bluuebunny/crossref_metadata_2025 huggingface dataset:
Healthy Steps as a Moderator: The Impact of Maternal Trauma on Child Social-Emotional Development
Authors: Briggs Rahil D. , Silver Ellen J. , Krug Laura M. , Mason Zachary S. , Schrag Rebecca D. A. , Chinitz Susan , Racine Andrew D.
Published: June 2014

Child social-emotional development is foundational for future success, and depends on the presence of caregiver–child relationships characterized by positive “serve and return” interactions, during which caregiver responses are reliable, consistent, and empathic. Caregivers with childhood trauma may be limited in their ability to provide this type of interaction, and child social-emotional development may be at risk. We describe a Healthy Steps (HS) program and the moderating effect of this program on the relationship between reported caregiver childhood trauma and child social-emotional development. In a quasi-experimental, longitudinal design, we determined the relationship between maternal report of childhood trauma and child social-emotional development on the Ages and Stages Questionnaires: Social-Emotional (ASQ:SE) at 36 months, adjusting for covariates, and tested for a moderating effect of participation in HS on this relationship. One hundred twenty-four children were assessed at 36 months. Children of mothers with childhood trauma had higher (worse) ASQ:SE mean scores than children of mothers without childhood trauma (75.9 vs. 35.9; p < .0001). Differences in adjusted mean ASQ:SE scores between children of mothers with and without childhood trauma were more apparent in the comparison group (90.4 vs. 28.3) than in HS (44.5 vs. 28.2; p < .001). Caregiver experiences of childhood trauma are related to deficits in social-emotional development in their 3-year-old children. HS, with a focus on caregiver trauma and child social-emotional development, may serve as a moderator of this association.
Development of a School-Based Obesity Intervention for Mexican Americans
Authors: Johnston Craig A. , Moreno Jennette P.
Published: June 2014

The goal of this article is to provide insight into the development of a school-based pediatric obesity intervention for urban, low-income, minority students. This program has demonstrated significant improvements in weight-based outcomes that were maintained long-term. First, an overview of the rationale for intervening in a school system is provided, and several relevant issues that health care providers face when working in communities are discussed. After this, the components and outcomes of a school-based intervention are listed, with particular attention given to necessary adaptations needed in a school setting. Finally, barriers and facilitators to engaging a school system, unanticipated issues, and overall thoughts on future directions that should be explored to support health care providers with a pediatric obesity focus in school settings are examined. Overall, this article attempts to address practical issues that are faced by individuals who are trying to improve the lives of children who are overweight and obese.
Is ostension any more than attention?
Authors: Szufnarowska Joanna , Rohlfing Katharina J. , Fawcett Christine , Gredebäck Gustaf
Published: June 2014

According to natural pedagogy theory, infants are sensitive to particular ostensive cues that communicate to them that they are being addressed and that they can expect to learn referential information. We demonstrate that 6-month-old infants follow others' gaze direction in situations that are highly attention-grabbing. This occurs irrespective of whether these situations include communicative intent and ostensive cues (a model looks directly into the child's eyes prior to shifting gaze to an object) or not (a model shivers while looking down prior to shifting gaze to an object). In contrast, in less attention-grabbing contexts in which the model simply looks down prior to shifting gaze to an object, no effect is found. These findings demonstrate that one of the central pillars of natural pedagogy is false. Sensitivity to gaze following in infancy is not restricted to contexts in which ostensive cues are conveyed.
MicroRNA-33b knock-in mice for an intron of sterol regulatory element-binding factor 1 (Srebf1) exhibit reduced HDL-C in vivo
Authors: Horie Takahiro , Nishino Tomohiro , Baba Osamu , Kuwabara Yasuhide , Nakao Tetsushi , Nishiga Masataka , Usami Shunsuke , Izuhara Masayasu , Nakazeki Fumiko , Ide Yuya , Koyama Satoshi , Sowa Naoya , Yahagi Naoya , Shimano Hitoshi , Nakamura Tomoyuki , Hasegawa Koji , Kume Noriaki , Yokode Masayuki , Kita Toru , Kimura Takeshi , Ono Koh
Published: June 2014

MicroRNAs (miRs) are small non-protein-coding RNAs that bind to specific mRNAs and inhibit translation or promote mRNA degradation. Recent reports, including ours, indicated that miR-33a located within the intron of sterol regulatory element-binding protein (SREBP) 2 controls cholesterol homeostasis and can be a possible therapeutic target for treating atherosclerosis. Primates, but not rodents, express miR-33b from an intron of SREBF1. Therefore, humanized mice, in which a miR-33b transgene is inserted within a Srebf1 intron, are required to address its function in vivo. We successfully established miR-33b knock-in (KI) mice and found that protein levels of known miR-33a target genes, such as ABCA1, ABCG1 and SREBP-1, were reduced compared with those in wild-type mice. As a consequence, macrophages from the miR-33b KI mice had a reduced cholesterol efflux capacity via apoA-I and HDL-C. Moreover, HDL-C levels were reduced by almost 35% even in miR-33b KI hetero mice compared with the control mice. These results indicate that miR-33b may account for lower HDL-C levels in humans than those in mice and that miR-33b is possibly utilized for a feedback mechanism to regulate its host gene SREBF1. Our mice will also aid in elucidating the roles of miR-33a/b in different genetic disease models.
Facile electrosynthesis of π-extended porphyrins
Authors: Fang Yuanyuan , Koszelewski Dominik , Kadish Karl M. , Gryko Daniel T.
Published: June 2014

Free-base porphyrins as well as their iridium and indium complexes have been electrochemically coupled, leading to π-extended macrocycles.
Entrapment of alkaloids within silver: from enantioselective hydrogenation to chiral recognition
Authors: Yang Hengpan , Chi Dinghui , Sun Qilong , Sun Wenwen , Wang Huan , Lu Jiaxing
Published: June 2014

An organically doped silver catalyst was synthesized for enantioselective electrohydrogenation and chiral recognition with high efficiency and remarkable recycle times.
Hydrothermal synthesis and electrochemical properties of tin titanate nanowires coupled with SnO2nanoparticles for Li-ion batteries
Authors: Wang Hongkang , Wang Man , Li Beibei , Yang Xia , Safarova Klara , Zboril Radek , Rogach Andrey L. , Leung Michael K. H.
Published: June 2014

Tin-titanate nanowires coupled with SnO2nanoparticles demonstrate enhanced electrochemical properties owing to atomic- and nano-scaled uniform distribution of tin elements.
Optimizing porphyrins for dye sensitized solar cells using large-scale ab initio calculations
Authors: Ørnsø Kristian B. , Pedersen Christian S. , Garcia-Lastra Juan M. , Thygesen Kristian S.
Published: June 2014

We present a systematic study of the level alignment of 5145 porphyrin based dyes for dye sensitized solar cells.
The influence of continuous vs. pulsed laser excitation on single quantum dot photophysics
Authors: Smyder Julie A. , Amori Amanda R. , Odoi Michael Y. , Stern Harry A. , Peterson Jeffrey J. , Krauss Todd D.
Published: June 2014

Important similarities and differences between pulsed and continuous excitation on the fluorescence dynamics of single quantum dots were discovered.
Lithium heterocuprates: the influence of the amido group on organoamidocuprate structures
Authors: Bomparola Roberta , Davies Robert P. , Hornaeur Stefan , White Andrew J. P.
Published: June 2014

The structural isomers of a number of lithium heteroamidocuprates LiCuR(NR′2) have been studied in the solid state and in solution, with the steric and electronic properties of the amido group (NR′2) shown to significantly influence the solid-state structures and the position of the solution equilibrium.
Proteome-scale identification of outer membrane proteins in Mycobacterium avium subspecies paratuberculosis using a structure based combined hierarchical approach
Authors: Rana Aarti , Rub Abdur , Akhter Yusuf
Published: June 2014

The overall strategy used for the proteome-wide comprehensive computational investigation to identify outer membrane proteins fromMycobacterium aviumsubsp.paratuberculosis.
Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability
Authors: Wei Katy , Moinat Maxim , Maarleveld Timo R. , Bruggeman Frank J.
Published: June 2014

Stochastic modelling of two-component signalling networks reveals active-state locking and growth-rate dependent bistability.
A versatile acid-labile linker for antibody–drug conjugates
Authors: Finniss Mathew C. , Chu Kevin S. , Bowerman Charles J. , Luft J. Christopher , Haroon Zishan A. , DeSimone Joseph M.
Published: June 2014

Silyl ether chemistry was used as the linker for an antibody drug conjugate to release a chemotherapeutic at low pH.
Integrating a thermoresponsive copolymer with host–guest interactions for fabricating molecular recognition surfaces
Authors: Shi Xiujuan , Chen Gaojian , Yuan Lin , Tang Zengchao , Liu Wei , Zhang Qiang , Haddleton David M. , Chen Hong
Published: June 2014

Thermoresponsive poly(NIPAAm-co-Ada) surfaces integrated with host–guest interactions were used as a platform for fabricating reusable and tunable molecular recognition surfaces.
Morphology control, luminescence and energy transfer properties of NaCeF4and NaCeF4:Tb3+/Yb3+nanocrystals
Authors: Lian Hongzhou , Dai Yunlu , Yang Dongmei , Cheng Ziyong , Li Chunxia , Hou Zhiyao , Shang Mengmeng , Lin Jun
Published: June 2014

Growth mechanism and photoluminescence properties of NaCeF4:Tb3+/Yb3+nanocrystals have been investigated for potential applications in enhancing the efficiency of solar cells.
Metal-free aerobic C–H oxidation of cyclic enones
Authors: Peixoto P. A. , Cormier M. , Ekosso Epane J. , Jean A. , Maddaluno J. , De Paolis M.
Published: June 2014

A metal-free procedure is described for the aerobic and complete C–H methylene oxidation of Hajos–Parrish enones to versatile dihydroindenediones.
4-Oxo- or 1-oxo-N7O+? A computational and experimental study
Authors: Yu Tao , Liu Ying-Zhe , Haiges Ralf , Christe Karl O. , Lai Wei-Peng , Wu Bo
Published: June 2014

Results from a combined computational and experimental study show that 1-oxo-N7O+(right) is much less stable than 4-oxo-N7O+(left), and that its facile decomposition to N5+and N2O impedes the synthesis of 4-oxo-N7O+from NF2O+or N3NFO+and excess HN3.
Anticancer metallodrugs of glutamic acid sulphonamides: in silico, DNA binding, hemolysis and anticancer studies
Authors: Ali Imran , Wani Waseem A. , Saleem Kishwar , Hsieh Ming-Fa
Published: June 2014

In response to an increased demand for effective anticancer drugs, a series of disodium sulphonamides ofl-glutamic acid (L1–L3) was synthesized. Sulphonamides were complexed with copper(ii), nickel(ii) and ruthenium(iii) ions, separately and respectively.
Guanidine based self-assembled monolayers on Au nanoparticles as artificial phosphodiesterases
Authors: Salvio Riccardo , Cincotti Antonio
Published: June 2014

Gold nanoparticles passivated with a catalytic monolayer based on guanidine exhibit high cooperativity and efficiency in the cleavage of phosphodiesters.
An efficient and new protocol for phosphine-free Suzuki coupling reaction using palladium-encapsulated and air-stable MIDA boronates in an aqueous medium
Authors: Mendes da Silva Joaquim Fernando , Yepes Perez Andres Felipe , Pinto de Almeida Natália
Published: June 2014

A simple methodology for Suzuki–Miyaura cross-coupling reactions using microencapsulated palladium and (het)aryl MIDA boronates in water–alcohol under phosphine-free conditions was developed.
Infrared photo-initiated fabrication of monolithic porous layer open tubular (monoPLOT) capillary columns for chromatographic applications
Authors: Collins David A. , Nesterenko Ekaterina P. , Paull Brett
Published: June 2014

Investigation into the development of a fabrication approach for capillary porous layer open tubular (PLOT) chromatographic columns via infrared (IR) photo-initiated polymerisation and the optimisation of the technique is presented in this work.
Selective iodide chemosensing through a redox-active Cu-corrole
Authors: Basumatary Biju , Ayoub Kaloo Masood , Kumar Singh Vineet , Mishra Ruchika , Murugavel Muthuchamy , Sankar Jeyaraman
Published: June 2014

A one-electron redox couple between iodide and Cu(iii)-corrole serves as the basis for selective sensing of iodide.
Biocatalyst mediated functionalization of salannin, an insecticidal limonoid
Authors: Haldar Saikat , Kolet Swati P. , Dandekar Devdutta S. , Kale Balaji S. , Gonnade Rajesh G. , Thulasiram Hirekodathakallu V.
Published: June 2014

Novel and efficient modification was achieved on the furan moiety of salannin by fungi mediated biocatalysis.
Asymmetric construction of quaternary stereocenters by magnesium catalysed direct amination of β-ketoesters using in situ generated nitrosocarbonyl compounds as nitrogen sources
Authors: Maji Biplab , Baidya Mahiuddin , Yamamoto Hisashi
Published: June 2014

An oxophilic magnesium salt in combination with a chiral N,N′-dioxide ligand switches the chemoselectivity of an ambident nitrosocarbonyl species to nitrogen for the highly enantioselective α-amination of β-ketoesters.
Double-layered hyaluronic acid/stearic acid-modified polyethyleneimine nanoparticles encapsulating (−)-gossypol: a nanocarrier for chiral anticancer drugs
Authors: Liu Hao , Li Ke , Lan Lan , Ma Jingwen , Zeng Yun , Xu Liang , Wu Daocheng
Published: June 2014

The double-layered nanoparticles encapsulating the chiral drug (−)-gossypol possess tumor-targeting ability, a sustained release profile, and evident tumor-inhibition effects.
Photo-induced fluorescence quenching in conjugated polymers dispersed in solid matrices at low concentration
Authors: Sahoo Dibakar , Tian Yuxi , Sforazzini Giuseppe , Anderson Harry L. , Scheblykin Ivan G.
Published: June 2014

Quenching by long-living photoproducts limits the fluorescence yield of conjugated polymers.
Scene text recognition by learning co‐occurrence of strokes based on spatiality embedded dictionary
Authors: Gao Song , Wang Chunheng , Xiao Baihua , Shi Cunzhao , Zhou Wen , Zhang Zhong
Published: June 2014

Text information contained in scene images is very helpful for high‐level image understanding. In this study, the authors propose to learn co‐occurrence of local strokes for scene text recognition by using a spatiality embedded dictionary (SED). Unlike spatial pyramid partitioning images into grids to incorporate spatial information, the authors SED associates every codeword with a particular response region and introduces more precise spatial information for robust character recognition. After localised soft coding and max pooling of the first layer, a sparse dictionary is learned to model co‐occurrence of several local strokes, which further improves classification performance. Experimental results on two scene character recognition datasets ICDAR2003 and CHARS74 K demonstrate that their character recognition method outperforms state‐of‐the‐art methods. Besides, competitive word recognition results are also reported for four benchmark word recognition datasets ICDAR2003, ICDAR2011, ICDAR2013 and street view text when combining their character recognition method with a conditional random field language model.
Synthesis, characterisation and antibacterial effects of sol–gel derived biphasic calcium phosphate nanopowders
Authors: Nazemi Zahra , Haghbin Nazarpak Masoumeh , Mehdikhani‐Nahrkhalaji Mehdi , Staji Hamid , Kalani Mohammad Mehdi
Published: June 2014

Hydroxyapatite (HA) and β‐tricalcium phosphate (β‐TCP) represent the main types of calcium phosphates used for the reconstruction of bone defects in maxillofacial, dental, orthopaedic and drug delivery applications. The bioactivity and bioresorbability of biphasic calcium phosphate (BCP) ceramics can be controlled by varying the HA/β‐TCP ratio. In this reported work, BCP nanopowders were prepared by a simple sol–gel method, in which Ca(NO3)2 · 4H2O and P2O5 were used as precursors for calcium and phosphate, respectively. The different phase ratios of HA/β‐TCP were obtained by changing the sintering temperature. X‐ray diffraction, inductive coupled plasma‐atomic emission spectroscopy, scanning electron microscopy, transmission electron microscopy and Fourier transformer infrared spectrophotometer results have shown that increasing the sintering temperature could cause more decomposition of HA into β‐TCP. Moreover, the size of the prepared nanoparticles was measured between 10 and 500 nm. Finally, the antibacterial activity was studied using Escherichia coli (ATCC 25922) as the Gram‐negative bacteria. The antibacterial effect of the BCP sample with 50% HA–50%β‐TCP phase ratio was tested at concentrations of 100, 200 and 300 mg/ml. The results showed bacterial growth reduction at a concentration of 300 mg/ml, which makes it a good candidate for the treatment of bone defects.
Self‐assembly of different graphene‐modified morphologies of TiO2: nanoparticle, nanorod and nanowire for bisphenol‐A photodecomposition
Authors: Hua Zulin , Zhang Xiaoyuan , Bai Xue , Ma Wenqiang , Yu Lu , Dai Zhangyan , Gu Li
Published: June 2014

Different graphene (GR)‐modified morphologies of TiO2 including nanoparticles, nanorods and nanowires were prepared by a simple and efficient electrostatic self‐assembly method followed by a hydrothermal reduction process. Characterisations reveal that different morphologies of TiO2 are distributed on GR and that they decrease the electron–hole recombination rate and extend the light absorption range compared with pure TiO2. The as‐prepared different morphologies of GR‐modified TiO2 nanocomposites are used to photodecompose bisphenol‐A in water under visible‐light irradiation. All morphologies of TiO2 anchored onto the surface of a GR sheet exhibit higher photocatalytic activity under irradiation than pure TiO2. Photocatalytic activity is also increased by the increase in length of TiO2 distributed on GR. The photodegradation activities of all GR/TiO2 nanocomposites are stable under light after three successive cycles.
Enhanced electroluminescence of all‐inorganic colloidal quantum dot light‐emitting diode by optimising the MoO3 intermediate layer
Authors: Tang Liyuan , Zhao Junliang , Zhang Xiaoli , Dai Haitao , Sun Xiaowei
Published: June 2014

The effects of the molybdenum trioxide (MoO3) intermediate layer on the performance of all‐inorganic colloidal quantum dot light‐emitting diodes (QD‐LEDs) with a structure of ITO/MoO3/NiO/QDs/ZnO/Al are explored. MoO3 layers with different thickness were inserted between the indium tin oxide and nickel oxide layer via a thermal evaporation process. The presented results show that an ultrathin (∼ 5 nm) MoO3 intermediate layer significantly enhanced the electroluminescence (EL) intensity of the QD‐LED, which was more than 100 times higher than the device without the MoO3 layer. It is suggested that the EL enhancement originates from the effectively facilitated injection of holes into quantum dots through the MoO3 intermediate layer.
Novel and Simple Synthesis of Brominated 1,10-Phenanthrolines
Authors: Výprachtický Drahomír , Kaňková Dana , Pokorná Veronika , Kmínek Ivan , Dzhabarov Vagif , Cimrová Věra
Published: June 2014

A novel, simple, and reasonably efficient synthesis of 3,8-dibromo-1,10-phenanthroline, 3,6-dibromo-1,10-phenanthroline, 3,5,8-tribromo-1,10-phenanthroline, and 3,5,6,8-tetrabromo-1,10-phenanthroline is presented herein. The crucial role of a new catalyst (sulfur dichloride – SCl2) for the bromination of 1,10-phenanthroline is reported. The bromination of 1,10-phenanthroline monohydrate in the presence of SCl2 and pyridine yielded the brominated compounds, previously only possible through the complicated multi-step and tedious Skraup synthesis method. The application of the bromination catalyst SCl2 as a medium-strength Lewis acid is demonstrated for the first time, and the results are compared with the behaviours of known weak (sulfur chloride – S2Cl2) and strong (thionyl chloride – SOCl2) bromination catalysts. A reaction mechanism was proposed.
Synthesis and Characteristics of Energetic Materials Based on 1,2-Dinitroguanidine
Authors: Hu Bingcheng , Jin Xinghui , Jia Huanqing , Liu Zuliang , Lv Chunxu
Published: June 2014

A series of energetic salts based on 1,2-dinitroguanidine were successfully synthesised and fully characterised using 1H NMR, 13C NMR, and IR spectroscopy, mass spectrometry, elemental analysis, and differential scanning calorimetry. The results show that all the salts possess higher detonation properties (detonation pressures and velocities ranging from 24.8 to 30.3 GPa and 7665 to 8422 m s–1, respectively) than those of trinitrotolouene (TNT, 2,4,6-trinitromethylbenzene). The thermal stability and thermal kinetic parameters were also investigated to give a better understanding of the physical and chemical properties of these energetic salts.
Preparation and Structural Studies of Non-Symmetric Guanidinate-Supported Zirconium Complexes
Authors: Fernández-Galán Rafael , Navarro Juan-Antonio , Carrillo-Hermosilla Fernando , Antiñolo Antonio , López-Solera Isabel , Villaseñor Elena
Published: June 2014

The new lithium guanidinate salt [Li{μ-κ1,κ2,N,N′-(NEt)(N-t-Bu)CNMe2}(THF)]2 (1) was obtained by the reaction of HNMe2 with n-BuLi and further reaction with the asymmetric carbodiimide EtN=C=N-t-Bu. Guanidinate-supported zirconium complexes [Zr{κ2,N,N′-(NEt)(N-t-Bu)CNMe2}(μ-Cl)Cl2]2 (2), [Zr{κ2,N,N′-(NEt)(N-t-Bu)CNMe2}3Cl] (4), [Zr{κ2,N,N′-(NEt)(N-t-Bu)CNMe2}2(η5-C5H5)Cl] (5) and [Zr{κ2,N,N′-(NEt)(N-t-Bu)CNMe2}(η5-C5H5)2Cl] (6) were prepared. Complexes 2, 4, and 6 were synthesized by the metathesis reaction of ZrCl4 or [ZrCl2(η5-C5H5)2] with 1. The previously described complex [Zr{κ2,N,N′-(NEt)(N-t-Bu)CNMe2}2Cl2] (3), which was prepared by the insertion reaction of EtN=C=N-t-Bu into a metal–amido bond of [Zr(NMe2)2Cl2(THF)2], allowed the new complex 5 to be obtained by reaction with NaC5H5. All of the new complexes were characterized spectroscopically and the molecular structures of 1, 4, and 6 were determined by single-crystal X-ray diffraction.
Swan grazing on seagrass: abundance but not grazing pressure varies over an annual cycle in a temperate estuary
Authors: Choney Gary E. , McMahon Kathryn , Lavery Paul S. , Collier Neil
Published: June 2014

Herbivorous waterfowl such as black swans are significant grazers in temperate waterbodies; their abundance, distribution and grazing rates vary over seasonal cycles. The present study examined spatial and temporal variation in the abundance and grazing rates of black swans in the Lower Swan River estuary, Western Australia, using visual surveys over 1 year (2009), and potential drivers of this variation, food sources and disturbance factors were assessed. We predicted that swan abundance and grazing pressure would be greater in summer and autumn when seasonal wetlands dry and the abundance of food sources would positively influence their distribution, whereas the level of disturbance would have a negative effect. Plant–grazer interactions are dynamic and complex; the present study revealed new findings on the seasonality of this relationship, where swan abundance but not grazing pressure varied over an annual cycle. Maximum swan abundance occurred in autumn (185) with minima in spring (53) but the swan grazing pressure did not vary between seasons, ranging from 6% to 25% of seagrass production consumed. Swan abundance was a function of season and the cover of seagrass. Key hot spots for swan abundance were identified where management efforts could be targeted by minimising human disturbances and protecting seagrass.
Reproductive biology of the Magellan skate, Bathyraja magellanica (Chondrichthyes, Rajidae), in the south-western Atlantic
Authors: Scenna Lorena B. , Díaz de Astarloa Juan M.
Published: June 2014

The knowledge of reproductive parameters is essential to develop effective management and conservation plans. The present study provides the first information on the reproductive biology of an abundant and important trawl by-catch skate, Bathyraja magellanica, along its geographic range in the south-western Atlantic (43–55°S). In total, 81 males (205–738 mm total length, TL) and 104 females (157–768 mm TL) were analysed. Length–frequency distributions were significantly different between sexes, with females being larger than males. However, no sexual dimorphism was observed in TL–total body weight relationship and liver size. Length at maturity was similar between males (638 mm TL) and females (653 mm TL), ~85% of maximum observed size. The mean number of vitellogenic oocytes per skate was 14.37 (±4.43), increasing with female TL. Egg cases of B. magellanica had striated surface, broad lateral keels, extremely long posterior horns, and its wall consisted of three layers. An important area for the reproduction of B. magellanica was found between 48°50′S and 50°30′S. The present results indicated that this species has a low reproductive efficiency, suggesting that the B. magellanica population should be monitored closely to avoid large-scale changes in skate community structure of the south-western Atlantic.
Carbonate production rates of encruster communities on a lagoonal patch reef: Vabbinfaru reef platform, Maldives
Authors: Morgan K. M. , Kench P. S.
Published: June 2014

Coral reefs are formed by the growth and calcification of primary coral framework and secondary encrusting organisms. Future scenarios of reef health predict global declines in coral cover and an increase in the relative importance of encrusting organisms to gross reef calcification. Numerous coral growth studies are available; however, there are few quantitative estimates of secondary carbonate production on reefs. The present study used vertically orientated PVC pipe to generate rates of carbonate production (g cm–2 year–1) by encruster communities on Vabbinfaru reef platform, Maldives (4°18′35″N, 73°25′26″E). Maximum carbonate production by encrusters was 0.112 g cm–2 year–1 (mean ± s.d.: 0.047 ± 0.019 g cm–2 year–1). Encruster community composition was dominated by non-geniculate coralline algae (mean ± s.d.: 76 ± 14.2%), with other encrusting taxa being quantitatively unimportant to total substrate cover (mean ± s.d.: 9 ± 16.7%). Rates of encruster calcification at Vabbinfaru fell within the range of values reported for other reef-building provinces. There is a particular need for more quantitative field-based measurements of reef-organism calcification rates because such values strengthen regional and global estimates of gross carbonate production and have direct implications for net reef accretion and the development of reef sedimentary environments.
Ecological effects of common carp (Cyprinus carpio) in a semi-arid floodplain wetland
Authors: Vilizzi Lorenzo , Thwaites Leigh A. , Smith Benjamin B. , Nicol Jason M. , Madden Chris P.
Published: June 2014

Common carp, Cyprinus carpio, is a highly invasive fish species across freshwater systems of south-eastern Australia, and especially in semi-arid floodplain wetlands. However, multi-component, large-scale experimental studies on carp effects on such ecosystems are scarce. This is in spite of demands to prioritise management and control of carp for the rehabilitation of habitats across the Murray–Darling Basin. A 2-year, large-scale field experiment in a terminal wetland of the lower River Murray (South Australia) evaluated the effects of free-ranging carp on water transparency, aquatic macrophytes (biomass and cover), zooplankton density, benthic invertebrates (density, richness and diversity) as well as native fish. Within 1 year since artificial inundation, transparency sharply decreased and this was accompanied by a decrease in aquatic macrophyte biomass and cover, a fluctuation in zooplankton density, and a decrease in benthic invertebrate richness and diversity. Also, the decreases in transparency and benthic invertebrate richness were significantly related to carp biomass, which averaged 68.0 kg ha–1 and induced a shift from clear- to turbid-water state. Following a flood event, increased connectivity caused carp to further access the newly inundated areas.
Periphyton control on stream invertebrate diversity: is periphyton architecture more important than biomass?
Authors: Tonkin Jonathan D. , Death Russell G. , Barquín José
Published: June 2014

There is little consensus on the form of the periphyton biomass–macroinvertebrate diversity relationship in streams. One factor that these relationships do not account for is the growth form of primary producers. We (1) examined the periphyton biomass–macroinvertebrate diversity relationship in 24 streams of Cantabria, Spain, in July 2007, and (2) determined whether this relationship was underpinned, and better explained, by specific responses to the growth form of the periphyton community. We hypothesised that macroinvertebrate diversity would be a log-linear function of periphyton biomass and would respond differently to two coarse divisions of the periphytic community; i.e. positively to %cover of non-filamentous algae and negatively to %cover of streaming filamentous algae. There was no relationship between benthic periphyton biomass and macroinvertebrate diversity in these streams but, as predicted, this relationship was underpinned by responses to the growth form of periphyton community. Generally, macroinvertebrate diversity responded positively to %cover of non-filaments and negatively to %cover of streaming filaments, although results were variable. These findings suggest that periphyton biomass–macroinvertebrate diversity relationships in streams can be underpinned by interactions with specific growth forms of periphyton. We suggest that further research is required to develop robust thresholds of %cover of filamentous algae cover that would benefit managers wishing to minimise negative effects of eutrophication on stream communities.
Insulin regulates primordial-follicle assembly in vitro by affecting germ-cell apoptosis and elevating oestrogen
Authors: Feng Xin-Lei , Sun Yuan-Chao , Zhang Min , Cheng Shun-Feng , Feng Yan-Ni , Liu Jing-Cai , Wang Hong-Hui , Li Lan , Qin Guo-Qing , Shen Wei
Published: June 2014

Insulin is a protein secreted by pancreatic β-cells, which plays an important role in the regulation of ovarian function. However, the specific molecular mechanism of its function remains largely unknown. This study aimed to assess the effect of insulin on mouse folliculogenesis using an in vitro ovary-culture model. The results demonstrated that insulin promoted the proliferation of ovarian granulosa cells in vitro, and thereby accelerated the progress of folliculogenesis (the percentage of oocytes in cysts declined from 42.6% to 29.3%); however, the percentage of apoptotic oocytes increased after insulin treatment. Further investigation indicated that apoptosis occurred mainly in germ-cell cysts. After 3 days of insulin treatment, oestrogen in the culture medium of mouse ovaries significantly increased (P < 0.01), while the lower dose of oestrogen promoted primordial-follicle assembly in vitro. In conclusion, insulin promoted folliculogenesis by facilitating germ-cell apoptosis within the cysts and upregulating oestrogen levels.
Effects of mowing regimes and climate variability on hay production of Leymus chinensis (Trin.) Tzvelev grassland in northern China
Authors: Baoyin Taogetao , Li Frank Yonghong , Bao Qinghai , Minggagud Hugjiltu , Zhong Yankai
Published: June 2014

Leymus chinensis (Trin.) Tzvelev grassland is the most widely distributed native steppe vegetation type suitable for haymaking in the semiarid pastoral regions of north-east Asia. The long-term effects of four mowing regimes (mowing once a year, twice a year, once every 2 years and twice every 3 years), and climatic variability on the hay production from L. chinensis grassland were investigated using permanent plots over 27 years. The results showed that (i) the overall cumulative annual herbage production over the 27 years was the highest under ‘mowing once a year’, and ‘mowing twice a year’ did not produce any significant change in the amount of harvested herbage; (ii) mowing induced a reduction in herbage production mostly in the first couple of years, and the reduction was larger under frequent than less frequent mowing. The annual herbage production in harvest years was higher under less frequent mowing (once every 2 years, or twice every 3 years) than that under annual mowing, but the higher herbage production in harvest years under less frequent mowing could not compensate for the herbage not made into hay in the years without harvest; (iii) annual herbage production generally increased with annual precipitation, but the response of annual herbage production to precipitation was best described by quadratic (instead of linear or logarithmic) equations, which suggested a decline in annual herbage production under the highest annual precipitation in the region, and the relationships stood under different mowing regimes; and (iv) an analysis of hay yield and quality, and costs of the mowing operation, showed that the haymaking from L. chinensis grassland was financially viable as long as the herbage production was not extremely low under drought. It is concluded that the best practice for haymaking from L. chinensis grassland should be based on the rule of ‘mowing once a year’ in high-production years and grazing in low-production years; and a light grazing early in the season may increase hay quality mowed in the autumn if the grassland grows well early in the season in high-production years.
Using categorical soil structure information to improve soil water retention estimates of tropical delta soils
Authors: Nguyen Phuong Minh , Le Khoa Van , Cornelis Wim M.
Published: June 2014

Models of soil water and solute transport require input data of soil hydraulic properties (e.g. soil water retention and hydraulic conductivity curves). Lack of such data, especially in tropical delta regions, has usually been the main constraint for the application of simulation models. Direct field or laboratory measurement of soil water retention is costly, laborious and time-consuming; therefore, indirect estimation from other easily measured soil properties has received great interest. However, indirect estimates are often unreliable. In this study, we hypothesise that including basic descriptive information of soil structure such as aspect of presence or absence of pedality can improve the prediction of the soil water retention characteristic (SWRC). Stepwise multiple linear regression was used to develop point pedotransfer functions (PTFs) to estimate soil water retention at eight pressure potentials (e.g. –1, –3, –6, –10, –20, –34, –100, –1500 kPa). Soil structural information was exploited as a preliminary grouping criterion to test our hypothesis. Soil samples were taken from 160 horizons distributed along the Mekong Delta, Vietnam. The results reveal that SWRC of tropical Mekong Delta soils could be satisfactorily estimated by typical predictors of PTFs (e.g. soil texture, organic carbon content and bulk density). Moreover, incorporating soil structure in developing PTFs did improve the prediction accuracy of SWRC, especially in the wet moisture range. Plastic limit was found to be a promising predictor for SWRC-PTFs of soils having a given degree of structural development.
Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens
Authors: Jin Chunyu , Yang Liuqing , Xie Min , Lin Chunru , Merkurjev Daria , Yang Joy C. , Tanasa Bogdan , Oh Soohwan , Zhang Jie , Ohgi Kenneth A. , Zhou Hongyan , Li Wenbo , Evans Christopher P. , Ding Sheng , Rosenfeld Michael G.
Published: June 2014

Significance

The emergence of powerful new chemical library-screening approaches and the generation of new types of chemical structures makes novel methods available to link candidate chemicals to potential target genes, e.g., as in the interaction with and effects on chromatin-bound targets. Here we report a method that can provide the genome-wide location of a candidate drug. One such synthetic chemical, SD70—first identified in a screen for inhibitors of tumor translocation events—was resynthesized with a tag permitting a ChIP-sequencing–like analysis, referred to as “Chemical affinity capture and massively parallel DNA sequencing (Chem-seq).” As a consequence of finding its recruitment on androgen receptor-bound functional enhancers, we were able to demonstrate that SD70 could inhibit the prostate cancer cell transcriptional program, in part by inhibition of the demethylase KDM4C.
Characterization of the xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus)
Authors: Fujii Tatsuya , Inoue Hiroyuki , Ishikawa Kazuhiko
Published: June 2014

We cloned a putative Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus) xlnR gene and isolated a xlnR disruptant strain. XlnR protein was localized in the nucleus. Xylanase production by the xlnR disruptant was lower than in the control strain at both the enzyme and transcriptional level. These data suggest that the XlnR protein regulates xylanase production in T. cellulolyticus.
‘Our imperiled age’: an unfinished dialogue between Carl Jung and Karl Stern
Authors: Burston Daniel Raphael
Published: June 2014

Karl Stern was a Catholic psychiatrist in Montreal who published extensively on psychoanalysis and religion from 1951 to 1965. He sent a copy of his second book,The Third Revolution(1954) to Jung, who responded warmly in a (hitherto unpublished) letter dated 30 April 1960. The paper ponders the similarities and differences between Stern and Jung's approach to the psychology of religion, and the impact that Jung's belated response to Stern's book might have had on Stern subsequently.
On the exterior Dirichlet problem for Hessian equations
Authors: Bao Jiguang , Li Haigang , Li Yanyan
Published: June 2014

In this paper, we establish a theorem on the existence of the solutions of the exterior Dirichlet problem for Hessian equations with prescribed asymptotic behavior at infinity. This extends a result of Caffarelli and Li (2003) for the Monge-Ampère equation to Hessian equations.
Properness of associated minimal surfaces
Authors: Alarcón Antonio , López Francisco
Published: June 2014

For any open Riemann surface

N

\mathcal {N}

and finite subset

Z

⊂

S

1

=
{
z
∈

C

|

|

z

|

=
1
}
,

\mathfrak {Z}\subset \mathbb {S}^1=\{z\in \mathbb {C}\,|\;|z|=1\},

there exist an infinite closed set

Z

N

⊂

S

1

\mathfrak {Z}_{\mathcal {N}} \subset \mathbb {S}^1

containing

Z

\mathfrak {Z}

and a null holomorphic curve

F
=
(

F
j

)

j
=
1
,
2
,
3

:

N

→

C

3

F=(F_j)_{j=1,2,3}:\mathcal {N}\to \mathbb {C}^3

such that the map
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="German upper Y colon German upper Z Subscript script upper N Baseline times script upper N right-arrow double-struck upper R squared comma German upper Y left-parenthesis German v comma upper P right-parenthesis equals Re left-parenthesis German v left-parenthesis upper F 1 comma upper F 2 right-parenthesis left-parenthesis upper P right-parenthesis right-parenthesis comma">

Y

:

Z

N

×

N

→

R

2

,

Y

(

v

,
P
)
=

Re

(

v

(

F
1

,

F
2

)
(
P
)

)

,

\mathfrak {Y}:\mathfrak {Z}_{\mathcal {N}}\times \mathcal {N} \to \mathbb {R}^2,\quad \mathfrak {Y}(\mathfrak {v},P)=\textrm {Re}\big (\mathfrak {v} (F_1,F_2)(P)\big ),

\]
is proper.

In particular,

Re

(

v

F

)

:

N

→

R

3

\textrm {Re}\big (\mathfrak {v} F\big ):\mathcal {N} \to \mathbb {R}^3

is a proper conformal minimal immersion properly projecting into

R

2

≡

R

2

×
{
0
}
⊂

R

3

,

\mathbb {R}^2\equiv \mathbb {R}^2\times \{0\} \subset \mathbb {R}^3,

for all

v

∈

Z

N

.

\mathfrak {v} \in \mathfrak {Z}_{\mathcal {N}}.
Tails Curtailed: Accounting for Nonlinear Dependence in Pricing Margin Insurance for Dairy Farmers
Authors: Bozic Marin , Newton John , Thraen Cameron S. , Gould Brian W.
Published: June 2014

Livestock Gross Margin Insurance for Dairy Cattle (LGM‐Dairy) is a risk management tool for protecting milk income over feed cost margins. In this article, we examine the assumptions underpinning the method used to determine LGM‐Dairy premiums. Analysis of the milk–feed dependence structure is conducted using copula methods, a rich set of tools that allow modelers to capture nonlinearities in dependence among variables of interest. We find a significant relationship between milk and feed prices that increases with time‐to‐maturity and severity of negative price shocks. Extremal, or tail, dependence is the propensity of dependence to concentrate in the tails of a distribution. A common theme in financial and actuarial applications and in agricultural crop revenue insurance is that tail dependence increases the risk to the underwriter and results in higher insurance premiums. We present, to our knowledge, the first case in which tail dependence may actually reduce actuarially fair premiums for an agricultural risk insurance product. We examine hedging effectiveness with LGM‐Dairy and show that, even in the absence of basis or production risk, hedging horizon plays an important role in the ability of this tool to smooth farm income over feed cost margins over time. Rating methodology that accounts for tail dependence between milk and feed prices extends the optimal hedging horizon and increases hedging effectiveness of the LGM‐Dairy program.
Large scale analysis of signal reachability
Authors: Todor Andrei , Gabr Haitham , Dobra Alin , Kahveci Tamer
Published: June 2014

Motivation: Major disorders, such as leukemia, have been shown to alter the transcription of genes. Understanding how gene regulation is affected by such aberrations is of utmost importance. One promising strategy toward this objective is to compute whether signals can reach to the transcription factors through the transcription regulatory network (TRN). Due to the uncertainty of the regulatory interactions, this is a #P-complete problem and thus solving it for very large TRNs remains to be a challenge.

Results: We develop a novel and scalable method to compute the probability that a signal originating at any given set of source genes can arrive at any given set of target genes (i.e., transcription factors) when the topology of the underlying signaling network is uncertain. Our method tackles this problem for large networks while providing a provably accurate result. Our method follows a divide-and-conquer strategy. We break down the given network into a sequence of non-overlapping subnetworks such that reachability can be computed autonomously and sequentially on each subnetwork. We represent each interaction using a small polynomial. The product of these polynomials express different scenarios when a signal can or cannot reach to target genes from the source genes. We introduce polynomial collapsing operators for each subnetwork. These operators reduce the size of the resulting polynomial and thus the computational complexity dramatically. We show that our method scales to entire human regulatory networks in only seconds, while the existing methods fail beyond a few tens of genes and interactions. We demonstrate that our method can successfully characterize key reachability characteristics of the entire transcriptions regulatory networks of patients affected by eight different subtypes of leukemia, as well as those from healthy control samples.

Availability: All the datasets and code used in this article are available at bioinformatics.cise.ufl.edu/PReach/scalable.htm.

Contact:  atodor@cise.ufl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
Authors: Cao Mengfei , Pietras Christopher M. , Feng Xian , Doroschak Kathryn J. , Schaffner Thomas , Park Jisoo , Zhang Hao , Cowen Lenore J. , Hescott Benjamin J.
Published: June 2014

Motivation: It has long been hypothesized that incorporating models of network noise as well as edge directions and known pathway information into the representation of protein–protein interaction (PPI) networks might improve their utility for functional inference. However, a simple way to do this has not been obvious. We find that diffusion state distance (DSD), our recent diffusion-based metric for measuring dissimilarity in PPI networks, has natural extensions that incorporate confidence, directions and can even express coherent pathways by calculating DSD on an augmented graph.

Results: We define three incremental versions of DSD which we term cDSD, caDSD and capDSD, where the capDSD matrix incorporates confidence, known directed edges, and pathways into the measure of how similar each pair of nodes is according to the structure of the PPI network. We test four popular function prediction methods (majority vote, weighted majority vote, multi-way cut and functional flow) using these different matrices on the Baker’s yeast PPI network in cross-validation. The best performing method is weighted majority vote using capDSD. We then test the performance of our augmented DSD methods on an integrated heterogeneous set of protein association edges from the STRING database. The superior performance of capDSD in this context confirms that treating the pathways as probabilistic units is more powerful than simply incorporating pathway edges independently into the network.

Availability: All source code for calculating the confidences, for extracting pathway information from KEGG XML files, and for calculating the cDSD, caDSD and capDSD matrices are available from http://dsd.cs.tufts.edu/capdsd

Contact:  lenore.cowen@tufts.edu or benjamin.hescott@tufts.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated detection and tracking of many cells by using 4D live-cell imaging data
Authors: Tokunaga Terumasa , Hirose Osamu , Kawaguchi Shotaro , Toyoshima Yu , Teramoto Takayuki , Ikebata Hisaki , Kuge Sayuri , Ishihara Takeshi , Iino Yuichi , Yoshida Ryo
Published: June 2014

Motivation: Automated fluorescence microscopes produce massive amounts of images observing cells, often in four dimensions of space and time. This study addresses two tasks of time-lapse imaging analyses; detection and tracking of the many imaged cells, and it is especially intended for 4D live-cell imaging of neuronal nuclei of Caenorhabditis elegans. The cells of interest appear as slightly deformed ellipsoidal forms. They are densely distributed, and move rapidly in a series of 3D images. Thus, existing tracking methods often fail because more than one tracker will follow the same target or a tracker transits from one to other of different targets during rapid moves.

Results: The present method begins by performing the kernel density estimation in order to convert each 3D image into a smooth, continuous function. The cell bodies in the image are assumed to lie in the regions near the multiple local maxima of the density function. The tasks of detecting and tracking the cells are then addressed with two hill-climbing algorithms. The positions of the trackers are initialized by applying the cell-detection method to an image in the first frame. The tracking method keeps attacking them to near the local maxima in each subsequent image. To prevent the tracker from following multiple cells, we use a Markov random field (MRF) to model the spatial and temporal covariation of the cells and to maximize the image forces and the MRF-induced constraint on the trackers. The tracking procedure is demonstrated with dynamic 3D images that each contain >100 neurons of C.elegans.

Availability:  http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014

Supplementary information:  Supplementary data are available at http://daweb.ism.ac.jp/yoshidalab/crest/ismb2014

Contact:  yoshidar@ism.ac.jp