bluuebunny/crossref_metadata_2025 huggingface dataset:
Ekofisk life-of-field seismic: Operations and 4D processing
Authors: Bertrand A. , Folstad P. G. , Lyngnes B. , Buizard S. , Hoeber H. , Pham N. , de Pierrepont S. , Schultzen J. , Grandi A.
Published: February 2014

In 2010, the world's largest optical permanent reservoir monitoring (PRM) system was installed in the southern part of the Norwegian North Sea at Ekofisk. The life-of-field seismic (LoFS) system consists of 3966 seabed multicomponent sensors along 200 km of mostly trenched fiber-optic seismic cables and covering about 60 km2 of Ekofisk field. Seismic data are acquired via a topside recording unit and a containerized source operated on a supply vessel. Six vintages of data were acquired between the end of 2010 and fall 2013. Different aspects of seismic operations at Ekofisk include seismic source, recording system, data transfer, quality control, and processing. One of the key factors in achieving the full value of a PRM system is to handle such operations in a safe, integrated, and efficient manner to deliver high-quality seismic volumes for interpretation with rapid turnaround. Key aspects of the 4D processing sequence include robustness and optimal turnaround. Integration of the different operational phases of the LoFS project and integration of expertise between client and contractor play a key role in delivering clean, well-resolvable 4D signals and low residual 4D noise with NRMS as low as 5%. The high-quality data delivered by operations and processing are now routinely used in well planning and reservoir-management workflows.
An efficient 4D processing flow for variable-depth streamer data
Authors: Hicks Erik , Hoeber Henning , Poole Gordon , King Ben
Published: February 2014

Variable-depth streamer acquisition is now widely used, achieving a bandwidth of more than 6 octaves (2.5 to 200 Hz) and excellent lateral resolution and providing improved impedance and reservoir analysis. This acquisition and processing method is based on towing the streamer deep, using a variable-depth profile optimized to ensure receiver notch diversity at the imaging stage and a deghosting method that takes advantage of the notch diversity. For 4D processing of monitors now acquired with variable-depth cables and with a baseline consisting of a flat towed streamer, we must deal with two processing issues. First, raypaths of traces acquired at the same surface locations differ; second, receiver ghosts lead to different wavelets. A 4D coprocessing flow is introduced that codatums 4D vintages to a common datum early in the sequence. Furthermore, a new deghosting technique is applied to variable-depth and conventional data. This processing flow gives excellent repeatability with 4D noise of less than 10% on a zero-time repeatability test with North Sea data from 2013.
Geotechnical Aspects of Disaster Recovery Planning in Residential Christchurch and Surrounding Districts Affected by Liquefaction
Authors: Rogers Nick , Williams Kate , Jacka Mike , Wallace Shamus , Leeves John
Published: February 2014

The Canterbury earthquake sequence of 2010–2011 consisted of six main earthquakes directly affecting more than 300,000 people. The earthquakes caused land and building damage to more than 100,000 residential properties across Canterbury. This paper focuses on the issues related to liquefaction in the residential areas. There has been a need for coordination of specialist geotechnical advice into broader Government policy and planning recovery decisions, such as determining which land is suitable for rebuilding on and improving residential construction standards to increase future resilience. From a technical perspective, these earthquakes have provided a valuable opportunity to study the role that specialized engineering knowledge plays in the recovery process. A particular lesson is the importance of systematically capturing technical or factual information in the aftermath of a disaster, thereby planning beyond the short-term response to ensure that the right information is collected to assist the long-term recovery.
Seismic Hazard Modeling for the Recovery of Christchurch
Authors: Gerstenberger Matthew , McVerry Graeme , Rhoades David , Stirling Mark
Published: February 2014

New time-dependent seismicity models for the Christchurch region reflect the greatly enhanced seismicity in the region at present, and the gradual decrease of the seismicity over the next few decades. These seismicity models, along with modified ground-motion prediction equations and revised hazard calculation procedures have been used to derive new seismic hazard estimates for timeframes from months to 50 years. The hazard estimates have been used for a variety of applications crucial to planning and implementing the recovery of Christchurch. The new model includes higher amplitude spectra for designing new structures and assessing existing ones, magnitude-weighted peak ground acceleration hazard curves that account for duration effects for liquefaction assessment and remediation, and peak ground acceleration curves for evaluating the probabilities of rock falls. Particularly challenging has been the incorporation of time-varying hazard components into the redesign levels.
Performance of Electric Power Systems in the 2010–2011 Christchurch, New Zealand, Earthquake Sequence
Authors: Kwasinski Alexis , Eidinger John , Tang Alex , Tudo-Bornarel Christophe
Published: February 2014

From late-2010 to mid-2011, Christchurch suffered a series of earthquakes and aftershocks that affected the city's power supply. The most relevant of these events occurred on 4 September 2010, 22 February 2011, and 13 June 2011. In all these events transmission level power restoration occurred rapidly—within one day. Except for the second event, similar relatively minor damage led to rapid restoration of distribution-level power outages. However, extensive damage to underground cables during the February 2011 earthquake caused some outages that lasted until early March. This damage seems to be amongst the only extensively-documented such failures to date. Despite recorded strong ground shakings, damage to other power infrastructure facilities was moderate to minor. This satisfactory performance of power infrastructure is attributed to a program implemented during the decade prior to this earthquake sequence to seismically upgrade almost all unreinforced masonry substation buildings and reinforce other infrastructure elements.
Select Liquefaction Case Histories from the 2010–2011 Canterbury Earthquake Sequence
Authors: Green Russell A. , Cubrinovski Misko , Cox Brady , Wood Clint , Wotherspoon Liam , Bradley Brendon , Maurer Brett
Published: February 2014

The 2010–2011 Canterbury earthquake sequence began with the 4 September 2010, Mw7.1 Darfield earthquake and includes up to ten events that induced liquefaction. Most notably, widespread liquefaction was induced by the Darfield and Mw6.2 Christchurch earthquakes. The combination of well-documented liquefaction response during multiple events, densely recorded ground motions for the events, and detailed subsurface characterization provides an unprecedented opportunity to add well-documented case histories to the liquefaction database. This paper presents and applies 50 high-quality cone penetration test (CPT) liquefaction case histories to evaluate three commonly used, deterministic, CPT-based simplified liquefaction evaluation procedures. While all the procedures predicted the majority of the cases correctly, the procedure proposed by Idriss and Boulanger (2008) results in the lowest error index for the case histories analyzed, thus indicating better predictions of the observed liquefaction response.
Seismic Performance of Vertical Nonstructural Components in the 22 February 2011 Christchurch Earthquake
Authors: Baird Andrew , Tasligedik Ali Sahin , Palermo Alessandro , Pampanin Stefano
Published: February 2014

A survey of 217 multistory buildings carried out following the 22 February 2011 Christchurch Earthquake further confirmed many of the known vulnerabilities vertical nonstructural components (VNSC) have to seismic movements. VNSC include facades, claddings, external infills, and internal partitions. In order to improve the seismic performance of such components, this paper will outline issues identified during damage reconnaissance following the Canterbury earthquake sequence. Displacement-based demands have been obtained using nonlinear response history analyses of a set of code-compliant, post-1990s reinforced concrete buildings when subjected to recorded ground motions of the major Canterbury earthquakes. The corresponding expected damage to VNSC based on informative guidance given in design codes and damage limits obtained experimentally are compared against the damage observed in post-earthquake assessments.
Transforming Governance: How National Policies and Organizations for Managing Disaster Recovery Evolved following the 4 September 2010 and 22 February 2011 Canterbury Earthquakes
Authors: Johnson Laurie A. , Mamula-Seadon Ljubica
Published: February 2014

Large-scale disasters simultaneously deplete capital stock and services which then requires many complex rebuilding and societal activities to happen in a compressed time period; one of those is governance. Governments often create new institutions or adapt existing institutions to cope with the added demands. Over two years following the 4 September 2010 and 22 February 2011 Canterbury earthquakes, governance transformations have increasingly centralized recovery authority and operations at the national level. This may have helped to strengthen coordination among national agencies and expedite policy and decision making; but the effectiveness of coordination among multiple levels of government, capacity building at the local and regional levels, and public engagement and deliberation of key decisions are some areas where the transformations may not have been as effective. The Canterbury case offers many lessons for future disaster recovery management in New Zealand, the United States, and the world.
NGA-West2 Ground Motion Model for the Average Horizontal Components of PGA, PGV, and 5% Damped Linear Acceleration Response Spectra
Authors: Campbell Kenneth W. , Bozorgnia Yousef
Published: February 2014

We used an expanded PEER NGA-West2 database to develop a new ground motion prediction equation (GMPE) for the average horizontal components of PGA, PGV, and 5% damped linear pseudo-absolute acceleration response spectra at 21 periods ranging from 0.01 s to 10 s. In addition to those terms included in our now superseded 2008 GMPE, we include a more-detailed hanging wall model, scaling with hypocentral depth and fault dip, regionally independent geometric attenuation, regionally dependent anelastic attenuation and site conditions, and magnitude-dependent aleatory variability. The NGA-West2 database provides better constraints on magnitude scaling and attenuation of small-magnitude earthquakes, where our 2008 GMPE was known to be biased. We consider our new GMPE to be valid for estimating horizontal ground motion from shallow crustal continental earthquakes in an active tectonic domain for rupture distances ranging from 0 km to 300 km and magnitudes ranging from 3.3 to 7.5–8.5, depending on source mechanism.
Pax genes: regulators of lineage specification and progenitor cell maintenance
Authors: Blake Judith A. , Ziman Melanie R.
Published: February 2014

Pax genes encode a family of transcription factors that orchestrate complex processes of lineage determination in the developing embryo. Their key role is to specify and maintain progenitor cells through use of complex molecular mechanisms such as alternate RNA splice forms and gene activation or inhibition in conjunction with protein co-factors. The significance of Pax genes in development is highlighted by abnormalities that arise from the expression of mutant Pax genes. Here, we review the molecular functions of Pax genes during development and detail the regulatory mechanisms by which they specify and maintain progenitor cells across various tissue lineages. We also discuss mechanistic insights into the roles of Pax genes in regeneration and in adult diseases, including cancer.
Foxa2 acts as a co-activator potentiating expression of the Nurr1-induced DA phenotype via epigenetic regulation
Authors: Yi Sang-Hoon , He Xi-Biao , Rhee Yong-Hee , Park Chang-Hwan , Takizawa Takumi , Nakashima Kinichi , Lee Sang-Hun
Published: February 2014

Understanding how dopamine (DA) phenotypes are acquired in midbrain DA (mDA) neuron development is important for bioassays and cell replacement therapy for mDA neuron-associated disorders. Here, we demonstrate a feed-forward mechanism of mDA neuron development involving Nurr1 and Foxa2. Nurr1 acts as a transcription factor for DA phenotype gene expression. However, Nurr1-mediated DA gene expression was inactivated by forming a protein complex with CoREST, and then recruiting histone deacetylase 1 (Hdac1), an enzyme catalyzing histone deacetylation, to DA gene promoters. Co-expression of Nurr1 and Foxa2 was established in mDA neuron precursor cells by a positive cross-regulatory loop. In the presence of Foxa2, the Nurr1-CoREST interaction was diminished (by competitive formation of the Nurr1-Foxa2 activator complex), and CoREST-Hdac1 proteins were less enriched in DA gene promoters. Consequently, histone 3 acetylation (H3Ac), which is responsible for open chromatin structures, was strikingly increased at DA phenotype gene promoters. These data establish the interplay of Nurr1 and Foxa2 as the crucial determinant for DA phenotype acquisition during mDA neuron development.
Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT)
Authors: Amin Nirav M. , Greco Todd M. , Kuchenbrod Lauren M. , Rigney Maggie M. , Chung Mei-I , Wallingford John B. , Cristea Ileana M. , Conlon Frank L.
Published: February 2014

The proper dissection of the molecular mechanisms governing the specification and differentiation of specific cell types requires isolation of pure cell populations from heterogeneous tissues and whole organisms. Here, we describe a method for purification of nuclei from defined cell or tissue types in vertebrate embryos using INTACT (isolation of nuclei tagged in specific cell types). This method, previously developed in plants, flies and worms, utilizes in vivo tagging of the nuclear envelope with biotin and the subsequent affinity purification of the labeled nuclei. In this study we successfully purified nuclei of cardiac and skeletal muscle from Xenopus using this strategy. We went on to demonstrate the utility of this approach by coupling the INTACT approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic methodologies to profile proteins expressed in the nuclei of developing hearts. From these studies we have identified the Xenopus orthologs of 12 human proteins encoded by genes, which when mutated in human lead to congenital heart disease. Thus, by combining these technologies we are able to identify tissue-specific proteins that are expressed and required for normal vertebrate organ development.
Integrin αvβ3 and thyroid hormones promote expansion of progenitors in embryonic neocortex
Authors: Stenzel Denise , Wilsch-Bräuninger Michaela , Wong Fong Kuan , Heuer Heike , Huttner Wieland B.
Published: February 2014

Neocortex expansion during evolution is associated with the enlargement of the embryonic subventricular zone, which reflects an increased self-renewal and proliferation of basal progenitors. In contrast to human, the vast majority of mouse basal progenitors lack self-renewal capacity, possibly due to lack of a basal process contacting the basal lamina and downregulation of cell-autonomous production of extracellular matrix (ECM) constituents. Here we show that targeted activation of the ECM receptor integrin αvβ3 on basal progenitors in embryonic mouse neocortex promotes their expansion. Specifically, integrin αvβ3 activation causes an increased cell cycle re-entry of Pax6-negative, Tbr2-positive intermediate progenitors, rather than basal radial glia, and a decrease in the proportion of intermediate progenitors committed to neurogenic division. Interestingly, integrin αvβ3 is the only known cell surface receptor for thyroid hormones. Remarkably, tetrac, a thyroid hormone analog that inhibits the binding of thyroid hormones to integrin αvβ3, completely abolishes the intermediate progenitor expansion observed upon targeted integrin αvβ3 activation, indicating that this expansion requires the binding of thyroid hormones to integrin αvβ3. Convergence of ECM and thyroid hormones on integrin αvβ3 thus appears to be crucial for cortical progenitor proliferation and self-renewal, and hence for normal brain development and the evolutionary expansion of the neocortex.
Macroglobulin complement-relatedencodes a protein required for septate junction organization and paracellular barrier function inDrosophila
Authors: Hall Sonia , Bone Courtney , Oshima Kenzi , Zhang Liang , McGraw Molly , Lucas Bethany , Fehon Richard G. , Ward Robert E.
Published: February 2014

Polarized epithelia play crucial roles as barriers to the outside environment and enable the formation of specialized compartments for organs to carry out essential functions. Barrier functions are mediated by cellular junctions that line the lateral plasma membrane between cells, principally tight junctions in vertebrates and septate junctions (SJs) in invertebrates. Over the last two decades, more than 20 genes have been identified that function in SJ biogenesis in Drosophila, including those that encode core structural components of the junction such as Neurexin IV, Coracle and several claudins, as well as proteins that facilitate the trafficking of SJ proteins during their assembly. Here we demonstrate that Macroglobulin complement-related (Mcr), a gene previously implicated in innate immunity, plays an essential role during embryonic development in SJ organization and function. We show that Mcr colocalizes with other SJ proteins in mature ectodermally derived epithelial cells, that it shows interdependence with other SJ proteins for SJ localization, and that Mcr mutant epithelia fail to form an effective paracellular barrier. Tissue-specific RNA interference further demonstrates that Mcr is required cell-autonomously for SJ organization. Finally, we show a unique interdependence between Mcr and Nrg for SJ localization that provides new insights into the organization of the SJ. Together, these studies demonstrate that Mcr is a core component of epithelial SJs and also highlight an interesting relationship between innate immunity and epithelial barrier functions.
Human embryonic epidermis contains a diverse Langerhans cell precursor pool
Authors: Schuster Christopher , Mildner Michael , Mairhofer Mario , Bauer Wolfgang , Fiala Christian , Prior Marion , Eppel Wolfgang , Kolbus Andrea , Tschachler Erwin , Stingl Georg , Elbe-Bürger Adelheid
Published: February 2014

Despite intense efforts, the exact phenotype of the epidermal Langerhans cell (LC) precursors during human ontogeny has not been determined yet. These elusive precursors are believed to migrate into the embryonic skin and to express primitive surface markers, including CD36, but not typical LC markers such as CD1a, CD1c and CD207. The aim of this study was to further characterize the phenotype of LC precursors in human embryonic epidermis and to compare it with that of LCs in healthy adult skin. We found that epidermal leukocytes in first trimester human skin are negative for CD34 and heterogeneous with regard to the expression of CD1c, CD14 and CD36, thus contrasting the phenotypic uniformity of epidermal LCs in adult skin. These data indicate that LC precursors colonize the developing epidermis in an undifferentiated state, where they acquire the definitive LC marker profile with time. Using a human three-dimensional full-thickness skin model to mimic in vivo LC development, we found that FACS-sorted, CD207- cord blood-derived haematopoietic precursor cells resembling foetal LC precursors but not CD14+CD16- blood monocytes integrate into skin equivalents, and without additional exogenous cytokines give rise to cells that morphologically and phenotypically resemble LCs. Overall, it appears that CD14- haematopoietic precursors possess a much higher differentiation potential than CD14+ precursor cells.
Spontaneous hair cell regeneration in the neonatal mouse cochlea in vivo
Authors: Cox Brandon C. , Chai Renjie , Lenoir Anne , Liu Zhiyong , Zhang LingLi , Nguyen Duc-Huy , Chalasani Kavita , Steigelman Katherine A. , Fang Jie , Cheng Alan G. , Zuo Jian
Published: February 2014

Loss of cochlear hair cells in mammals is currently believed to be permanent, resulting in hearing impairment that affects more than 10% of the population. Here, we developed two genetic strategies to ablate neonatal mouse cochlear hair cells in vivo. Both Pou4f3DTR/+ and Atoh1-CreER™; ROSA26DTA/+ alleles allowed selective and inducible hair cell ablation. After hair cell loss was induced at birth, we observed spontaneous regeneration of hair cells. Fate-mapping experiments demonstrated that neighboring supporting cells acquired a hair cell fate, which increased in a basal to apical gradient, averaging over 120 regenerated hair cells per cochlea. The normally mitotically quiescent supporting cells proliferated after hair cell ablation. Concurrent fate mapping and labeling with mitotic tracers showed that regenerated hair cells were derived by both mitotic regeneration and direct transdifferentiation. Over time, regenerated hair cells followed a similar pattern of maturation to normal hair cell development, including the expression of prestin, a terminal differentiation marker of outer hair cells, although many new hair cells eventually died. Hair cell regeneration did not occur when ablation was induced at one week of age. Our findings demonstrate that the neonatal mouse cochlea is capable of spontaneous hair cell regeneration after damage in vivo. Thus, future studies on the neonatal cochlea might shed light on the competence of supporting cells to regenerate hair cells and on the factors that promote the survival of newly regenerated hair cells.
TGFβ regulates epithelial-mesenchymal interactions through WNT signaling activity to control muscle development in the soft palate
Authors: Iwata Jun-ichi , Suzuki Akiko , Yokota Toshiaki , Ho Thach-Vu , Pelikan Richard , Urata Mark , Sanchez-Lara Pedro A. , Chai Yang
Published: February 2014

Clefting of the soft palate occurs as a congenital defect in humans and adversely affects the physiological function of the palate. However, the molecular and cellular mechanism of clefting of the soft palate remains unclear because few animal models exhibit an isolated cleft in the soft palate. Using three-dimensional microCT images and histological reconstruction, we found that loss of TGFβ signaling in the palatal epithelium led to soft palate muscle defects in Tgfbr2fl/fl;K14-Cre mice. Specifically, muscle mass was decreased in the soft palates of Tgfbr2 mutant mice, following defects in cell proliferation and differentiation. Gene expression of Dickkopf (Dkk1 and Dkk4), negative regulators of WNT-β-catenin signaling, is upregulated in the soft palate of Tgfbr2fl/fl;K14-Cre mice, and WNT-β-catenin signaling is disrupted in the palatal mesenchyme. Importantly, blocking the function of DKK1 and DKK4 rescued the cell proliferation and differentiation defects in the soft palate of Tgfbr2fl/fl;K14-Cre mice. Thus, our findings indicate that loss of TGFβ signaling in epithelial cells compromises activation of WNT signaling and proper muscle development in the soft palate through tissue-tissue interactions, resulting in a cleft soft palate. This information has important implications for prevention and non-surgical correction of cleft soft palate.
The ERECTA receptor kinase regulates Arabidopsis shoot apical meristem size, phyllotaxy and floral meristem identity
Authors: Mandel Tali , Moreau Fanny , Kutsher Yaarit , Fletcher Jennifer C. , Carles Cristel C. , Williams Leor Eshed
Published: February 2014

In plants, the shoot apical meristem (SAM) serves as a reservoir of pluripotent stem cells from which all above ground organs originate. To sustain proper growth, the SAM must maintain homeostasis between the self-renewal of pluripotent stem cells and cell recruitment for lateral organ formation. At the core of the network that regulates this homeostasis in Arabidopsis are the WUSCHEL (WUS) transcription factor specifying stem cell fate and the CLAVATA (CLV) ligand-receptor system limiting WUS expression. In this study, we identified the ERECTA (ER) pathway as a second receptor kinase signaling pathway that regulates WUS expression, and therefore shoot apical and floral meristem size, independently of the CLV pathway. We demonstrate that reduction in class III HD-ZIP and ER function together leads to a significant increase in WUS expression, resulting in extremely enlarged shoot meristems and a switch from spiral to whorled vegetative phyllotaxy. We further show that strong upregulation of WUS in the inflorescence meristem leads to ectopic expression of the AGAMOUS homeotic gene to a level that switches cell fate from floral meristem founder cell to carpel founder cell, suggesting an indirect role for ER in regulating floral meristem identity. This work illustrates the delicate balance between stem cell specification and differentiation in the meristem and shows that a shift in this balance leads to abnormal phyllotaxy and to altered reproductive cell fate.
An essential role for LPA signalling in telencephalon development
Authors: Geach Timothy J. , Faas Laura , Devader Christelle , Gonzalez-Cordero Anai , Tabler Jacqueline M. , Brunsdon Hannah , Isaacs Harry V. , Dale Leslie
Published: February 2014

Lysophosphatidic acid (LPA) has wide-ranging effects on many different cell types, acting through G-protein-coupled receptors such as LPAR6. We show that Xenopus lpar6 is expressed from late blastulae and is enriched in the mesoderm and dorsal ectoderm of early gastrulae. Expression in gastrulae is an early response to FGF signalling. Transcripts for lpar6 are enriched in the neural plate of Xenopus neurulae and loss of function caused forebrain defects, with reduced expression of telencephalic markers (foxg1, emx1 and nkx2-1). Midbrain (en2) and hindbrain (egr2) markers were unaffected. Foxg1 expression requires LPAR6 within ectoderm and not mesoderm. Head defects caused by LPAR6 loss of function were enhanced by co-inhibiting FGF signalling, with defects extending into the hindbrain (en2 and egr2 expression reduced). This is more severe than expected from simple summation of individual defects, suggesting that LPAR6 and FGF have overlapping or partially redundant functions in the anterior neural plate. We observed similar defects in forebrain development in loss-of-function experiments for ENPP2, an enzyme involved in the synthesis of extracellular LPA. Our study demonstrates a role for LPA in early forebrain development.
Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins
Authors: Rafiq Kiran , Shashikant Tanvi , McManus C. Joel , Ettensohn Charles A.
Published: February 2014

A central challenge of developmental and evolutionary biology is to understand the transformation of genetic information into morphology. Elucidating the connections between genes and anatomy will require model morphogenetic processes that are amenable to detailed analysis of cell/tissue behaviors and to systems-level approaches to gene regulation. The formation of the calcified endoskeleton of the sea urchin embryo is a valuable experimental system for developing such an integrated view of the genomic regulatory control of morphogenesis. A transcriptional gene regulatory network (GRN) that underlies the specification of skeletogenic cells (primary mesenchyme cells, or PMCs) has recently been elucidated. In this study, we carried out a genome-wide analysis of mRNAs encoded by effector genes in the network and uncovered transcriptional inputs into many of these genes. We used RNA-seq to identify >400 transcripts differentially expressed by PMCs during gastrulation, when these cells undergo a striking sequence of behaviors that drives skeletal morphogenesis. Our analysis expanded by almost an order of magnitude the number of known (and candidate) downstream effectors that directly mediate skeletal morphogenesis. We carried out genome-wide analysis of (1) functional targets of Ets1 and Alx1, two pivotal, early transcription factors in the PMC GRN, and (2) functional targets of MAPK signaling, a pathway that plays an essential role in PMC specification. These studies identified transcriptional inputs into >200 PMC effector genes. Our work establishes a framework for understanding the genomic regulatory control of a major morphogenetic process and has important implications for reconstructing the evolution of biomineralization in metazoans.
Silicon Compounds with Inverted Geometry around Silicon Atoms
Authors: Iwamoto Takeaki , Ishida Shintaro
Published: February 2014

In the last decade, several stable silicon compounds with nonclassical inverted geometry around silicon atoms have been synthesized. Their unusual structures, bonding, and reactivity have been investigated extensively by X-ray analysis, spectroscopy, and theoretical calculations. In this highlight review, recent progress on chemistry of silicon compounds with inverted geometry around silicon atoms is summarized.
Nanometer-sized Polynuclear Cluster and Oxide Nanocrystal Formation via Aging-condition-dependent Hydrolysis of Zirconium Oxychloride
Authors: Takasaki Fumiyuki , Fujiwara Kazuhiko , Nakajima Yasushi , Nishikawa Taku , Ogawa Nobuaki
Published: February 2014

Aqueous solutions of zirconium oxychloride aged at temperatures between 298 and 333 K for 0–26 days were investigated. Nanoparticles with different size distributions depending on aging temperature and duration were detected by dynamic light-scattering measurements. Extended X-ray absorption fine structure analysis and scanning transmission electron microscopy measurements revealed the nanoparticles formed in the samples to be zirconium polynuclear complexes and zirconium dioxide nanocrystals under mild condition, which was previously unexplored.
Functional abdominal pain causing Scurvy, Pellagra, and Hypovitaminosis A
Authors: Ho Edith Y. , Mathy Christian
Published: February 2014

Severe vitamin deficiency disease is rarely seen in developed countries. We present an atypical case of a young man with scurvy, pellagra, and hypovitaminosis A, caused by longstanding functional abdominal pain that severely limited his ability to eat.
Matched molecular pair-based data sets for computer-aided medicinal chemistry
Authors: Hu Ye , de la Vega de León Antonio , Zhang Bijun , Bajorath Jürgen
Published: February 2014

Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the latest release of the ChEMBL database for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.
Saul Gass, a Tribute to Him and to His Leadership in Model Assessment and Validation
Authors: Murphy Frederic H.
Published: February 2014

Saul Gass was one of the early pioneers of operations research. His common-sense approach to model assessment and validation has had an impact on the building and use of policy models for several decades. We discuss his pioneering work in this area.
Operations Research Transforms Baosteel’s Operations
Authors: Tang Lixin , Meng Ying , Wang Gongshu , Chen Zhi-Long , Liu Jiyin , Hu Guofen , Chen Lijun , Zhang Bo
Published: February 2014

Shanghai Baoshan Iron and Steel Complex (Baosteel) is China’s largest and the world’s third-largest steel company. In 2005, our research team was tasked with developing advanced operations research-based planning tools to improve the operational efficiency of Baosteel’s Shanghai plant. In the following six years, we developed novel optimization algorithms and tailored metaheuristics, and implemented four decision support systems (DSSs) to replace the manual planning methods at the Shanghai plant. The DSSs have brought scientific operations management to Baosteel and transformed the plant’s production and final-product delivery operations. Baosteel estimates that from 2007 to 2012, they provided a cumulative economic benefit of 77 million. Based on their current usage at this plant, they also estimate that these DSSs will continue to provide an annual economic benefit of 20 million, which represents a 17 percent improvement of Baosteel’s information technology and operations management capability. They have also reduced Baosteel’s carbon dioxide emissions by 585,770 tons annually.
Dell’s Channel Transformation: Leveraging Operations Research to Unleash Potential Across the Value Chain
Authors: Martin Karl , Chitalia Parag , Pugalenthi Murugan , Rau K. Raghava , Maity Sudeep , Kumar Rahul , Saksena Rohit , Hebbar Randhir , Krishnan Mahesh , Hegde Ganesh , Kesanapally Chandrasekhar , Bimbraw Tejinder Kaur , Subramanian Sumathi
Published: February 2014

Dell pioneered the direct sales model by offering its customers technology solutions through full-system configurability. In 2007, Dell launched several strategic initiatives to drive channel transformation by offering fixed configurations through online channels, retailers, distributors, and other channel partners. Dell's center of excellence (CoE) in analytics developed solutions that apply operations research (OR) to address key challenges across the value chain and enable profitable growth in the new channels. These solutions include (1) a configuration optimizer to reduce product complexity by identifying fixed hardware configurations (FHCs), which Dell builds and stocks, (2) an online conversion rate accelerator to improve the online customer purchase experience, leading to increased revenues and customer satisfaction, and (3) a retail margin maximizer to improve forecasts, mitigate inventory risk, and recommend promotions to increase margins. Since 2007, OR has helped Dell solve complex business problems and has facilitated its growth in the FHC business to $15 billion. Since 2010, these OR solutions have delivered a margin impact of more than $140 million by reducing markdown expenditures, improving online conversion rates, increasing ocean shipments, and enhancing customer satisfaction.
Bayesian Inference Using Gibbs Sampling in Applications and Curricula of Decision Analysis
Authors: Diaz Mauricio , Frances Daniel M.
Published: February 2014

Applications and curricula of decision analysis currently do not include methods to compute Bayes' rule and obtain posteriors for nonconjugate prior distributions. The current convention is to force the decision maker's belief to take the form of a conjugate distribution, leading to a suboptimal decision. Bayesian inference using Gibbs sampling (BUGS) software, which uses Markov chain Monte Carlo methods, numerically obtains posteriors for nonconjugate priors. By using the decision maker's true nonconjugate belief, the problems explored suggest that BUGS can produce a posterior distribution that leads to optimal decision making. Other methods exist that can use nonconjugate priors, but they must be implemented ad hoc because they do not have any supporting software. BUGS offers the distinct advantage of being implemented in existing software, and with simple coding can solve a wide range of decision analysis problems. BUGS is useful in making optimal decisions, and it is easy to learn and implement; therefore, including BUGS in decision analysis curricula is valuable.
The semantics of possessives
Authors: Peters Stanley , Westerståhl Dag
Published: February 2014

We investigate what possessives mean by examining a wide range of English examples, pre-and postnominal, quantified and nonquantified, to arrive at general, systematic truth conditions for them. In the process, we delineate a rich class of paradigmatic possessives having crosslinguistic interest, exploiting characteristic semantic properties. One is that all involve (implicit or explicit) quantification over possessed entities. Another is that this quantification always carries existential import, even when the quantifier over possessed entities itself does not. We show that this property, termed possessive existential import, is intimately related to the notion of narrowing (Barker 1995). Narrowing has implications for compositionally analyzing possessives’ meaning. We apply the proposed semantics to the issues of the definiteness of possessives, negation of possessives, partitives and prenominal possessives, postnominal possessives and complements of relational nouns, freedom of the possessive relation, and the semantic relationship between pre- and postnominal possessives.
Relationship Types and Contraceptive Use Within Young Adult Dating Relationships
Authors: Manlove Jennifer , Welti Kate , Wildsmith Elizabeth , Barry Megan
Published: February 2014

CONTEXT

Although expanding research has found that relationship characteristics can shape contraceptive use among young adults, limited research has examined how relationship characteristics intersect to form distinct types of relationships and how relationship types are linked to contraceptive use.

METHODS

Data from the 2002–2005 rounds of the National Longitudinal Survey of Youth 1997 cohort were used to examine contraceptive use in 3,485 young adult dating relationships. Latent class analysis was employed to develop a typology of relationships using measures of relationship structure (duration) and quality (intimacy, commitment and conflict). Multinomial logistic regression analyses were used to estimate associations between relationship type and contraceptive use and method choice at last sex.

RESULTS

Four types of relationships were identified, two shorter term and two longer term, differentiated by levels of intimacy, commitment and conflict. Young adults in longer term relationships with greater conflict and lower intimacy and commitment were less likely than those in other long‐term relationships to use hormonal and dual methods versus no method (relative risk ratios, 0.6–0.7). Hormonal method use, versus no method use or condom use, was more prevalent in short‐term relationships with greater intimacy and commitment and lower conflict than in other short‐term relationships (1.7 and 1.9, respectively).

CONCLUSIONS

Classifying short‐term relationships as “casual” or long‐term ones as “serious” may ignore heterogeneity within these categories that may have implications for contraceptive use. Future qualitative research could provide a better understanding of relationship types and couples’ fertility intentions and access to and use of contraceptives.
Unfulfilled bodily rights in higher education: Development of sexual harassment policies during the past two decades
Authors: Heikkinen Mervi , Sunnari Vappu
Published: February 2014

Various researchers contend that realizations of citizenship rights in the sphere of the individual are influenced by official citizenship status, age, social class, nationality, disability, religion, sexuality and gender. These dimensions that define citizenship are significant within organizations. Thus citizenship is a useful, important concept in elaborating the equality of conditions in educational institutions such as universities. This article focuses on sexual harassment in universities, which the authors consider a violation of citizenship rights. The article explores the shortcomings and insufficiencies of university sexual harassment policies and developments that have occurred since the university in northern Finland renewed and revised its sexual harassment policies. This study employs a qualitative method and is characterized by a gender-sensitive approach. The message that sexual harassment is forbidden at university has remained the same in policy documents over the past two decades; however, the issue of sexual harassment at university has become increasingly visible. Despite the existing policies and their development from 1990 to 2011, students and staff have experienced – and continue to experience – sexual harassment that hinders the full realization of their citizenship, that is, the intertwined fulfilment of bodily and intellectual rights at university.
The presence of an absence: Youth participation in macro-level educational reform
Authors: Herriot Lindsay
Published: February 2014

Youth are traditionally excluded from meaningful decision-making in macro-level educational reform. An example of this absence is made present by youths’ voluntary dialogue and engagement through social media about a significant piece of educational reform in the province of Alberta called Bill 44. The findings indicate significant possibilities for the inclusion of student voice as part of active citizenship education in macro level educational policy and reform proceedings.
‘Let me in, I have the right to be here’: Black youth struggle for equal education and full citizenship after the Brown decision, 1954–1969
Authors: Willis Vincent
Published: February 2014

An area often neglected in the historiography of public education in the United States is the contributions made by black youth in the fight for equal education. During the 1950s and 1960s, when the struggle for equal education reached its apex, black youth were an essential part of the struggle. This article centeres the activism of black youth by illuminating how they actively fought for educational equality after the Brown decision and how their activism was linked to a larger struggle for full citizenship. Moreover, I examine the multiple forms of direct action black students utilized to promote citizenship education. By elevating their usage of walk-ins, walkouts and sit-ins, I argue that black youth advocated for more than just access into a building previously denied to them. Their activism was deeply rooted in the tenets of citizenship education. Using empirical data from the National Association for the Advancement of Colored People (NAACP) files, A. Philip Randolph papers, Bayard Rustin papers and historical black and national newspapers, this article shows how equal education was inextricably linked to citizenship education and both would have to be accomplished before educational equality could be obtained. While the Brown decision legally reshaped public schools in the United States, it was the advocacy of black youth – particularly those living in the South, along with civil rights and teacher organizations that declared second-class education unacceptable. This work adds to scholarly works on citizenship education by illuminating the various ways black youth used civic participation as a tool to achieve educational equality. I conclude by suggesting that teachers and students can benefit from this historical work because it portrays the different ways students can participate in educational reform while simultaneously giving teachers ideas of how to support and empower their students for civic engagement.
Education being citizenship: Citizenship education through The Rise of Li’ Ttledot game and curricular programme
Authors: Lim Kenneth Y T , Ong Matthew Y C
Published: February 2014

This article reports on an intervention that leverages game-based learning in citizenship education. The Rise of Li’ Ttledot represents a curricular programme for citizenship education that was trialed in a primary school in 2011. It draws inspiration from prior research-based interventions in Singapore and attempts to translate key design principles from these earlier enactments to a younger demographic cohort of learners. It seeks to do so by providing a rich in-game experience and subsequently facilitating the abstraction of key citizenship values through a post-game programme of dialogic interaction between teacher and students. The article presents data that seems to support the degree and nature of scaffolding provided to facilitate these abstractions among younger learners.
Defect-related properties of optical coatings
Authors: Cheng Xinbin , Wang Zhanshan
Published: February 2014

Defects in optical coatings are a major factor degrading their performance. Based on the nature of defects, we classified them into two categories: visible defects and non-visible defects. Visible defects result from the replication of substrate imperfections or particulates within the coatings by subsequent layers and can increase scattering loss, produce critical errors in extreme ultraviolet lithography, weaken mechanical and environmental stability, and reduce laser damage resistance. Non-visible defects mainly involve a decrease in laser damage resistance but typically have no influence on other properties of optical coatings. In the case of widely used HfO2/SiO2 dielectric coatings, metallic Hf nano-clusters, off-stoichiometric HfO2 nano-clusters, or areas of high-density electronic defects have been postulated as possible sources for non-visible defects. The emphasis of this review is devoted to discussing localized defect-driven laser-induced damage (LID) in optical coatings used for nanosecond-scale pulsed laser applications, but consideration is also given to other properties of optical coatings such as scattering, environmental stability, etc. The low densities and diverse properties of defects make the systematic study of LID initiating from localized defects time-consuming and very challenging. Experimental and theoretical studies of localized defect-driven LID using artificial defects whose properties can be well controlled are highlighted.
Microwave-assisted oxidation of benzyl alcohols using supported cobalt based nanomaterials under mild reaction conditions
Authors: Hosseinpour Reza , Pineda Antonio , Ojeda Manuel , Garcia Angel , Romero Antonio A. , Luque Rafael
Published: February 2014

Supported Co3O4nanoparticles (NPs) on Al-SBA-15 were synthesized by means of a mechanochemical protocol, to yield catalytically active materials in the microwave (MW)-assisted selective oxidation of benzyl alcohols to their corresponding aldehydes, using hydrogen peroxide as green oxidant. The catalysts were found to be relatively stable upon reutilization under the investigated conditions.
Tetracycline antibiotics and resistance mechanisms
Authors: Nguyen Fabian , Starosta Agata L. , Arenz Stefan , Sohmen Daniel , Dönhöfer Alexandra , Wilson Daniel N.
Published: February 2014

The ribosome and protein synthesis are major targets within the cell for inhibition by antibiotics, such as the tetracyclines. The tetracycline family of antibiotics represent a large and diverse group of compounds, ranging from the naturally produced chlortetracycline, introduced into medical usage in the 1940s, to second and third generation semi-synthetic derivatives of tetracycline, such as doxycycline, minocycline and more recently the glycylcycline tigecycline. Here we describe the mode of interaction of tetracyclines with the ribosome and mechanism of action of this class of antibiotics to inhibit translation. Additionally, we provide an overview of the diverse mechanisms by which bacteria obtain resistance to tetracyclines, ranging from efflux, drug modification, target mutation and the employment of specialized ribosome protection proteins.