bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational protein design as a tool for fold recognition
Authors: Schmidt am Busch Marcel , Mignon David , Simonson Thomas
Published: March 2009

Computationally designed protein sequences have been proposed as a basis to perform fold recognition and homology searching. To investigate this possibility, an automated procedure is used to completely redesign 24 SH3 proteins and 22 SH2 proteins. We use the experimental backbone coordinates as fixed templates in the folded state and a molecular mechanics model to compute the pairwise interaction energies between all sidechain types and conformations. Energy calculations are done with the Proteins@Home volunteer computing platform. A heuristic algorithm is then used to scan the sequence and conformational space for optimal solutions. We produced 200,000—450,000 sequences for each backbone template. The designed sequences ressemble moderately‐distant, natural homologues of the initial templates, according to their identity scores and their similarity with respect to the Pfam sets of SH2 and SH3 domains. Standard homology detection tools document their native‐like character: the Conserved Domain Database recognizes 61% (52%) of our low‐energy sequences as SH3 (SH2) domains; the SUPERFAMILY, Hidden‐Markov Model library recognizes 81% (84%). Conversely, position specific scoring matrices (PSSMs) derived from our designed sequences can be used to detect natural homologues in sequence databases. Within SwissProt, a set of natural SH3 PSSMs detects 772 SH3 domains, for example; our designed PSSMs detect 67% of these, plus one additional sequence and two false positives. If six amino acids involved in substrate binding (a selective pressure not accounted for in our design) are reset to their experimental types, then 77% of the experimental SH3 domains are detected. Results for the SH2 domains are similar. Several directions to improve the method further are discussed. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies
Authors: Sun Weitao , He Jing
Published: March 2009

Secondary structure topology in this article refers to the order and the direction of the secondary structures, such as helices and strands, with respect to the protein sequence. Even when the locations of the secondary structure Cα atoms are known, there are still (N!2N)(M!2M) different possible topologies for a protein withNhelices andMstrands. This work explored the question if the native topology is likely to be identified among a large set of all possible geometrically constrained topologies through an evaluation of the residue contact energy formed by the secondary structures, instead of the entire chain. We developed a contact pair specific and distance specific multiwell function based on the statistical characterization of the side chain distances of 413 proteins in the Protein Data Bank. The multiwell function has specific parameters to each of the 210 pairs of residue contacts. We illustrated a general mathematical method to extend a single well function to a multiwell function to represent the statistical data. We have performed a mutation analysis using 50 proteins to generate all the possible geometrically constrained topologies of the secondary structures. The result shows that the native topology is within the top 25% of the list ranked by the effective contact energies of the secondary structures for all the 50 proteins, and is within the top 5% for 34 proteins. As an application, the method was used to derive the structure of the skeletons from a low resolution density map that can be obtained through electron cryomicroscopy. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Identification of trypsin‐inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor
Authors: Chen Ting , Lee Tian‐Ren , Liang Wei‐Guang , Chang Wun‐Shaing Wayne , Lyu Ping‐Chiang
Published: March 2009

Human serine proteinase inhibitor Kazal‐type 2 (SPINK2) functions as a trypsin/acrosin inhibitor and is synthesized mainly in the testis and seminal vesicle where its activity is engaged in fertility. The SPINK2 protein contains a typical Kazal domain composed by six cysteine residues forming three disulfide bridges. The expression of SPINK2 is closely related to cancer such as lymphomas, in that a high transcript level of SPINK2 in patients with primary cutaneous follicle center cell lymphomas have better prognosis with lower mortality. To clarify the role of SPINK2 in cancer, we performed quantitative real‐time PCR and showed that the expression level of SPINK2 is significantly elevated in most leukemia cell lines except B‐lymphoblast TK‐6 cells. The molecular function and structural features of SPINK2 were also investigated by employing the recombinant active and mutant inactive SPINK2 proteins to determine its key P2‐P2' (Pro23‐Arg24‐His25‐Phe26) active site. The inhibition assay results demonstrated that Arg24 at the P1 site is crucial for the specificity of SPINK2 on target enzyme. Although His25 at the P1' and Phe26 at the P2' residues are also involved in trypsin‐SPINK2 interaction, Pro23 at the P2 site may not be directly participated in interacting with trypsin. In addition, we determined the 3D solution structure of SPINK2 and used this structure to predict the SPINK2‐proteinase complex structure and binding properties. These studies not only provide critical information about the structural properties and biophysical features of the SPINK2 proteinase inhibitor, but also suggest its important role in tumor progression and response to treatment. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Modular coenzyme specificity: A domain‐swopped chimera of glutamate dehydrogenase
Authors: Sharkey Michael A. , Engel Paul C.
Published: March 2009

Domain‐swopped chimeras of the glutamate dehydrogenases from Clostridium symbiosum (CsGDH) (NAD+‐specific) and Escherichia coli (EcGDH) (NADP+‐specific) have been produced, with the aim of testing the localization of determinants of coenzyme specificity. An active chimera consisting of the substrate‐binding domain (Domain I) of CsGDH and the coenzyme‐binding domain (Domain II) of EcGDH has been purified to homogeneity, and a thorough kinetic analysis has been carried out. Results indicate that selectivity for the phosphorylated coenzyme does indeed reside solely in Domain II; the chimera utilizes NAD+ at 0.8% of the rate observed with NADP+, similar to the 0.5% ratio for EcGDH. Positive cooperativity toward L‐glutamate, characteristic of CsGDH, has been retained with Domain I. An unforeseen feature of this chimera, however, is that, although glutamate cooperativity occurs only at higher pH values in the parent CsGDH, the chimeric protein shows it over the full pH range explored. Also surprising is that the chimera is capable of catalysing severalfold higher reaction rates (Vmax) in both directions than either of the parent enzymes from which it is constructed. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The behavior of clomazone in the soil environment
Authors: Gunasekara Amrith S , dela Cruz Imma Donna P , Curtis Matthew J , Claassen Victor P , Tjeerdema Ronald S
Published: March 2009

BACKGROUND: Clomazone is a herbicide used to control broadleaf weeds and grasses. Clomazone use in agriculturally important crops and forests for weed control has increased and is a potential water contaminant given its high water solubility (1100 µg mL−1). Soil sorption is an environmental fate parameter that may limit its movement to water systems. The authors used model rice and forest soils of California to test clomazone sorption affinity, capacity, desorption, interaction with soil organic matter and behavior with black carbon.

RESULTS: Sorption of clomazone to the major organic matter fraction of soil, humic acid (HA) (Kd = 29–87 L kg−1), was greater than to whole soils (Kd = 2.3–11 L kg−1). Increased isotherm non‐linearity was observed for the whole soils (N = 0.831–0.893) when compared with the humic acids (N = 0.954–0.999). Desorption isotherm results showed hysteresis, which was greatest at the lowest solution concentration of 0.067 µg mL−1 for all whole soils and HA extracts. Aliphatic carbon content appeared to contribute to increased isotherm linearity.

CONCLUSION: The results indicate that clomazone does not sorb appreciably to sandy or clay soils. Its sorption affinity and capacity is greater in humic acid, and consequently clomazone has difficulty desorbing from soil organic matter. Sorption appears to follow processes explained by the dual‐mode model, the presence of fire residues (black carbon) and a recently proposed sorption mechanism. Copyright © 2009 Society of Chemical Industry
Peptide conjugates of therapeutically used antitubercular isoniazid—design, synthesis and antimycobacterial effect
Authors: Horváti Kata , Mező Gábhor , Szabó Nóra , Hudecz Ferenc , Bősze Szilvia
Published: March 2009

Tuberculosis (TB) is a bacterial infectious disease caused by Mycobacterium tuberculosis, a slow‐growing, powerful human pathogen which can survive in the host macrophages. In the chemotherapy of such intracellular pathogens it is necessary to achieve relatively high level of the drug in blood to attain therapeutically effective concentration in infected cells, which presumably has several serious side effects on healthy tissues. The elimination of M. tuberculosis from infected phagocytes could be more efficient with target cell‐directed delivery of antituberculars. A particularly promising approach is to conjugate a drug moiety to a peptide based carrier. The conjugates are chemically constructed to target release by hydrolysis (enzymatic and/or chemical) to liberate the active compound. Here we report the synthesis, characterisation and antimycobacterial evaluation of isoniazid (INH) peptide conjugates. As carrier moiety T‐cell epitope of immundominant 16‐kDa protein of M. tuberculosis and tuftsin‐derived peptides were used. To conjugate INH two synthetic methods were developed, where INH was coupled directly to the peptides or through a heterobifunctional reagent. We found that all of the INH conjugates were effective against M. tuberculosis and the minimal inhibitory concentration (MIC) values were comparable to the free INH moiety. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Decay kinetics of the luminescence of Ag– centers doped in alkali halide crystals
Authors: Kawai Taketoshi , Akai Ichiro , Ichida Hideki , Kanematsu Yasuo , Mizoguchi Kohji , Karasawa Tsutomu
Published: March 2009

Decay kinetics of the luminescence of Ag– centers doped in NaCl, KBr, and CsBr single crystals have been investigated in the temperature range from 4 K to 260 K. At low temperature, the radiative transitions from the 1T1u states in the Ag– centers exhibit the luminescence with the decay time constants of about 1.3 ns. With increasing temperature, the decay time constants decrease, reflecting a thermally activated non‐radiative transition process from the 1T1u to 3T1u states. On the other hand, the luminescence due to the radiative transitions from the 3T1u states have the decay time constants of about 1.0 ms at low temperature and about 10 μs above 80 K. From the analysis of the temperature dependence of the decay time constants, the parameters of a three‐level model and a thermally activated non‐radiative process from the 1T1u to 3T1u states are obtained. The parameters are discussed as compared with those of other Tl+‐type centers doped in alkali halide crystals. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantifying uncertainty in estimation of hydrologic metrics for ecohydrological studies
Authors: Kennard Mark J. , Mackay Stephen J. , Pusey Bradley J. , Olden Julian D. , Marsh Nick
Published: March 2009

Hydrologic metrics have been used extensively in ecology and hydrology to summarize the characteristics of riverine flow regimes at various temporal scales but there has been limited evaluation of the sources and magnitude of uncertainty involved in their computation. Variation in bias, precision and overall accuracy of these metrics influences the ability to correctly describe flow regimes, detect meaningful differences in hydrologic characteristics through time and space, and define flow‐ecological response relationships. Here, we examine the effects of two primary factors—discharge record length and time period of record—on uncertainty in the estimation of 120 separate hydrologic metrics commonly used by researchers to describe ecologically relevant components of the hydrologic regime. Metric bias rapidly decreased and precision and overall accuracy markedly increased with increasing record length, but tended to stabilize >15 years and did not change substantially >30 years. We found a strong positive relationship between the degree of overlap of discharge record and similarity in hydrologic metrics when based on 15‐ and 30‐year discharge periods calculated within a 36‐year temporal window (1965–2000), although hydrologic metrics calculated for a given stream gauge tended to vary only within a restricted range through time. Our study provides critical guidance for selecting an appropriate record length and temporal period of record given a degree of metric bias and precision deemed acceptable by a researcher. We conclude that: (1) estimation of hydrologic metrics based on at least 15 years of discharge record is suitable for use in hydrologic analyses that aim to detect important spatial variation in hydrologic characteristics; (2) metric estimation should be based on overlapping discharge records contained within a discrete temporal window (ideally >50% overlap among records); and (3) metric uncertainty varies greatly and should be accounted for in future analyses. Copyright © 2009 John Wiley & Sons, Ltd.
Advancing STEM teaching and learning with research teams
Authors: Coppola Brian P.
Published: March 2009

An overlooked role for faculty members in advancing teaching and learning is that of the research advisor who teams with students interested in faculty careers.
The national perspective: Fostering the enhancement of STEM undergraduate education
Authors: Ramaley Judith A.
Published: March 2009

This chapter considers how best to integrate STEM education into the larger context of the undergraduate experience to address important national concerns.
Preparing STEM doctoral students for future faculty careers
Authors: Austin Ann E. , Campa Henry , Pfund Christine , Gillian‐Daniel Donald L. , Mathieu Robert , Stoddart Judith
Published: March 2009

This chapter describes programs created to improve the preparation of future STEM faculty for their roles as educators.
Climate change: Creating conditions conducive to quality STEM undergraduate education
Authors: Baldwin Roger G.
Published: March 2009

Lasting reform of STEM undergraduate education must engage stakeholders from the individual classroom and laboratory to the national policy level.
Genotoxic effects of a particular mixture of acetamiprid and α‐cypermethrin on chromosome aberration, sister chromatid exchange, and micronucleus formation in human peripheral blood lymphocytes
Authors: Kocaman Ayşe Yavuz , Topaktaş Mehmet
Published: March 2009

The genotoxic effects of a particular mixture of acetamiprid (Acm, neonicotinoid insecticide) and α‐cypermethrin (α‐cyp, pyrethroid insecticide) on human peripheral lymphocytes were examined in vitro by chromosomal aberrations (CAs), sister chromatid exchange (SCE), and micronucleus (MN) tests. The human peripheral lymphocytes were treated with 12.5 + 2.5, 15 + 5, 17.5 + 7.5, and 20 + 10 μg/mL of Acm+α‐cyp, respectively, for 24 and 48 h. The mixture of Acm+α‐cyp induced the CAs and SCEs at all concentrations and treatment times when compared with both the control and solvent control and these increases were concentration‐dependent in both treatment times. MN formation was significantly induced at 12.5 + 2.5, 15 + 5, 17.5 + 7.5, μg/mL of Acm+α‐cyp when compared with both controls although these increases were not concentration‐dependent. Binuclear cells could not be detected sufficiently in the highest concentration of the mixture (20 + 10 μg/mL) for both the 24‐ and 48‐h treatment times. Mitotic index (MI), proliferation index (PI) and nuclear division index (NDI) significantly decreased because of the cytotoxic and cytostatic effects of the mixture, at all concentrations for two treatment periods. Significant decreases in MI and PI were concentration dependent at both treatment times. The decrease in NDI was also concentration‐dependent at 48‐h treatment period. In general, Acm+α‐cyp inhibited nuclear division more than positive control, mitomycin C (MMC) and showed a higher cytostatic effect than MMC. Furthermore, in this article, the results of combined effects of Acm+α‐cyp were compared with the results of single effects of Acm or α‐cyp (Kocaman and Topaktas,2007,2009, respectively). In conclusion, the particular mixture of Acm+α‐cyp synergistically induced the genotoxicity/cytotoxicity in human peripheral blood lymphocytes. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.
FreeMobility: dynamic location computing using GIS
Authors: Ji Yiming , Sproul Gordon
Published: March 2009

This paper presents the design, implementation and evaluation of the FreeMobility localization system—a distributed system that allows access points (APs) or cellular towers to dynamically determine the location of a mobile user using only received signal strength (SS) and mobility information (direction and traveled distance) from the mobile. FreeMobility does not require special infrastructure or installation, and it is readily applicable to commodity devices like laptops, PDAs and cell phones using existing Wi‐Fi and/or cellular networks. This paper introduces mathematical methodology that dynamically predicts the location of the mobile; the paper also presents detailed analysis and experimental results that explore practical issues in implementing the system. FreeMobility was evaluated using: (1) measurements from IEEE 802.11 networks at both the University of South Carolina, Beaufort (USC Beaufort) and a residential neighborhood in Columbia, SC; and (2) online data resources from war‐driving community and other research communities. The results demonstrate that FreeMobility provides reliable location estimates, and the localization error is comparable with other existing systems. With the assistance of the geographic information system (GIS), FreeMobility does not require dense tower deployment, and it is able to provide location attributes in addition to pure coordinates from most other systems. Copyright © 2009 John Wiley & Sons, Ltd.
Preferential removal of non‐injured seeds by an omnivorous ant, Tetramorium tsushimae Emery, in the seed dispersal of Chamaesyce maculata (L.) small
Authors: Ohnishi Yoshihiro K. , Suzuki Nobuhiko
Published: March 2009

To elucidate roles of an omnivorous ant, Tetramorium tsushimae Emery, against pre‐dispersal seed consumers in the seed dispersal of Chamaesyce maculata (L.) Small, the effects of the seed injury by a stinkbug, Nysius plebeius Distat, on the seed removal by the ant and the germination rate were examined in laboratory experiments. The ants of T. tsushimae removed more frequently non‐injured seeds than injured seeds. Therefore, low removal frequency of injured seeds by T. tsushimae ants might facilitate the increase in removal frequency of non‐injured seeds, consequently leading to efficient seed dispersal of C. maculata. The germination rate of injured seeds that N. plebeius nymphs sucked was conspicuously lower than the non‐injured seeds. The germination rate of seeds that T. tsushimae ants carried out of their nest was similar to that of the non‐injured seeds. Thus, seed removal by T. tsushimae ants has hardly effects on the germination of these seeds. Therefore, the preferential removal of non‐injured seeds by T. tsushimae ants might contribute to the dispersal success of C. maculata seeds. These results might show a novel interaction between myrmecochorous plants and ants in which the assessment of seed quality by ants contributes to the reproductive success of plants.
Utilizing a Simulated Tendon to Teach Tendon Repair Technique
Authors: Ingraham J. M. , Weber R. A. , Weber R. A.
Published: March 2009

To evaluate the effectiveness of teaching core tendon repairs using a simulation model, ten surgical residents with no prior experience repairing flexor tendons were taught a four-strand cruciate repair. The residents then performed ten repairs each on a simulated tendon (a round synthetic bait worm 10 mm in diameter) while being timed and graded by a hand surgeon using a global rating scale (1 to 5). Six residents also performed a zone IV flexor tendon repair on a fresh frozen cadaver—three residents who had practiced and three other residents who had no practice on the simulated tendon. The mean initial quality score was 2.4/5.0 which improved to 4.8/5.0 by the tenth trial. There was a significant incremental improvement in mean performance from trial 1 to 10 ( p<0.0001). The mean times to complete the first and last repairs were 5.4 and 3.0 min, respectively. In the cadaver trial, there was statistically significant evidence ( p=0.05, one-sided Wilcoxon exact test) that the three residents previously trained with the simulated tendon had a higher median performance (4.4, min=4.3, max=4.8) than the three who had not been trained (1.8, min=1.7, max=2.1). The mean times to complete the repairs were 4.0 and 5.8 min, respectively. In conclusion, this inexpensive model mimics an in vivo tendon repair experience with sufficient fidelity to justify its use in training residents to perform a tendon repair.
Isolated Symmetrical Brachymetacarpia of the Thumb—Case Report
Authors: Suresh S. S. , Abraham Raju , Ravi Pullanikattil
Published: March 2009

The authors report a case of isolated symmetrical metacarpia of the first metacarpal in a 33-year-old serving soldier. The patient was totally unaware of the deformity, which was found incidentally while radiographs were done for the wrist to rule out scaphoid fracture. To the best of our knowledge, there have been no similar reports in the English literature before.
Chemical Composition and Characteristics of Commiphora wightii (Arnott) Bhandari Seed Oil
Authors: Patel B. H. , Thakore S. , Nagar Padamnabhi Shanker
Published: March 2009

The seeds of Commiphora wightii (Arnott) Bhandari contain 9.8 ± 0.7% oil. The fatty acid composition and chemical properties of the extracted oil were determined. Gas liquid chromatography of the methyl esters of the fatty acids shows the presence of 46.62% saturated fatty acids and 51.40% unsaturated fatty acids. The fatty acid composition is as follows: capric acid 3.50%, myristic acid 14.51%, palmitic acid 6.68%, stearic acid 4.70%, arachidic acid 3.18%, behenic acid 14.05%, myristoleic acid 1.34%, palmitoleic acid 12.07%, oleic acid 14.15%, eicosenoic acid 0.11%, linoleic acid 22.34% and alpha linoleic acid 1.37%.
Structure, Protein Interactions and In Vitro Protease Accessibility of Extruded and Pressurized Full‐Fat Soybean Flakes
Authors: Jung Stephanie , Mahfuz Abdullah , Maurer Devin
Published: March 2009

The objectives of the present study were to determine how extrusion (barrel temperature of 100 °C) and high‐pressure processing (HPP, 200 and 500 MPa, 15 min, 25 °C) of full‐fat soybean flakes (FFSF) modified the structure of soybean cotyledon cells, the protein interactions and the in vitro protease accessibility. Cellular disruption of the cotyledon cells was only observed for extruded FFSF. Extrusion and HPP at 500 MPa favored formation of insoluble protein aggregates, in which oil was entrapped. High pressure size exclusion chromatography (HPSEC) and extraction methods using buffers containing SDS and 2‐mercaptoethanol suggested that noncovalent interactions were the main forces in protein aggregate formation during HPP 500 MPa and extrusion. Intermolecular cross‐linking by disulfide bonding was also involved in insoluble aggregates, but at a lesser extent than noncovalent interactions. Extrusion and HPP 500‐MPa treatment enhanced the proteolytic attack, while treatment at 200 MPa had no impact. Drastic changes in the peptide profile of the extracted proteins were, however, only observed for the enzyme‐treated 500‐MPa FFSF. Optimal oil and protein extraction yields required cellular disruption of cotyledon cells and hydrolysis of protein aggregates, which were obtained with enzyme‐assisted aqueous extraction of extruded FFSF.
Intraoperative use of cone‐beam computed tomography in a cadaveric ossified cochlea model
Authors: Barker Emma , Trimble Keith , Chan Harley , Ramsden James , Nithiananthan Sajendra , James Adrian , Bachar Gideon , Daly Mike , Irish Jonathan , Siewerdsen Jeff
Published: March 2009

Objectives

To describe a cadaveric temporal bone model of labyrinthitis ossificans and investigate the utility of intraoperative cone‐beam computed tomography (CBCT) in the facilitating cochlear implantation.

Design

Cadaveric temporal bone study.

Methods

Five cadaveric heads had cement introduced into the 10 cochleas. CBCT and a conventional CT scan were compared to assess the extent of cochlear obliteration. The cement was drilled‐out (under CBCT guidance, if required) and cochlear implant electrode arrays (from 3 different manufacturers) inserted.

Results

CBCT images demonstrated temporal bone anatomy and the extent of cochlear obliteration as clearly as conventional CT in all cases. Intraoperative CBCT guided drilling and facilitated electrode placement in two of five heads (3 of 10 ears). Streak‐artifact from the electrodes of two devices partially obscured image clarity.

Conclusions

The obliterated cochlear model reproduced a disease‐ossified cochlear both radiographically and surgically. CBCT is useful for intraoperative imaging to facilitate electrode array placement in the obliterated or congenitally abnormal cochlea.
Test‐retest reliability of drug‐induced sleep endoscopy
Authors: Rodriguez‐Bruno Krista , Goldberg Andrew N. , McCulloch Charles E. , Kezirian Eric J.
Published: March 2009

Objective

To determine the test‐retest reliability of drug‐induced sleep endoscopy (DISE).

Methods

Prospective cohort study. Patients with OSA underwent two separate DISE examinations. The following outcomes were measured: a global assessment of obstruction at the palate and/or hypopharynx; the degree of obstruction at the palate and hypopharynx; and the contribution of individual structures (palate, tonsils, tongue, epiglottis, and lateral pharyngeal walls) to obstruction.

Results

Thirty‐two patients underwent two separate DISE examinations. The preoperative sleep study apnea‐hypopnea index was 40.7 ± 21.1, and the lowest oxygen saturation was 79.8 ± 17.4 percent. Point estimates for the intraclass correlation coefficient analogs related to palatal obstruction ranged from 0.41 to 0.89; related to the hypopharyngeal airway, the point estimates ranged from 0.57 to 0.84.

Conclusion

The test‐retest reliability of DISE appears good, especially in the evaluation of the hypopharyngeal airway. Larger studies can generate more precise confidence interval estimates and test the generalizability of these findings.
Trap for Women or Freedom to Choose? The Struggle over Cash for Child Care Schemes in Finland and Sweden
Authors: HIILAMO HEIKKI , KANGAS OLLI
Published: March 2009

Debates on welfare reforms have revolved around institutional inertias with the emphasis on institutions as structures. We argue that political discourses work in the same vein and create continuities constraining the array of possible policy options – political frames as carriers of institutional inertia and path dependence. The data are based on political debates on child home care in Finland and Sweden. The ‘trap for women’ frame became dominant in the Swedish discourse, while in Finland ‘freedom to choose’ has been hegemonic. According to the Swedish frame, public day care offers children the best preconditions for later development and enhances social equality, whereas in Finland care at home with all its positive characteristics was contrasted with bureaucratic institutional care. The article highlights how politicians have used these hegemonic discourses to maintain the legitimacy of certain policy options.
Popular Explanations of Poverty: A Critical Discussion of Empirical Research
Authors: LEPIANKA DOROTA , VAN OORSCHOT WIM , GELISSEN JOHN
Published: March 2009

Various authors point to the connection between public perceptions of poverty and institutionalised strategies of dealing with the poor. The way the general public perceives the poor, and especially the causes of poverty, is generally assumed to have a profound influence on the legitimacy of anti-poverty policies. Yet studies on popular perceptions of and attributions for poverty are relatively infrequent. Moreover, a considerable share of existing research appears conceptually and/or methodologically inadequate. This article provides a critical review of existing literature that is interwoven into the discussion of the two most common approaches to studying lay poverty attributions: the factor analytical approach and the forced-choice-question approach. With respect to the latter, we present an empirical analysis and interpretation of the four response categories that constitute the core of the forced-choice question included in Eurobarometer.
Second language acquisition by low-literate learners: An under-studied population
Authors: Tarone Elaine
Published: March 2009

Many adolescent and adult L2 learners in language classrooms, both in the US and other countries, have little or no alphabetic print literacy. Language teachers may turn to SLA research for assistance, yet almost all research on oral SLA has focused on educated, highly-literate learners (Bigelow & Tarone 2004; Tarone, Bigelow & Hansen 2009). The assumption seems to have been that the findings of this research hold for ALL learners, including learners with little to no literacy. However, research in cognitive and experimental psychology shows that the acquisition of grapheme–phoneme correspondence – the ability to associate a phoneme and a visual symbol – changes the way oral language is processed. The present paper shows the relevance of these findings for SLA. It summarizes a three-part study on oral L2 processing, a partial replication of previous SLA research, carried out in a population of low-literate adolescent Somali learners of L2 English. The findings confirm that alphabetic print literacy level had a significant impact on oral L2 processing. The paper concludes with a call to replicate current SLA studies and findings with populations of learners who have little or no alphabetic literacy.
Engineering spatial concepts
Authors: Micucci Daniela , Tisato Francesco , Adorni Marzia
Published: March 2009

The success of a software system strongly depends on the ability of turning a precise domain analysis into a concrete architecture. Even if the domain model relies on sound ontological bases, there is often a wide semantic gap between the conceptual model and the concrete components that should reify it. To fill the semantic gap, relevant domain concepts should be engineered by identifying the corresponding architectural abstractions, which can be realized by concrete software components. Space plays a crucial role in many application domains, but surprisingly, related architectural abstractions have not emerged yet. This paper proposes space-related abstractions derived from the application of classical software engineering principles; in particular, the information hiding principle that leads to an operational definition of space. Basic abstractions are refined to deal with architectural aspects. As the underlying software engineering principles are close to principles that underlie the definition of space ontologies, the conjecture is that the proposed space architectural abstractions might be the basis for a formalization in ontological terms.
The concepts of model in information systems engineering: a proposal for an ontology of models
Authors: Sánchez Diana M. , Cavero José María , Marcos Esperanza
Published: March 2009

Modelling is one of the most frequent tasks in the area of information systems (ISs), with models such as schemata, ontologies, patterns and architectures forming the bases for their creation. Very often, however, the difference between these types of models is not clear and causes confusion and erratic use of the terms. The aim of this paper is to clarify the concept of model through a study of some of the more common ones used in ISs. This proposal is presented through an ontology, where we show how we conceptualize models according to their role in the development of an IS: the model understood as the representation of a domain or as a reality serving as an example.
‘I cannot keep my place without being deascent’: Pauper Letters, Parish Clothing and Pragmatism in the South of England, 1750–1830
Authors: JONES PETER D.
Published: March 2009

This paper examines the issue of pauper agency under the old poor law. It relies on an examination of the ‘voice’ of paupers as it appears in a hitherto neglected source, pauper letters. The ‘face-to-face’ nature of poor relief has often been commented upon by historians, yet despite an ongoing historical preoccupation with all aspects of its administration, the question of how paupers actually interacted with, let alone were able to influence, the provision of that relief remains largely unexamined. Concentrating on requests for, or involving the issue of, clothing, this paper argues that paupers not only demonstrated a keen awareness of the imperatives underpinning relief policy in the locality, but also utilised aspects of many long-standing and powerful cultural discourses to strengthen their case for clothing relief.
The Environmental Effects of Blood Sports in Lowland England since 1750
Authors: JONES ERIC L.
Published: March 2009

This paper considers the effects of blood sports on the landscape, wildlife and farming, and assesses the implications of the topic for some matters of historical interpretation. Histories of individual sports written by practitioners are rarely candid about the environmental costs and even descriptions by professional historians tend to neglect the dynamic ecological consequences. Ritualised foxhunting supplanted more effective control and encouraged pests. Any benign consequences were incidental. Thanks to commercial money, shooting intensities held up well even during agricultural depressions. Game preservation, notably of pheasants, meant heavy pressure on birds of prey and other wild species; planting woodland was the main benign effect, although this simultaneously fostered so-called pests. Killing species that competed with game eliminated some wildlife but often proved self-defeating in the long term. Angling had mixed implications for waterside wildlife, although riverine habitats were lastingly modified when sport-fishing replaced fishing for food. Hunting and shooting meant some withdrawal of land from farming and interference with rotations: these activities reduced productivity. That the national economy could ‘afford’ to divert so many resources to elite sports contradicts the dominant view that England came up against a resources barrier.
The Dependent Poor? (Re)constructing The Lives of Individuals ‘On the Parish’ in Rural Dorset, 1800–1832
Authors: SHAVE SAMANTHA A.
Published: March 2009

Social commentators in the early decades of the nineteenth century considered the ‘poor classes’ to be a homogenous sub-group of society dependent on parish poor relief. Whilst in recent decades studies of the Old Poor Law have added much to our understandings of the complexity of poor relief practices, the concept of dependency has proved remarkably durable. This article challenges this central assumption by focusing upon the very individuals who constituted this supposedly homogenous dependent group. The relief histories of eight individuals from two cohorts who resided in the Dorset parish of Motcombe are (re)constructed and linked to demographic data to produce detailed biographies. On the basis of these biographies it is argued that even in north Dorset, where opportunities for employment and alternative forms of subsistence were few, ‘the poor’ experienced complex fluctuations of dependence on, and independence from, poor relief. It is also shown that traditional assumptions about the factors prompting relief, including the expansion of the family, did not have a uniform impact on all individuals. Such a methodology also makes it possible to explore how the parish managed to respond to the differing and similar needs of individuals. It is thus stressed that instead of following one policy for all, parish officials applied and tailored relief to suit each individual.
Uncertainty and the double dividend hypothesis
Authors: SARTZETAKIS EFTICHIOS S. , TSIGARIS PANAGIOTIS D.
Published: March 2009

This paper examines the double dividend hypothesis in the presence of labour income uncertainty. Empirical evidence shows that uncertainty over labour income is particularly significant in developing, while not negligible in developed countries. Under uncertainty, and assuming incomplete capital markets, the tax system plays a role in providing social insurance, and a green tax reform influences its effectiveness. We show that the increase in environmental tax reduces consumption risk, while the balanced budget decrease in labour income tax increases income risk. We find that the total welfare effect of a green tax reform differs substantially from the case of certainty. The critical parameters determining the existence of a second dividend are the lump-sum transfers, the relative substitutability of the two goods for leisure, and the initial tax rates relative to their optimal that determine also the response of labour supply to a change in the tax mix.
Distributions of N2O and its air‐sea fluxes in seawater along cruise tracks between 30°S–67°S and in Prydz Bay, Antarctica
Authors: Zhan Liyang , Chen Liqi
Published: March 2009

Air and surface seawater samples were taken during the 22nd Chinese National Antarctic Research Expedition, November 2005 to March 2006, and analyzed for N2O concentrations. The results show that the concentration of N2O in surface seawater increased from 8.9 ± 0.2 nM to 17.9 ± 0.3 nM along the cruise tracks southward from 30°S–67°S latitude and correlated well with sea surface temperature (SST). The saturation anomaly along the cruise tracks changed from negative (south) to positive (north) with the turning point located between 50 and 55°S latitude coincident with the location of the Subantarctic Front (SAF). Positive saturation found north of the SAF is due to the seasonal SST variation, while the undersaturation of N2O south of the SAF may be due to a combination of SST variation and intrusion of N2O‐depleted ice meltwater during summer. Air‐sea fluxes measured on the cruise tracks north of the SAF were positive, ranging between 5 and 10 μmol m−2 d−1, while fluxes south of the SAF were close to zero. N2O in the surface water of Prydz Bay was in near equilibrium with the atmosphere: the corresponding air‐sea flux was about −0.3 ± 0.8 μmol m−2 d−1, not different from zero.
Dynamics of three anomalous SST events in the Coral Sea
Authors: Schiller A. , Ridgway K. R. , Steinberg C. R. , Oke P. R.
Published: March 2009

Variability of the circulation in the Coral Sea, accompanied by large heat transport anomalies, has the potential to have detrimental impacts on underlying ecosystems, including the Great Barrier Reef. In this study we analyze the dynamics of three events, characterized by extremes in sea‐surface temperature, as simulated in an eddy‐resolving ocean reanalysis. We show that a cooling in April 1997 results from strong wind anomalies and is supported by vertical and horizontal advective heat losses. A warm event in October 1998 is attributable to a heat gain by horizontal advection. A heat budget of the mixed‐layer within a closed box shows that warm anomalies in January 2002 involve a quasi‐balance between horizontal advection and vertical entrainment with a large local heat gain through the ocean surface near‐shore that apparently caused a coral bleaching event. The dynamics of these extreme events are all quite different, with both local and remote influences.
Reconstructing annual inflows to the headwater catchments of the Murray River, Australia, using the Pacific Decadal Oscillation
Authors: McGowan Hamish A. , Marx Samuel K. , Denholm John , Soderholm Joshua , Kamber Balz S.
Published: March 2009

The Pacific Decadal Oscillation (PDO) is a major forcing of inter‐decadal to quasi‐centennial variability of the hydroclimatology of the Pacific Basin. Its effects are most pronounced in the extra‐tropical regions, while it modulates the El Niño Southern Oscillation (ENSO), the largest forcing of global inter‐annual climate variability. Palaeo‐PDO indices are now available for at least the past 500 years. Here we show that the >500 year PDO index of Shen et al. (2006) is highly correlated with inflows to the headwaters of Australia's longest river system, the Murray‐Darling. We then use the PDO to reconstruct annual inflows to the Murray River back to A.D. 1474. These show penta‐decadal and quasi‐centennial cycles of low inflows and a possible 500 year cycle of much greater inflow variability. Superimposed on this is the likely influence of recent anthropogenic global warming. We believe this may explain the exceptionally low inflows of the past decade, the lowest of the previous 529 years.
Near‐surface circulation in the South China Sea during the winter monsoon
Authors: Centurioni L. R. , Niiler P. N. , Lee D.‐K.
Published: March 2009

Original velocity measurements at 15 m depth from Surface Velocity Program drifters are used to calculate the circulation in the South China Sea during the Winter Monsoon. The Ekman currents are computed with a new method and subtracted from drifter's velocity to calculate the residual circulation, which is approximately in geostrophic balance. The Ekman flow is nearly zonal and comparable to the zonal geostrophic flow in the northern basin. The geostrophic flow is cyclonic and extends into the southern Luzon Strait. Strong jets occur south of Hainan, off Vietnam and, to the south, off peninsular Malaysia. The Vietnam jet is concentrated inshore of the 200 m isobath, with mean speeds in excess of 1 m s−1. The onshore Ekman transport and pumping velocity computed from the wind stress curl offer a qualitative explanation of the existence and behavior of such jets.
Tracking nucleation, growth, and sublimation in cirrus clouds using ARM millimeter‐wavelength radar observations
Authors: Ivanova K. , Ackerman T. P.
Published: March 2009

On the basis of a case study we outline a stochastic approach to investigate the internal structure of radiative properties of cirrus clouds and place it into the context of the state of the large‐scale atmosphere. We analyze radar reflectivity η(t) measurements obtained with the ground‐based millimeter‐wavelength radar of the Atmospheric Radiation Measurements (ARM) Program of the Department of Energy at its Southern Great Plains facility. We demonstrate that the evolution of observed non‐Gaussian, time‐dependent probability distribution functions of η(t) at each of various depths into cloud relative to cloud top is governed by the Fokker‐Planck equation with linear drift D1(x) and stochastic multiplicative noise D2(x). The former is tentatively identified with larger‐scale forcing, and the latter is identified with in‐cloud circulations and turbulence. Obtained quadratic dependence of D2(x) leads to a noise‐induced drift that presents the influence of the small‐scale noise on the slow, large‐scale deterministic processes. Obtained larger values of the noise‐induced drift for the middle 50% of cirrus versus both the upper and lower 25% is anticipated from an ice crystal growth and deposition region. We find that the probability distribution functions of the cirrus that developed above a low‐pressure system exhibit behavior at larger scales, e.g., delay times of 2 h, that is consistent with the structure of cirrus based on aircraft in situ measurements and with results from ground‐based Raman lidar studies of cirrus. In contrast, the tails of the probability distribution functions of the cirrus over high‐pressure system do not show the structure of properties that is distinctive for the cirrus above low‐pressure synoptics.
Statistical approaches to error identification for plane‐parallel retrievals of optical and microphysical properties of three‐dimensional clouds: Bayesian inference
Authors: Gabriel P. , Barker H. W. , O'Brien D. , Ferlay N. , Stephens G. L.
Published: March 2009

This paper addresses the effects of three‐dimensional (3‐D) radiative transfer on the retrieval of optical depth for inhomogeneous stratiform liquid water clouds from passive satellite imagery. A nonparametric Bayesian classifier is developed to identify locations in a scene where plane‐parallel retrievals fail to meet the requirements of a criterion that dictates a specified level of accuracy. Receiver operating characteristics are introduced that provide useful metrics that assess the quality of the error identification procedure as functions of illumination‐viewing geometry. By fixing droplet effective radii, distributions of errors for retrieved optical depth are estimated at a scale of 120 m. These estimates suggest the best performance that can be expected for optical depth retrievals when 3‐D radiative transfer cannot be ignored. The developments in this paper were made possible through the use of Monte Carlo radiative transfer simulations on stratiform clouds that were generated by a cloud system‐resolving model. Plane‐parallel retrievals employ the CloudSat optical depth retrieval algorithm.
Aerosol analysis and forecast in the European Centre for Medium‐Range Weather Forecasts Integrated Forecast System: Forward modeling
Authors: Morcrette J.‐J. , Boucher O. , Jones L. , Salmond D. , Bechtold P. , Beljaars A. , Benedetti A. , Bonet A. , Kaiser J. W. , Razinger M. , Schulz M. , Serrar S. , Simmons A. J. , Sofiev M. , Suttie M. , Tompkins A. M. , Untch A.
Published: March 2009

This paper presents the aerosol modeling now part of the ECMWF Integrated Forecasting System (IFS). It includes new prognostic variables for the mass of sea salt, dust, organic matter and black carbon, and sulphate aerosols, interactive with both the dynamics and the physics of the model. It details the various parameterizations used in the IFS to account for the presence of tropospheric aerosols. Details are given of the various formulations and data sets for the sources of the different aerosols and of the parameterizations describing their sinks. Comparisons of monthly mean and daily aerosol quantities like optical depths against satellite and surface observations are presented. The capability of the forecast model to simulate aerosol events is illustrated through comparisons of dust plume events. The ECMWF IFS provides a good description of the horizontal distribution and temporal variability of the main aerosol types. The forecast‐only model described here generally gives the total aerosol optical depth within 0.12 of the relevant observations and can therefore provide the background trajectory information for the aerosol assimilation system described in part 2 of this paper.