bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses
Authors: Deihimi Tahereh , Niazi Ali , Ebrahimi Mansour , Kajbaf Kimia , Fanaee Somaye , Bakhtiarizadeh Mohammad Reza , Ebrahimie Esmaeile 
Published: October 2012

Abstract
Regarding the possible multiple functions of a specific gene, finding the alternative roles of genes is a major challenge. Huge amount of available expression data and the central role of the promoter and its regulatory elements provide unique opportunely to address this issue. The question is that how the expression data and promoter analysis can be applied to uncover the different functions of a gene. A computational approach has been presented here by analysis of promoter regulatory elements, coexpressed gene as well as protein domain and prosite analysis. We applied our approach on Thaumatin like protein (TLP) as example. TLP is of group 5 of pathogenesis related proteins which their antifungal role has been proved previously. In contrast, Osmotin like proteins (OLPs) are basic form of TLPs with proved role only in abiotic stresses. We demonstrated the possible outstanding homolouges involving in both biotic and abiotic stresses by analyzing 300 coexpressed genes for each Arabidopsis TLP and OLP in biotic, abiotic, hormone, and light microarray experiments based on mutual ranking. In addition, promoter analysis was employed to detect transcription factor binding sites (TFBs) and their differences between OLPs and TLPs. A specific combination of five TFBs was found in all TLPs presenting the key structure in functional response of TLP to fungal stress. Interestingly, we found the fungal response TFBs in some of salt responsive OLPs, indicating the possible role of OLPs in biotic stresses. Thirteen TFBS were unique for all OLPs and some found in TLPs, proposing the possible role of these TLPs in abiotic stresses. Multivariate analysis showed the possibility of estimating models for distinguishing biotic and abiotic functions of TIPs based on promoter regulatory elements. This is the first report in identifying multiple roles of TLPs and OLPs in biotic and abiotic stresses. This study provides valuable clues for screening and discovering new genes with possible roles in tolerance against both biotic and abiotic stresses. Interestingly, principle component analysis showed that promoter regulatory elements of TLPs and OLPs are more variable than protein properties reinforcing the prominent role of promoter architecture in determining gene function alteration.
Adaptation to different salinities exposes functional specialization in the intestine of the sea bream (Sparus aurata L.)
Authors: Gregório Sílvia F. , Carvalho Edison S. M. , Encarnação Sandra , Wilson Jonathan M. , Power Deborah M. , Canário Adelino V. M. , Fuentes Juan 
Published: October 2012

Summary
In addition to high drinking rates, processing of intestinal fluid is essential for osmoregulation in marine fish. This study analyzed the long-term response of the sea bream (Sparus aurata L.) to relevant changes of external salinity 12, 35 and 55ppt focusing on the anterior intestine and in the less often studied rectum. Intestinal water absorption, epithelial HCO3- secretion and gene expression of the main molecular mechanisms (SLC26a6, SLC26a3, SLC4a4, atp6v1b, CFTR, NKCC1 and NKCC2) involved in Cl- and HCO3- movements were examined. The anion transporters SLC26a6 and SLC26a3 are several fold more expressed in the anterior intestine, while the expression of Atp6v1b (V-type H+-ATPase β subunit) several fold higher in the rectum. Prolonged exposure to altered external salinity was without effect on water absorption but associated with concomitant changes in intestinal fluid content, epithelial HCO3- secretion and salinity dependent expression of SLC26a6, SLC26a3 and SLC4a4 in the anterior intestine. However, the most striking response to external salinity was obtained in the rectum, where a 4-5-fold increase in water absorption was paralleled by a 2-3-fold increase in HCO3- secretion in response to 55 ppt. In addition, the rectum of high salinity acclimated fish shows a sustained (and enhanced) secretory current (Isc) identified in vitro in Ussing chambers, confirmed by the higher expression CFTR and NKCC1 and established by protein localization with immunohistochemistry. Taken together the present results suggest a functional anterior-posterior specialization with regards to intestinal fluid processing and subsequently to salinity adaptation of the sea bream. The rectum becomes more active at higher salinities and functions as the final controller of the intestinal function in osmoregulation.
Inter-leg coordination in the control of walking speed inDrosophila
Authors: Wosnitza Anne , Bockemühl Till , Dübbert Michael , Scholz Henrike , Büschges Ansgar 
Published: October 2012

SummaryLegged locomotion is the most common behavior of terrestrial animals and it is assumed to have become highly optimized during evolution. Quadrupeds, for instance, use distinct gaits which are optimal with regard to metabolic cost and have characteristic kinematic features and patterns of inter-leg coordination. In insects, the situation is not as clear. In general, insects are able to alter inter-leg coordination systematically with locomotion speed, producing a continuum of coordination patterns. This notion, however, is based on the study of not one but several insect species. These species differ greatly in size and weight and each species tends to walk at a rather narrow range of speeds. We have addressed these issues and examined four strains of Drosophila, which are similar in size and weight, but tend to walk at different speed ranges. Our data suggest that Drosophila controls its walking speed almost exclusively via step frequency. At high walking speeds we invariably found tripod coordination the quality of which increased with speed as indicated by a simple measure of tripod coordination strength (TCS). At low speeds we also observed tetrapod coordination and wave gait-like walking patterns. These findings suggest not only a clear speed dependence of inter-leg coordination, but imply that inter-leg coordination is flex-ible. This was further supported by amputation experiments in which we examined walking behavior in animals after the removal of a hind leg. These animals show immediate adaptations in body posture, leg kinematics, and inter-leg coordination thereby maintaining their ability to walk.
Tribocharged Polymer Surfaces: Solvent Effect on Pattern Formation and Modification
Authors: Francisco Kelly R , Burgo Thiago A L , Galembeck Fernando 
Published: October 2012

Abstract
Commonly used liquids have a powerful effect on the tribocharge patterns formed by rubbing polyethylene (PE) and poly(tetrafluoroethylene) surfaces. Solvents previously absorbed on PE specifically suppress positive tribocharge deposition. When applied to previously tribocharged surfaces, they also behave as charge-suppressing agents or transfer media. All these unprecedented results verify a new mechanochemical model that was recently introduced to explain the hitherto challenging problem of triboelectricity formation.
Specific Chromatographic Retentions on Polymer Pore Surface of Macroporous Spongy Monoliths
Authors: Tanigawa Tetsuya , Kubo Takuya , Hosoya Ken 
Published: October 2012

Abstract
We examined chromatographic retention properties of macroporous spongy monolithic columns. Detailed chromatographic evaluations showed that planar compounds were strongly retained on poly(ethylene-co-vinyl acetate)-based monoliths, whereas sterically bulky or hydrophilic compounds were weakly retained. The comparison results with commonly used columns suggested that the specific retention abilities were a result of the differences in the polymer-chain orientation on polymer pore surface.
Why No Electrostatic Attraction in DLVO Theory?
Authors: Ise Norio 
Published: October 2012

Abstract
The Fowler–Guggenheim–McQuarrie analysis of the Debye–Hückel theory shows that electrostatic Helmholtz and Gibbs free energies (Fel and Gel, respectively) are not equal. The difference term (Fel − Gel)/V (V: system volume) is the osmotic pressure pel. The DLVO theory is based on the assumption that Fel = Gel, suggesting that this theory can be justified only for small pel, namely for weakly charged systems. The experiments show that the DLVO theory provides seemingly satisfactory pictures for weakly charged colloidal systems but not for strongly interacting ones. The widely accepted view that the mean-field approach should predict only repulsion is not justified. The intrinsic reason why the DLVO theory has provided only repulsion seems to be due to the assumption Fel = Gel.
The Small-Strain Shear Modulus and Damping Ratio of Quartz and Volcanic Sands
Authors: Senetakis Kostas , Anastasiadis Anastasios , Pitilakis Kyriazis 
Published: October 2012

Abstract
The dynamic properties of soils in the region of very small strains are essential for any seismic design. This paper aims to investigate the dynamic small-strain shear modulus (GO) and damping ratio (DO) of reconstituted dry sands of variable mineralogy, shape, and grain-size distribution. In particular, the low-amplitude torsional resonant column test results of 31 specimens are synthesized, 19 specimens of natural and quarry sands predominately composed of quartz particles, and 12 specimens of volcanic sands composed of rhyolitic glassy rock of porous particles. It is concluded that the volcanic sands exhibit significantly lower GO values and slightly lower DO values in comparison to the quartz ones whilst the response of the quartz sands is significantly affected by the shape of the particles. The differences in the observed responses between quartz and volcanic sands are partially attributed to the variability in particles density, morphology, and mineralogy, as well as the higher void ratio and the lower dry density that the volcanic sands exhibit in comparison to the quartz ones. Overall, the effects of the mean effective confining pressure (σm′), the void ratio (e), and the grain-size distribution on the dynamic response of the volcanic soils follow a similar trend as in the quartz sands. Using the general form of available relationships presented in the literature, and after modifying the “constant” parameters, appropriate equations, stemming from the low-amplitude resonant column data test, are proposed that may be used for the estimation of the small-strain shear modulus and damping ratio separately for natural quartz sands, quarry quartz sands, and volcanic granular soils.
Precision Tool Condition Monitoring for Grinding Wheel in IC Manufacturing of Silicon Wafer
Authors: Hsu Ya-Chen , Pearn W. L. , Chuang Ya-Fei 
Published: October 2012

AbstractIn integrated circuit (IC) manufacturing industries, wafer grinding is an important step because it improves wafer flatness and thickness. The diamond-grinding wheel used for grinding the wafers is expensive. Inevitably, the diamond-grinding wheel wears gradually during the grinding process, and the wafer surface is contaminated by grinding chips. Consequently, the fraction of defectives gradually becomes significant. In this situation, cost reduction is important for silicon wafer suppliers in the global market. Therefore, it is essential to monitor the grinding wheel in order to reduce the manufacturing cost and minimize the fraction of defectives. In this paper, we consider the grinding-wheel replacement problem in IC factories with the aim of determining the optimal replacement time for the grinding wheels. In order to maintain high wafer process quality and minimize the production cost, we propose a tool condition monitoring procedure for assessing the true capability at each time period of the grinding process and then find the optimal time for tool replacement. The procedure can be used practically for the silicon wafer manufacturing industry.
MECHANICAL AND MICROSTRUCTURAL EFFECTS ON MEDIUM CARBON STEEL WELD JOINTS WHEN A GMAW PROCESS IS USED TO REPAIR STRUCTURAL COMPONENTS USED IN THE MANUFACTURING OF HEAVY MINING EQUIPMENT
Authors: Valenzuela Eduardo , López Víctor 
Published: October 2012

AbstractMeet the technical specifications defined by the designengineering department is a critical factor to haveof a good performance during the normal life cycle of heavy mining equipment. This study was done to determine how the repair process carried out in order to recover structuralcomponents that did not meet the proper quality criteria after the inspection process,can alter the microstructure and the mechanical properties of the product used in the construction of heavy miningequipment.As the repair process can be donenot only once, but twice and until three times using a manual GMAW process, this study was carried out under controlled conditions and using similar process parameters as those used in the manufacturing process. A set of four specimens were prepared, one without any repair, and the other three with one, two and three repairs. In order to evaluate the sanity of the welded unions and also the materials behavior of each one of the specimens, tensile, microhardness, macroetch, charpy, and metallographic testswere carried out
Analysis of the Heat Generated by Welding Process for Solid State two dissimilar metals.
Authors: Rodríguez Ramos Ezequiel R. , Zambrano Robledo P. del C. , Juárez Hernández A. , Reyes Valdéz A. 
Published: October 2012

AbstractThis article presents an analysis of the heat generated by welding two different metals by friction. The welded samples were a DP600 steel and aluminum 6063. To perform this analysis it study the heat conducted in this system using Fourier’s Law and respective specific heat of each metal. We analyzed the integral equations that make up the model and the heat flow analysis to predict the optimal combination of alloys, in an ideal process.
Évolution de la place du végétal dans la ville, de l’espace vert a la trame verte
Authors: Mehdi Lotfi , Weber Christiane , Pietro Francesca Di , Selmi Wissal 
Published: October 2012

La place attribuée aux espaces verts par les politiques urbaines depuis le XIXe siècle en France a connu plusieurs phases. Selon les tendances urbanistiques adoptées, trois périodes principales peuvent être identifiées : il s’agit de l’ère de l’urbanisme fonctionnaliste, de celle de l’urbanisme durable et enfin l’émergence de l’urbanisme écologique. Tout au long de ces périodes, de nouvelles pratiques de gestion et différentes typologies d’espaces verts sont apparues. Les espaces végétalisés urbains ont ainsi évolué par rapport à un « gradient de naturalité », allant des jardins privés à forte valeur ornementale à la trame verte urbaine multifonctionnelle. De nos jours, les études menées sur « la nature » en ville se structurent en fonction de deux orientations principales : (i) l’évaluation des services écosystémiques rendus par la biodiversité et (ii) la mise en connectivité des habitats particuliers. L’objectif de cet article est de proposer une synthèse de l’évolution de la place du végétal en ville à la fois dans les diverses théories urbanistiques et dans les pratiques urbanistiques.
A Polystyrene‐Supported, Highly Recyclable Squaramide Organocatalyst for the Enantioselective Michael Addition of 1,3‐Dicarbonyl Compounds to β‐Nitrostyrenes
Authors: Kasaplar Pinar , Riente Paola , Hartmann Caroline , Pericàs Miquel A. 
Published: October 2012

AbstractA chiral squaramide has been supported onto a polystyrene (PS) resin through a copper‐catalyzed azide–alkyne cycloaddition (CuAAC) reaction and used as a very active, easily recoverable and highly reusable organocatalyst for the asymmetric Michael addition of 1,3‐dicarbonyl compounds to β‐nitrostyrenes. The PS‐supported squaramide could be recycled up to 10 times.
Enantioselective Addition of Dialkylzincs to Aldehydes Catalyzed by (−)‐MITH
Authors: Cheng Ying‐Ni , Wu Hsyueh‐Liang , Wu Ping‐Yu , Shen Ying‐Ying , Uang Biing‐Jiun 
Published: October 2012

AbstractAn effective catalytic system that imparts high enantioselectivity has been disclosed for the synthesis of optically active alcohols, which may undergo further chemical transformations. The enantioselective alkylation of aldehydes with dialkylzincs to afford the corresponding optically active alcohols with excellent enantioselectvities has been achieved in the presence of 0.1–0.5 mol % of the camphor‐derived chiral ligand (−)‐2‐exo‐morpholinoisobornane‐10‐thiol (MITH) (1) at room temperature or at 0 °C.
Facile Synthesis of Well‐Dispersed Silver Nanoparticles on Hierarchical Flower‐like Ni3Si2O5(OH)4 with a High Catalytic Activity towards 4‐Nitrophenol Reduction
Authors: Jin Renxi , Xing Yan , Yu Xiaodan , Sun Shaolin , Yu Donghui , Wang Fangfang , Wu Wenbin , Song Shuyan 
Published: October 2012

AbstractLayered nickel silicate nanoflowers (NSFs) with a hierarchical nanostructure have been successfully fabricated by a template‐free solvothermal method. The as‐prepared nanoflowers were composed of many interconnected edge‐curving lamellae with a thickness of about 15 nm and had a high specific surface area (279 m2 g−1) and large pore volume (0.67 cm3 g−1). The highly dispersed small silver nanoparticles (AgNPs) were immobilized on the surface of NSFs through the in situ reduction of Ag+ by Sn2+. The AgNP/NSF nanocomposites showed a high performance in the catalytic reduction of 4‐nitrophenol. In particular, there was no visible decrease in the catalytic activity of the reused catalysts even after being recycled four times. The as‐prepared AgNP/NSF nanocomposites might be an excellent catalyst owing to their availability, formability, chemical and thermal stability, and high specific surface area.
DNA Sequence and Ancillary Ligand Modulate the Biexponential Emission Decay of Intercalated [Ru(L)2dppz]2+Enantiomers
Authors: McKinley Andrew W. , Andersson Johanna , Lincoln Per , Tuite Eimer M. 
Published: October 2012

AbstractThe bi‐exponential emission decay of [Ru(L)2dppz]2+(L=N,N′‐diimine ligand) bound to DNA has been studied as a function of polynucleotide sequence, enantiomer, and nature of L (phenanthroline vs. bipyridine). The lifetimes (τi) and pre‐exponential factors (αi) depend on all three parameters. With [poly(dA‐dT)]2, the variation ofαiwith [Nu]/[Ru] has little dependence on L for Λ‐[Ru(L)2dppz]2+but a substantial dependence for Δ‐[Ru(L)2dppz]2+. With [poly(dG‐dC)]2, by contrast, the Λ‐enantiomerαivalues depend strongly on the nature of L, whereas those of the Δ‐enantiomer are relatively unaffected. DNA‐bound linked dimers show similar photophysical behaviour. The lifetimes are identified with two geometries of minor‐groove intercalated [Ru(L)2dppz]2+, resulting in differential water access to the phenazine nitrogen atoms. Interplay of cooperative and anti‐cooperative binding resulting from complex–complex and complex–DNA interactions is responsible for the observed variations ofαiwith binding ratio. [Ru(phen)2dppz]2+emission is quenched by guanosine in DMF, which may further rationalise the shorter lifetimes observed with guanine‐rich DNA.
Die chemische Formelsprache – (un‐)vermeidbare Hürden auf dem Weg zu einer Verständnisentwicklung?
Authors: Bernholt Sascha , Fischer Insa , Heuer Sandra , Taskin Vahide , Martens Jürgen , Parchmann Ilka 
Published: October 2012

AbstractDie chemische Formelsprache prägt den Kompetenzbereich Kommunikation in einer besonderen, fachspezifischen Weise. Sie stellt einen eigenen Lerngegenstand dar, repräsentiert aber auch chemische Prozesse und Fachkonzepte nach präzisen Regeln. Für das Lernen und Kommunizieren in und über Chemie ist sie folglich unverzichtbar. Zahlreiche Untersuchungen zeigen jedoch nach wie vor, dass Schülerinnen und Schüler große Probleme in der Interpretation und Verwendung von Symbolen, Formeln und Reaktionsgleichungen haben. Dieser Beitrag knüpft zunächst an bekannte Ergebnisse aus der Lehr‐Lern‐Forschung an. Er hinterfragt weiterhin das Verständnis üblicher Darstellungen in Lehrbüchern. Aufbauend auf eine Querschnittsuntersuchung werden schließlich Anregungen für die Unterrichtspraxis gegeben, deren weitere Diskussion die Autoren mit diesem Beitrag anstoßen möchten.
Recent Advances in the Research of Heterocyclic Compounds as Antitubercular Agents
Authors: Yan Mi , Ma Shutao 
Published: October 2012

AbstractTuberculosis (TB) is a major health problem, with approximately one‐third of the world′s population infected with Mycobacterium tuberculosis, eight million people in the active disease state, and two million dying annually. Furthermore, the prevalence of TB/HIV co‐infection, and the emergence of multidrug‐resistant tuberculosis (MDR‐TB) and extensively drug‐resistant tuberculosis (XDR‐TB) have further aggravated the spread of this disease and thus mortality by it. There is an urgent need for novel antitubercular agents with improved properties, such as lower toxicity, shortened duration of therapy, rapid bactericidal action, and enhanced activity against MDR strains. Fortunately, a number of new potential antitubercular candidate drugs with heterocyclic rings, which are most likely to be effective against resistant strains, have entered clinical trials in recent years. This review highlights recent advances in the research of novel heterocyclic compounds, with particular focus on their antimycobacterial activity, mechanisms of action, toxicity, and structure–activity relationships (SARs).
μ3‐ vs. μ‐Hydroxido Bridges – Peripheral Function Controls the Nuclearity of Hydroxido‐Bridged Copper(II) Complexes
Authors: Chiboub Fellah Fatima Zohra , Costes Jean‐Pierre , Vendier Laure , Duhayon Carine , Ladeira Sonia , Tuchagues Jean‐Pierre 
Published: October 2012

AbstractThe synthesis and characterization of three monohydroxido‐bridged dinuclear CuII complexes, [{Cu2(L1)2(μ‐OH)}(ClO4){Cu2(L1)2(μ‐OH)}](ClO4)·5.5H2O (1), Cu2(L2)2(OH)(ClO4)(H2O)2 (2), [{Cu2(L3)2(μ‐OH)(ClO4)}2]·5H2O (3) and three monohydroxido‐bridged trinuclear CuII complexes, [Cu3(L4)3(μ3‐OMe)(ClO4)2] (4), [Cu3(L5)3(μ3‐OH) (ClO4)2]·0.5{(CH3)2CO}·0.5(H2O) (5), [Cu3(L6)3(μ3‐OH)(ClO4)2] (6), is reported (HL1–HL6 = tridentate N2O ligands resulting from the Schiff base condensation of salicylaldehyde or 3‐methoxysalicylaldehyde with ethylenediamine, 1,2‐diaminopropane, 2‐methylpropane‐1,2‐diamine or 1,2‐diaminocyclohexane). The six new complexes are obtained through aggregation of the corresponding mononuclear precursor Cu(Li)(py)(ClO4) in the presence of HO– (MeO–) anions in methanol. The nuclearity of the resulting complex depends on the steric requirement of Li: in the presence of an OMe substituent α to the Ophenoxido atom (L1–L3), μ‐HO– single‐bridged dinuclear compounds are obtained (1–3); in the absence of an α‐substituent (L4–L6), the aggregation proceeds to the μ3‐OH– (μ3‐OMe–) bridged trinuclear compounds 4–6. The molecular structures of 1, 3 and 4–6 have been established through single‐crystal X‐ray studies. Antiferromagnetic interactions operate in 1 (J = –57 cm–1, –2JS1S2 formalism), 2 is paramagnetic, and 3 is the first example of a ferromagnetic monohydroxido‐bridged dinuclear CuII complex (J = 16 cm–1). The structural and magnetic parameters for the 22 μ‐HO– single‐bridged dinuclear CuII compounds reported to date are compared. Antiferromagnetic interactions operate in all three monohydroxido‐bridged trinuclear CuII complexes 4, 5, and 6 (J = –16.9, –6.3, and –6.7 cm–1, respectively). The structural and magnetic parameters for the seven μ3‐hydroxido (methoxido) bridged trinuclear CuII compounds presently known in the series based on tridentate Schiff bases that result from condensation of diamines with salicylaldehydes are compared.