

Reprogramming of mouse fibroblasts toward a myocardial cell fate by forced expression of cardiac transcription factors or microRNAs has recently been demonstrated. The potential clinical applicability of these findings is based on the minimal regenerative potential of the adult human heart and the limited availability of human heart tissue. An initial but mandatory step toward clinical application of this approach is to establish conditions for conversion of adult human fibroblasts to a cardiac phenotype. Toward this goal, we sought to determine the optimal combination of factors necessary and sufficient for direct myocardial reprogramming of human fibroblasts. Here we show that four human cardiac transcription factors, including GATA binding protein 4, Hand2, T-box5, and myocardin, and two microRNAs, miR-1 and miR-133, activated cardiac marker expression in neonatal and adult human fibroblasts. After maintenance in culture for 4–11 wk, human fibroblasts reprogrammed with these proteins and microRNAs displayed sarcomere-like structures and calcium transients, and a small subset of such cells exhibited spontaneous contractility. These phenotypic changes were accompanied by expression of a broad range of cardiac genes and suppression of nonmyocyte genes. These findings indicate that human fibroblasts can be reprogrammed to cardiac-like myocytes by forced expression of cardiac transcription factors with muscle-specific microRNAs and represent a step toward possible therapeutic application of this reprogramming approach.
Effective responses: Protestants, Catholics and the provision of health care in the post-war Kivus
Authors: Seay Laura
                      E.
Published: March 2013

In extremely weak states, why are some civil society organisations better at providing health care than others? The case of health-care provision in the Kivu provinces of the eastern DRC provides a useful context in which to examine this question. Faced with the negative effects of more than 15 years of conflict, civil society organisations are the only institutions capable of providing social services. This article uses a series of case studies of local, faith-based health-care providers to argue that a number of historical, demographic and institutional factors cause some groups to develop stronger social capital networks than others. This in turn affects the degree of effectiveness that an organisation will have in providing social services in the state's absence. In doing so, they effectively substitute for the state in its role as a provider and regulator of public goods.

[Réponses efficaces : les Protestants, les Catholiques et la prévention des soins sanitaires dans le Kivu d'après-guerre]. Dans les états extrêmement faibles, pourquoi certaines organisations de la société civile sont plus efficaces pour fournir les soins sanitaires que d'autres? Le cas de prévention des soins sanitaires dans les provinces du Kivu à l'est de la RDC fournit un contexte pertinent pour examiner cette question. Faisant face aux effets négatifs de plus de 15 ans de conflits, les organisations de la société civile sont les seules institutions capables de fournir des services sociaux. Cet article utilise une série d'études de cas de fournisseurs de soins de santé confessionnels opérant au niveau local, pour soutenir qu'un certain nombre de facteurs historiques, démographiques et institutionnels permettent à certains groupes de développer de plus forts réseaux sociaux que d'autres. Ceci affecte à son tour le degré d'efficacité d'une organisation dans la fourniture de services sociaux en l'absence de l'État. De cette manière, ils se substituent effectivement à l'État dans son rôle de fournisseur et régulateur de biens publics.

Mots-clés : RDC ; soins de santé, religion ; les Protestants, les Catholiques ; Kivu
Ontogenetic Development of the Digestive Tract in Larvae of American Shad
Authors: Hong X Y , Zhu X P , Chen K C , Pan D B , Li K B
Published: March 2013

The American Shad Alosa sapidissima was introduced into China for aquaculture in 2003. The histological characteristics of the digestive tract of American Shad larvae were examined from hatching to 33 d after hatching (DAH) with the aim of cultivating the larvae efficiently. The fertilized American Shad eggs were imported from Oregon and incubated in barrels with spring water maintained at 20.3–21.9°C in Qingyuan, Guangdong Province, China. The larvae were transferred to cement pools (water temperature at 24.0–25.0°C) at 13 DAH. Larvae were fed Artemia nauplii starting at 3 DAH, Artemia nauplii supplemented with gradually increasing proportions of commercial formulated feed after 18 DAH, and then only the formulated feed by 30 DAH. Based on the source of nutrition and structural changes in the digestive tract, larval development was divided into three stages: (1) lecitotrophic (0–2 DAH), (2) lecitoexotrophic (3 DAH), and (3) exotrophic (4–33 DAH). At 0 DAH of the lecitotrophic stage, the digestive system was undifferentiated and contained a large acidophilic yolk sac. By 1 DAH, the mouth and anus opened, the liver appeared, and the buccopharynx and intestine began to differentiate. The lecitoexotrophic stage began at the start of exogenous feeding, which led to the disappearance of the yolk sac. During the exotrophic stage, the esophagus could be differentiated into two different regions by 4 DAH. The intestinal tract developed quickly and differentiated into an obvious foregut and hindgut by 11 DAH. The primary stomach formed by 8 DAH and completely developed by 19 DAH with the presence of a few gastric glands. By 25 DAH, many gastric glands and a number of pyloric ceca were observed. The results of the study show the quick development of the digestive system in American Shad and we suggest initiating the weaning process at 23–25 DAH in the larvae.
Matching Cue Size and Task Properties in Exogenous Attention
Authors: Burnett Katherine E. , d'Avossa Giovanni , Sapir Ayelet
Published: March 2013

Exogenous attention is an involuntary, reflexive orienting response that results in enhanced processing at the attended location. The standard view is that this enhancement generalizes across visual properties of a stimulus. We test whether the size of an exogenous cue sets the attentional field and whether this leads to different effects on stimuli with different visual properties. In a dual task with a random-dot kinematogram (RDK) in each quadrant of the screen, participants discriminated the direction of moving dots in one RDK and localized one red dot. Precues were uninformative and consisted of either a large or a small luminance-change frame. The motion discrimination task showed attentional effects following both large and small exogenous cues. The red dot probe localization task showed attentional effects following a small cue, but not a large cue. Two additional experiments showed that the different effects on localization were not due to reduced spatial uncertainty or suppression of RDK dots in the surround. These results indicate that the effects of exogenous attention depend on the size of the cue and the properties of the task, suggesting the involvement of receptive fields with different sizes in different tasks. These attentional effects are likely to be driven by bottom-up mechanisms in early visual areas.
BATF is required for normal expression of gut-homing receptors by T helper cells in response to retinoic acid
Authors: Wang Chuanwu , Thangamani Shankar , Kim Myunghoo , Gu Bon-Hee , Lee Jee H. , Taparowsky Elizabeth J. , Kim Chang H.
Published: March 2013

CCR9 and α4β7 are the major trafficking receptors for lymphocyte migration to the gut, and their expression is induced during lymphocyte activation under the influence of retinoic acid (RA). We report here that BATF (basic leucine zipper transcription factor, ATF-like), an AP-1 protein family factor, is required for optimal expression of CCR9 and α4β7 by T helper cells. BATF-deficient (knockout [KO]) mice had reduced numbers of effector T and regulatory T cells in the intestine. The intestinal T cells in BATF KO mice expressed CCR9 and α4β7 at abnormally low levels compared with their wild-type (WT) counterparts, and BATF KO CD4+ T cells failed to up-regulate the expression of CCR9 and α4β7 to WT levels in response to RA. Defective binding of RARα and histone acetylation at the regulatory regions of the CCR9 and Itg-α4 genes were observed in BATF KO T cells. As a result, BATF KO effector and FoxP3+ T cells failed to populate the intestine, and neither population functioned normally in the induction and regulation of colitis. Our results establish BATF as a cellular factor required for normal expression of CCR9 and α4β7 and for the homeostasis and effector functions of T cell populations in the intestine.
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
Authors: Chu Hsueh-Ting , Hsiao William W. L. , Chen Jen-Chih , Yeh Tze-Jung , Tsai Mong-Hsun , Lin Han , Liu Yen-Wenn , Lee Sheng-An , Chen Chaur-Chin , Tsao Theresa T. H. , Kao Cheng-Yan
Published: March 2013

Motivation: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.

Results: EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases.

Availability and implementation: EBARDenovo is available at http://ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only.

Contact:  cykao@csie.ntu.edu.tw, htchu@asia.edu.tw or postergrey@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package
Authors: Kemena Carsten , Bussotti Giovanni , Capriotti Emidio , Marti-Renom Marc A. , Notredame Cedric
Published: March 2013

Motivation: Aligning RNAs is useful to search for homologous genes, study evolutionary relationships, detect conserved regions and identify any patterns that may be of biological relevance. Poor levels of conservation among homologs, however, make it difficult to compare RNA sequences, even when considering closely evolutionary related sequences.

Results: We describe SARA-Coffee, a tertiary structure-based multiple RNA aligner, which has been validated using BRAliDARTS, a new benchmark framework designed for evaluating tertiary structure–based multiple RNA aligners. We provide two methods to measure the capacity of alignments to match corresponding secondary and tertiary structure features. On this benchmark, SARA-Coffee outperforms both regular aligners and those using secondary structure information. Furthermore, we show that on sequences in which <60% of the nucleotides form base pairs, primary sequence methods usually perform better than secondary-structure aware aligners.

Availability and implementation: The package and the datasets are available from http://www.tcoffee.org/Projects/saracoffee and http://structure.biofold.org/sara/.

Contact:  cedric.notredame@crg.es

Supplementary information:  Supplementary data are available at Bioinformatics online
SplicingCompass: differential splicing detection using RNA-Seq data
Authors: Aschoff Moritz , Hotz-Wagenblatt Agnes , Glatting Karl-Heinz , Fischer Matthias , Eils Roland , König Rainer
Published: March 2013

Motivation: Alternative splicing is central for cellular processes and substantially increases transcriptome and proteome diversity. Aberrant splicing events often have pathological consequences and are associated with various diseases and cancer types. The emergence of next-generation RNA sequencing (RNA-seq) provides an exciting new technology to analyse alternative splicing on a large scale. However, algorithms that enable the analysis of alternative splicing from short-read sequencing are not fully established yet and there are still no standard solutions available for a variety of data analysis tasks.

Results: We present a new method and software to predict genes that are differentially spliced between two different conditions using RNA-seq data. Our method uses geometric angles between the high dimensional vectors of exon read counts. With this, differential splicing can be detected even if the splicing events are composed of higher complexity and involve previously unknown splicing patterns. We applied our approach to two case studies including neuroblastoma tumour data with favourable and unfavourable clinical courses. We show the validity of our predictions as well as the applicability of our method in the context of patient clustering. We verified our predictions by several methods including simulated experiments and complementary in silico analyses. We found a significant number of exons with specific regulatory splicing factor motifs for predicted genes and a substantial number of publications linking those genes to alternative splicing. Furthermore, we could successfully exploit splicing information to cluster tissues and patients. Finally, we found additional evidence of splicing diversity for many predicted genes in normalized read coverage plots and in reads that span exon–exon junctions.

Availability: SplicingCompass is licensed under the GNU GPL and freely available as a package in the statistical language R at http://www.ichip.de/software/SplicingCompass.html

Contact:  m.aschoff@dkfz.de or r.koenig@dkfz.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
RCPedia: a database of retrocopied genes
Authors: Navarro Fábio C. P. , Galante Pedro A. F.
Published: March 2013

Motivation: Retrocopies are copies of mature RNAs that are usually devoid of regulatory sequences and introns. They have routinely been classified as processed pseudo-genes with little or no biological relevance. However, recent findings have revealed functional roles for retrocopies, as well as their high frequency in some organisms, such as primates. Despite their increasing importance, there is no user-friendly and publicly available resource for the study of retrocopies.

Results: Here, we present RCPedia, an integrative and user-friendly database designed for the study of retrocopied genes. RCPedia contains a complete catalogue of the retrocopies that are known to be present in human and five other primate genomes, their genomic context, inter-species conservation and gene expression data. RCPedia also offers a streamlined data representation and an efficient query system.

Availability and implementation: RCPedia is available at http://www.bioinfo.mochsl.org.br/rcpedia.

Contact:  pgalante@mochsl.org.br

Supplementary information:  Supplementary data are available at Bioinformatics online.
Direct distance measurements to SN 2009ip
Authors: Potashov M. , Blinnikov S. , Baklanov P. , Dolgov A.
Published: March 2013

We demonstrate the applicability of our new method (the Dense Shell Method or DSM) for the determination of astronomical distances by calculating the distance to SN 2009ip. The distance to this supernova has been accurately determined in the standard approach via the cosmic distance ladder and has been found to be 20.4 Mpc. Our direct method, assuming the most reasonable parameter values, gives a very close result, namely ≈20.1 ± 0.8 (68 per cent CL) Mpc to SN 2009ip.
Effect of Milling Temperature and Postmilling Cooling Procedures on Rice Milling Quality Appraisals
Authors: Pan Zhongli , Khir Ragab , Thompson James F.
Published: March 2013

The objective of this research was to study the effects of different milling conditions and postmilling handling procedures on appraised milling quality of rough rice. Rough rice (M202) with moisture content of 11.5 ± 0.2% was used for this study. The samples were milled with a McGill number 3 mill under four milling conditions, including normal milling, milling at high temperature, milling with cooling using ice water, and room temperature water. The milled rice samples were cooled in closed and open plastic containers and in open pans with three temperatures: 15, 23, and 35°C. The effects of milling and postmilling conditions on milled rice temperature, moisture loss, cooling rate, single and multiple fissuring rates, total rice yield (TRY), head rice yield (HRY), whiteness index (WI), and total lipid content (TLC) were evaluated. Results showed that high single and multiple fissuring rates and low TRY and HRY were inherent in improper milling and postmilling conditions. Single fissuring rates were 15.9 and 17.6% and multiple fissuring rates were 3.5 and 7.2% for rice samples milled under normal and high‐temperature conditions, respectively. Cooling methods that used open containers and pans had more moisture losses and further resulted in lowering appraised milling quality than methods that used closed containers. Low‐temperature milling conditions followed by cooling in closed containers significantly reduced single and multiple fissuring rates and improved TRY and HRY by 0.9 and 1.5 percentage points, respectively. The effects of tested milling and postmilling conditions on WI and TLC were not significant. Obtained results constitute valuable information for developing milling and cooling procedures to achieve consistent, accurate, and reliable milling quality appraisals for rough rice.
Validity of the Lipid Sink as a Mechanism for the Reversal of Local Anesthetic Systemic Toxicity
Authors: Kuo Ilin , Akpa Belinda S.
Published: March 2013

Background:

In vitro observations support the lipid sink theory of therapeutic action by confirming the capacity of lipid emulsions to successfully uptake bupivacaine from aqueous media. However, competing hypotheses and some in/ex vivo small animal studies suggest that a metabolic or positive inotropic effect underlies the dramatic effects of lipid therapy. Controlled clinical tests to establish causality and mechanism of action are an impossibility. In an effort to quantitatively probe the merits of a “sink” mechanism, a physiologically based pharmacokinetic model has been developed that considers the binding action of plasma lipid.

Methods:

The model includes no fitting parameters and accounts for concentration dependence of plasma protein and lipid:anesthetic binding as well as the metabolism of the lipid scavenger. Predicted pharmacokinetics were validated by comparison with data from healthy volunteers administered a nontoxic dose of bupivacaine. The model was augmented to simulate lipid therapy and extended to the case of accidental IV infusion of bupivacaine at levels known to cause systemic toxicity.

Results:

The model yielded quantitative agreement with available pharmacokinetic data. Simulated lipid infusion following an IV overdose was predicted to yield (1) an increase in total plasma concentration, (2) a decrease in unbound concentration, and (3) a decrease in tissue content of bupivacaine.

Conclusions:

Results suggest that the timescale on which tissue content is reduced varies from organ to organ, with the concentration in the heart falling by 11% within 3 min. This initial study suggests that, in isolation, the lipid sink is insufficient to guarantee a reversal of systemic toxicity.
Herbaspirillum

psychrotolerans sp. nov., a member of the family

Oxalobacteraceae

from a glacier forefield
Authors: Bajerski Felizitas , Ganzert Lars , Mangelsdorf Kai , Lipski André , Busse Hans-Jürgen , Padur Lisa , Wagner Dirk
Published: March 2013

A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1T was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1T has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1T is able to grow between −5 °C and 30 °C with optimum growth at 14–20 °C. Glycerol, dl-arabinose, d-xylose, d-galactose, d-fructose, d-lyxose, d-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10 %) for PB1T are C16 : 0 (19.1 %), C16 : 1ω7cis (44.6 %) and C18 : 1ω7cis (16.2 %). The major polyamines are putrescine [54.9 µmol (g dry weight)−1] and 2-hydroxy putrescine [18.5 µmol (g dry weight)−1]. DNA G+C content is 62.5 mol%. Strain PB1T is phylogenetically related to species of the genus

Herbaspirillum

, with highest 16S rRNA gene sequence similarities to

Herbaspirillum canariense

(97.3 %),

Herbaspirillum aurantiacum

(97.2 %),

Herbaspirillum soli

(97.2 %) and

Herbaspirillum frisingense

(97.0 %). The DNA–DNA relatedness values were below 30 % between PB1T and the type strains of

Herbaspirillum canariense

,

Herbaspirillum aurantiacum

and

Herbaspirillum soli

. The different geographical origin of strain PB1T from its closest phylogenetic relatives resulted in different phenotypic and genotypic specifications, whereby strain PBT represents a novel species of the genus

Herbaspirillum

, for which the name

Herbaspirillum

psychrotolerans is proposed. The type strain is PB1T (DSM 26001T = LMG 27282T).
Morphology and morphogenesis of a soil ciliate, Rigidohymena candens (Kahl, 1932) Berger, 2011 (Ciliophora, Hypotricha, Oxytrichidae), with notes on its molecular phylogeny based on small-subunit rDNA sequence data
Authors: Chen Xumiao , Yan Ying , Hu Xiaozhong , Zhu Mingzhuang , Ma Honggang , Warren Alan
Published: March 2013

The morphology and morphogenesis of the stylonychine hypotrich Rigidohymena candens (Kahl, 1932) Berger, 2011, isolated from garden soil in Qingdao, China, were investigated using live observation and protargol impregnation methods. The Qingdao isolate possesses all diagnostic morphological characters of R. candens. The main events during binary fission are as follows: (i) the proter retains the parental adoral zone of membranelles entirely, whereas the old undulating membranes dedifferentiate into an anlage that gives rise to the leftmost frontal cirrus and the new undulating membranes of the proter; (ii) five streaks of fronto-ventral-transverse cirral anlagen are segmented in the pattern 3 : 3 : 3 : 4 : 4 from left to right, which form two frontal, four frontoventral, one buccal, five ventral and five transverse cirri, respectively; (iii) dorsal morphogenesis is in the typical Oxytricha pattern; (iv) three caudal cirri are formed, one at the posterior end of each of dorsal kineties 1, 2 and 4; and (v) the postoral ventral cirrus V/3 is not involved in primordia formation. The morphological and morphogenetic observations and phylogenetic analyses based on the small-subunit rDNA sequence data support the validity of Rigidohymena Berger, 2011 and its systematic position in the subfamily Stylonychinae.
Streptomyces

aidingensis sp. nov., an actinomycete isolated from lake sediment
Authors: Xia Zhan-Feng , Ruan Ji-Sheng , Huang Ying , Zhang Li-Li
Published: March 2013

A novel actinomycete strain, designated TRM 46012T, was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64′ N 89° 26′ E), north-west China. The strain was aerobic and Gram-staining-positive with an optimum NaCl concentration for growth of 0–5 % (w/v). The isolate had sparse aerial mycelium and produced bud-shaped spores at the end of the aerial mycelium on ISP medium 4. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and three unidentified glycolipids. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The G+C content of the DNA was 74.4 mol%. Phylogenetic analysis showed that strain TRM 46012T had 16S rRNA gene sequence similarity of 95.7 % with the most closely related species with a validly published name,

Streptomyces cheonanensis

, and it could be distinguished from all species in the genus

Streptomyces

by using the data from this polyphasic taxonomic study. On the basis of these data, strain TRM 46012T should be designated as a representative of a novel species of the genus

Streptomyces

, for which the name

Streptomyces

aidingensis sp. nov. is proposed. The type strain is TRM 46012T ( = CGMCC 4.5739T = NBRC 108211T).
Kaistia hirudinis sp. nov., isolated from the skin of Hirudo verbana
Authors: Glaeser Stefanie P. , Galatis Harald , Martin Karin , Kämpfer Peter
Published: March 2013

A Gram-negative, rod-shaped bacterium was isolated from the skin of the medical leech Hirudo verbana and studied for its taxonomic allocation. 16S rRNA gene sequence similarities to other strains showed that the strain was closely related to species of the genus

Kaistia

.

Kaistia geumhonensis

was shown to be the most closely related species (96.8 %), followed by

Kaistia soli

(96.6 %) and

Kaistia dalseonensis

(96.2 %). All other species of the genus

Kaistia

showed 16S rRNA gene sequence similarities <96 %. Chemotaxonomic data for strain E94T (major ubiquinone: Q-10; major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylserine, unknown phospholipids, aminolipids and aminophospholipids; and major fatty acids: C18 : 1ω7c, C19 : 0ω8c cylco, C16 : 0 and C18 : 0) supported the affiliation of the isolate to the genus

Kaistia

. Phenotypic differentiation of strain E94T from all species of the genus

Kaistia

was possible using different physiological characters. Strain E94T represents a novel species of the genus

Kaistia

, for which the name Kaistia hirudinis sp. nov. is proposed, with the type strain E94T ( = LMG 26925T = CIP 110381T = CCM 8401T).
Odor–Taste Learning Assays in Drosophila Larvae
Authors: Gerber Bertram , Biernacki Roland , Thum Jeannette
Published: March 2013

The Drosophila larva is an emerging model for studies in behavioral neurogenetics because of its simplicity in terms of cell number. Despite this simplicity, basic features of neuronal organization and key behavior faculties are shared with adult flies and with mammals. Here, we describe a Pavlovian-type learning assay in fruit fly larvae. A group of larvae is sequentially exposed to specific odors in the presence or the absence of sugar, and then tested to determine whether they prefer the odor previously experienced with the reward. The protocol uses a two-group, reciprocal training design: One group of Drosophila larvae is exposed to n-amyl acetate (AM) with a sugar reward (+), then subsequently exposed to 1-octanol (OCT) with no reward (denoted AM+/OCT). The other group receives the reciprocal training (AM/OCT+). The two groups of larvae are then tested for their choices between AM and OCT. Relatively higher preferences for AM after AM+/OCT training than after AM/OCT+ training reflect associative learning and are quantified by the learning index (LI). This method offers a robust, simple, cheap, and reasonably quick test for learning ability (an aversive version is available as well, using either high-concentration salt or quinine as punishment). With the concerted efforts of the Drosophila research community, we anticipate it will allow us to unravel the full circuitry underlying odor–taste learning on a single-cell level.
A Rapid Western Blotting Protocol for the Xenopus Oocyte
Authors: Lin-Moshier Yaping , Marchant Jonathan S.
Published: March 2013

Often experimentalists require a quantitative assessment of the levels of heterologously expressed proteins to best interpret changed Ca2+ signaling patterns. Here, we detail a rapid and convenient western blotting method for individual Xenopus oocytes. The method exploits recently introduced rapid blotting systems, commercially available from Invitrogen (iBlot) or Bio-Rad (Trans-Blot Turbo). The key advantage is speed: from live cell to transferred membrane in <1 h. Therefore, oocytes can be conveniently processed for western blotting to assess relative expression levels, even after a long day of Ca2+ imaging experiments.
Two-Photon Imaging of Immune Cells in Neural Tissue
Authors: Niesner Raluca , Siffrin Volker , Zipp Frauke
Published: March 2013

To develop new therapeutic strategies for many central nervous system (CNS) diseases, it is essential to observe the motility and function of immune cells within neural tissue. Two-photon laser-scanning microscopy is an outstanding technique for imaging these phenomena under in vivo-like conditions. To gain deeper insight into the pathological phenomena that occur during chronic neuroinflammation of the CNS, we use it to view acute murine hippocampal slices cocultured with different subpopulations of immune cells and to view in vivo the brain stem of anesthetized transgenic mice affected by experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis. This protocol describes the preparation of cocultures of acute hippocampal slices with antigen-specific T helper 17 (Th17) cells migrating into the parenchyma, and the preparation of anesthetized mice for imaging the brain stem. We also discuss technical aspects of dual-color, two-photon laser-scanning microscopy that is used to image these samples and that allows for greater flexibility in the choice of fluorophores.
The Xenopus Oocyte: A Single-Cell Model for Studying Ca2+ Signaling
Authors: Lin-Moshier Yaping , Marchant Jonathan S.
Published: March 2013

In the four decades since the Xenopus oocyte was first demonstrated to have the capacity to translate exogenous mRNAs, this system has been exploited for many different experimental purposes. Typically, the oocyte is used either as a “biological test tube” for heterologous expression of proteins without any particular cell biological insight or, alternatively, it is used for applications where cell biology is paramount, such as investigations of the cellular adaptations that power early development. In this article, we discuss the utility of the Xenopus oocyte for studying Ca2+ signaling in both these contexts.
Protein-Coding cis-Natural Antisense Transcripts Have High and Broad Expression in Arabidopsis
Authors: Zhan Shuhua , Lukens Lewis
Published: March 2013

Pairs of genes within eukaryotic genomes are often located on opposite DNA strands such that transcription generates cis-natural sense antisense transcripts (cis-NATs). This orientation of genes has been associated with the biogenesis of splice variants and natural antisense small RNAs. Here, in an analysis of currently available data, we report that within Arabidopsis (Arabidopsis thaliana), protein-coding cis-NATs are also characterized by high abundance, high coexpression, and broad expression. Our results suggest that a permissive chromatin environment may have led to the proximity of these genes. Compared with other genes, cis-NAT-encoding genes have enriched low-nucleosome-density regions, high levels of histone H3 lysine-9 acetylation, and low levels of H3 lysine-27 trimethylation. Promoters associated with broadly expressed genes are preferentially found in the 5′ regulatory sequences of cis-NAT-encoding genes. Our results further suggest that natural antisense small RNA production from cis-NATs is limited. Small RNAs sequenced from natural antisense small RNA biogenesis mutants including dcl1, dcl2, dcl3, and rdr6 map to cis-NATs as frequently as small RNAs sequenced from wild-type plants. Future work will investigate if the positive transcriptional regulation of overlapping protein-coding genes contributes to the prevalence of these genes within other eukaryotic genomes.
A bromine analogue of picoplatin: a new substance from the group of platinum-based chemotherapeutics
Authors: Pažout Richard , Maixner Jaroslav , Hrdá Michaela , Loužilová Tereza , Kačer Petr
Published: March 2013

A new substance,cis-amminedibromido(2-methylpyridine-κN)platinum(II),cis-[PtBr2(C6H7N)(NH3)], which is a potential platinum-based antineoplastic agent for the treatment of patients with solid tumors, has been synthesized and structurally characterized. There is one molecule in the asymmetric unit and molecules are linkedviatwo symmetry-independent N—H...Br hydrogen bonds into zigzag chains running parallel to thecaxis. C—H...Br hydrogen bonds crosslink these chains to give a layer parallel to (010). N—H...Br hydrogen bonds and π–π stacking interactions between pairs of pyridine rings stack the layers alongb.
Similarities and differences in the structures of 5-bromo-6-hydroxy-7,8-dimethylchroman-2-one and 6-hydroxy-7,8-dimethyl-5-nitrochroman-2-one
Authors: Goswami Shailesh K. , Hanton Lyall R. , McAdam C. John , Moratti Stephen C. , Simpson Jim
Published: March 2013

The title compounds, C11H11BrO3, (I), and C11H11NO5, (II), respectively, are derivatives of 6-hydroxy-5,7,8-trimethylchroman-2-one substituted at the 5-position by a Br atom in (I) and by a nitro group in (II). The pyranone rings in both molecules adopt half-chair conformations, and intramolecular O—H...Br [in (I)] and O—H...Onitro[in (II)] hydrogen bonds affect the dispositions of the hydroxy groups. Classical intermolecular O—H...O hydrogen bonds are found in both molecules but play quite dissimilar roles in the crystal structures. In (I), O—H...O hydrogen bonds form zigzagC(9) chains of molecules along theaaxis. Because of the tetragonal symmetry, similar chains also form alongb. In (II), however, similar contacts involving an O atom of the nitro group form inversion dimers and generateR22(12) rings. These also result in a close intermolecular O...O contact of 2.686 (4) Å. For (I), four additional C—H...O hydrogen bonds combine with π–π stacking interactions between the benzene rings to build an extensive three-dimensional network with molecules stacked along thecaxis. The packing in (II) is much simpler and centres on the inversion dimers formed through O—H...O contacts. These dimers are stacked through additional C—H...O hydrogen bonds, and further weak C—H...O interactions generate a three-dimensional network of dimer stacks.
The influence of ERP implementation on the division of power at the production‐sales interface
Authors: de Vries Jan , Boonstra Albert
Published: March 2013

Purpose

The purpose of this paper is to develop and validate a model that demonstrates the influence of enterprise resource planning (ERP) implementation on the power and interests of actors at the production‐sales interface, and vice versa.

Design/methodology/approach

An empirical in‐depth longitudinal case study examines how a medium‐sized company in the graphics industry implemented an ERP system and how this has affected the interests and power distribution between the manufacturing and sales departments.

Findings

The case study reveals that the power division among key players at the production‐sales interface has been affected by the ERP implementation. These changes influence their attitudes and behaviours as well as the usage of the ERP system.

Research limitations/implications

Limitations are associated with the inherent weaknesses of any research based on a single‐case study: theoretical, but not statistical, generalisations are possible.

Practical implications

The findings imply that those implementing ERP systems in production‐sales environments should, from the outset of the project, identify potential changes in the division of power and seek to reconcile stakeholder interests.

Originality/value

This is one of the few studies that has examined in‐depth the potential effects of ERP implementation on power division at the production‐sales interface.
Logistics supplier integration in the automotive industry
Authors: Bennett David , Klug Florian
Published: March 2013

Purpose

In recent decades the automotive industry has established a variety of new forms of logistics integration between automobile assemblers and their suppliers, in particular those in the first tier. The purpose of this paper is to outline which form of logistics integration original equipment manufacturer (OEM) assembly plants use to link up with proximate suppliers, and to classify and compare different types of logistics supplier integration.

Design/methodology/approach

The data and insights for this paper come from a literature review of research and practitioner papers and studies to survey logistics integration models in theory and practice. In addition, data are collected through semi‐structured interviews and site visits.

Findings

The main findings are summarised in five conditions which characterise logistics supplier integration in the automotive industry. These conditions vary significantly between local dedicated supply as discussed in this paper and the traditional supply, which is distant and scattered around suppliers. These main conditions are “geographical proximity”, “delivery contents, volume and sequence”, “shared investment and asset specificity”, “information sharing and information technology system integration” as well as “transport system”. Although all of the five conditions were considered relevant for the description of existing integration forms, only the “geographical proximity” dimension is emerged as most suited for a formal typology. Therefore, a seven‐step integration model was developed which allows for a categorisation and comparison of existing logistics integration forms of proximate supply.

Research limitations/implications

This research aims to support the academic study of cross‐company and inter‐organisational supplier integration by providing consistent criteria for cross‐site comparisons. A holistic and consistent understanding of different logistics integration types will be necessary, which will help in evaluating the actual integration forms such as supplier parks.

Originality/value

The majority of studies into the supplier integration phenomenon conclude that logistical concerns are the driving factor behind supplier co‐location. Therefore, the focus of this research is on the spectrum of vertical integration in logistics between the vehicle manufacturers and their suppliers.
An evaluation of problem‐based assessment in teaching operations management
Authors: Bamford David , Karjalainen Katri , Jenavs Ernest
Published: March 2013

Purpose

The aim of this paper is to respond to calls for in‐depth studies of production and operations management (OM) teaching by providing an analysis of the relative effectiveness of a continuous problem‐based assessment and a traditional final exam assessment in OM.

Design/methodology/approach

An undergraduate OM module is used to assess how well a problem‐based assessment method performs against a more traditional final exam in terms of impact on student learning, student classification and feasibility. Quantitative data on student performance, feedback and satisfaction are used.

Findings

The analysis shows that the problem‐based assessment provides a better learning experience for the students, but is a worse classificatory of student results than the conventional exam. In terms of feasibility, problem‐based assessment can be a cost‐effective assessment method.

Research limitations/implications

This study analyses the assessment method used on one module for nine years; to increase the generalizability of the findings further research is needed with different modules and contexts.

Practical implications

This paper gives guidance to OM educators on how to improve assessment methods to achieve both improved learning effects as well as an accurate classification of student performance.

Originality/value

This study extends the literature on problem‐based learning to assessments and provides an empirical analysis of one such method. This study also provides detailed analysis of different assessment methods in OM based on longitudinal data.
Identifying critical enablers and pathways to high performance supply chain quality management
Authors: Lin Chinho , Kuei Chu‐hua , Chai Kang‐Wei
Published: March 2013

Purpose

The aim of this paper is threefold: first, to examine the content of supply chain quality management (SCQM); second, to identify the structure of SCQM; and third, to show ways for finding improvement opportunities and organizing individual institution's resources/actions into collective performance outcomes.

Design/methodology/approach

To meet the goals of this work, the paper uses abductive reasoning and two qualitative methods: content analysis and formal concept analysis (FCA). Primary data were collected from both original design manufacturers (ODMs) and original equipment manufacturers (OEMs) in Taiwan.

Findings

According to the qualitative empirical study, modern enterprises need to pay immediate attention to the following two pathways: a compliance approach and a voluntary approach. For the former, three strategic content variables are identified: training programs, ISO, and supplier quality audit programs. As for initiating a voluntary effort, modern lead firms need to instill “motivation” into a supply chain quality system.

Practical implications

The findings based on the abductive model reveal numerous strategic and tactical enablers, key sequences to move firms from their current situation to their preferred one, and critical opportunities for supply chain‐wide quality system designs.

Originality/value

This study will be of great value to supply chain policy makers, supply chain operators, and decision makers in lead firms in a supply chain setting and their channel partners. The proactive use of the authors' proposed research procedure is indispensable to effective supply chain quality planning.
An exploratory case study of aspect‐oriented metrics for fault proneness, content and fixing effort prediction
Authors: Elish Mahmoud O. , AL‐Rahman AL‐Khiaty Mojeeb , Alshayeb Mohammad
Published: March 2013

Purpose

The purpose of this paper is to investigate the relationships between some aspect‐oriented metrics and aspect fault proneness, content and fixing effort.

Design/methodology/approach

An exploratory case study was conducted using an open source aspect‐oriented software consisting of 76 aspects, and 13 aspect‐oriented metrics were investigated that measure different structural properties of an aspect: size, coupling, cohesion, and inheritance. In addition, different prediction models for aspect fault proneness, content and fixing effort were built using different combinations of metrics' categories.

Findings

The results obtained from this study indicate statistically significant correlation between most of the size metrics and aspect fault proneness, content and fixing effort. The cohesion metric was also found to be significantly correlated with the same. Moreover, it was observed that the best accuracy in aspect fault proneness, content and fixing effort prediction can be achieved as a function of some size metrics.

Originality/value

Fault prediction helps software developers to focus their quality assurance activities and to allocate the needed resources for these activities more effectively and efficiently; thus improving software reliability. In literature, some aspect‐oriented metrics have been evaluated for aspect fault proneness prediction, but not for other fault‐related prediction problems such as aspect fault content and fixing effort.
A framework for Six‐Sigma driven RFID‐enabled supply chain systems
Authors: Zare Mehrjerdi Yahia
Published: March 2013

Purpose

This paper aims to propose a new framework for selecting strategies from the pools of RFID strategies, Six‐Sigma strategies and supply chain strategies. To gain a better understanding of the proposed model, three case studies are investigated and all related strategies are presented and discussed.

Design/methodology/approach

This article proposes a new framework for Six‐Sigma driven RFID‐enabled supply chain systems. Theory building is comprised of four parts where each part is discussed clearly in the content of the article. However, it is through such tools that management can identify new systems for matching the needs of his/her organization with all of the right strategies.

Findings

In a journey to business excellence, an organization is successful if specific goals for critical processes of the organization are identified. The quality management programs implemented can modernize and simplify activities towards the ultimate goal of the business. To do so, this author's discussions on Six‐Sigma strategies, supply chain strategies, and radio frequency identification are converted into a framework that can be used for developing an appropriate model for organizational strategy selection. There are some cases in the literature that can support such a model building and framework identification. Three of such cases are presented for the readers' familiarity with the subject.

Practical implications

The use of these three methodologies can bring significant changes to an organization. This can be done by taking into consideration the key strategies of supply chain management, Six‐Sigma, and RFID playing a big role in the success of the organization.

Originality/value

For each methodology considered, strategies are examined and a framework based upon such methodologies is proposed. Cases supporting the proposed framework are reviewed from the literature for clarification purposes.
The common ground of relationships and exchange: towards a contractual foundation of marketing
Authors: Ehret Michael , Haase Michaela
Published: March 2013

Purpose

The aim of this paper is to argue for an explicit foundation of market exchange on person‐to‐person relationships as an alternative to the foundation on person‐to‐goods relationship underlying the exchange model inherited from neoclassical economics and classical contract law and used in a large significant share of marketing studies.

Design/methodology/approach

The paper provides a unifying theoretical framework to the analysis of transactions and relationships that links institutional approaches from economics, sociology, and law.

Findings

Relational contract theory provides a common ground for phenomena studied by both traditional exchange‐based and relationship marketing approaches. Relational contract theory conceives all types of market exchange as based on person‐to‐person relationships and provides an anchor for institutional, social and economic approaches in marketing.

Research limitations/implications

The concept of transaction provides a common foundation for the analysis of marketing phenomena that holds in diverse environments, including arms‐length transactions and close‐linked relationships. It provides an interface between marketing theory on the one hand and institutional, social and economic disciplines on the other.

Practical implications

Contracts specify how the parties to a transaction can realize action options opened up by property rights arrangements. Contracting strategy is the vital backbone of an industrial service strategy. Sound design of business models starts with the identification of the optimal owner of a resource, i.e. the actor who is in the best position to manage uncertainties or take on responsibilities associated with resource use.

Originality/value

This is the first investigation of a contractual foundation of marketing theory. It embeds the concept of exchange in an institutional framework and adapts it to the evolving business reality shaped by co‐operating firms and the rising share of services in value creation.