bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptotically Unbiased Estimation of Autocovariances and Autocorrelations with Panel Data in the Presence of Individual and Time Effects
Authors: Okui Ryo 
Published: July 2013

AbstractThis article proposes asymptotically unbiased estimators of autocovariances and autocorrelations for panel data with both individual and time effects. We show that the conventional autocovariance estimators suffer from the bias caused by the elimination of individual and time effects. The bias related to individual effects is proportional to the long-run variance, and it related to time effects is proportional to the value of the estimated autocovariance. For the conventional autocorrelation estimators, the elimination of time effects does not cause a bias while the elimination of individual effects does. We develop methods to estimate the long-run variance and propose bias-corrected estimators based on the proposed long-run variance estimator. We also consider the half-panel jackknife estimation for bias correction. The theoretical results are given by employing double asymptotics under which both the number of observations and the length of the time series tend to infinity. Monte Carlo simulations show that the asymptotic theory provides a good approximation to the actual bias and that the proposed bias-correction methods work well.
Oxidative Damage and Mutagenesis in Saccharomyces cerevisiae: Genetic Studies of Pathways Affecting Replication Fidelity of 8-Oxoguanine
Authors: Shockley Arthur H , Doo David W , Rodriguez Gina P , Crouse Gray F 
Published: July 2013

Abstract
Oxidative damage to DNA constitutes a major threat to the faithful replication of DNA in all organisms and it is therefore important to understand the various mechanisms that are responsible for repair of such damage and the consequences of unrepaired damage. In these experiments, we make use of a reporter system in Saccharomyces cerevisiae that can measure the specific increase of each type of base pair mutation by measuring reversion to a Trp+ phenotype. We demonstrate that increased oxidative damage due to the absence of the superoxide dismutase gene, SOD1, increases all types of base pair mutations and that mismatch repair (MMR) reduces some, but not all, types of mutations. By analyzing various strains that can revert only via a specific CG → AT transversion in backgrounds deficient in Ogg1 (encoding an 8-oxoG glycosylase), we can study mutagenesis due to a known 8-oxoG base. We show as expected that MMR helps prevent mutagenesis due to this damaged base and that Pol η is important for its accurate replication. In addition we find that its accurate replication is facilitated by template switching, as loss of either RAD5 or MMS2 leads to a significant decrease in accurate replication. We observe that these ogg1 strains accumulate revertants during prolonged incubation on plates, in a process most likely due to retromutagenesis.
Functional variable method to study nonlinear evolution equations
Authors: Eslami Mostafa , Mirzazadeh Mohammad 
Published: July 2013

Abstract
The functional variable method is a powerful solution method for obtaining exact solutions of nonlinear evolution equations. This method presents a wider applicability for handling nonlinear wave equations. In this paper, the functional variable method is used to construct exact solutions of Davey-Stewartson equation, generalized Zakharov equation, K(m, n) equation with generalized evolution term, (2 + 1)-dimensional long-wave-short-wave resonance interaction equation and nonlinear Schrödinger equation with power law nonlinearity. The obtained solutions include solitary wave solutions, periodic wave solutions.
Anaerobic wastewater treatment using anaerobic baffled bioreactor: a review
Authors: Hassan Siti , Dahlan Irvan 
Published: July 2013

Abstract
Anaerobic wastewater treatment is receiving renewed interest because it offers a means to treat wastewater with lower energy investment. Because the microorganisms involved grow more slowly, such systems require clever design so that the microbes have sufficient time with the substrate to complete treatment without requiring enormous reactor volumes. The anaerobic baffled reactor has inherent advantages over single compartment reactors due to its circulation pattern that approaches a plug flow reactor. The physical configuration of the anaerobic baffled reactor enables significant modifications to be made; resulting in a reactor which is proficient of treating complex wastewaters which presently require only one unit, ultimately significant reducing capital costs. This paper also concerns about mechanism, kinetic and hydrodynamic studies of anaerobic digestion for future application of the anaerobic baffled reactor for wastewater treatment.
Australia's ethical framework for when animals are used for scientific purposes
Authors: Rose M , Grant E 
Published: July 2013

AbstractThe basic tenet of theAustralian Code of Practice for the Care and Use of Animals for Scientific Purposes(the Code) is that there is an ethical imperative in our decisions as to if and how animals are used in these circumstances. The Code provides a framework for ethical review which incorporates a set of guiding principles and establishes institutional Animal Ethics Committees with responsibilities for oversight of these activities; the nexus between animal welfare and scientific outcomes and the recognition that such ethical decisions are not matters for the scientific community alone but must involve the wider community are notions central to the effective implementation of the Code. The Code identifies the responsibilities of the parties involved such that arrangements within which individuals exercise their responsibilities are clarified and processes for accountability are transparent. First published in 1969 as an initiative of the scientific community under the auspices of the National Health and Medical Research Council, the seventh edition of the Code was published in 2004. The Code is a living document with changing community views and scientific developments reflected in each revision. The time course of the development of the Code provides a background to examine the way in which policies governing the use of animals for scientific purposes have evolved in Australia. This paper will provide an overview of these developments and discuss the influences which have shaped the key elements of this approach.
Attitudes towards catch-and-release recreational angling, angling practices and perceptions of pain and welfare in fish in New Zealand
Authors: Muir R , Keown AJ , Adams NJ , Farnworth MJ 
Published: July 2013

AbstractAlthough there is still some debate regarding whether fish have the capacity to feel pain, recent scientific research seems to support the notion that fish can indeed suffer. However, the continued scientific discourse has led to questions regarding how members of the public perceive issues of pain and welfare in fish. A questionnaire was developed and randomly distributed to 700 members of the general public in New Zealand. Questionnaires gathered basic demographic information, information regarding respondents’ participation in and opinions on angling practice, and opinions about fish welfare and pain. The response rate was 62.4% (437/700). The primary aim of the study was to assess public concerns for the impact of catch-and-release angling (CRA) on the welfare of fish. Most respondents indicated a belief that fish are capable of feeling some pain although older respondents scored the capacity of fish to feel pain lower than younger respondents. Likewise, most respondents believed that CRA causes pain and compromises survival in fish. Principle Component Analysis identified two major components within responses. These were: i) importance placed on good fishing techniques; and ii) concern for pain and survival of fish. Female respondents showed more concern about angling practices and their impact on pain and survival of fish than male respondents. Respondents who participate in CRA and considered it acceptable showed less concern for pain and survival in fish than both respondents who do not participate and those who considered CRA unacceptable. The majority of respondents considered angling an acceptable pastime (65%; 284/435) but also indicated support for the introduction of guidelines and regulations to improve fish welfare in the future (76.4%; 334/434). Those respondents that did not believe regulations were necessary provided statistically lower importance scores for both pain and survival in fish and good angling practices than respondents that did. Education about good angling practices may provide the best route by which fish welfare can be improved.
Statistical power, effect size and animal welfare: recommendations for good practice
Authors: Hawkins D , Gallacher E , Gammell M 
Published: July 2013

AbstractDespite the particular relevance of statistical power to animal welfare studies, we noticed an apparent lack of sufficient information reported in papers published inAnimal Welfareto facilitatepost hoccalculation of statistical power for use in meta-analyses. We therefore conducted a survey of all papers published inAnimal Welfarein 2009 to assess compliance with relevant instructions to authors, the level of statistical detail reported and the interpretation of results regarded as statistically non-significant. In general, we found good levels of compliance with the instructions to authors except in relation to the level of detail reported for the results of each test. Although not requested in the instructions to authors, exactP-values were reported in just over half of the tests but effect size was not explicitly reported for any test, there was no reporting ofa prioristatistical analyses to determine sample size and there was no formal assessment of non-significant results in relation to type II errors. As a first stage to addressing this we recommend more reporting ofa prioripower analyses, more comprehensive reporting of the results of statistical analysis and the explicit consideration of possible statistical power issues when interpretingP-values. We also advocate the calculation of effect sizes and their confidence intervals and a greater emphasis on the interpretation of the biological significance of results rather than just their statistical significance. This will enhance the efforts that are currently being made to comply with the 3Rs, particularly the principle of reduction.
Loading density and welfare of goat kids during long distance road transport
Authors: Hindle VA , Reimert HGM , van der Werf JTN , Lambooij E 
Published: July 2013

AbstractMany goat kids(Capra aegagrus hircus)are transported live from The Netherlands for slaughter in France or Spain. Current standards indicate that goats (<35 kg) should have sufficient space at 0.2-0.30 m2per animal (approximately 5 goats per m2). Research was devised to assess behaviour and physiological responses of goat kids transported at different space allowances. After weaning, goat kids were fed milk for six weeks using a lambar-type feeder and then transported to Spain(circa1,400 km). These kids (8-10 kg, maximum eight weeks old) were transported at space allowances of 0.2, 0.13 and 0.1 m2per animal (ie loading densities 5, 7.5 or 10 animals per m2, respectively) in three journeys. Before loading and upon arrival, six goats per compartment were weighed, blood sampled and had rectal temperature measured. Three goats per compartment were equipped with ECG loggers. On average, kids lost approximately 4% in bodyweight and rectal temperature fell 0.2°C during 20 h transport. Heart rate ranged between 100-190 bpm irrespective of loading density during actual transport. All animals stood at the beginning but were never all recumbent independent of loading density. Kids tended to huddle together at lower loading densities. High loading density restricted movement. Blood concentrations of haemoglobin and haematocrit increased, as did osmolality indicating dehydration. It is recommended that water be supplied using a drinking system to which animals are accustomed. Since movement was restricted it is recommended that kids be transported at nine animals per m2(maximum).
Development and testing of an on-farm welfare assessment protocol for dairy goats
Authors: Muri K , Stubsjøen SM , Valle PS 
Published: July 2013

AbstractTo ensure that farm animal welfare issues are identified and addressed appropriately, there is a need for robust on-farm welfare assessment protocols. This paper describes the development of a comprehensive welfare assessment protocol for dairy goats(Capra hircus)and its testing on 30 commercial dairy goat farms in Norway. The protocol combines animal-based welfare indicators with measures of husbandry provisions to enable the identification of welfare problems and challenges inherent to the production system. The study also includes a first report of group level qualitative behavioural assessments (QBA) of goats. Due to reliability and validity issues related to behavioural assessments of human-animal interactions, indices of stockperson attitudes were incorporated as a complementary assessment of stockmanship. The most prevalent physical conditions observed were ocular discharge, skin lesions, udder asymmetry, calluses on knees and hocks, and overgrown claws. Moreover, fear levels appeared to be of particular concern in some herds. Significant associations were found between qualitative behavioural assessments and measures of health and stockmanship. Floor type was associated with four animal-based welfare outcomes. Reliability and validity of goat welfare indicators need to be further tested, and intervention plans and thresholds need to be determined so that advice can be tailored to the specific problems identified on each farm. We conclude that the protocol can work as a tool to identify welfare issues in dairy goat herds, and that this study may be a valuable contribution to the development of a much-needed welfare assessment protocol for dairy goats.
4‐Hydroxyphenylpyruvate Dioxygenase Inhibitors in Combination with Safeners: Solutions for Modern and Sustainable Agriculture
Authors: Ahrens Hartmut , Lange Gudrun , Müller Thomas , Rosinger Chris , Willms Lothar , van Almsick Andreas 
Published: July 2013

AbstractInhibitors of 4‐hydroxyphenylpyruvate dioxygenase (HPPD) prevent plant carotenoid pigment formation, which in turn leads to chlorophyll degradation. This “bleaching” herbicide mode of action provides weed‐control products for various crops, such as rice, corn, and cereals. Combinations with suitable safeners allow the full exploitation of the potential of this compound class to selectively control major weed problems, including rapidly increasing cases of resistance against other important herbicide classes.
Tropical cyclogenesis induced by ITCZ breakdown in association with synoptic wave train over the western North Pacific
Authors: Cao Xi , Chen Guanghua , Chen Wen 
Published: July 2013

AbstractCompared to the eastern Pacific and eastern Atlantic, tropical cyclogenesis associated with breakdown of the intertropical convergence zone (ITCZ) was less documented over the western North Pacific (WNP). A typical case in boreal summer 2006 over the WNP, in which tropical cyclogenesis is induced by ITCZ breakdown in association with synoptic‐scale wave train (SWT), is examined through observation analysis and numerical simulations. Observational analysis displays that a northwest–southeast‐oriented SWT developed and propagated northwestward several days prior to ITCZ breakdown. Furthermore, the comparisons of simulation results reveal the role of the SWT in ITCZ breakdown. On one hand, the SWT within the ITCZ region is conducive to break down the ITCZ by enhancing the potential vorticity (PV), strengthening the meridional PV gradient and producing an evident sign reversal of PV gradient. On the other hand, the anomalous anticyclonic circulation related to the SWT north of ITCZ can reduce the meridional scale of PV band and thus increase the meridional PV gradient to accelerate ITCZ breakdown.
The self‐association of the cyclotide kalata B2 in solution is guided by hydrophobic interactions
Authors: Rosengren K. Johan , Daly Norelle L. , Harvey Peta J. , Craik David J. 
Published: July 2013

ABSTRACTThe cyclotides are a family of small head‐to‐tail cyclic plant defense proteins. In addition to their cyclic backbone, cyclotides comprise three disulfide bonds in a knotted arrangement, resulting in a highly cross‐braced structure that provides exceptional chemical and proteolytic stability. A number of bioactivities have been associated with cyclotides, including insecticidal, antimicrobial, anti‐viral and cytotoxic, and these activities are related to an ability to target and disrupt biological membranes. Kalata B2 and to a lesser extent kalata B1, isolated from Oldenlandia affinis, self‐associate to tetramers and octamers in aqueous buffers, and this oligomerization has been suggested to be relevant for their ability to form pores in membranes. Here we demonstrate by solution NMR spectroscopy analysis that the oligomerization of kalata B2 is concentration dependent and that it involves the packing of hydrophobic residues normally exposed on the surface of kalata B2 into a multimeric hydrophobic core. Interestingly, the hydrophobic surface that is “quenched” has previously been shown to be responsible for the ability of kalata B2 to insert into membranes. Thus, it seems unlikely that the oligomers observed in aqueous solution are related to any multimeric state present in a membrane environment, and responsible for the formation of pores. The ability to self‐associate might alternatively provide a mechanism for preventing self‐toxicity when stored at high concentrations in intracellular compartments. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 453–460, 2013.
Regioselective Deacetylation of Disaccharides via Immobilized Aspergillus niger Esterase(s)‐catalyzed Hydrolysis in Aqueous and Non‐aqueous Media
Authors: Bavaro Teodora , Torres‐Salas Pamela , Antonioli Nicola , Morelli Carlo F. , Speranza Giovanna , Terreni Marco 
Published: July 2013

AbstractPurified lipase fractions from crude commercial extract of Aspergillus niger lipase (ANL) were selectively immobilized on hydrophobic supports. A significant percentage of esterase activity remains in the supernatant, derived from esterase(s) unable to become adsorbed onto the employed matrices. These residual proteins were covalently immobilized on epoxy‐acrylic resin. Immobilized hydrolases were tested in the hydrolysis of acetylated disaccharides in water‐cosolvent systems. ANL‐Esterase was able to catalyze regioselective deprotection of acetylated β‐O‐methyl lactoside in C‐2 position and β‐O‐methyl lactosaminide in C‐3′ position. The hydrolyzed products, never reported before, can be considered new building blocks for the synthesis of oligosaccharides of biological relevance. Furthermore, preparative hydrolyses were also performed in tert‐butanol. This solvent is compatible with ANL‐esterase stability and it appears to be a novel and promising approach because of its green status.
Diarylprolinol in an Asymmetric, Direct Cross‐Aldol Reaction with Alkynyl Aldehydes
Authors: Hayashi Yujiro , Kojima Masahiro , Yasui Yusuke , Kanda Yuta , Mukaiyama Takasuke , Shomura Hiroki , Nakamura Daichi , Ritmaleni  , Sato Itaru 
Published: July 2013

AbstractThe direct cross‐aldol reaction of alkynyl aldehydes catalyzed by a trifluoromethylated diarylprolinol provides a practical route for the highly enantioselective synthesis of chiral β‐alkynyl‐β‐hydroxy aldehydes. Good anti selectivity and excellent enantioselectivity were obtained in the reactions of silylpropynals, which afford synthetically useful chiral building blocks.
A groundwater–soil–plant–atmosphere continuum approach for modelling water stress, uptake, and hydraulic redistribution in phreatophytic vegetation
Authors: Gou Si , Miller Gretchen 
Published: July 2013

ABSTRACTModelling groundwater uptake provides a powerful tool for examining the tight linkage of phreatophytic vegetation with spatial and temporal variations in groundwater and soil moisture. Here, a physically based modelling framework was developed to simulate groundwater uptake and hydraulic redistribution (HR), as driven by the potential gradients along the groundwater–soil–plant–atmosphere continuum. A new water stress function, based on the ‘vulnerability curve’ theory, was introduced; it integrates the influence of both soil water and groundwater on transpiration. The model was then implemented using a system dynamics approach and applied to simulate groundwater uptake of Quercus douglasii (blue oak) in a California savanna. It showed good agreement with the measured evapotranspiration, soil moisture, and leaf water potential data. The model results indicated that the dominant water source for blue oaks switched from soil water in the wet season to groundwater in the dry season. During the dry period, cavitation led to a hydraulic conductivity loss of approximately 85% in the shallow roots, and groundwater uptake contributed over 80% of transpiration. The dry, shallow soil layers received water from groundwater and deep soil layers at night through HR. The new water stress function performed well when simulating daily transpiration (r2 = 0·69). The model indicated that blue oaks maintained only a small portion of deep roots (15% of the total) to uptake groundwater and mitigate the impacts of drought. The proposed model framework can be incorporated into coupled climate, hydrological, and ecological models to improve their performance when studying ecohydrological process and climate feedbacks. Copyright © 2013 John Wiley & Sons, Ltd.
An Eco‐Friendly Asymmetric Organocatalytic Conjugate Addition of Malonates to α,β‐Unsaturated Aldehydes: Application on the Synthesis of Chiral Indoles
Authors: Feu Karla Santos , Deobald Anna Maria , Narayanaperumal Senthil , Corrêa Arlene G. , Weber Paixão Márcio 
Published: July 2013

AbstractThe asymmetric Michael addition of malonates to α,β‐unsaturated aldehydes using a modified Jørgensen–Hayashi organocatalyst in EtOH:brine solvent media is reported. The procedure proceeds smoothly to afford the corresponding Michael adducts in good yields with excellent enantioselectivities. The resulting Michael adducts represent excellent building blocks for the synthesis of chiral indoles.
Assignment of Configuration in a Series of Dioxolanone‐Type Secondary Metabolites from Guignardia bidwellii – A Comparison of VCD and ECD Spectroscopy
Authors: Andernach Lars , Sandjo Louis P. , Liermann Johannes C. , Buckel Iris , Thines Eckhard , Opatz Till 
Published: July 2013

AbstractThe absolute configurations of a series of phytotoxic dioxolanone‐type secondary metabolites isolated from culture filtrates of the grape black rot fungus Guignardia bidwellii were determined by vibrational circular dichroism (VCD) spectroscopy in the mid‐IR frequency range. Comparison of the recorded data with DFT calculations showed good agreement between experiment and theory for VCD, whereas electronic circular dichroism (ECD) data for the compounds matched poorly with the predicted spectra obtained by time‐dependent DFT (TDDFT) calculations at the same level of theory.