bluuebunny/crossref_metadata_2025 huggingface dataset:
A new method for high‐resolution characterization of hydraulic conductivity
Authors: Liu Gaisheng , Butler James J. , Bohling Geoffrey C. , Reboulet Edward , Knobbe Steve , Hyndman David W.
Published: August 2009

A new probe has been developed for high‐resolution characterization of hydraulic conductivity (K) in shallow unconsolidated formations. The probe was recently applied at the Macrodispersion Experiment (MADE) site in Mississippi where K was rapidly characterized at a resolution as fine as 0.015 m, which has not previously been possible. Eleven profiles were obtained with K varying up to 7 orders of magnitude in individual profiles. Currently, high‐resolution (0.015‐m) profiling has an upper K limit of 10 m/d; lower‐resolution (≈0.4‐m) mode is used in more permeable zones pending modifications. The probe presents a new means to help address unresolved issues of solute transport in heterogeneous systems.
Indirect observation of periodic charge polarization in silicon isolated double quantum dots
Authors: Tanner M. G. , Chapman P. , Podd G. , Williams D. A.
Published: August 2009

This paper presents a simulation-supported experimental investigation into the properties of trench isolated highly doped (nphosphorus∼2.9×1019 cm−3) n-type silicon on insulator isolated double quantum dots (IDQDs) with integrated single electron transistor (SET) for charge sensing. IDQD and SET features are successfully distinguished through the gate dependence of their dc responses at 4.2 K and through comparison with SET only devices, demonstrating controlled semiperiodic charge polarization in silicon IDQDs over a large gate range. Simulation of the observed SET-IDQD electronic response is quantitatively matched to the experiment, giving insight into the device coupling. A dynamic mechanism of charge sensing in the SET is proposed, supported by simulation. The controllable potential structure is suitable for quantum information processing.
Subwavelength focusing of terahertz/far-infrared radiation via phonon-polariton resonance in polar salt antenna structures
Authors: Chien Wei-Yin , Szkopek Thomas
Published: August 2009

We calculate the terahertz/far-infrared focusing properties of polar salt antennas exploiting the sharp optical-phonon resonances in polar salts. We report a fundamental formula for the quality factor of local surface phonon-polariton modes in the electrostatic limit, wherein the frequency of the mode alone determines the quality factor. We consider the resonance properties of both cylindrical polar salt antennas and antennas composed of self-similar assemblies of micro/nanospheres. The deepest subwavelength antenna operation is found to occur at the high frequency end of the reststrahlen band where the dielectric function approaches −1. Through numerical simulations, we predict local electric field enhancements as high as 800 in self-similar GaP λ0/8 antenna structures.
Resistance switching effect in Nb-doped SrTiO3 (100) bicrystal with (100) ∼45° twist boundary
Authors: Hirose Sakyo , Nishimura Hitoshi , Niimi Hideaki
Published: August 2009

We have fabricated Nb-doped SrTiO3 bicrystals with (100) ∼45° twist boundary by changing the fabricating conditions and demonstrated that they can exhibit a large resistance switching effect. Nb:SrTiO3 bicrystals cooled at the rate of −300 K/h show an asymmetric large hysteresis in current-voltage characteristics and the magnitude of resistance change attains two orders of magnitude. The resistance state can also be switched by the application of voltage pulses with different polarity and both states can be memorized for over 5 h at room temperature. From experimental results, it can be speculated that the twist boundary could be an origin of large resistance switching and memory effects and it behaves like an electrode interface in SrRuO3/Nb:SrTiO3 Schottky junction devices.
Comparative study of thermally grown oxides on n-type free standing 3C-SiC (001)
Authors: Esteve R. , Schöner A. , Reshanov S. A. , Zetterling C.-M. , Nagasawa H.
Published: August 2009

Alternative ways to improve the oxidation process of free standing 3C-SiC (001) are developed and tested with the aim to reduce the fixed and mobile charges in the oxide and at the SiO2/3C-SiC interface. The postoxidation annealing step in wet oxygen (O2+H2) is demonstrated to be beneficial for n-type 3C-SiC metal-oxide-semiconductor capacitors resulting in significant reduction in flat band voltage shift, effective oxide charge density, and density of interface traps. The inefficiency of nitridation for the improvement of the oxide quality on 3C-SiC is discussed.
Thermionic emission energy distribution from nanocrystalline diamond films for direct thermal-electrical energy conversion applications
Authors: Uppireddi Kishore , Westover Tyler L. , Fisher Timothy S. , Weiner Brad R. , Morell Gerardo
Published: August 2009

In the ongoing quest for energy production by nonconventional methods, energy conversion by vacuum and solid-state thermionic emission devices is one of the potentially efficient pathways for converting thermal energy directly into electrical power. The realization of practical of thermionic energy conversion devices strongly depends on achieving low work function materials, which is thus far a limiting factor. In an attempt to develop a new low work function thermionic material, this work reports thermionic emission energy distributions (TEEDs) from nanocrystalline diamond (NCD) films in the temperature range from 700 to 900 °C that reveal a consistent effective work function of 3.3 eV. The NCD films also exhibit emission peaks corresponding to higher work functions as indicated by shifts in their energy position and relative intensity as a function of temperature. These shifts thus appear to be related to instabilities in the NCD’s surface chemistry. The analysis of these data yields information on the origin of the low effective work function of NCD.
Entrapment of magnetic microcrystals for on-chip electron spin resonance studies
Authors: Groll N. , Bertaina S. , Pati M. , Dalal N. S. , Chiorescu I.
Published: August 2009

On-chip electron spin resonance (ESR) of magnetic molecules requires the ability to precisely position nanosized samples in antinodes of the electromagnetic field for maximal magnetic interaction. A method is developed to entrap microcrystals containing spins in a well defined location on a substrate’s surface. Traditional cavity ESR measurements are then performed on a mesoscopic crystal at 34 GHz. Polycrystalline diluted Cr5+ spins are entrapped as well and measured while approaching the lower limit of the ESR sensitivity. This method suggests the feasibility of on-chip ESR measurements at dilution refrigerator temperatures by enabling the positioning of samples atop an on-chip superconducting cavity.
Thermodynamic and structural properties of finely discretized on-lattice hard-sphere fluids: Virial coefficients, free energies, and direct correlation functions
Authors: Siderius Daniel W. , Gelb Lev D.
Published: August 2009

Using both molecular simulation and theory, we examine fluid-phase thermodynamic and structural properties of on-lattice hard-sphere fluids. Our purpose in this work is to provide reference data for on-lattice density functional theories [D. W. Siderius and L. D. Gelb, Langmuir 25, 1296 (2009)] and related perturbation theories. In this model, hard spheres are located at sites on a finely discretized cubic lattice where the spacing between lattice sites is between one-tenth and one-third the hard-sphere diameter. We calculate exactly the second, third, and fourth virial coefficients as functions of the lattice spacing. Via Monte Carlo simulation, we measure the excess chemical potential as a function of density for several lattice spacings. These results are then parametrized with a convenient functional form and can immediately be used in on-lattice density functional theories. Of particular interest is to identify those lattice spacings that yield properties similar to those of the off-lattice fluid. We find that the properties of the on-lattice fluid are strongly dependent on lattice spacing, generally approaching those of the off-lattice fluid with increasing lattice resolution, but not smoothly. These observations are consistent with results for larger lattice spacings [A. Z. Panagiotopoulos, J. Chem. Phys. 123, 104504 (2005)]. Certain lattice spacings are found to yield fluid properties in particularly good agreement with the off-lattice fluid. We also find that the agreement of many different on- and off-lattice hard-sphere fluid properties is predicted quite well by that of the virial coefficients, suggesting that they may be used to identify favorable lattice spacings. The direct correlation function at a few lattice spacings and a single density is obtained from simulation. The on-lattice fluid is structurally anisotropic, exhibiting spherical asymmetry in correlation functions. Interestingly, the anisotropies are properly captured in the Percus–Yevick-based calculation of the direct correlation function. Lastly, we speculate on the possibility of obtaining a theoretical equation of state of the on-lattice hard-sphere fluid computed in the Percus–Yevick approximation.
Enhanced plasticity in a Zr-based bulk metallic glass composite with in situ formed intermetallic phases
Authors: Chen G. , Bei H. , Cao Y. , Gali A. , Liu C. T. , George E. P.
Published: August 2009

An in situ formed intermetallic phase/bulk metallic glass composite with high strength and good plasticity was fabricated by casting Zr55.0Cu29.0Ni8.0Al8.0 melts. In situ formed tetragonal structured (Zr,Ni,Al)2(Cu,Ni,Al) intermetallic particles with a hardness of 9.6±0.3 GPa improve the fracture strength of the composite. Micrographs of the fractured samples reveal that the shear band spacing is smaller than the intermetallic particles, indicating that they can effectively block shear band propagation before catastrophic fracture.
Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency
Authors: Makarov Dmitrii E. , Plaxco Kevin W.
Published: August 2009

Recent years have seen a number of investigations in which distances within unfolded proteins, polypeptides, and other biopolymers are probed via fluorescence resonance energy transfer, a method that relies on the strong distance dependence of energy transfer between a pair of dyes attached to the molecule of interest. In order to interpret the results of such experiments it is commonly assumed that intramolecular diffusion is negligible during the excited state lifetime. Here we explore the conditions under which this “frozen chain” approximation fails, leading to significantly underestimated donor-acceptor distances, and describe a means of correcting for polymer dynamics in order to estimate these distances more accurately.
An in-plane, variable optical attenuator using a fluid-based tunable reflective interface
Authors: Lapsley Michael Ian , Lin Sz-Chin Steven , Mao Xiaole , Huang Tony Jun
Published: August 2009

We introduce an optofluidic based variable optical attenuator with high stability, high reliability, simple and inexpensive fabrication, and an attenuation performance comparable to commercial devices. A standard soft lithography process produces a single-layered polydimethylsiloxane (PDMS) microfluidic device integrated with optical fibers. By altering the refractive index of the fluid within the microchannel, we can control the reflectivity of the fluid/PDMS interface and thus achieve variable attenuation. Theoretical calculations are conducted based on Snell’s law of refraction and the Fresnel equations of reflection, and the calculated attenuation response matches well with experimental data.
Local bonding effect on the defect states of oxygen vacancy in amorphous HfSiO4
Authors: Noh Hyeon-Kyun , Ryu Byungki , Choi Eun-Ae , Bang Junhyeok , Chang K. J.
Published: August 2009

We perform first-principles calculations to investigate the defect properties of O vacancies in amorphous HfSiO4. For atomic models generated from molecular dynamics simulations, we find that O vacancies, which have only Hf atoms or a mixture of Hf and Si in the neighborhood, behave as charge trap centers, similar to those in HfO2. On the other hand, O vacancies surrounded by only Si atoms are energetically most favorable and have very high trap energies for both electron and hole carriers. Thus, these defects are suggested to be responsible for the reduction of threshold voltage instability.
Rate equation analysis of efficiency droop in InGaN light-emitting diodes
Authors: Ryu Han-Youl , Kim Hyun-Sung , Shim Jong-In
Published: August 2009

Efficiency droop in InGaN light-emitting diodes (LEDs) is analyzed based on the rate equation model. By using the peak point of the efficiency versus current-density relation as the parameters of the rate equation analysis, internal quantum efficiency and each recombination current at arbitrary current density can be unambiguously determined without any knowledge of A, B, and C coefficients. The theoretical analysis is compared with measured efficiency of a LED sample and good agreement between the model and experiment is found. The investigation of recombination coefficients shows that Auger recombination alone is not sufficient to explain the efficiency droop of InGaN LEDs.
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
Authors: Fei Jingyi , Bronson Jonathan E. , Hofman Jake M. , Srinivas Rathi L. , Wiggins Chris H. , Gonzalez Ruben L.
Published: August 2009

Determining the mechanism by which tRNAs rapidly and precisely transit through the ribosomal A, P, and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics of the L1 stalk, a structural element of the large ribosomal subunit that is implicated in directing tRNA movements during translation. Within pretranslocation ribosomal complexes, the L1 stalk exists in a dynamic equilibrium between open and closed conformations. Binding of elongation factor G (EF-G) shifts this equilibrium toward the closed conformation through one of at least two distinct kinetic mechanisms, where the identity of the P-site tRNA dictates the kinetic route that is taken. Within posttranslocation complexes, L1 stalk dynamics are dependent on the presence and identity of the E-site tRNA. Collectively, our data demonstrate that EF-G and the L1 stalk allosterically collaborate to direct tRNA translocation from the P to the E sites, and suggest a model for the release of E-site tRNA.
Quantifying superstrate and substrate influence
Authors: Holm John , Intumbo Incanha
Published: August 2009

To quantify the degree to which the structure of superstrate and substrate languages influence that of a creole, this paper compares the nearly 100 grammatical features of Guiné-Bissau Creole Portuguese surveyed in Baptista, Mello, & Suzuki (2007) with the corresponding structures in Balanta (one of the creole’s substrate/adstrate languages) and Portuguese (its superstrate), proceeding from one area of syntax to another. However, tables summarizing the presence or absence of features in each of the three languages are not organized by area of syntax but rather by the patterns of the features’ presence or absence in the three languages, allowing a quantification of the various patterns of influence, e.g. the percentage of cases in which a feature is found in the creole only, in the creole and its superstrate only, in the creole and its substrate only, or in all three. These percentages are then discussed regarding what support they might lend to the various hypotheses purporting to explain the sources of creole language structures: the influence of superstrate and substrate languages, universals, creole-internal innovations, and the convergence of all or some of these. The issue of Balanta being both a substrate and an adstrate language with many speakers bilingual in the creole is also discussed, as is the dated bias in the very grammatical categories chosen for the survey, which assumes an Atlantic creole prototype based on ‘Kwa’ rather than West Atlantic languages, the Niger-Congo subfamily to which Balanta belongs.
Developmental trajectories in mastery of paragraphing
Authors: Myhill Debra
Published: August 2009

Learning to write paragraphs and thus learning how to sub-divide a text for topical and organisational coherence is an accepted part of acquiring writing maturity, and most teachers of writing will include explicit teaching of paragraphing techniques within their writing instruction classes. However, there is relatively little pedagogical or empirical attention devoted to understanding the nature of development in paragraphing — how writers increase in sophistication in managing paragraphs, and the pathways of development from not using paragraphs to secure mastery. The study reported here, therefore, set out to answer the research question — what developmental trajectories are evident in mastering paragraphing in secondary-aged writers? The article draws on a detailed linguistic analysis of a corpus of writing samples from 359 students stratified by age (13 or 15) and gender and posits a model of development in which the trajectory is from graphical organisation through to topical organisation and finally to textual organisation. However, the trajectory is not simply linear as the demands of longer, more complex texts create new challenges in paragraph organisation for able writers.
Literacy predictors and early reading and spelling skills as a factor of orthography
Authors: Zaretsky Elena , Kraljevic Jelena Kuvac , Core Cynthia , Lencek Mirjana
Published: August 2009

The majority view of reading development maintains the importance of specific cognitive and linguistic abilities, e.g. phonological awareness (PA) and vocabulary and verbal working memory (VWM). Another factor in attaining literacy may be the language of exposure, e.g. whether it has a transparent or a deep orthography. This study examines the interaction between known predictors for literacy development and the orthography. It focuses on early levels of literacy (decoding and spelling) amongst children with typical language development. English-speaking (deep orthography) and Croatian-speaking (transparent orthography) kindergarteners were assessed on measures of vocabulary, PA, functions of verbal working memory, and early literacy skills at the beginning of the kindergarten year. The results indicate that a transparent orthography (Croatian) increases early decoding and encoding skills and they show expected correlations between PA, vocabulary, and early literacy abilities. English speakers did not show these correlations at the onset of the kindergarten year. We postulate that the nature of the deep orthography requires some instructional time for English-speaking children before PA and vocabulary will show predictive validity for reading acquisition.
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Authors: Keller Andreas , Backes Christina , Gerasch Andreas , Kaufmann Michael , Kohlbacher Oliver , Meese Eckart , Lenhof Hans-Peter
Published: August 2009

Motivation: Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for studying the activity of the signaling cascades and for understanding the information flow in the networks.

Results: We present a novel dynamic programming algorithm for detecting deregulated signaling cascades. The so-called FiDePa (Finding Deregulated Paths) algorithm interprets differences in the expression profiles of tumor and normal tissues. It relies on the well-known gene set enrichment analysis (GSEA) and efficiently detects all paths in a given regulatory or signaling network that are significantly enriched with differentially expressed genes or proteins. Since our algorithm allows for comparing a single tumor expression profile with the control group, it facilitates the detection of specific regulatory features of a tumor that may help to optimize tumor therapy. To demonstrate the capabilities of our algorithm, we analyzed a glioma expression dataset with respect to a directed graph that combined the regulatory networks of the KEGG and TRANSPATH database. The resulting glioma consensus network that encompasses all detected deregulated paths contained many genes and pathways that are known to be key players in glioma or cancer-related pathogenic processes. Moreover, we were able to correlate clinically relevant features like necrosis or metastasis with the detected paths.

Availability: C++ source code is freely available, BiNA can be downloaded from http://www.bnplusplus.org/.

Contact:  ack@bioinf.uni-sb.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
UniMaP: finding unique mass and peptide signatures in the human proteome
Authors: Alexandridou Anastasia , Tsangaris George Th. , Vougas Konstantinos , Nikita Konstantina , Spyrou George
Published: August 2009

Summary: The uniqueness of a measured molecular mass or peptide sequence plays a very important role in the fields of protein identification and peptide/protein-biomarker investigation. We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. These unique tags are remarkably important in research related to protein identification or biomarker discovery and measurements.

Availability: UniMaP web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/

Contact:  gspyrou@bioacademy.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Spatial discrimination reversal learning in weanling rats is impaired by striatal administration of an NMDA-receptor antagonist
Authors: Watson Deborah J. , Stanton Mark E.
Published: August 2009

The striatum plays a major role in both motor control and learning and memory, including executive function and “behavioral flexibility.” Lesion, temporary inactivation, and infusion of an N-methyl-d-aspartate (NMDA)-receptor antagonist into the dorsomedial striatum (dmSTR) impair reversal learning in adult rats. Systemic administration of MK-801 disrupts reversal learning in developing rats, as reported in an earlier work by Chadman et al., but it is not known whether NMDA-receptor function within the dmSTR plays a role in this effect. In Experiment 1, reversal learning was dose-dependently impaired following bilateral dmSTR administration of MK-801 (either 2.5 or 5.0 μg) only during the reversal phase relative to saline in postnatal day (P) 26 rats. In Experiment 2, separate groups of P26 rats were trained on the same reversal learning task, but were administered bilateral dmSTR infusions during acquisition only (MK–SAL), reversal only (SAL–MK), both phases (MK–MK), or neither phase (SAL–SAL). The MK-801 effect was specific to the reversal training phase. The drug did not alter acquisition of the initial discrimination. Analysis of the pattern of errors indicates that dmSTR MK-801 treatment increased perseveration of the choice response trained in acquisition. NMDA receptors in the dmSTR play a role in reversal learning in the weanling rat.
The APP-interacting protein FE65 is required for hippocampus-dependent learning and long-term potentiation
Authors: Wang Yan , Zhang Ming , Moon Changjong , Hu Qubai , Wang Baiping , Martin George , Sun Zhongsheng , Wang Hongbing
Published: August 2009

FE65 is expressed predominantly in the brain and interacts with the C-terminal domain of β-amyloid precursor protein (APP). We examined hippocampus-dependent memory and in vivo long-term potentiation (LTP) at the CA1 synapses with isoform-specific FE65 knockout (p97FE65−/−) mice. When examined using the Morris water maze, p97FE65−/− mice were impaired for the hidden platform task but showed normal performance in the probe test. To further discriminate the role of FE65 in acquisition and memory consolidation, we examined p97FE65−/− mice with temporal dissociative passive avoidance (TDPA) and contextual fear conditioning (CFC). p97FE65−/− mice showed impaired short-term memory for both TDPA and CFC when tested 10 min after training. After multiple TDPA training sessions, the crossover latency of some p97FE65−/− mice reached the cutoff value, but it significantly decayed in 8 d. At the Schaffer collateral-CA1 synapses, p97FE65−/− mice showed defective early-phase LTP (E-LTP). These results demonstrate novel roles of FE65 in synaptic plasticity, acquisition, and retention for certain forms of memory formation.
Concerns regarding the use of amphibians as metrics of critical biological thresholds: a comment on Welsh & Hodgson (2008)
Authors: KROLL ANDREW J. , HAYES MARC P. , MACCRACKEN JAMES G.
Published: August 2009

1. Welsh & Hodgson (2008)argued that stream‐associated amphibians (Ascaphus truei,Dicamptodon tenebrosusandRhyacotriton variegatus) are reliable indicators of ecosystem health in the Pacific Northwest (PNW), U.S.A. We demonstrate that their assertions rely on circular reasoning as well as logical and empirical assumptions that have not received rigorous evaluation.

2. Welsh & Hodgson (2008)based their arguments on data collected in northwestern California, U.S.A. However, all three taxa occur across a wide range of environmental gradients in the PNW, and other research results suggest that the taxa respond differentially to environmental perturbations across their geographical distribution. Hence, differences in abundance are not always reliable indicators of the state of an ecosystem, as population numbers can be influenced by factors that may not be associated with habitat quality (e.g. predation and disease).

3. Welsh & Hodgson (2008)present indices (rather than estimates) of abundance, which contain an unquantifiable amount of uncertainty not reliably attributable to either environmental or management factors. Evaluating parameters such as reproductive success and survival are more likely to provide strong inference about factors influencing population size than correlative studies that associate some measure of relative abundance with individual habitat features.

4. We argue that direct measurement of physical features (water temperature, sediment and wood), for whichWelsh & Hodgson (2008)suggest using amphibians as surrogates, is more accurate, efficient and cost effective compared with monitoring cryptic species with methods that are unable to quantify spatial and temporal uncertainty in biological responses.

5. Headwater streams are critical components of catchments in the PNW, and all three amphibian taxa show strong associations with low‐order streams. However, we think research and monitoring of headwater streams should be guided by hypotheses that evaluate causal mechanisms, rather than relying on descriptive patterns that are limited in geographical scope and which support only weak inference about ecosystem processes. Other studies provide direct links between physical features and responses of target populations (i.e. fish). Adding a second correlative link (i.e. amphibians) provides no added benefit, and increases uncertainty in the association between management actions and changes in population size.
Ecological and socio‐economic impacts of invasive water hyacinth (Eichhornia crassipes): a review
Authors: VILLAMAGNA A. M. , MURPHY B. R.
Published: August 2009

1. Water hyacinth (Eichhornia crassipes) is one of the world’s most invasive aquatic plants and is known to cause significant ecological and socio‐economic effects.

2. Water hyacinth can alter water clarity and decrease phytoplankton production, dissolved oxygen, nitrogen, phosphorous, heavy metals and concentrations of other contaminants.

3. The effects of water hyacinth on ecological communities appear to be largely nonlinear. Abundance and diversity of aquatic invertebrates generally increase in response to increased habitat heterogeneity and structural complexity provided by water hyacinth but decrease due to decreased phytoplankton (food) availability.

4. Effects of water hyacinth on fish are largely dependent on original community composition and food‐web structure. A more diverse and abundant epiphytic invertebrate community may increase fish abundance and diversity, but a decrease in phytoplankton may decrease dissolved oxygen concentrations and planktivorous fish abundance, subsequently affecting higher trophic levels.

5. Little is known about the effects of water hyacinth on waterbird communities; however, increases in macroinvertebrate and fish abundance and diversity suggest a potentially positive interaction with waterbirds when water hyacinth is at moderate density.

6. The socio‐economic effects of water hyacinth are dependent on the extent of the invasion, the uses of the impacted waterbody, control methods and the response to control efforts. Ecosystem‐level research programmes that simultaneously monitor the effects of water hyacinth on multiple trophic‐levels are needed to further our understanding of invasive species.
Inversion of controlled‐source electromagnetic data using a model‐based approach
Authors: Li Maokun , Abubakar Aria , Habashy Tarek M. , Zhang Yan
Published: August 2009

A two‐and‐half dimensional model‐based inversion algorithm for the reconstruction of geometry and conductivity of unknown regions using marine controlled‐source electromagnetic (CSEM) data is presented. In the model‐based inversion, the inversion domain is described by the so‐called regional conductivity model and both geometry and material parameters associated with this model are reconstructed in the inversion process. This method has the advantage of using a priori information such as the background conductivity distribution, structural information extracted from seismic and/or gravity measurements, and/or inversion results a priori derived from a pixel‐based inversion method. By incorporating this a priori information, the number of unknown parameters to be retrieved becomes significantly reduced. The inversion method is the regularized Gauss‐Newton minimization scheme. The robustness of the inversion is enhanced by adopting nonlinear constraints and applying a quadratic line search algorithm to the optimization process. We also introduce the adjoint formulation to calculate the Jacobian matrix with respect to the geometrical parameters. The model‐based inversion method is validated by using several numerical examples including the inversion of the Troll field data. These results show that the model‐based inversion method can quantitatively reconstruct the shapes and conductivities of reservoirs.
Thrombin generation testing in haemophilia comprehensive care centres
Authors: DARGAUD Y. , NEGRIER C.
Published: August 2009

Summary.  Haemophilia comprehensive care centres (HCCC) were first created more than 50 years ago. Their first objective was educating the patient and healthcare professionals in the management of bleeding. Today HCCCs are centres of excellence with multidisciplinary specialists, which continue to provide essential services that are continually reassessed in light of new scientific information. In addition, HCCCs make significant research contributions by studying new methods to improve the well‐being of patients with haemophilia. Laboratory expertise is one of the central pillars of HCCCs with a direct impact on diagnosis and management of the haemophilia disease. Vast efforts have been made for the standardization of factor VIII (FVIII) and FIX measurements and inhibitor detection. Molecular biology has improved diagnostics and made it possible to develop new, more secure FVIII and FIX concentrates for replacement therapy. However, phenotyping of each haemophilia patient with an accurate prediction of the individual bleeding risk and also the individual response of patients to antihaemophilic treatment still remains a challenge. In the last 5 years, an expanding interest of haematologists for thrombin generation testing (TGT) reflects the need for new laboratory tools able to evaluate the overall coagulating capacity of patients. This study will review unmet laboratory needs in haemophilia and the potential applications of TGT in the management of haemophiliacs. Furthermore, technical and standardization issues of the method will be discussed.
Differences in genetic instability and cellular phenotype among Barrett’s, cardiac, and gastric intestinal metaplasia in a Japanese population with Helicobacter pylori
Authors: Watari Jiro , Moriichi Kentaro , Tanabe Hiroki , Sato Ryu , Fujiya Mikihiro , Miwa Hiroto , Das Kiron M , Kohgo Yutaka
Published: August 2009

Aims:  Intestinal metaplasia is considered to be a precursor lesion in both Barrett’s and intestinal‐type gastric cancer. The aim was to clarify the differences in molecular pathology between specialized intestinal metaplasia (SIM) in Barrett’s oesophagus (BO), cardiac (CIM) and gastric intestinal metaplasia (GIM).

Methods and results:  Eighty‐eight SIM cases with BO, 30 CIM cases and 52 GIM cases in patients with or without Helicobacter pylori infectionwere analysed for genetic instability and Das‐1. Microsatellite instability and a loss of heterozygosity were evaluated at five microsatellite loci. The incidence of genetic instability was 55.7% in SIM, 40.0% in CIM and 23.1% in GIM, revealing a significant difference between SIM and GIM (P < 0.0005). For each microsatellite marker analysed, there were obvious differences in frequency among the three conditions. Das‐1 reactivity was significantly higher in SIM than in CIM or GIM (P < 0.0001, both). Interestingly, both genetic instability and Das‐1 reactivity in SIM showed a significantly higher incidence in patients with H. pylori infection than in those without (P < 0.005 and P < 0.01, respectively).

Conclusions:  SIM is distinct from CIM and GIM, and the pathogenesis of SIM, like that of GIM, is associated to some degree with H. pylori infection in a Japanese population.
Intraductal tubular adenoma (pyloric gland‐type) of the pancreas: a reappraisal and possible relationship with gastric‐type intraductal papillary mucinous neoplasm
Authors: Chetty Runjan , Serra Stefano
Published: August 2009

Aims:  Intraductal tubular adenoma (ITA) is an uncommon intraluminal polypoid lesion that occurs in the main pancreatic duct and involves the main pancreatic duct in the region of head or body. Three cases of ITA are presented, the literature reviewed and their association with intraductal papillary mucinous neoplasm (IPMN) is postulated.

Methods and results:  ITA is composed of tightly packed tubular structures with focal cystic dilation and papillary areas lined by gastric/pyloric epithelium showing minimal to mild cytological atypia. Pancreatic intraepithelial neoplasia (PanIN) 1A and B was present in smaller ducts of all cases. In addition, in the cases in this report and 50% of cases reported in the literature, an associated gastric‐type IPMN was present in the same duct as the ITA or in adjacent ducts. The coexistence of ITA and IPMN and the similarities of their epithelial lining (gastric/pyloric mucosa) suggest a possible pathogenic link.

Conclusions:  ITA can occur without (type A) or with (type B) an associated gastric‐type IPMN. ITA could represent a localized, polypoid form of gastric‐type IPMN.It is a benign lesion with no evidence of invasion and no direct tumour‐related deaths. Its relationship to intraductal tubular carcinoma remains to be elucidated.
Evolutionary ecology of human birth sex ratio under the compound influence of climate change, famine, economic crises and wars
Authors: Helle Samuli , Helama Samuli , Lertola Kalle
Published: August 2009

1.  Human sex ratio at birth at the population level has been suggested to vary according to exogenous stressors such as wars, ambient temperature, ecological disasters and economic crises, but their relative effects on birth sex ratio have not been investigated. It also remains unclear whether such associations represent environmental forcing or adaptive parental response, as parents may produce the sex that has better survival prospects and fitness in a given environmental challenge.

2.  We examined the simultaneous role of wars, famine, ambient temperature, economic development and total mortality rate on the annual variation of offspring birth sex ratio and whether this variation, in turn, was related to sex‐specific infant mortality rate in Finland during 1865–2003.

3.  Our findings show an increased excess of male births during the World War II and during warm years. Instead, economic development, famine, short‐lasting Finnish civil war and total mortality rate were not related to birth sex ratio. Moreover, we found no association between annual birth sex ratio and sex‐biased infant mortality rate among the concurrent cohort.

4.  Our results propose that some exogenous challenges like ambient temperature and war can skew human birth sex ratio and that these deviations likely represent environmental forcing rather than adaptive parental response to such challenges.
Blood surveillance and detection on platelet bacterial contamination associated with septic events
Authors: Hsueh J. C. , Ho C. F. , Chang S. H. , Pan F. Z. , Chen S. C. , Shi M. D. , Chien S. T.
Published: August 2009

summary.

The objective of this study was to evaluate the risk of transfusion‐associated septic events in Taiwan. In Taiwan, most blood components are provided from blood centres; so platelet (PLT) bacterial contaminations are rarely reported. The study's aim is to investigate the prevalence of PLT bacterial contamination in Kaoshiung Armed Forces General Hospital by using BacT/ALERT system for routine screening.

A total of 82 apheresis and 2256 whole blood‐derived PLT units were tested. A measured quantity of 1 mL aliquots were taken as samplings from all blood bag tubing of PLT units, and then further incubated in a bacterial detection system (BacT/ALERT). The subcultures of true‐positive bottles underwent bacterial identification by using Vitek system, microscopic observation and culture‐based methods. Eight units (0·34%, 8 of 2338) were found to have bacterial contamination. The true‐positive rate of the whole blood‐derived and apheresis PLTs was 0·31% (7 of 2256) and 1·22% (1 of 82), respectively. Six microorganisms were identified with the most dominate being Staphylococcus epidermidis. One case of transfusion‐associated sepsis was confirmed; in addition, the holding period of PLTs (F = 4·522, P = 0·034) and positive detection of PLT bacterial contamination (F = 46·605,P < 0·001) were associated with post‐transfusion sepsis. Thus, in this study, although the transfusion‐associated septic event was rarely found and PLT units were provided from blood centres, bacterial screening was necessary to safely quarantine the transfusion. The holding period of PLT units should be no more than 4 days in order to avoid possible bacterial contamination.
Patient involvement in assessing consultation quality: a quantitative study of the Patient Enablement Instrument in Poland
Authors: Pawlikowska Teresa R.B. , Walker Jeremy J. , Nowak Pawel R. , Szumilo‐Grzesik Wieslawa
Published: August 2009

Background  Promoting a more patient‐responsive service has been the focus of policy initiatives in newer EU states. One measure of success should be the patient’s assessment of their consultation with their doctor.

Objectives  To measure consultation quality in Polish primary care using patient enablement (a patient‐driven instrument developed in the UK) and to test its theoretical framework. To compare the patient enablement outcome of different types of doctor delivering primary care in Poland following reform.

Design  Cross‐sectional quantitative questionnaire survey.

Setting  Random sample of primary care doctors practising within a 60‐km radius of Gdansk, Poland.

Subjects and outcome measures  Patient Enablement Instrument and correlates were measured in 7924 consecutive adult consultations of 48 doctors, stratified according to training: family medicine specialists (diploma holders), non‐diplomates and general medicine doctors (polyclinic internists).

Results  Completion was high (78%). The mean patient enablement score in Poland was 4.0 (SD 3.3) and mean consultation length was 10.3 min (SD 5.4 min). Consultation length and knowing the doctor are independently related to patient enablement in the Polish context. Variation between doctors is significant, but earlier differences in enablement between alternative providers have largely been ameliorated in practice.

Conclusion  It is feasible to use patient enablement on a large scale at routine consultation in primary care in Poland: acceptability was good in diverse environments. The internal consistency of enablement and its relationships broadly mirror those found in the UK. The effect of patient expectations shaped by social and cultural issues influencing enablement outcome requires further investigation.
The longitudinal course of cognition in older adults with bipolar disorder
Authors: Gildengers Ariel G , Mulsant Benoit H , Begley Amy , Mazumdar Sati , Hyams Adriana V , Reynolds III Charles F , Kupfer David J , Butters Meryl A
Published: August 2009

Objectives:  Epidemiological studies suggest that elders with bipolar disorder (BD) may be at increased risk for dementia compared to the general population. We sought to investigate whether older adults with BD would present with more cognitive dysfunction than expected for their age and education, and whether they would experience a more rapid cognitive decline over three‐year prospective follow‐up.

Methods:  Thirty‐three subjects age ≥ 50, mean (SD) age 69.7 (7.9) years, with BD I (n = 28) and II (n = 5) had neuropsychological examination at baseline and longitudinally over three years. All subjects were administered the Dementia Rating Scale (DRS) when euthymic. Thirty‐six mentally healthy comparators (‘controls’), equated on age and education, were selected from ongoing studies in our research center examining the longitudinal relationship between late‐life mood disorders and cognitive function.

Results:  Compared to mentally healthy comparators, subjects with BD performed significantly worse on the DRS at baseline [mean (SD) 135.2 (4.7); n = 33 versus 139.5 (3.3); n = 36], and over follow‐up [131.9 (7.7); n = 14 versus 139.1 (3.4); n = 22]. There was a group‐by‐time interaction between the subjects with BD and the controls [group × time: F(1,64) = 5.07, p = 0.028].

Conclusions:  In our study, older adults with BD had more cognitive dysfunction and more rapid cognitive decline than expected given their age and education. Cognitive dysfunction and accelerated cognitive decline may lead to decreased independence, with increased reliance on family and community supports, and potential placement in assisted‐living facilities.
Renal cell carcinoma in patients with end‐stage renal disease: relationship between histological type and duration of dialysis
Authors: Nouh Mohammed A.A.M. , Kuroda Naoto , Yamashita Motoki , Hayashida Yushi , Yano Toshifumi , Minakuchi Jun , Taniguchi Susumu , Nomura Isaku , Inui Masashi , Sugimoto Mikio , Kakehi Yoshiyuki
Published: August 2009

Study Type – Prognosis (case series) Level of Evidence 4

OBJECTIVE

To evaluate the clinical outcomes and histological types of renal cell carcinoma (RCC) arising in patients with end‐stage renal disease (ESRD), and to analyse the relationship of histopathological features with the duration of dialysis.

PATIENTS AND METHODS

Clinical characteristics and outcomes of 34 patients who had a radical nephrectomy for RCC arising in ESRD between November 1994 and June 2008 were investigated. Archive paraffin‐embedded tissue specimens obtained from 27 patients were histochemically and immunohistochemically analysed to determine the histopathological type.

RESULTS

There was one death from cancer and one patient with local progression within a median observation period of 29.5 months. Acquired cystic disease (ACD)‐associated RCC, clear cell‐papillary RCC, mucinous tubular and spindle‐cell carcinoma, and Xp11.2 translocation/TFE3 gene fusion were identified in eight, two, three and one patient, respectively. Conventional clear‐cell RCC was the predominant histological type (nine of 15) in patients with a duration of dialysis of <10 years, while ACD‐associated RCC was predominant (seven of 12) in those with dialysis for ≥10 years. Sarcomatoid foci were identified in three patients with dialysis for ≥10 years. Papillary adenoma was microscopically identified as a satellite tumour in 10 patients.

CONCLUSION

The spectrum of histological types of RCCs arising in ESRD is distinct from that of sporadic RCCs. Patients with a longer duration of dialysis should have particular attention for progression and metastasis. Immunohistochemical profiling is efficient in the histological classification of RCCs arising in ESRD, although knowledge about genetic changes remains to be accumulated.
The Politics of Memory in Annexed Lorraine: The Conflicts between Germanification and French Stalwarts at the beginning of the 20th Century
Authors: HAMMAN PHILIPPE
Published: August 2009

The article examines how the uses of memory in turn‐of‐the‐century Lorraine structured political discourse and presented enduring difficulties for the actions of German administrators and local community leaders. In this border region, memory was always contested and challenged, and thereby unstable. This paper approaches “the politics of French memory” through the examination of various pro‐French “memory societies” and networks such as the Souvenir Français. The central question is how did conflicts over memory impact Lorraine's political life and its place in the German Empire in the years leading up to the Great War? Regarding this point, the growth of nationalism is analysed as a phenomenon that reached far beyond French nationalist circles.
Ways of Forgetting: Israel and the Obliterated Memory of the Palestinian Nakba
Authors: RAM URI
Published: August 2009

This study analyses national ways of forgetting. Following the eminent British Anthropologists Mary Douglas, I relate here to “forgetting” as “selective remembering, misremembering and disremembering” (Douglas 2007: 13). The case study offered here is that of the Israeli‐Jewish forgetting of the uprooting of the Palestinians in the war of 1948. This paper discusses three facets of the collective forgetting: Inthe first subchapterI analyze the foundations of the Israeli regime of forgetting and discern three mechanisms of removing from memory of selected events:narrative forgetting:the formation and dissemination of an historical narrative;physical forgetting:the destruction of physical remains; andsymbolic forgetting:the creation of a new symbolic geography of new places and street names. Inthe second subchapter, I look at the tenacious ambiguity that lies in the regime of forgetting, as it does not completely erase all the traces of the past. And finally, inthe third subchapter, I discuss the growth of subversive memory and counter‐memory that at least indicates the option of a future revision of the Israeli regime of forgetting.