bluuebunny/crossref_metadata_2025 huggingface dataset:
dbGSH: a database of S-glutathionylation
Authors: Chen Yi-Ju , Lu Cheng-Tsung , Lee Tzong-Yi , Chen Yu-Ju
Published: May 2014

Summary:  S-glutathionylation, the reversible protein posttranslational modification (PTM) that generates a mixed disulfide bond between glutathione and cysteine residue, critically regulates protein activity, stability and redox regulation. Due to its importance in regulating oxidative/nitrosative stress and balance in cellular response, a number of methods have been rapidly developed to study S-glutathionylation, thus expanding the dataset of experimentally determined glutathionylation sites. However, there is currently no database dedicated to the integration of all experimentally verified S-glutathionylation sites along with their characteristics or structural or functional information. Thus, the dbGSH database has been created to integrate all available datasets and to provide the relevant structural analysis. As of January 31, 2014, dbGSH has manually collected >2200 experimentally verified S-glutathionylated peptides from 169 research articles using a text-mining approach. To solve the problem of heterogeneity of the data collected from different sources, the sequence identity of the reported S-glutathionylated peptides is mapped to UniProtKB protein entries. To delineate the structural correlations and consensus motifs of these S-glutathionylation sites, the dbGSH database also provides structural and functional analyses, including the motifs of substrate sites, solvent accessibility, protein secondary and tertiary structures, protein domains and gene ontology.

Availability and implementation: dbGSH is now freely accessible at http://csb.cse.yzu.edu.tw/dbGSH/. The database content is regularly updated with new data collected by the continuous survey of research articles.

Contact:  francis@saturn.yzu.edu.tw or yujuchen@gate.sinica.edu.tw

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Detecting clustering and ordering binding patterns among transcription factors via point process models
Authors: Cha Maria , Zhou Qing
Published: May 2014

Motivation: Recent development in ChIP-Seq technology has generated binding data for many transcription factors (TFs) in various cell types and cellular conditions. This opens great opportunities for studying combinatorial binding patterns among a set of TFs active in a particular cellular condition, which is a key component for understanding the interaction between TFs in gene regulation.

Results: As a first step to the identification of combinatorial binding patterns, we develop statistical methods to detect clustering and ordering patterns among binding sites (BSs) of a pair of TFs. Testing procedures based on Ripley’s K-function and its generalizations are developed to identify binding patterns from large collections of BSs in ChIP-Seq data. We have applied our methods to the ChIP-Seq data of 91 pairs of TFs in mouse embryonic stem cells. Our methods have detected clustering binding patterns between most TF pairs, which is consistent with the findings in the literature, and have identified significant ordering preferences, relative to the direction of target gene transcription, among the BSs of seven TFs. More interestingly, our results demonstrate that the identified clustering and ordering binding patterns between TFs are associated with the expression of the target genes. These findings provide new insights into co-regulation between TFs.

Availability and implementation: See ‘www.stat.ucla.edu/∼zhou/TFKFunctions/’ for source code.

Contact:  zhou@stat.ucla.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Neuroanaesthesia
Authors: Kigozi Michele , Newton Mary , James Paul , Moppett Iain
Published: May 2014

Successful management of neurological emergencies such as subarachnoid haemorrhage (SAH) and traumatic brain injury (TBI) requires rapid decision making and intervention with the anaesthetist playing a key role. The cases in this chapter explore the management and controversies relating to SAH (case 4.1) and TBI (case 4.2) both at initial presentation and during ongoing care. SAH is a sudden and potentially devastating condition with a high associated mortality and morbidity rate. Developments in endovascular occlusion techniques (coiling) have significantly altered the anaesthetic management of SAH, though thorough knowledge of the complications arising from SAH (delayed cerebral ischaemia, sodium disturbances, cardiovascular and pulmonary complications) is essential. When managing TBI the anaesthetist must modify their technique to prioritise cerebral perfusion and prevent secondary brain injury whilst working closely with neurosurgeons as part of a team to ensure the best functional outcomes.
Acute pain management
Authors: Key William , Nicholls Barry , Law Simon , Cashman Jeremy
Published: May 2014

Achieving excellent analgesia for acute pain can be a significant challenge which often falls to the anaesthetist. This chapter describes techniques for achieving analgesia for pain resulting from multiple trauma (case 7.2), and explores the potential benefits from paravertebral blockade (PVB) following mastectomy (case 7.1). Accurate, reliable, repeated assessment of pain is vital and forms an essential component of an analgesic strategy. Multimodal anaesthesia, and appropriate use of regional anaesthetic techniques may achieve the best results. A low threshold for investigating potential complications of neuraxial techniques is important. Optimal control of acute pain may reduce the incidence of chronic pain. PVB may provide superior acute pain relief and a reduction in the incidence of chronic pain following breast surgery compared to opioid based techniques. Avoidance of epidural-related complications support use of PVB for unilateral thoracic and breast surgery. Various mechanisms are postulated suggesting that paravertebral blockade may impact on cancer recurrence rates.
Progenitor constraints on the Type-Ia supernova SN2011fe from pre-explosion Hubble Space Telescope He ii narrow-band observations
Authors: Graur Or , Maoz Dan , Shara Michael M.
Published: May 2014

We present Hubble Space Telescope (HST) imaging observations of the site of the Type-Ia supernova SN2011fe in the nearby galaxy M101, obtained about 1 yr prior to the event, in a narrow band centred on the He ii λ4686 Å emission line. In a ‘single-degenerate’ progenitor scenario, the hard photon flux from an accreting white dwarf (WD), burning hydrogen on its surface over ∼1 Myr should, in principle, create a He iii Strömgren sphere or shell surrounding the WD. Depending on the WD luminosity, the interstellar density, and the velocity of an outflow from the WD, the He iii region could appear unresolved, extended, or as a ring, with a range of possible surface brightnesses. We find no trace of He ii λ4686 Å line emission in the HST data. Using simulations, we set 2σ upper limits on the He ii λ4686 Å luminosity of LHeii < 3.4 × 1034 erg s−1 for a point source, corresponding to an emission region of radius r < 1.8 pc. The upper limit for an extended source is LHeii < 1.7 × 1035 erg s−1, corresponding to an extended region with r ∼ 11 pc. The largest detectable shell, given an interstellar-medium density of 1 cm−3, has a radius of ∼6 pc. Our results argue against the presence, within the ∼105 yr prior to the explosion, of a supersoft X-ray source of luminosity Lbol ≳ 3 × 1037 erg s−1, or of a super-Eddington accreting WD that produces an outflowing wind capable of producing cavities with radii of 2–6 pc.
Poliomyelitis in transgenic mice expressing CD155 under the control of the Tage4 promoter after oral and parenteral poliovirus inoculation
Authors: Khan Shaukat , Toyoda Hidemi , Linehan Melissa , Iwasaki Akiko , Nomoto Akio , Bernhardt Günter , Cello Jeronimo , Wimmer Eckard
Published: May 2014

An important step in poliovirus (PV) infection by the oral route in humans is replication of the virus in lymphatic tissues of the gastrointestinal (GI) tract, thought to be mainly in the Peyer’s patches of the small intestine. No immunocompetent transgenic (tg) mice that express human PV receptor (CD155) under the control of different promoters can be infected orally. The mouse orthologue of human CD155 is Tage4, a protein expressed at the surface of enterocytes and in the Peyer’s patches. We describe here the generation of a tg mouse model in which the Tage4 promoter was used to drive expression of the human PV receptor-coding region (Tage4-CD155tg mice). In this model, CD155 expression was observed by immunostaining in different regions in the Peyer’s patches but not in their germinal centres. Although a similar pattern of staining was observed between 3- and 6-week-old Tage4-CD155tg mice, poliomyelitis was only seen in the younger mice after PV infection by the oral route. When compared with TgPVR21 mice that expressed CD155 driven by its human promoter, 3-week-old Tage4-CD155tg mice were more susceptible to gut infection and paralysis following feeding with PV. Also, Tage4-CD155tg mice exhibited higher susceptibility to poliomyelitis after parenteral inoculation of PV. Remarkably, the LD50after intracerebral inoculation of PV was similar in both CD155 tg mouse strains. The CD155 tg mouse model reported here, although moderately susceptible to oral infection, may be suitable to study mechanisms of PV replication in the gastrointestinal tract and to dissect important aspects of PV neuroinvasiveness.
Ontogenic, phenotypic, and functional characterization of XCR1+ dendritic cells leads to a consistent classification of intestinal dendritic cells based on the expression of XCR1 and SIRPα
Authors: Becker Martina , Güttler Steffen , Bachem Annabell , Hartung Evelyn , Mora Ahmed , Jäkel Anika , Hutloff Andreas , Henn Volker , Mages Hans Werner , Gurka Stephanie , Kroczek Richard A.
Published: May 2014

In the past, lack of lineage markers confounded the classification of dendritic cells (DC) in the intestine and impeded a full understanding of their location and function. We have recently shown that the chemokine receptor XCR1 is a lineage marker for cross-presenting DC in the spleen. Now we provide evidence that intestinal XCR1+ DC largely, but not fully, overlap with CD103+ CD11b- DC, the hypothesized correlate of cross-presenting DC in the intestine, and are selectively dependent in their development on the transcription factor Batf3. XCR1+ DC are located in the villi and epithelial crypts of the lamina propria of the small intestine, the T cell zones of Peyers Patches, and in the T cell zones and sinuses of the draining mesenteric lymph node. Functionally, we could demonstrate for the first time that XCR1+ / CD103+ CD11b- DC excel in the cross-presentation of orally applied antigen. Together, our data show that XCR1 is a lineage marker for cross-presenting DC also in the intestinal immune system. Further, extensive phenotypic analyses reveal that expression of the integrin SIRPα consistently demarcates the XCR1- DC population. We propose a simplified and consistent classification system for intestinal DC based on the expression of XCR1 and SIRPα.
Accounting for sources of bias and uncertainty in copy number-based statistical deconvolution of heterogeneous tumour samples
Authors: Yau Christopher
Published: May 2014

Deconvolving heterogeneous tumour samples to identify constituent cell populations with differing copy number profiles using whole genome sequencing data is a challenging problem. Copy number calling algorithms have differential detection rates for different sizes and classes of copy number alterations. This paper describes how uncertainty in classification and differential detection rates can introduce biases in measures of clonal diversity. A simulation strategy is introduced that allows differential detection rates to be adjusted for and this process is shown to minimise bias.
Loss of β-catenin triggers oxidative stress and impairs hematopoietic regeneration
Authors: Lento William , Ito Takahiro , Zhao Chen , Harris Jeffrey R. , Huang Wei , Jiang Chen , Owzar Kouros , Piryani Sadhna , Racioppi Luigi , Chao Nelson , Reya Tannishtha
Published: May 2014

Accidental or deliberate ionizing radiation exposure can be fatal due to widespread hematopoietic destruction. However, little is known about either the course of injury or the molecular pathways that regulate the subsequent regenerative response. Here we show that the Wnt signaling pathway is critically important for regeneration after radiation-induced injury. Using Wnt reporter mice, we show that radiation triggers activation of Wnt signaling in hematopoietic stem and progenitor cells. β-Catenin-deficient mice, which lack the ability to activate canonical Wnt signaling, exhibited impaired hematopoietic stem cell regeneration and bone marrow recovery after radiation. We found that, as part of the mechanism, hematopoietic stem cells lacking β-catenin fail to suppress the generation of reactive oxygen species and cannot resolve DNA double-strand breaks after radiation. Consistent with the impaired response to radiation, β-catenin-deficient mice are also unable to recover effectively after chemotherapy. Collectively, these data indicate that regenerative responses to distinct hematopoietic injuries share a genetic dependence on β-catenin and raise the possibility that modulation of Wnt signaling may be a path to improving bone marrow recovery after damage.
Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARγ-driven enhancers
Authors: Step Sonia E. , Lim Hee-Woong , Marinis Jill M. , Prokesch Andreas , Steger David J. , You Seo-Hee , Won Kyoung-Jae , Lazar Mitchell A.
Published: May 2014

Rosiglitazone (rosi) is a powerful insulin sensitizer, but serious toxicities have curtailed its widespread clinical use. Rosi functions as a high-affinity ligand for peroxisome proliferator-activated receptor γ (PPARγ), the adipocyte-predominant nuclear receptor (NR). The classic model, involving binding of ligand to the NR on DNA, explains positive regulation of gene expression, but ligand-dependent repression is not well understood. We addressed this issue by studying the direct effects of rosi on gene transcription using global run-on sequencing (GRO-seq). Rosi-induced changes in gene body transcription were pronounced after 10 min and correlated with steady-state mRNA levels as well as with transcription at nearby enhancers (enhancer RNAs [eRNAs]). Up-regulated eRNAs occurred almost exclusively at PPARγ-binding sites, to which rosi treatment recruited coactivators, including MED1, p300, and CBP. In contrast, transcriptional repression by rosi involved a loss of coactivators from eRNA sites devoid of PPARγ and enriched for other transcription factors, including AP-1 factors and C/EBPs. Thus, rosi activates and represses transcription by fundamentally different mechanisms that could inform the future development of anti-diabetic drugs.
PI3K-mediated PDGFRα signaling regulates survival and proliferation in skeletal development through p53-dependent intracellular pathways
Authors: Fantauzzo Katherine A. , Soriano Philippe
Published: May 2014

Previous studies have identified phosphatidylinositol 3-kinase (PI3K) as the main downstream effector of PDGFRα signaling during murine skeletal development. Autophosphorylation mutant knock-in embryos in which PDGFRα is unable to bind PI3K (PdgfraPI3K/PI3K) exhibit skeletal defects affecting the palatal shelves, shoulder girdle, vertebrae, and sternum. To identify proteins phosphorylated by Akt downstream from PI3K-mediated PDGFRα signaling, we immunoprecipitated Akt phosphorylation substrates from PDGF-AA-treated primary mouse embryonic palatal mesenchyme (MEPM) lysates and analyzed the peptides by nanoliquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS). Our analysis generated a list of 56 proteins, including 10 that regulate cell survival and proliferation. We demonstrate that MEPM cell survival is impaired in the presence of a PI3K inhibitor and that PdgfraPI3K/PI3K-derived MEPMs do not proliferate in response to PDGF-AA treatment. Several of the identified Akt phosphorylation targets, including Ybox1, mediate cell survival through regulation of p53. We show that Ybox1 binds both the Trp53 promoter and the p53 protein and that expression of Trp53 is significantly decreased upon PDGF-AA treatment in MEPMs. Finally, we demonstrate that introduction of a Trp53-null allele attenuates the vertebral defects found in PdgfraPI3K/PI3K neonates. Our findings identify p53 as a novel effector downstream from PI3K-engaged PDGFRα signaling that regulates survival and proliferation during skeletal development in vivo.
Structural analysis of the KANSL1/WDR5/KANSL2 complex reveals that WDR5 is required for efficient assembly and chromatin targeting of the NSL complex
Authors: Dias Jorge , Van Nguyen Nhuong , Georgiev Plamen , Gaub Aline , Brettschneider Janine , Cusack Stephen , Kadlec Jan , Akhtar Asifa
Published: May 2014

The subunits of the nonspecific lethal (NSL) complex, which include the histone acetyltransferase MOF (males absent on the first), play important roles in various cellular functions, including transcription regulation and stem cell identity maintenance and reprogramming, and are frequently misregulated in disease. Here, we provide the first biochemical and structural insights into the molecular architecture of this large multiprotein assembly. We identified several direct interactions within the complex and show that KANSL1 acts as a scaffold protein interacting with four other subunits, including WDR5, which in turn binds KANSL2. Structural analysis of the KANSL1/WDR5/KANSL2 subcomplex reveals how WDR5 is recruited into the NSL complex via conserved linear motifs of KANSL1 and KANSL2. Using structure-based KANSL1 mutants in transgenic flies, we show that the KANSL1–WDR5 interaction is required for proper assembly, efficient recruitment of the NSL complex to target promoters, and fly viability. Our data clearly show that the interactions of WDR5 with the MOF-containing NSL complex and MLL/COMPASS histone methyltransferase complexes are mutually exclusive. We propose that rather than being a shared subunit, WDR5 plays an important role in assembling distinct histone-modifying complexes with different epigenetic regulatory roles.
Investigating Physical Chromatin Associations Across the Xenopus Genome by Chromatin Immunoprecipitation
Authors: Gentsch George E. , Smith James C.
Published: May 2014

Chromatin immunoprecipitation (ChIP) combined with genomic analysis techniques provide a global snapshot of protein–DNA interactions in the context of chromatin, yielding insights into which genomic loci might be regulated by the DNA-associated protein under investigation. This protocol describes how to perform ChIP on intact or dissected Xenopus embryos. The ChIP-isolated DNA fragments are suitable for high-throughput sequencing (ChIP-Seq) or for quantitative PCR (ChIP-qPCR). In this protocol, embryonic tissue is harvested from Xenopus tropicalis or Xenopus laevis at the developmental stage of interest, and DNA-associated proteins are immobilized to their endogenous genomic binding sites with formaldehyde. Nuclei are extracted from embryos and subjected to sonication so as to shear the chromatin to a size that allows sufficient positional resolution of protein binding to genomic DNA. Chromatin fragments bound by the protein of interest are immunoprecipitated using antibody-coupled beads, washed under high-stringency conditions, and stripped from the beads with anionic detergents. The chemical cross-links are reversed, and the coimmunoprecipitated DNA is purified. The resulting DNA fragments can be analyzed by qPCR or used to create a ChIP-Seq library. General advice for qPCR and for making ChIP-Seq libraries is offered, and approaches for analyzing ChIP-Seq data are outlined.
Inducing RNAi in Drosophila Cells by Soaking with dsRNA
Authors: Zhou Rui , Mohr Stephanie , Hannon Gregory J. , Perrimon Norbert
Published: May 2014

RNA interference (RNAi) triggered by synthetic long double-stranded RNAs (dsRNAs) has been applied in many Drosophila cell lines to study the functions of individual genes or for genome-wide scans. One contributor to the popularity of this approach is that many fly cell lines spontaneously take up dsRNAs from media, obviating the need for assisted uptake methods such as transfection. In this protocol, RNAi is induced in Drosophila S2 cells by soaking with dsRNA. Cell lines other than S2 can also be used, although the ability of each line to passively take up dsRNA does vary. Therefore, the efficiency of passive uptake should be carefully verified for each line.
Identification and Staining of Distinct Populations of Secretory Organelles in Astrocytes
Authors: Bezzi Paola , Volterra Andrea
Published: May 2014

Increasing evidence indicates that astrocytes, the most abundant glial cell type in the brain, respond to an elevation in cytoplasmic calcium concentration ([Ca2+]i) by releasing chemical transmitters (also called gliotransmitters) via regulated exocytosis of heterogeneous classes of organelles. By this process, astrocytes exert modulatory influences on neighboring cells and are thought to participate in the control of synaptic circuits and cerebral blood flow. Studying the properties of exocytosis in astrocytes is a challenge, because the cell biological basis of this process is incompletely defined. Astrocytic exocytosis involves multiple populations of secretory vesicles, including synaptic-like microvesicles (SLMVs), dense-core granules (DCGs), and lysosomes. Here we summarize the available information for identifying individual populations of secretory organelles in astrocytes, including DCGs, SLMVs, and lysosomes, and present experimental procedures for specifically staining such populations.
Imaging Exocytosis and Recycling of Synaptic-Like Microvesicles in Astrocytes
Authors: Bezzi Paola , Volterra Andrea
Published: May 2014

Optical imaging techniques are well suited for following the dynamics of physiological processes in living cells. Total internal reflection fluorescence (TIRF) microscopy based on evanescent wave illumination (EWi) allows spectacular, real-time visualization of individual vesicle movements, fusions, and retrievals at the cell surface (i.e., within 100 nm of the plasma membrane). TIRF microscopy is an ideal approach for studying the properties of exocytosis and recycling in cultured astrocytes, particularly because these cells have a rather flat surface and contain secretory vesicles with sparse distribution. Among all populations of secretory vesicles, we focus here on synaptic-like microvesicles (SLMVs). We illustrate how TIRF microscopy using EWi is useful to study exocytosis and recycling of SLMVs at the single-vesicle level and, when combined with epifluorescence illumination (EPIi), can provide detailed information on the kinetics of exocytosis, endocytosis, and re-acidification at the whole-cell level.
Chronic Calcium Imaging of Neurons in the Mouse Visual Cortex Using a Troponin C–Based Indicator
Authors: Santos Alexandre Ferrão , Hübener Mark
Published: May 2014

This protocol describes the use of the genetically encoded troponin C–based calcium indicator TN-XXL to chronically monitor the functional properties of single neocortical neurons in the mouse visual cortex. A cranial window is implanted over the brain of a mouse expressing TN-XXL in pyramidal neurons of the cerebral cortex. Several days later, the visual cortex is mapped and photographed to facilitate repeated imaging of the same region using two-photon microscopy. Initial two-photon imaging may be done ∼2 wk after the window is implanted. We show the application of this technique for long-term in vivo imaging of stimulus response properties. Beyond providing functional information, long-term imaging of TN-XXL–labeled neurons also enables the simultaneous monitoring of structural properties down to the level of single dendritic spines.
Confocal Spot Detection of Presynaptic Ca2+ Domains
Authors: DiGregorio David
Published: May 2014

Advances in rapid imaging of fluorescence probes are crucial to the study of neuronal signaling and information processing within the nervous system. Fluorescence indicators of cellular signaling (e.g., Ca2+ or voltage) can report changes on the millisecond timescale and signals can be localized to submicrometer structures. There are significant methodological challenges, however, involved in making measurements at such high temporal and spatial resolution. I describe here the principle and implementation of a confocal spot detection method for rapid and localized detection of fluorescence changes, which we have used for the detection of action potential-induced presynaptic Ca2+ domains.
On the assessment of time-resolved diffraction results
Authors: Fournier Bertrand , Coppens Philip
Published: May 2014

Data collected during dynamic structure pump–probe crystallography experiments require appropriate indicators of agreement and tools to visualize the electron-density distribution changes. Agreement factors based on the ratio of intensitiesRwith and without the external perturbation are shown to be analogous to the {\cal R}1andw{\cal R}2{\cal R} factors widely used in standard crystallographic refinements. The η-based {\cal R} factors, normalized by the average relative intensity change, are significantly larger thanR-based values. It is shown that the relative intensity change η-based {\cal R} factors are not suitable for comparing different data sets. Fourier photodifference maps allow the visualization of the externally induced structural changes in the crystal, but also can be used during refinement to observe residual peaks not yet accounted for by the model and thus monitor the progress of the refinement. The photodeformation maps are a complementary tool to confirm the validity of the final model. Photodeformation maps with equalized laser-on and laser-off thermal motion are used to highlight the structural changes.
Hidden Law‐Making in the Province of Medical Jurisprudence
Authors: Montgomery Jonathan , Jones Caroline , Biggs Hazel
Published: May 2014

Judges articulate their role in controversial cases of medical ethics in terms of deference toParliament, lest their personal morality be improperly brought to bear. This hides a wide range of law‐making activities, as parliamentary sovereignty is diffused by ‘intermediate law‐makers’, and judicial activity is more subtle than the deference account implies. The nature of litigation raises questions about the contributions of other legal personnel and also the nature of the parties' interests in test‐cases. While judges demonstrate an awareness of some of these issues and anxiety about the constitutional legitimacy of their work, a more nuanced account is needed of their proper role. This may be built onAustin's theory of tacit legislation. It may draw from human rights law. However, considerable work is required before the complexities of hidden law‐making can be properly incorporated into the province of medical jurisprudence.
Animal Defenders International v United Kingdom: Sensible Dialogue or a Bad Case of Strasbourg Jitters?
Authors: Lewis Tom
Published: May 2014

In Animal Defenders International v United Kingdom a majority of the Grand Chamber of the European Court of Human Rights held that the UK's statutory broadcasting ban on political advertisements under the Communications Act 2003 did not breach the right to freedom of expression under Article 10 of the European Convention on Human Rights. The judgment departs from the Court's established case law and, it is argued, raises several issues of concern both with regard to freedom of expression, and for human rights adjudication more generally. In particular, the Court's use of a doctrine of ‘general measures’ led it to place a great deal of reliance on the quality and quantity of legislative debate that preceded the UK ban, rather than its actual impact upon the applicant.
Evaluation of Potassium‐Clavulanate‐Supplemented Modified Charcoal‐Cefoperazone‐Deoxycholate Agar for Enumeration of Campylobacter in Chicken Carcass Rinse
Authors: Chon Jung‐Whan , Kim Hong‐Seok , Kim Hyunsook , Oh Deog‐Hwan , Seo Kun‐Ho
Published: May 2014

Potassium‐clavulanate‐supplemented modified charcoal‐cefoperazone‐deoxycholate agar (C‐mCCDA) that was described in our previous study was compared with original mCCDA for the enumeration of Campylobacter in pure culture and chicken carcass rinse. The quantitative detection of viable Campylobacter cells from a pure culture, plated on C‐mCCDA, is statistically similar (P > 0.05) to mCCDA. In total, 120 chickens were rinsed using 400 mL buffered peptone water. The rinses were inoculated onto C‐mCCDA and mCCDA followed by incubation at 42 °C for 48 h. There was no statistical difference between C‐mCCDA (45 of 120 plates; mean count, 145.5 CFU/mL) and normal mCCDA (46 of 120 plates; mean count, 160.8 CFU/mL) in the isolation rate and recovery of Campylobacter (P > 0.05) from chicken carcass rinse. The Pearson correlation coefficient value for the number of Campylobacter cells recovered in the 2 media was 0.942. However, the selectivity was much better on C‐mCCDA than on mCCDA plates (P < 0.05). Significantly fewer C‐mCCDA plates (33 out of 120 plates; mean count, 1.9 CFU/mL) were contaminated with non‐Campylobacter cells than the normal mCCDA plates (67 out of 120 plates; mean count, 27.1 CFU/mL). The C‐mCCDA may provide improved results for enumeration of Campylobacter in chicken meat alternative to mCCDA with its increased selectivity the modified agar possess.
Viability of the Lactobacillus rhamnosus HN001 Probiotic Strain in Swiss‐ and Dutch‐Type Cheese and Cheese‐Like Products
Authors: Cichosz Grażyna , Aljewicz Marek , Nalepa Beata
Published: May 2014

The objective of this study was to determine the viability of the probiotic Lactobacillus rhamnosus HN001 in Swiss‐type and Dutch‐type cheese and cheese‐like products (milk fat is substituted by stearin fraction of palm fat) during manufacture, ripening, and storage. The use of the probiotic L. rhamnosus HN001 in Dutch‐type cheese and cheese‐like products significantly (P = 0.1) changed their chemical composition (protein and fat content) and an insignificant increase (approximately 1.6% in cheese‐like products and approximately 0.3% in cheese) in yield. L. rhamnosus HN001 did not affect the rate of changes in the pH of ripened cheese and cheese‐like products. A minor increase in probiotic counts was observed in initial stages of production and were partially removed with whey. Ripened cheese and cheese‐like products were characterized by high survival rates of probiotic bacteria which exceeded 8 log CFU/g after ripening. An insignificant reduction in the number of viable probiotic cells was noted during storage of Swiss‐type and Dutch‐type cheese, whereas a significant increase in probiotic cell counts was observed in cheese‐like products during storage.
Population‐level effects of fitness costs associated with repressible female‐lethal transgene insertions in two pest insects
Authors: Harvey‐Samuel Tim , Ant Thomas , Gong Hongfei , Morrison Neil I. , Alphey Luke
Published: May 2014

Genetic control strategies offer great potential for the sustainable and effective control of insect pests. These strategies involve the field release of transgenic insects with the aim of introducing engineered alleles into wild populations, either permanently or transiently. Their efficacy can therefore be reduced if transgene‐associated fitness costs reduce the relative performance of released insects. We describe a method of measuring the fitness costs associated with transgenes by analyzing their evolutionary trajectories when placed in competition with wild‐type alleles in replicated cage populations. Using this method, we estimated lifetime fitness costs associated with two repressible female‐lethal transgenes in the diamondback moth and olive fly as being acceptable for field suppression programs. Furthermore, using these estimates of genotype‐level fitness costs, we were able to project longer‐term evolutionary trajectories for the transgenes investigated. Results from these projections demonstrate that although transgene‐associated fitness costs will ultimately cause these transgenes to become extinct, even when engineered lethality is repressed, they may persist for varying periods of time before doing so. This implies that tetracycline‐mediated transgene field persistence in these strains is unlikely and suggests that realistic estimates of transgene‐associated fitness costs may be useful in trialing ‘uncoupled’ gene drive system components in the field.
New Method for Continuous Transmissivity Profiling in Fractured Rock
Authors: Keller Carl E. , Cherry John A. , Parker Beth L.
Published: May 2014

A new method is presented to search for hydraulically transmissive features in open boreholes in bedrock. A flexible borehole liner made of a watertight, nylon fabric is filled with water to create a constant driving head to evert (reverse of invert) the liner down the hole so that the liner pushes the borehole water out into transmissive fractures or other permeable features. The descent rate is governed by the bulk transmissivity of the remaining permeable features below the liner. Initially, the liner descent rate or velocity is a measure of transmissivity (T) of the entire hole. As the everting liner passes and seals each permeable feature, changes in the liner velocity indicate the position of each feature and an estimate of T using the Thiem equation for steady radial flow. This method has been performed in boreholes with diameters ranging from 96 to 330 mm. Profiling commonly takes a few hours in holes 200‐ to 300‐m long. After arrival of the liner at the bottom of the hole, the liner acts as a seal preventing borehole cross connection between transmissive features at different depths. Liner removal allows the hole to be used for other purposes. The T values determined using this method in a dolostone aquifer were found to be similar to the values from injection tests using conventional straddle packers. This method is not a replacement for straddle‐packer hydraulic testing of specific zones where greater accuracy is desired; however, it is effective and efficient for scanning entire holes for transmissive features.
The safety and effectiveness of Da Vinci surgical system compared with open surgery and laparoscopic surgery: a rapid assessment
Authors: Yu Jiajie , Wang Yingqiang , Li Youping , Li Xianglian , Li Cuicui , Shen Jiantong
Published: May 2014

Objective

The primary objectives of this rapid assessment were to assess the clinical evidence of Da Vinci surgical system (DVSS) comparing with open procedures and laparoscopic procedures, and in order to provide the evidence for health decision makers and clinician.

Methods

A comprehensive search of electronic databases (EMbase, PubMed, The Cochrane Library, Web of Science, CNKI, VIP, CBM and Wanfang) and HTA websites were completed up to 9 October, 2013. Two reviews (Jiajie Yu and Yingqiang Wang) independently extracted data of the manuscripts, and assessed quality of included studies using AMSTAR tools. Qualitative description and GRADE were used to report the outcomes and evidence quality.

Outcomes

A total of 17 studies were included: 3 were HTA and 14 were SR/meta‐analysis. The included studies focused on prostatectomy, nephrectomy, hysterectomy colorectal surgery, and cardiac surgery. DVSS was shown to be associated with statistically significant reduction in length of hospital stay, blood loss, and transfusion rate compared with open and laparoscopic surgery, but increase in operative time when compared with open surgery.

Conclusion

Based on the evidence included in this rapid assessment, DVSS has a limited impact on several clinical outcomes. Considering no available data from randomized controlled trials and much higher cost, decisions will be complex and need to be made carefully. Decision makers should cut down the quantity of purchasing and reasonable allocate them.
Genome‐wide identification, evolution, and expression analysis of RNA‐binding glycine‐rich protein family in maize
Authors: Zhang Jianhua , Zhao Yanxin , Xiao Hailin , Zheng Yonglian , Yue Bing
Published: May 2014

The RNA‐binding glycine‐rich protein (RB‐GRP) family is characterized by the presence of a glycine‐rich domain arranged in (Gly)n‐X repeats and an RNA‐recognition motif (RRM).RB‐GRPsparticipate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23RB‐GRPsdistributed on 10 chromosomes were identified in maize (Zea maysL.), and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified, while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of theRB‐GRPsin maize. Comparative analysis ofRB‐GRPsin maize,Arabidopsis(Arabidopsis thalianaL.), rice (Oryza sativaL.), and wheat (Triticum aestivum) revealed that two exclusive subgroups were only identified in maize. Expression of eightZmRB‐GRPswas significantly regulated by at least two kinds of stresses. In addition,cis‐elements predicted in the promoter regions of theZmRB‐GRPsalso indicated that theseZmRB‐GRPswould be involved in stress response of maize. The preliminary genome‐wide analysis of theRB‐GRPsin maize would provide useful information for further study on the function of theZmRB‐GRPs.
Bottle and sippy cup use is associated with diet and energy intake in toddlers
Authors: Ben‐Avraham Sivan , Hyden Christel J. , Fletcher Jason , Bonuck Karen A.
Published: May 2014

The second year of life incorporates a continued shift from a liquid‐ to solid‐based diet. Little is known about the prevalence and dietary impact of bottle and sippy cup use. This paper describes associations between percent of energy consumed via drinking containers (bottles and sippy cups combined) and dietary outcomes, between 1 and 2 years of age. This observational study recruited n = 299 low‐income, nutrition programme clients from the Bronx, NY, whose 12 month olds consumed ≥ 2 non‐water bottles per day. The main exposure variable was percent of energy intake via drinking containers (PEDC), dichotomized at the median into low‐percent–energy‐from‐drinking‐containers (LOW‐C) and high‐percent–energy‐from‐drinking‐containers (HIGH‐C) groups, assessed quarterly, for 1 year. We report 24‐hour dietary recall nutrient and food serving data by LOW‐C vs. HIGH‐C. We employed linear mixed models to study associations between PEDC and nutrient intake. PEDC decreased from 52% to 33% between 1 and 2 years of age in both groups. The LOW‐C group had higher intake of energy, dietary fibre, iron and sodium, grains, protein‐rich foods and sweets. Conversely, LOW‐C group had lower intake of Vitamin D and calcium vs. the HIGH‐C group. PEDC was inversely associated with total energy intake in a model controlling for baseline age, baseline‐weight‐for‐length and gender (β = −5.8, P = 0.029, 95% confidence interval (−10.96, −0.6). Lower bottle and sippy cup use had significant, albeit mixed association with diet quality in the second year of life, and was associated with higher energy intake. Evidence‐based guidelines are needed to determine the appropriate use of those feeding methods.
Association between maternal depressive symptoms in the early post‐natal period and responsiveness in feeding at child age 2 years
Authors: Mallan Kimberley M. , Daniels Lynne A. , Wilson Jacinda L. , Jansen Elena , Nicholson Jan M.
Published: May 2014

Maternal depression is a known risk factor for poor outcomes for children. Pathways to these poor outcomes relate to reduced maternal responsiveness or sensitivity to the child. Impaired responsiveness potentially impacts the feeding relationship and thus may be a risk factor for inappropriate feeding practices. The aim of this study was to examine the longitudinal relationships between self‐reported maternal post‐natal depressive symptoms at child age 4 months and feeding practices at child age 2 years in a community sample. Participants were Australian first‐time mothers allocated to the control group of the NOURISH randomized controlled trial when infants were 4 months old. Complete data from 211 mothers (of 346 allocated) followed up when their children were 2 years of age (51% girls) were available for analysis. The relationship between Edinburgh Postnatal Depression Scale (EPDS) score (child age 4 months) and child feeding practices (child age 2 years) was tested using hierarchical linear regression analysis adjusted for maternal and child characteristics. Higher EPDS score was associated with less responsive feeding practices at child age 2 years: greater pressure [β = 0.18, 95% confidence interval (CI): 0.04–0.32, P = 0.01], restriction (β = 0.14, 95% CI: 0.001–0.28, P = 0.05), instrumental (β = 0.14, 95% CI: 0.005–0.27, P = 0.04) and emotional (β = 0.15, 95% CI: 0.01–0.29, P = 0.03) feeding practices (ΔR2 values: 0.02–0.03, P < 0.05). This study provides evidence for the proposed link between maternal post‐natal depressive symptoms and lower responsiveness in child feeding. These findings suggest that the provision of support to mothers experiencing some levels of depressive symptomatology in the early post‐natal period may improve responsiveness in the child feeding relationship.
Pica during pregnancy among Mexican‐born women: a formative study
Authors: Lin Janice W. , Temple Luisa , Trujillo Celina , Mejia‐Rodriquez Fabiola , Rosas Lisa Goldman , Fernald Lia , Young Sera L.
Published: May 2014

Although pica, the craving and purposive consumption of non‐food substances, is common among many populations, especially during pregnancy, the health consequences are not well understood. Further, very little is known about pica among Mexican populations in the United States and Mexico. Therefore, we conducted formative research to understand pica in this understudied population. Our objectives were to identify the frequency and types of pica behaviours, to understand perceived aetiologies and consequences of pica and to ascertain if the behaviour was common enough to warrant a larger study. We held nine focus group discussions (three in the Salinas Valley, California; six in Xoxocotla, Morelos, Mexico) with 76 Mexican‐born women who were currently pregnant or had delivered within the past 2 years. Earth, adobe, bean stones and ice were the most commonly reported pica substances. Twenty‐eight of the 76 participants (37%) reported ever engaging in pica; 22 participants (29%) reported doing so during pregnancy. The proportion of women reporting pica in the United States and Mexico was 43% and 34%, respectively. Women attributed pica to the overwhelming organoleptic appeal of pica substances (especially smell and texture) and to micronutrient deficiencies. Perceived consequences of unfulfilled pica cravings were birthmarks or fetal loss; fulfilled pica cravings were also thought to be generally harmful to the mother or child, with several women specifying toxic lead, pesticides or ‘worms’. In sum, pica among Mexican women is common enough to warrant a larger epidemiologic study of its sociodemographic correlates and physiological consequences.
The reliability of weight‐for‐length/height Z scores in children
Authors: Mwangome Martha K. , Berkley James A.
Published: May 2014

The World Health Organisation (WHO) recommends weight‐for‐length/height (WFL/H), represented as a Z score for diagnosing acute malnutrition among children aged 0 to 60 months. Under controlled conditions, weight, height and length measurements have high degree of reliability. However, the reliability when combined into a WFL/H Z score, in all settings is unclear. We conducted a systematic review of published studies assessing the reliability of WFL/Hz on PubMed and Google scholar. Studies were included if they presented reliability scores for the derived index of WFL/Hz, for children under 5 years. Meta‐analysis was conducted for a pooled estimate of reliability overall, and for children above and below 24 months old. Twenty six studies on reliability of anthropometry were identified but only three, all community‐based studies, reported reliability scores for WFL/Hz. The overall pooled intra‐class correlation coefficient (ICC) estimate for WFL/Hz among children aged 0 to 60 months was 0.81 (95% CI 0.64 to 0.99). Among children aged less than 24 months the pooled ICC estimate from two studies was 0.72 (95% CI 0.67 to 0.77) while the estimate reported for children above 24 months from one study was 0.97 (95% CI 0.97 to 0.99). Although WFL/Hz is recommended for diagnosis of acute under nutrition among children below 5 years, information on its reliability in all settings is sparse. In community settings, reliability of WFL/Hz is considerably lower than for absolute measures of weight and length/height, especially in younger children. The reliability of WFL/Hz needs further evaluation.
In-situ optical microscopy observations of the growth of individual carbon nanocoils
Authors: Gohara Takehiro , Takei Kuniharu , Arie Takayuki , Akita Seiji
Published: May 2014

The authors investigate individual carbon nanocoil (CNC) growth by in-situ observations using optical microscopy. From the temperature dependence of growth rate, the activation energy for CNC growth was found to be 0.5 eV. A higher activation energy of 1.1 eV was required to form noncoiled fibers. Comparing these activation energies indicated that incorporating Sn within the Fe matrix lowered the activation energy for carbon diffusion, within or on catalyst particles. The authors also found that the smooth growth of some CNCs was inhibited by the collision of catalyst particles at the tips of the CNCs.
High-throughput fabrication of compact and flexible bilayer nanowire grid polarizers for deep-ultraviolet to infrared range
Authors: Wang Li , Schift Helmut , Gobrecht Jens , Ekinci Yasin , Kristiansen Per Magnus , Solak Harun H. , Jefimovs Konstantins
Published: May 2014

The authors present the design and fabrication of a bilayer metallic wire-grid polarizer with a period of 80 nm on a flexible polymeric substrate optimized for broadband operation ranging from the infrared down to the deep-ultraviolet range. Their high-throughput fabrication over large areas is realized by nanoimprint lithography by producing the imprint master stamps using extreme ultraviolet interference lithography. Optical measurements show that the fabricated bilayer polarizer covers a broad spectral range, starting from wavelength of 280 nm. Transverse magnetic transmission of 70% and an extinction ratio of 30 dB were realized.
Probing Exchange Pathways in One-Dimensional Aggregates with Super-Resolution Microscopy
Authors: Albertazzi Lorenzo , van der Zwaag Daan , Leenders Christianus M. A. , Fitzner Robert , van der Hofstad Remco W. , Meijer E. W.
Published: May 2014

Examining Supramolecular Exchange

Microtubules are a natural example of a one-dimensional (1D) supramolecular structure. Synthetic examples of 1D fibrils often have monomers linked by weak noncovalent interactions that allow monomers to exchange in and out of the fibrils.

Albertazzi
et al.

(p.
491
) used a combination of super-resolution microscopy on individual fibrils and stochastic simulation to study monomer exchange in fibrils formed from stacked 1,3,5-benzenetricarboxamide motifs. Exchange did not require large-scale depolymerization and repolymerization, or reassembly of fragments, but proceeded through individual monomers exchanging homogeneously throughout the fibrils.
Forming Terrestrial Planets
Authors: Chambers John
Published: May 2014

Recent numerical models may provide a clearer understanding of the forces that shape planetary systems.