bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of biochar on soil physical properties and winter wheat growth
Authors: Devereux Rachel C. , Sturrock Craig J. , Mooney Sacha J. 
Published: March 2013

ABSTRACTBiochar has been reported to improve soil quality and crop yield; however, less is known about its effects on the physical and, in particular, structural properties of soil. This study examines the potential ability of biochar to improve water retention and crop growth through a pot trial using biochar concentrations of 0%, 1·5%, 2·5% and 5% w/w. X-ray computed tomography was used to measure soil structure via pore size characteristics; this showed that pore size is significantly affected by biochar concentration. Increasing biochar is associated with decreasing average pore size, which we hypothesise would impact heavily on hydraulic performance. At the end of the experiment, average pore size had decreased from 0·07 mm2 in the 0% biochar soil to 0·046 mm2 in the 5% biochar soil. Increased biochar concentration also significantly decreases saturated hydraulic conductivity and soil bulk density. It was also observed that increased biochar significantly decreases soil water repellency. Increased water retention was also observed at low matric potentials, where it was shown that increased biochar is able to retain more water as the soil dried out. The application of biochar had little effect on short-term (<10 weeks) wheat growth, but did improve water retention through a change in soil porosity, pore size, bulk density and wetting ability.
Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3
Authors: Kanaparthi Dheeraj , Pommerenke Bianca , Casper Peter , Dumont Marc G 
Published: March 2013

Abstract
Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitrate-dependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitrate-dependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 × 104 autotrophic and 1 × 107 heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to ∼0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using 13CO2 was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.
Crossing-sign discrimination and knot-reduction for a lattice model of strand passage
Authors: Soteros Chris , Szafron Michael 
Published: March 2013

By performing strand-passages on DNA, type II topoisomerases are known to resolve topological constraints that impede normal cellular functions. The full details of this enzyme–DNA interaction mechanism are, however, not completely understood. To better understand this mechanism, researchers have proposed and studied a variety of random polygon models of enzyme-induced strand-passage. In the present article, we review results from one such model having the feature that it is amenable to combinatorial and asymptotic analysis (as polygon length goes to infinity). The polygons studied, called Θ-SAPs, are on the simple-cubic lattice and contain a specific strand-passage structure, called Θ, at a fixed site. Another feature of this model is the availability of Monte Carlo methods that facilitate the estimation of crossing-sign-dependent knot-transition probabilities. From such estimates, it has been possible to investigate how knot-reduction depends on the crossing-sign and the local juxtaposition geometry at the strand-passage site. A strong relationship between knot-reduction and a crossing-sign-dependent crossing-angle has been observed for this model. In the present article, we review these results and present heuristic geometrical arguments to explain this crossing-sign and angle-dependence. Finally, we discuss potential implications for other models of type II topoisomerase action on DNA.
The topology of plasmid-monomerizing Xer site-specific recombination
Authors: Colloms Sean D. 
Published: March 2013

Xer site-specific recombination at cer and psi converts bacterial plasmid multimers into monomers so that they can be efficiently segregated to both daughter cells at cell division. Recombination is catalysed by the XerC and XerD recombinases acting at ~30 bp core sites, and is regulated by the action of accessory proteins bound to accessory DNA sequences adjacent to the core sites. Recombination normally occurs only between sites in direct repeat in a negatively supercoiled circular DNA molecule, and yields two circular products linked together in a right-handed four-node catenane with antiparallel sites. These and other topological results are explained by a model in which the accessory DNA sequences are interwrapped around the accessory proteins, trapping three negative supercoils so that strand exchange by the XerC and XerD yields the observed four-node catenane.
Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations
Authors: Olson Wilma K. , Grosner Michael A. , Czapla Luke , Swigon David 
Published: March 2013

Bacterial gene expression is regulated by DNA elements that often lie far apart along the genomic sequence, but come close together during genetic processing. The intervening residues form loops, which are organized by the binding of various proteins. For example, the Escherichia coli Lac repressor protein binds DNA operators, separated by 92 or 401 bp, and suppresses the formation of gene products involved in the metabolism of lactose. The system also includes several highly abundant architectural proteins, such as the histone-like (heat-unstable) HU protein, which severely deform the double helix upon binding. In order to gain a better understanding of how the naturally stiff DNA double helix forms the short loops detected in vivo, we have developed new computational methods to study the effects of various non-specific binding proteins on the three-dimensional configurational properties of DNA sequences. The present article surveys the approach that we use to generate ensembles of spatially constrained protein-decorated DNA structures (minicircles and Lac repressor-mediated loops) and presents some of the insights gained from the correspondence between computation and experiment about the potential contributions of architectural and regulatory proteins to DNA looping and gene expression.
Decoding the SUMO signal
Authors: Hay Ronald T. 
Published: March 2013

SUMO (small ubiquitin-like modifier) emerged from the shadow of the well-established ubiquitin some 15 years ago when it was shown that a distinct conjugation pathway was responsible for SUMO modification. Since then it has been established that SUMO modifies over a thousand substrates and plays diverse roles in many important biological processes. Recognition of SUMO is mediated by short peptide sequences known as SIMs (SUMO-interaction motifs) that allow effector proteins to engage SUMO-modified substrates. Like ubiquitin, SUMO can form polymeric chains, and these chains can be recognized by proteins containing multiple SIMs. One protein that contains such a sequence of SIMs also contains a RING (really interesting new gene) domain that is the hallmark of a ubiquitin E3 ligase. This ubiquitin ligase known as RNF4 (RING finger protein 4) has the unique property that it can recognize SUMO-modified proteins and target them for ubiquitin-mediated proteolysis. Structural and biochemical analyses of RNF4 has shed light on the long sought after mechanism of ubiquitin transfer and illustrates how its RING domain primes the ubiquitin-loaded E2 for catalysis.
UWB bandpass filter with notch‐band based on transversal signal‐interaction concepts
Authors: Mirzaee M. , Virdee B. S. 
Published: March 2013

Presented is a structure to design a compact ultra‐wideband (UWB) bandpass filter (BPF) with excellent selectivity that enables inclusion of notch‐band characteristics within the filter's passband to mitigate interfering signals that coexist within the UWB spectrum. The proposed filter topology utilises two signal paths with different electrical lengths made up of two wideband BPFs that are connected in parallel. The mechanism of generating notch‐band is delineated based on transversal signal‐interaction concepts. Good agreement is observed between simulated and measured performances of the UWB filter, demonstrating a fractional bandwidth of 123% (2.66–11.2 GHz) with a sharp notch‐band at 5.21 GHz.
Junctionless Π‐gate transistor with indium gallium arsenide channel
Authors: Guo H.X. , Zhang X. , Zhu, Z. , Kong E.Y.J. , Yeo Y.‐C. 
Published: March 2013

The fabrication and characterisation of a gate‐first In0.7Ga0.3As channel Π‐gate junctionless transistor by a CMOS‐compatible top‐down approach is reported for the first time. The structure uses a simple layer structure and process flow. 3D device simulation shows that the Π‐gate structure can deplete the channel carriers more effectively compared with planar and tri‐gate devices. The fabricated device with 200 nm gate length shows good transfer characteristics with a Ion/Ioff ratio of ∼104 and subthreshold swing of ∼210 mV/decade. The results indicate the suitability of the proposed structure for junctionless transistor operation.
Si wire array waveguide grating with parallel star coupler configuration fabricated by ArF excimer immersion lithography
Authors: Okayama H. , Shimura D. , Takahashi H. , Seki M. , Toyama M. , Sano T. , Koshino K. , Yokoyama N. , Ohtsuka M. , Sugiyama A. , Ishitsuka S. , Tsuchizawa T. , Nishi H. , Yamada K. , Yaegashi H. , Horikawa T. , Sasaki H. 
Published: March 2013

An Si wire array waveguide grating wavelength demultiplexer fabricated using immersion ArF lithography is reported. The tilt directions of the input and output star couplers are aligned in the same direction to avoid phase error generated at the curved waveguides. A 16 channel device with 200 GHz wavelength spacing was fabricated.
Experimental study on parametric tunable dispersion compensation for WDM channels with mixed OOK and QPSK formats
Authors: Inoue T. , Tanizawa K. , Namiki S. 
Published: March 2013

Presented is a parametric tunable dispersion compensation (PTDC) for 43 Gbit/s WDM channels with mixed modulation formats of OOK and QPSK. The residual dispersion for the OOK channels is successfully compensated for, while the QPSK channels with digital coherent detection maintain a good signal quality regardless of various settings of PTDC that involve nonlinear processes of wavelength conversion based on four‐wave mixing. Specific design issues on PTDC are discussed, considering the characteristics of the modulation formats of the received channels.
70 GSa/s and 51 GHz bandwidth track‐and‐hold amplifier in InP DHBT process
Authors: Deza J. , Ouslimani A. , Konczykowska A. , Kasbari A. , Godin J. , Pailler G. 
Published: March 2013

A differential 70 GSa/s track‐and‐hold amplifier has been designed and fabricated in a 320 GHz‐fT InP double heterojunction bipolar transistor process. Measurements show a 51 GHz small‐signal bandwidth with an S11 parameter lower than −15 dB up to 56 GHz. The transient operation is verified up to 70 GSa/s. 60 GSa/s spectral measurements give total harmonic distortion <−46 dB up to 7 GHz and <−37 dB over the whole measurement range.
Preparation of in‐situ surface‐modified nanosilica and its application in separating oil from water
Authors: Liu Kai , Zheng Nan , Li Xiaohong , Zhang Zhijun 
Published: March 2013

A report is presented on the preparation of surface‐functionalised nanosilica from silicon tetrachloride (SiCl4, one of the major by‐products in the polycrystalline silicon industry) by in‐situ surface modification in aqueous solution. The approach uses both SiCl4 and sodium metasilicate as the silicon sources to generate nanosilica, whereas the proportion of sodium metasilicate and SiCl4 is adjusted to control the pH value of the reaction system. In this way, desired SiO2 nanoparticles were in‐situ surface‐modified by hexamethyldisilazane as soon as they were generated in the reaction solution, which makes it feasible to prevent the severe aggregation of nanosilica that often happens during the hydrolytic process. The obtained nanosilica with uniform particle size distribution (mean diameter 35–40 nm) shows superhydrophobicity (a water contact angle of 165°) and excellent organic dispersibility. Thanks to the low cost of raw materials as well as the superhydrophobicity and lipophilicity of as‐prepared nanosilica, its application for improving the selective penetration of oil is primarily investigated. The result shows that quartz sand modified by as‐prepared nanosilica can separate diesel oil from water successfully, which could be significant for improving crude oil recovery efficiency.
Nanoimprinting of TiO2–SiO2 photocurable materials with high titanium concentration for CF4/O2 etch selectivity
Authors: Takei Satoshi 
Published: March 2013

The nanofabrication of nanometre‐scale multiple‐level structures by nanoimprint lithography and CF4/O2 etching rates was investigated for nanoelectro mechanical systems and three‐dimensional (3D) wafer‐level packaging. A TiO2–SiO2 sol–gel photocurable material with high titanium concentration of 20.9 wt% was developed for CF4/O2 etch selectivity with a pattern transferring carbon layer in a bi‐layer process. The nanostructures of 3D micropatterns, holes with 200 nm diameter and 130 nm‐wide dense lines with line edge roughness of ∼10 nm were provided. The CF4/O2 etching rate of the TiO2–SiO2 photocurable material was ∼3.7 times lower than that of the referenced SiO2 sol–gel photocurable material. The CF4/O2 etch rates of titanium‐based photocurable materials were confirmed for deep plasma etching processes.
The Effects of Juvenile American Shad Planktivory on Zooplankton Production in Columbia River Food Webs
Authors: Haskell Craig A. , Tiffan Kenneth F. , Rondorf Dennis W. 
Published: March 2013

AbstractColumbia River reservoirs support a large population of nonnative American Shad Alosa sapidissima that consume the zooplankton that native fishes also rely on. We hypothesized that the unprecedented biomass of juvenile American Shad in John Day Reservoir is capable of altering the zooplankton community if these fish consume a large portion of the zooplankton production. We derived taxon‐specific estimates of zooplankton production using field data and a production model from the literature. Empirical daily ration was estimated for American Shad and expanded to population‐level consumption using abundance and biomass data from hydroacoustic surveys. Daphnia spp. production was high in early summer but declined to near zero by September as shad abundance increased. American Shad sequentially consumed Daphnia spp., copepods, and Bosmina spp., which tracked the production trends of these taxa. American Shad evacuation rates ranged from 0.09 to 0.24/h, and daily rations ranged from 0.008 to 0.045 g·g−1·d−1 (dry weight) over all years. We observed peak American Shad biomass (45.2 kg/ha) in 1994, and daily consumption (1.6 kg/ha) approached 30% (5.3 kg/ha) of zooplankton production. On average, American Shad consumed 23.6% of the available zooplankton production (range, <1–83%). The changes in the zooplankton community are consistent with a top‐down effect of planktivory by American Shad associated with their unprecedented biomass and consumption, but the effects are likely constrained by temperature, nutrient flux, and the seasonal production patterns of zooplankton in John Day Reservoir. American Shad add to the planktivory exerted by other species like Neomysis mercedis to reduce the capacity of the reservoir to support other planktivorous fishes. The introduction of American Shad and other nonnative species will continue to alter the food web in John Day Reservoir, potentially affecting native fishes, including Pacific salmon Oncorhynchus spp.
Reproductive Biology of Pacific Ocean Perch and Northern Rockfish in the Aleutian Islands
Authors: TenBrink Todd T. , Spencer Paul D. 
Published: March 2013

Abstract
Estimates of maturity (i.e., the proportion of mature individuals at age) play an important role in assessing stock productivity; however, this information has not been published for rockfishes in the Aleutian Islands. Ovary and otolith samples were collected from Pacific Ocean Perch Sebastes alutus and Northern Rockfish S. polyspinis during both fishery-independent and fishery-dependent cruises in 2010 to investigate maturity and other aspects of reproductive biology. Histological examination of ovaries indicated that both species exhibited general parturition in April, while specimens caught in the summer and fall were maturing and generally exhibited progressive stages of vitellogenesis. Histological analysis was more reliable when characterizing ovary condition than were macroscopic or visual assessments during the developing period. Estimates of natural mortality, based on a relationship with the gonadosomatic index, were 0.040 for Pacific Ocean Perch and 0.042 for Northern Rockfish. Mean fecundity estimates calculated for Northern Rockfish (89,320 oocytes) were correlated more with length and weight than age. Estimates of age and length at 50% maturity were 9.1 years at 32.4 cm for Pacific Ocean Perch and 7.6 years at 27.7 cm for Northern Rockfish and indicate maturation at younger ages than do previous studies from the Gulf of Alaska. This information on reproductive biology will improve estimation of fishing mortality reference points and management of these commercially important species in the Aleutian Islands.
Received June 22, 2012; accepted December 10, 2012
Egg mortality of northeast Arctic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus)†
Authors: Langangen Øystein , Stige Leif C. , Yaragina Natalia A. , Vikebø Frode B. , Bogstad Bjarte , Gusdal Yvonne 
Published: March 2013

Abstract
High and variable mortality during the egg and larval stages is thought to be an important source of interannual variability in stock size in many marine fish. However, quantitative information about the mortality during these life stages, especially interannual variability, is sparse. Here, we used a time-series covering 35 years (1959–1993) of survey data to estimate mortality during the egg stages of northeast Arctic cod (Gadus morhua) and Northeast Arctic haddock (Melanogrammus aeglefinus). Using a regression approach based on the numbers of eggs in different developmental stages, we calculated the mean instantaneous mortality rate of cod eggs to be 0.17 d−1 (95% CI: 0.15–0.19), which is significantly higher than that for haddock, 0.09 d−1 (95% CI: 0.07–0.12). Interannual variability in egg mortality ranges from ∼0.12 to ∼0.22 d−1 for cod and from ∼0.04 to ∼0.12 d−1 for haddock. The accuracy of these estimates was evaluated by the analysis of synthetic data constructed from a coupled physical–biological model, suggesting that mean mortality and the magnitude of interannual variability were estimated reliably, but not mortality for any given year.
Impact of the Carbon and Nitrogen Supply on Relationships and Connectivity between Metabolism and Biomass in a Broad Panel of Arabidopsis Accessions
Authors: Sulpice Ronan , Nikoloski Zoran , Tschoep Hendrik , Antonio Carla , Kleessen Sabrina , Larhlimi Abdelhalim , Selbig Joachim , Ishihara Hirofumi , Gibon Yves , Fernie Alisdair R. , Stitt Mark 
Published: March 2013

AbstractNatural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism and growth. Profiling of metabolic traits combined with network-based and statistical analyses allow the comparison of conditions and identification of sets of traits that predict biomass. However, it often remains unclear why a particular set of metabolites is linked with biomass and to what extent the predictive model is applicable beyond a particular growth condition. A panel of 97 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions was grown in near-optimal carbon and nitrogen supply, restricted carbon supply, and restricted nitrogen supply and analyzed for biomass and 54 metabolic traits. Correlation-based metabolic networks were generated from the genotype-dependent variation in each condition to reveal sets of metabolites that show coordinated changes across accessions. The networks were largely specific for a single growth condition. Partial least squares regression from metabolic traits allowed prediction of biomass within and, slightly more weakly, across conditions (cross-validated Pearson correlations in the range of 0.27–0.58 and 0.21–0.51 and P values in the range of &lt;0.001–&lt;0.13 and &lt;0.001–&lt;0.023, respectively). Metabolic traits that correlate with growth or have a high weighting in the partial least squares regression were mainly condition specific and often related to the resource that restricts growth under that condition. Linear mixed-model analysis using the combined metabolic traits from all growth conditions as an input indicated that inclusion of random effects for the conditions improves predictions of biomass. Thus, robust prediction of biomass across a range of conditions requires condition-specific measurement of metabolic traits to take account of environment-dependent changes of the underlying networks.
Store‐operated Ca2+ entry is not required for store refilling in skeletal muscle
Authors: Cully Tanya R , Launikonis Bradley S 
Published: March 2013

Summary

The present review describes store‐operated Ca2+ entry (SOCE) in skeletal muscle.

Fundamental discoveries in the field of skeletal muscle SOCE are described and the techniques that were used to make these. The advantages and limitations in these techniques are discussed to provide a means of questioning and determining the physiological role(s) of SOCE in skeletal muscle.

It is concluded that SOCE has little or no role in the filling of the sarcoplasmic reticulum with Ca2+ at rest or during a single contracture. It is likely that SOCE is activated during fatigue, although direct measurements of SOCE are lacking and the physiological significance remains uncertain.