bluuebunny/crossref_metadata_2025 huggingface dataset:
Using a data triangle to understand molecular nutrition
Authors: Evelo Chris
Published: April 2011

Until recently nutrigenomics was mainly about transcriptomics related data. That already confronted us with overwhelming analytical problems. We learned to mathematically and statistically treat genome wide expression studies and studies directed to gene expression regulation. Nutrigenomics researchers had to become bilingual speaking: English and R1 and learned to think about co-expression, clusters and false discovery rates. The latter in fact proofed to be a trap. Removing all the false positives made us loose the information we were really interested in. To understand the results of our genomics experiments we often had to confront what we were measuring with what we already knew. After all false positives are not likely to all be related to the same meaningful biological process. That asked for the development of new analytical tools like Cytoscape for network analysis and PathVisio for pathway analysis. More importantly we had to structure what we know. Text mining and data mining helped us to do that, but what was really needed was mobilization of all the knowledge that is present in the heads of the scientific community. WikiPathways was our contribution to the rapidly emerging field of community curation. Thus we started to become able to integrate different types of technologies that span the full gene expression pipeline and to understand that in the biological context.Today the story repeats itself. Genome wide genetics is becoming real. We can do Genome Wide Association Studies and soon we can sequence individual genomes in relation to food intake and phenotypic responses. And then what? How can we deal with that new avalanche of data? The oversampling problems will be a few orders of magnitude larger; after all there can be hundreds of SNPs in every gene. There will just be too many to understand which SNPs are important from the data alone. We will again have to relate them to the biological processes. But is that enough? I think not. We will only understand the outcome of those large scale genetics studies if we not only attribute the SNPs to genes and thereby to pathways. We will also have to consider the actual sequences and see what the functional effect is that the SNP causes. Is it likely to influence transcription factor binding, miRNA effects, or protein-protein interactions? This calls for new types of data integration, for which we already have the tools. And it calls for new creative ways to do that. What we really need is teams of creative minds. Some new initiatives seem to show that these are already being formed.1: http://www.r-project.org
Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax
Authors: Bar Daniel
Published: April 2011

The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes. This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous sequences were found to be predominantly within short contigs. Re-sequencing of candidate sites using distinct isolations of P. vivax genomic DNA showed deletions not found in the human genome, and with much greater similarity to the P. vivax than human genome. Moreover, the identified fragments were enriched for mRNA coding sequences and genes that are known to be functionally important for P. vivax, including nitric oxide synthase 1 (neuronal) adaptor and Interleukin-1 family, suggesting a functional role. These results are important for two reasons. First, a directional massive horizontal transfer of genetic material from humans to another eukaryote is shown for the first time. This sheds light on parasite evolution, co-adaptation and immune evasion. Second, the DNA found is enriched for Interleukin-1 family, which is known to be essential for malaria protection. This indicates a functional role and might serve to better understand how Plasmodium vivax and the immune system interact.
Development of a method for phenotyping Black Rot (Guignardia bidwellii) resistance on grapevine (Vitis_ spp.)
Authors: Rex Friederike , Fechter Iris , Hausmann Ludger , Töpfer Reinhard
Published: April 2011

Black Rot of grapevine is caused by the Ascomycet Guignardia bidwellii. The pathogen was introduced from North America to Europe in the 19th century. Since 2002, increased effects of the disease have been noticed, causing significant yield losses in the region of Mosel and infections in all German wine-growing regions. For that reason, it is important to breed Black Rot-resistant grapevine cultivars. A method has been developed to characterize lots of vines in a fast and reliable way concerning their susceptibility. Initial data has been collected and can be used for genetic analysis (here QTL). The aim of the project is to develop a molecular marker correlating with Black Rot resistance which can be used to select juvenile plants and therefore support the breeding of resistant cultivars.
Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Authors: Mishra Sonal , Meena Abha , Singh Sema , Yadav Dharmendra Kumar , Khan Feroz , Shukla Rakesh
Published: April 2011

The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as those involved in the conversion of (R)-reticuline to salutaridine-7-O-acetate are already characterized. The inversion of (S)-reticuline to (R)-reticuline represent the important steps in morphine biosynthesis. Wound induced transcript accumulation in Papaver reveals a novel wound inducible EST (NCBI DbEST: GO238757) showing homology with (R,S)-reticuline 7-O-methyltransferase (ID: Q6WUC2) isolated from Papaver somniferum. We compare the substrate binding homology of this novel wound inducible (R,S)-reticuline 7-O-methyltransferase (7-OMT) using template of P. somniferum (Q6WUC2; gb∣AAQ01668) as experimental control. Homology modeling with 70% identity & 85% similarity with catalytic site of template protein i.e., (Q6WUC2) short chain dehydrogenase/reductase (SDR), showed docking energy -69.9 and -75.8 kcal/mol with (S)-Reticuline (CID:439653) and (R)-Reticuline (CID:440586) respectively, which are comparable with experimental control binding site interaction energies. Docking of S- & R-reticuline into the active site revealed eight (F(5), E(18), W(24), C(47), F(44), P(45), C(46) and I(47) amino acids presumably responsible for the high substrate specificity of (R,S)-reticuline 7-O-methyltransferase.
Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Authors: Derry Jonathan , Mangravite Lara , Suver Christine , Furia Matt , Henderson David , Schildwachter Xavier , Izant Jonathan , Sieberts Solveig , Kellen Michael , Friend Stephen
Published: April 2011

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Attention induces dynamic changes in coherence between monkey area V1 and V4
Authors: Grothe Iris , Neitzel Simon , Mandon Sunita , Kreiter Andreas
Published: April 2011

Neurons receive a vast number of synaptic inputs at the same time. To successfully process a relevant piece of information, a neuron needs to select relevant, while suppressing irrelevant signals. In order to dynamically route a meaningful set of signals through processing pathways, neurons need to have a fast and flexible mechanism to change their effective connectivity. Here, we hypothesize that attention changes effective connectivity by modulating the synchrony between neuronal populations.We investigated whether attention dynamically changes effective connectivity between area V4 neurons and their V1 input. Single unit activity, multi unit activity and local field potentials (LFP) were recorded simultaneously from macaque monkeys’ areas V1 and V4. While maintaining their gaze on a fixation spot, the monkeys had to attend to one of two continuously morphing shapes and respond to reoccurrence of the initial sample shape in the attended stream. Size and position of the shapes were adjusted such that both fitted into a single V4 receptive field (RF) while covering two separate, non-overlapping V1 RFs.We found strong phase-coherence of gamma-band LFPs between the V1 populations responding to the attended stimulus and the V4 population. At the same time, V1 populations responding to the unattended stimulus showed only weak LFP phase-coherence with the V4 population. Furthermore, spike-triggered averages (STAs) of at least 40% of the recording pairs revealed that spikes recorded from area V4 were precisely timed with respect to the phase of the gamma oscillation in the upstream area V1. More importantly, almost all these cases showed an increased effect with attention. These results support the hypothesis that attention induces dynamic changes in the effective connectivity between two anatomically hard-wired neuronal populations by selectively modulating synchrony.
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version1.0
Authors: White James , Arze Cesar , Matalka Malcolm , Team The CloVR , Angiuoli Samuel , Fricke W. Florian
Published: April 2011

The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Mothur [1] – a C++ - based software package used for clustering 16SrRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);B)The Ribosomal Database (RDP) naive Bayesian classifier [2] assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;C) Qiime [3] – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac [4]) for within- (alpha diversity) and between- (beta diversity) sample analysis;D) Metastats [5] and custom R scripts used to generate additional statistical and graphical evaluations.Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyrotagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.
A robust near infrared luminescent ytterbium metal–organic framework for sensing of small molecules
Authors: Guo Zhiyong , Xu Hui , Su Shengqun , Cai Jianfeng , Dang Song , Xiang Shengchang , Qian Guodong , Zhang Hongjie , O’Keeffe Michael , Chen Banglin
Published: April 2011

The first near-infrared luminescent ytterbium metal–organic framework has been realized for the highly selective and sensitive sensing of small molecules.
Peak experiences and strategic IT alignment at Vermont Teddy Bear
Authors: Gogan Janis L , Lewis Mark O
Published: April 2011

In winter 2010 Bob Stetzel, the new Chief Information Officer (CIO) at Vermont Teddy Bear (VTB), hopes to replace or modernize many of the company's existing systems and invest in some new applications. This catalog marketer (via online and print catalogs) offers three separately managed brands: Vermont Teddy Bear (VTB), PajamaGrams, and Calyx Flowers. Sales are highly seasonal, with peak volumes at Christmas, Valentine's Day and Mother's Day. Stetzel has spent his first few months on the job cataloging systems and databases, learning about the ‘spider web’ of middleware connecting various applications and platforms, and locating employees with expertise to fix them. The company has survived an economic downturn and several costly strategic missteps. The CEO is seeking new sources of revenue and ways to leverage their well-known brand, while the CIO needs to set Information Technology (IT) priorities: should they invest in a full-featured Enterprise Resource Planning (ERP) package or take other steps that would more quickly yield tangible results? Whatever choice he makes, Stetzel will have to convince the CEO and the Board of Directors to provide the necessary resources. This case provides students with an opportunity to place themselves in the shoes of a CIO wrestling with strategic IT alignment challenges at a time when resources are severely constrained and competitive rivalry is fierce.
Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex
Authors: Gold Matthew G. , Stengel Florian , Nygren Patrick J. , Weisbrod Chad R. , Bruce James E. , Robinson Carol V. , Barford David , Scott John D.
Published: April 2011

A-kinase anchoring protein 79 (AKAP79) is a human anchoring protein that organizes cAMP-dependent protein kinase (PKA), Ca
2+
/calmodulin (CaM)-dependent protein phosphatase (PP2B), and protein kinase C (PKC) for phosphoregulation of synaptic signaling. Quantitative biochemical analyses of selected AKAP79 complexes have determined the quaternary structure of these signaling complexes. We show that AKAP79 dimerizes, and we demonstrate that, upon addition of a lysine-reactive cross-linker, parallel homomeric dimers are stabilized through K328–K328 and K333–K333 cross-links. An assembly of greater complexity comprising AKAP79, PP2B, a type II regulatory subunit fragment (RII 1–45) of PKA, and CaM was reconstituted in vitro. Using native MS, we determined the molecular mass of this complex as 466 kDa. This indicates that dimeric AKAP79 coordinates two RII 1–45 homodimers, four PP2B heterodimers, and two CaM molecules. Binding of Ca
2+
/CaM to AKAP79 stabilizes the complex by generating a second interface for PP2B. This leads to activation of the anchored phosphatases. Our architectural model reveals how dimeric AKAP79 concentrates pockets of second messenger responsive enzyme activities at the plasma membrane.
Dual origin of mesenchymal stem cells contributing to organ growth and repair
Authors: Feng Jifan , Mantesso Andrea , De Bari Cosimo , Nishiyama Akiko , Sharpe Paul T.
Published: April 2011

In many adult tissues, mesenchymal stem cells (MSCs) are closely associated with perivascular niches and coexpress many markers in common with pericytes. The ability of pericytes to act as MSCs, however, remains controversial. By using genetic lineage tracing, we show that some pericytes differentiate into specialized tooth mesenchyme-derived cells—odontoblasts—during tooth growth and in response to damage in vivo. As the pericyte-derived mesenchymal cell contribution to odontoblast differentiation does not account for all cell differentiation, we identify an additional source of cells with MSC-like properties that are stimulated to migrate toward areas of tissue damage and differentiate into odontoblasts. Thus, although pericytes are capable of acting as a source of MSCs and differentiating into cells of mesenchymal origin, they do so alongside other MSCs of a nonpericyte origin. This study identifies a dual origin of MSCs in a single tissue and suggests that the pericyte contribution to MSC-derived mesenchymal cells in any given tissue is variable and possibly dependent on the extent of the vascularity.
Establishing a molecular relationship between chondritic and cometary organic solids
Authors: Cody George D. , Heying Emily , Alexander Conel M. O. , Nittler Larry R. , Kilcoyne A. L. David , Sandford Scott A. , Stroud Rhonda M.
Published: April 2011

Multidimensional solid-state NMR spectroscopy is used to refine the identification and abundance determination of functional groups in insoluble organic matter (IOM) isolated from a carbonaceous chondrite (Murchison, CM2). It is shown that IOM is composed primarily of highly substituted single ring aromatics, substituted furan/pyran moieties, highly branched oxygenated aliphatics, and carbonyl groups. A pathway for producing an IOM-like molecular structure through formaldehyde polymerization is proposed and tested experimentally. Solid-state
13
C NMR analysis of aqueously altered formaldehyde polymer reveals considerable similarity with chondritic IOM. Carbon X-ray absorption near edge structure spectroscopy of formaldehyde polymer reveals the presence of similar functional groups across certain Comet 81P/Wild 2 organic solids, interplanetary dust particles, and primitive IOM. Variation in functional group concentration amongst these extraterrestrial materials is understood to be a result of various degrees of processing in the parent bodies, in space, during atmospheric entry, etc. These results support the hypothesis that chondritic IOM and cometary refractory organic solids are related chemically and likely were derived from formaldehyde polymer. The fine-scale morphology of formaldehyde polymer produced in the experiment reveals abundant nanospherules that are similar in size and shape to organic nanoglobules that are ubiquitous in primitive chondrites.
The RecA/RAD51 protein drives migration of Holliday junctions via polymerization on DNA
Authors: Rossi Matthew J. , Mazina Olga M. , Bugreev Dmitry V. , Mazin Alexander V.
Published: April 2011

The Holliday junction (HJ), a cross-shaped structure that physically links the two DNA helices, is a key intermediate in homologous recombination, DNA repair, and replication. Several helicase-like proteins are known to bind HJs and promote their branch migration (BM) by translocating along DNA at the expense of ATP hydrolysis. Surprisingly, the bacterial recombinase protein RecA and its eukaryotic homologue Rad51 also promote BM of HJs despite the fact they do not bind HJs preferentially and do not translocate along DNA. RecA/Rad51 plays a key role in DNA double-stranded break repair and homologous recombination. RecA/Rad51 binds to ssDNA and forms contiguous filaments that promote the search for homologous DNA sequences and DNA strand exchange. The mechanism of BM promoted by RecA/RAD51 is unknown. Here, we demonstrate that cycles of RecA/Rad51 polymerization and dissociation coupled with ATP hydrolysis drives the BM of HJs.
IκB kinase ε and TANK-binding kinase 1 activate AKT by direct phosphorylation
Authors: Xie Xiaoduo , Zhang Denghong , Zhao Bin , Lu Min-Kan , You Ming , Condorelli Gianluigi , Wang Cun-Yu , Guan Kun-Liang
Published: April 2011

AKT activation requires phosphorylation of the activation loop (T308) by 3-phosphoinositide-dependent protein kinase 1 (PDK1) and the hydrophobic motif (S473) by the mammalian target of rapamycin complex 2 (mTORC2). We recently observed that phosphorylation of the AKT hydrophobic motif was dramatically elevated, rather than decreased, in mTOR knockout heart tissues, indicating the existence of other kinase(s) contributing to AKT phosphorylation. Here we show that the atypical IκB kinase ε and TANK-binding kinase 1 (IKKε/TBK1) phosphorylate AKT on both the hydrophobic motif and the activation loop in a manner dependent on PI3K signaling. This dual phosphorylation results in a robust AKT activation in vitro. Consistently, we found that growth factors can induce AKT (S473) phosphorylation in Rictor
−/−
cells, and this effect is insensitive to mTOR inhibitor Torin1. In IKKε/TBK1 double-knockout cells, AKT activation by growth factors is compromised. We also observed that TBK1 expression is elevated in the mTOR knockout heart tissues, and that TBK1 is required for Ras-induced mouse embryonic fibroblast transformation. Our observations suggest a physiological function of IKKε/TBK1 in AKT regulation and a possible mechanism of IKKε/TBK1 in oncogenesis by activating AKT.
Shape selection of twist-nematic-elastomer ribbons
Authors: Sawa Yoshiki , Ye Fangfu , Urayama Kenji , Takigawa Toshikazu , Gimenez-Pinto Vianney , Selinger Robin L. B. , Selinger Jonathan V.
Published: April 2011

How microscopic chirality is reflected in macroscopic scale to form various chiral shapes, such as straight helicoids and spiral ribbons, and how the degree of macroscopic chirality can be controlled are a focus of studies on the shape formation of many biomaterials and supramolecular systems. This article investigates both experimentally and theoretically how the chiral arrangement of liquid crystal mesogens in twist-nematic-elastomer films induces the formation of helicoids and spiral ribbons because of the coupling between the liquid crystalline order and the elasticity. It is also shown that the pitch of the formed ribbons can be tuned by temperature variation. The results of this study will facilitate the understanding of physics for the shape formation of chiral materials and the designing of new structures on basis of microscopic chirality.
Real-time label-free monitoring of adipose-derived stem cell differentiation with electric cell-substrate impedance sensing
Authors: Bagnaninchi Pierre O. , Drummond Nicola
Published: April 2011

Real-time monitoring of stem cells (SCs) differentiation will be critical to scale-up SC technologies, while label-free techniques will be desirable to quality-control SCs without precluding their therapeutic potential. We cultured adipose-derived stem cells (ADSCs) on top of multielectrode arrays and measured variations in the complex impedance Z* throughout induction of ADSCs toward osteoblasts and adipocytes. Z* was measured up to 17 d, every 180 s, over a 62.5–64kHz frequency range with an ECIS Zθ instrument. We found that osteogenesis and adipogenesis were characterized by distinct Z* time-courses. Significant differences were found (
P
= 0.007) as soon as 12 h post induction. An increase in the barrier resistance (Rb) up to 1.7 ohm·cm
2
was associated with early osteo-induction, whereas Rb peaked at 0.63 ohm·cm
2
for adipo-induced cells before falling to zero at
t
= 129 h. Dissimilarities in Z* throughout early induction (<24 h) were essentially attributed to variations in the cell-substrate parameter α. Four days after induction, cell membrane capacitance (Cm) of osteo-induced cells (Cm = 1.72 ± 0.10 μF/cm
2
) was significantly different from that of adipo-induced cells (Cm = 2.25 ± 0.27 μF/cm
2
), indicating that Cm could be used as an early marker of differentiation. Finally, we demonstrated long-term monitoring and measured a shift in the complex plane in the middle frequency range (1 kHz to 8 kHz) between early (
t
= 100 h) and late induction (
t
= 380 h). This study demonstrated that the osteoblast and adipocyte lineages have distinct dielectric properties and that such differences can be used to perform real-time label-free quantitative monitoring of adult stem cell differentiation with impedance sensing.
Repression of tumor suppressor miR-451 is essential for NOTCH1-induced oncogenesis in T-ALL
Authors: Li Xiaoyu , Sanda Takaomi , Look A. Thomas , Novina Carl D. , von Boehmer Harald
Published: April 2011

The NOTCH1 signaling pathway is a critical determinant of cell fate decisions and drives oncogenesis through mechanisms that are incompletely understood. Using an established mouse model of T cell acute lymphoblastic leukemia (T-ALL), here we report that induction of intracellular Notch1 (ICN1) leads to repression of miR-451 and miR-709. ICN1 decreases expression of these miRNAs by inducing degradation of the E2a tumor suppressor, which transcriptionally activates the genes encoding miR-451 and miR-709. Both miR-451 and miR-709 directly repress Myc expression. In addition, miR-709 directly represses expression of the Akt and Ras-GRF1 oncogenes. We also show that repression of miR-451 and miR-709 expression is required for initiation and maintenance of mouse T-ALL. miR-451 but not miR-709 is conserved in humans, and human T-ALLs with activating NOTCH1 mutations have decreased miR-451 and increased MYC levels compared with T-ALLs with wild-type NOTCH1. Thus, miR-451 and miR-709 function as potent suppressors of oncogenesis in NOTCH1-induced mouse T-ALL, and miR-451 influences MYC expression in human T-ALL bearing NOTCH1 mutations.
Clonal selection in xenografted human T cell acute lymphoblastic leukemia recapitulates gain of malignancy at relapse
Authors: Clappier Emmanuelle , Gerby Bastien , Sigaux François , Delord Marc , Touzri Farah , Hernandez Lucie , Ballerini Paola , Baruchel André , Pflumio Françoise , Soulier Jean
Published: April 2011

Genomic studies in human acute lymphoblastic leukemia (ALL) have revealed clonal heterogeneity at diagnosis and clonal evolution at relapse. In this study, we used genome-wide profiling to compare human T cell ALL samples at the time of diagnosis and after engraftment (xenograft) into immunodeficient recipient mice. Compared with paired diagnosis samples, the xenograft leukemia often contained additional genomic lesions in established human oncogenes and/or tumor suppressor genes. Mimicking such genomic lesions by short hairpin RNA–mediated knockdown in diagnosis samples conferred a selective advantage in competitive engraftment experiments, demonstrating that additional lesions can be drivers of increased leukemia-initiating activity. In addition, the xenograft leukemias appeared to arise from minor subclones existing in the patient at diagnosis. Comparison of paired diagnosis and relapse samples showed that, with regard to genetic lesions, xenograft leukemias more frequently more closely resembled relapse samples than bulk diagnosis samples. Moreover, a cell cycle– and mitosis-associated gene expression signature was present in xenograft and relapse samples, and xenograft leukemia exhibited diminished sensitivity to drugs. Thus, the establishment of human leukemia in immunodeficient mice selects and expands a more aggressive malignancy, recapitulating the process of relapse in patients. These findings may contribute to the design of novel strategies to prevent or treat relapse.
Gluten Enhances Cooking, Textural, and Sensory Properties of Oat Noodles
Authors: Zhou Bai‐Ling , Zhu Fan , Shan Fang , Cai Yi‐Zhong , Corke Harold
Published: April 2011

Whole grain oats are widely regarded as conferring significant health benefits. Composite flour of whole grain oat flour, wheat flour, and tapioca starch in the ratio 1:1:0.16 was formulated to make oat noodles with the addition of gluten at various levels. The influence of gluten on pasting and gelling properties of composite flour, and on cooking, textural, and sensory properties of salted oat noodles was evaluated. Addition of gluten decreased the paste viscosity, reduced hardness and springiness of gel, reduced cooking yield, cooking loss, and broken ratio during cooking, and increased the tensile strength and firmness of cooked noodles. Scanning electron microscopy showed that gluten tightened the network of protein in the noodles by forming oriented fibrils. Addition of gluten had little effect on the color of raw and cooked oat noodles, which were somewhat yellow. Sensory evaluation indicated that addition of gluten could enhance the overall acceptability of cooked oat noodles. This study may stimulate further interest in using functional whole grain cereal ingredients in developing healthy staple foods.
Incidence of Gastroesophageal Reflux During Transpyloric Feeds
Authors: Rosen Rachel , Hart Kristen , Warlaumont Mary
Published: April 2011

Objectives:

Transpyloric feeding has been proposed as an alternative method for controlling gastroesophageal reflux, but there have been no pediatric studies to determine how transpyloric feeding affects reflux burden. The aim of the present study was to determine the reflux burden in patients receiving transpyloric feeds.

Patients and Methods:

We reviewed the multichannel intraluminal impedance tracings of patients who had persistent symptoms and were fed transpylorically during the multichannel intraluminal impedance recording. We compared the reflux profiles during feed and nonfeed periods. We also compared the number of reflux‐related hospitalizations at Children's Hospital Boston in the year before and the year after the initiation of transpyloric feeds.

Results:

The mean number of reflux events per hour was 1.4 ± 1.3 and 0.8 ± 1.1 during feed and nonfeed periods, respectively (P = 0.06). There was no significant difference in the percentage of time that boluses were present in the esophagus during feed periods (1.0% ± 1.4%) compared with the nonfeed periods (0.6% ± 1.1%, P = 0.5). There was no significant difference in the mean number of reflux‐related hospitalizations in the year before (1.2 ± 1.4) or after (1.4 ± 1.2, P = 0.7) the initiation of transpyloric feeds.

Conclusions:

There is more reflux during transpyloric feeding periods than nonfeeding periods, which may explain why some patients continue to have reflux‐related hospitalizations even after the initiation of transpyloric feeds.
Portal Gastropathy and Duodenopathy in Children With Extrahepatic and Intrahepatic Portal Hypertension: Endoscopic Diagnosis and Histologic Scoring
Authors: Aydoğan Ayşen , Güllüoğlu Mine , Önder Semen Yeşil , Gökçe Selim , Çeltik Coşkun , Durmaz Özlem
Published: April 2011

Objectives:

The aim of the study was to determine the frequency of portal gastropathy (PG) and duodenopathy (PD) in children, to document the correlation of various clinical and laboratory parameters associated with portal hypertensive gastroduodenal lesions, to compare the endoscopic portal hypertensive lesions with different histologic findings, and to evaluate the use of a possible histologic scoring system.

Methods:

All children undergoing endoscopic investigation for portal hypertension (PH) between January 2006 and November 2007 were analysed retrospectively. Clinical and demographical data and endoscopic and histologic findings were recorded. Histologic findings suggestive of PG and PD (capillary dilation, increased numbers of capillaries, histologic bleeding, and edema) were scored.

Results:

Of 51 consecutive children (29 boys, mean age 10.1± 3.6 years [range 2.5–15.8 years]), 28 were cirrhotic. PG was diagnosed in 58.8% endoscopically. Children with cirrhotic PH had the highest rate of PG (64.3%), whereas those with extrahepatic or intrahepatic noncirrhotic PH were alike (50% and 54.5%, respectively). Baveno PG scores were higher in children with cirrhosis with higher Child‐Pugh scores. Capillary dilation was the only histologic finding showing significant association with the endoscopic diagnosis. Only 9% had PD on endoscopy. None of the histologic findings correlated with endoscopic diagnosis of PD.

Conclusions:

PG and PD are seen in children with extrahepatic and intrahepatic PH at rates similar to those reported in adult studies. Baveno PG scores increased in parallel with Child‐Pugh class in children with cirrhosis. Capillary dilation was the only histologic finding showing significant association with the endoscopic diagnosis of PG in this study.
Pathophysiology, Diagnosis, and Management of Pediatric Ascites
Authors: Giefer Matthew J , Murray Karen F , Colletti Richard B
Published: April 2011

The pediatric population has a number of unique considerations related to the diagnosis and treatment of ascites. This review summarizes the physiologic mechanisms for cirrhotic and noncirrhotic ascites and provides a comprehensive list of reported etiologies stratified by the patient's age. Characteristic findings on physical examination, diagnostic imaging, and abdominal paracentesis are also reviewed, with particular attention to those aspects that are unique to children. Medical and surgical treatments of ascites are discussed. Both prompt diagnosis and appropriate management of ascites are required to avoid associated morbidity and mortality.
Targeted Mutagenesis of Duplicated Genes in Soybean with Zinc-Finger Nucleases
Authors: Curtin Shaun J. , Zhang Feng , Sander Jeffry D. , Haun William J. , Starker Colby , Baltes Nicholas J. , Reyon Deepak , Dahlborg Elizabeth J. , Goodwin Mathew J. , Coffman Andrew P. , Dobbs Drena , Joung J. Keith , Voytas Daniel F. , Stupar Robert M.
Published: April 2011

We performed targeted mutagenesis of a transgene and nine endogenous soybean (Glycine max) genes using zinc-finger nucleases (ZFNs). A suite of ZFNs were engineered by the recently described context-dependent assembly platform—a rapid, open-source method for generating zinc-finger arrays. Specific ZFNs targeting DICER-LIKE (DCL) genes and other genes involved in RNA silencing were cloned into a vector under an estrogen-inducible promoter. A hairy-root transformation system was employed to investigate the efficiency of ZFN mutagenesis at each target locus. Transgenic roots exhibited somatic mutations localized at the ZFN target sites for seven out of nine targeted genes. We next introduced a ZFN into soybean via whole-plant transformation and generated independent mutations in the paralogous genes DCL4a and DCL4b. The dcl4b mutation showed efficient heritable transmission of the ZFN-induced mutation in the subsequent generation. These findings indicate that ZFN-based mutagenesis provides an efficient method for making mutations in duplicate genes that are otherwise difficult to study due to redundancy. We also developed a publicly accessible Web-based tool to identify sites suitable for engineering context-dependent assembly ZFNs in the soybean genome.
Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade
Authors: Hocher Valérie , Alloisio Nicole , Auguy Florence , Fournier Pascale , Doumas Patrick , Pujic Petar , Gherbi Hassen , Queiroux Clothilde , Da Silva Corinne , Wincker Patrick , Normand Philippe , Bogusz Didier
Published: April 2011

Comparative transcriptomics of two actinorhizal symbiotic plants, Casuarina glauca and Alnus glutinosa, was used to gain insight into their symbiotic programs triggered following contact with the nitrogen-fixing actinobacterium Frankia. Approximately 14,000 unigenes were recovered in roots and 3-week-old nodules of each of the two species. A transcriptomic array was designed to monitor changes in expression levels between roots and nodules, enabling the identification of up- and down-regulated genes as well as root- and nodule-specific genes. The expression levels of several genes emblematic of symbiosis were confirmed by quantitative polymerase chain reaction. As expected, several genes related to carbon and nitrogen exchange, defense against pathogens, or stress resistance were strongly regulated. Furthermore, homolog genes of the common and nodule-specific signaling pathways known in legumes were identified in the two actinorhizal symbiotic plants. The conservation of the host plant signaling pathway is all the more surprising in light of the lack of canonical nod genes in the genomes of its bacterial symbiont, Frankia. The evolutionary pattern emerging from these studies reinforces the hypothesis of a common genetic ancestor of the Fabid (Eurosid I) nodulating clade with a genetic predisposition for nodulation.
Two‐year follow‐up of the ‘Families for Health’ programme for the treatment of childhood obesity
Authors: Robertson W. , Thorogood M. , Inglis N. , Grainger C. , Stewart‐Brown S.
Published: April 2011

Background  The high prevalence of obesity in children in the UK warrants continuing public health attention. ‘Families for Health’ is a family‐based group programme for the treatment of childhood obesity. Significant improvements in body mass index (BMI) z‐score (−0.21, 95% CI: −0.35 to −0.07, P= 0.007) and other health outcomes were seen in children at a 9‐month follow‐up.

Aim  To undertake a 2‐year follow‐up of families who attended ‘Families for Health’ in Coventry, to assess long‐term outcomes and costs.

Methods  ‘Families for Health’ is a 12‐week programme with parallel groups for parents and children, addressing parenting skills, healthy lifestyles and emotional well‐being. The intervention was delivered at a leisure centre in Coventry, England, with 27 overweight or obese children aged 7–13 years (18 girls, 9 boys) and their parents, from 21 families. A ‘before‐and‐after’ evaluation was completed with 19 (70%) children followed up at 2 years. The primary outcome was change in BMI z‐score from baseline; secondary outcomes were children's quality of life, parent–child relationships, eating/activity habits and parents' mental health. Costs to deliver the intervention and to families were recorded.

Results  Mean change in BMI z‐score from baseline was −0.23 (95% CI: −0.42 to −0.03, P= 0.027) at the 2‐year follow‐up and eight (42%) children had a clinically significant reduction in BMI z‐score. Significant improvements were seen in children's quality of life and eating habits in the home, while there were sustained reductions in unhealthy foods and sedentary behaviour. Fruit and vegetable consumption and parent's mental health were not significantly different at 2 years. Costs of the programme were £517 per family (£402 per child), equivalent to £2543 per unit reduction in BMI z‐score.

Conclusions  Improvements in BMI z‐score and certain other outcomes associated with the ‘Families for Health’ programme were sustained at the 2‐year follow‐up. ‘Families for Health’ is a promising new childhood obesity intervention, and a randomized controlled trial is now indicated.
Formation of modern dolomite in hypersaline pans of the Western Cape, South Africa
Authors: MAUGER CARLA L. , COMPTON JOHN S.
Published: April 2011

Authigenic calcite and dolomite and biogenic aragonite occur in Holocene pan sediments in a Mediterranean‐type climate on the western coastal plain of South Africa. Sediment was analysed from a Late Pleistocene coastal pan at Yzerfontein and four Holocene inland pans ranging from brackish to hypersaline. The pans are between 0·08 and 0·14 km2 in size. The δ18OPDB values of carbonate minerals in the pan sediments range from −2·41 to 5·56‰ and indicate precipitation from evaporative waters. Covariance of total organic content and percentage carbonate minerals, and the δ13CPDB values of pan carbonate minerals (−8·85 to −1·54‰) suggest that organic matter degradation is a significant source of carbonate ions. The precipitation of the carbonate minerals, especially dolomite, appears to be mediated by sulphate‐reducing bacteria in the black sulphidic mud zone found in the brine‐type hypersaline pans. The knobbly, sub‐spherical texture of the carbonate minerals suggests that the precipitation of the carbonate minerals, particularly dolomite, is related to microbial processes. The 87Sr/86Sr ratios of pan carbonate minerals (0·7108 to 0·7116) are slightly higher than modern sea water and indicate a predominantly sea water (marine aerosol) source for calcium (Ca2+) ions with relatively minor amounts of Ca2+ derived from the chemical weathering of bedrock.
The sedimentary response to a pioneer geo‐engineering project: Tracking the Kander River deviation in the sediments of Lake Thun (Switzerland)
Authors: WIRTH STEFANIE B. , GIRARDCLOS STÉPHANIE , RELLSTAB CHRISTIAN , ANSELMETTI FLAVIO S.
Published: April 2011

Human activities such as river corrections and deviations, lake‐level regulations and installations of hydropower plants affect and often strongly modify natural processes in lacustrine systems. In 1714, the previously bypassing Kander River was deviated into peri‐alpine Lake Thun. This pioneering geo‐engineering project, the first river correction of such dimensions in Switzerland, doubled the water and sediment input to the lake. In order to evaluate the sedimentary consequences of the Kander River deviation, the lacustrine sediments were investigated using a combined approach of high‐resolution (3·5 kHz) reflection seismic data and sediment cores (maximum length 2·5 m). The significance of this study is increased by the possible hazard represented by ammunition dumped into the lake (from 1920 to 1960) and by the recent installation of a gas pipeline on the lake floor in 2007/2008. The first 130 years after the river deviation were dominated by an extremely high sediment input, which led to the frequent occurrence of subaquatic mass movements. Slope failures primarily occur due to rapid sediment accumulation, but were occasionally triggered in combination with earthquake‐induced shocks and lake‐level fluctuations. After 1840, mass‐movement activity and sedimentation rates decreased due to a reduced sediment input as the Kander River adjusted to its new base level and, to a smaller degree, by further engineering of the Kander River bed and gravel withdrawal at the Kander Delta. A further consequence of the Kander River deviation is that the shores around Lake Thun have been more frequently affected by flooding due to the increased water input. In the time span from 1850 to 2006, six historically and/or instrumentally documented flood events could be correlated to flood turbidites in the sediment cores. This study demonstrates the significant usefulness of lacustrine sediments, not only in archiving natural hazards and human impact but also in assessing the consequences of future anthropogenic interventions on lacustrine systems.
Primary squamous cell carcinoma of fallopian tube accompanied by gastric metaplasia of female genital tract: Case report and review
Authors: Satoh Hiroshi , Baba Tsukasa , Mandai Masaki , Suzuki Ayako , Matsumura Noriomi , Konishi Ikuo
Published: April 2011

Primary squamous cell carcinoma arising from the fallopian tube (SCCFT) is extremely rare with only six reported cases. We report a case of primary SCCFT accompanied by multifocal pyloric glandular metaplasia in the genital tract. An accompanying review of the literature describes the characteristics of this rare histological subtype invading into the muscular layer of the fallopian tube to involve adjacent pelvic organs, while the most common serous type tends to spread into the abdominal cavity through tubal ducts. Due to the low response rate of adjuvant therapies, the 5‐year survival rate of patients bearing primary SCCFT at stage II–IV is very poor, only accounting for 25%. All patients were alive without disease where optimal resection had been successfully achieved. These findings imply that radical tumor resection is mandatory for satisfactory treatment of primary SCCFT.
Retrospective evaluation of perinatal outcome in women with mild gestational hyperglycemia
Authors: Kaymak Oktay , Iskender Can T. , Ustunyurt Emin , Yıldız Yasemin , Doganay Melike , Danisman Nuri
Published: April 2011

Aim:  To assess maternal and perinatal complications associated with mild gestational hyperglycemia (MGH).

Material and Methods:  This retrospective study was conducted in the perinatology division of Zekai Tahir Burak Women's Hospital between January and June 2009. Four hundred and eighty one patients with MGH and 212 patients with pre‐gestational diabetes or gestational diabetes mellitus (GDM) were recruited in the study. The control group consisted of 479 patients with normal glucose challenge test. Patients with MGH and the control group were compared in terms of maternal and neonatal complications.

Results:  The rates of large‐for‐gestational‐age (LGA) or macrosomic infants, pregnancy induced hypertension, primary cesarean delivery, preterm delivery and neonatal hypoglycemia were significantly higher in patients with MGH, GDM or preexisting diabetes. The rates of spontaneous preterm labor, shoulder dystocia, hyperbilirubinemia, low 1‐min Apgar score, fetal malformations and neonatal morbidity did not differ between the groups.

Conclusion:  MGH is associated with an increased risk of primary cesarean delivery, preterm delivery, pregnancy induced hypertension, and macrosomic and LGA infants.
Successful recovery from delayed amniotic fluid embolism with prolonged cardiac resuscitation
Authors: Hosono Kanako , Matsumura Noriomi , Matsuda Naoyuki , Fujiwara Hiroshi , Sato Yukiyasu , Konishi Ikuo
Published: April 2011

Amniotic fluid embolisms (AFE) are one of the most fatal complications of pregnancy. We describe a case of AFE that occurred 2 h after vaginal delivery at 41 weeks of gestation. The diagnosis of AFE was made by symptoms of dyspnea, coagulopathy, and severe hypotension. ZnCP‐1, the characteristic component of meconium, was elevated in the serum. Cardiac compressions after repeated cardiac arrests were required during the initial 2 h of resuscitation. Primary resuscitation was performed with airway management and aggressive fluid management, including infusion of 33 units of red cell concentrates and 57 units of fresh frozen plasma. The patient recovered without any aftereffects. This case report warrants that AFE should be considered when coagulopathy and dyspnea are observed during the postpartum period.
Principal Costs in Initial Public Offerings
Authors: Dalziel Thomas , White Robert E. , Arthurs Jonathan D.
Published: April 2011

abstract

The initial public offering (IPO) of a new venture's stock often results in significant changes to the firm's ownership structure. Because firm owners (principals) often have heterogeneous interests, conflicts can arise among the principals. While governance mechanisms are often effective in limiting agency problems, we suggest that principals can also attempt to use governance mechanisms to their own advantage in IPO settings. Specifically, when principal–principal conflict exists, powerful principals may exert control via governance mechanisms to pursue their own interests in ways that create inefficiencies in the form of ‘principal costs’.
Regulatory Burden, Rule of Law, and Entry of Strategic Entrepreneurs: An International Panel Study
Authors: Levie Jonathan , Autio Erkko
Published: April 2011

abstract

Entry into entrepreneurship is a strategic act for individuals who seek an optimal way to exploit their human, social, and financial capital. Trade‐offs associated with this choice are influenced by institutional conditions. We use signalling theory, employment choice theory, and theory on strategic entry to develop hypotheses on the effect of business regulations and rule of law on strategic and non‐strategic entrepreneurial entry. Analysing a six‐year panel of 54 countries, we find lighter burden of regulation associated with a higher rate and relative prevalence of strategic entrepreneurial entry. Rule of law moderates this effect such that regulation has a significant effect on strategic entry only when rule of law is strong. These findings are robust against alternative proxies. Implications are drawn for prospective entrepreneurs, existing organizations, policy, and further research.
Intuitive Analysis of Variance – A Formative Assessment Approach
Authors: Trumpower David
Published: April 2011

This article describes an assessment activity that can show students how much they intuitively understand about statistics, but also alert them to common misunderstandings. How the activity can be used formatively to help improve students' conceptual understanding of analysis of variance is discussed.