bluuebunny/crossref_metadata_2025 huggingface dataset:
A scheme for spin transistor with extremely large on/off current ratio
Authors: Wang L. , Shen K. , Cho S. Y. , Wu M. W.
Published: December 2008

Quantum wires with periodic local Rashba spin-orbit couplings are proposed for a higher performance of spin field-effect transistor. Fano–Rashba quantum interference due to the spin-dependent modulated structure gives rise to a broad energy range of vanishingly small transmission. Tuning Rashba spin-orbit couplings can provide the on or off currents with extremely large on/off current ratios even in the presence of a strong disorder.
Enhanced 1.47 μm emission and lowered upconversion of Tm3+-doped gallate-germanium-bismuth-lead glass by codoping rare earths
Authors: Shi D. M. , Zhang Q. Y.
Published: December 2008

An intense broadband 1.47 μm emission with a full width at half maximum of 125 nm and a peak emission cross section of 4.056×10−21 cm2 of the Tm3+-doped gallate-germanium-bismuth-lead (GGBP) glass has been obtained upon 808 nm diode-laser excitation. Effects of rare-earth (RE3+=Ho3+, Tb3+, Eu3+, Dy3+) codoping on the spectroscopic properties of the Tm3+-doped GGBP glass have been investigated. It is found that the incorporation of RE3+ into the Tm3+-doped GGBP glass can effectively improve the 1.47 μm emission and can deduce the upconversion luminescence, which makes the GGBP glass more attractive to use in S-band optical fiber amplifiers.
Ionization-induced surface tension reduction of water droplets
Authors: Weon Byung Mook , Je Jung Ho
Published: December 2008

Ionization has been proposed to change natural properties of liquids by influencing surface tension; however, microphysical mechanism has not been well established. Our general physical model to link surface tension and ionization rate shows that radiation-induced ionization may significantly lower the surface tension of tiny water droplets (1–100 nm). Our estimation shows that a few electric charges are sufficient to reduce the surface tension, for instance, of a water droplet with 10 nm radius. Ionization-induced surface tension phenomenon may have impact on many industrial and natural situations, for instance, linking a possible microphysical route to cloud formation by cosmic rays.
Ice nucleation activity of bacteria isolated from snow compared with organic and inorganic substrates
Authors: Mortazavi Roya , Hayes Christopher T. , Ariya Parisa A.
Published: December 2008

Environmental context. Biological ice nucleators have been found to freeze water at very warm temperatures. The potential of bio-aerosols to greatly influence cloud chemistry and microphysics is becoming increasingly apparent, yet detailed knowledge of their actual role in atmospheric processes is lacking. The formation of ice in the atmosphere has significant local, regional and global influence, ranging from precipitation to cloud nucleation and thus climate. Ice nucleation tests on bacteria isolated from snow and laboratory-grown bacteria, in comparison with those of known organic and inorganic aerosols, shed light on this issue. Abstract. Ice nucleation experiments on bacteria isolated from snow as well as grown in the laboratory, in comparison with those of known organic and inorganic aerosols, examined the importance of bio-aerosols on cloud processes. Snow samples were collected from urban and suburban sites in the greater Montreal region in Canada (45°28′N, 73°45′W). Among many snow bacterial isolates, eight types of bacterial species, none belonging to known effective ice nucleators such as Pseudomonas or Erwinia genera, were identified to show an intermediate range of ice nucleation activity (–12.9 ± 1.3°C to –17.5 ± 2.8°C). Comparable results were also obtained for molten snow samples and inorganic suspensions (kaolin and montmorillonite) of buffered water solutions. The presence of organic molecules (oxalic, malonic and succinic acids) had minimal effect (<2°C) on ice nucleation. Considering experimental limitations, and drawing from observation in snow samples of a variety of bacterial populations with variable ice-nucleation ability, a shift in airborne-species population may significantly alter glaciation processes in clouds.
Identification of predators using a novel photographic tethering device
Authors: Bassett D. K. , Jeffs A. G. , Montgomery J. C.
Published: December 2008

Tethering prey is often used to help determine the impact of predators in aquatic communities. In this study, a novel photographic tethering device was used to make digital recordings of predation events on juveniles of the spiny lobster, Jasus edwardsii. Predation of lobsters was significantly higher during the day (76%) than at night (33.4%). This was consistent with a SCUBA survey that found greater numbers of diurnal predators than nocturnal predators at the study site. However, the abundance of predators was not consistent with the number of predation events for individual species as recorded by the photographic tethering device. The snapper, Pagrus auratus, was the most abundant species at the study site (45% of all diurnally active fishes), but was only responsible for 12% of predation events during the day. In contrast, wrasse species were responsible for the greatest number of predation events during the day (60%), yet made up only a small proportion of the diurnal fish population (25%). The results of this study indicate the importance of determining the identity of potential predators, through the use of a photographic tethering device, for increasing the value of results generated from tethering experiments.
Distribution and early life-history characteristics of anguillid leptocephali in the western South Pacific
Authors: Kuroki Mari , Aoyama Jun , Miller Michael J. , Watanabe Shun , Shinoda Akira , Jellyman Donald J. , Feunteun Eric , Tsukamoto Katsumi
Published: December 2008

Freshwater eels are important fisheries species in parts of the western South Pacific, but little is known about their oceanic early life history or spawning areas. The age, growth, morphology and geographic distribution of five species of genetically identified anguillid leptocephali collected in 1995, 2000 and 2005 were compared. The sizes and ages of the leptocephali collected, Anguilla australis (n = 18), Anguilla marmorata (n = 15), Anguilla reinhardtii (n = 12), Anguilla megastoma (n = 2) and Anguilla obscura (n = 1), ranged from 19.0 to 50.9 mm and from 25 to 155 days, respectively. Leptocephali were mostly collected in the South Equatorial Current region. The total myomere ranges overlapped among species, but anodorsal myomere numbers clearly divided shortfinned and longfinned eels. The myomere ranges of the leptocephali were similar to the reported ranges of the numbers of vertebrae in adults. Larval growth rates suggested that the temperate species A. australis had slightly slower growth than the tropical species A. reinhardtii. The present study suggests that both temperate and tropical anguillid eels use the South Equatorial Current region for spawning and larval development, although some species might have different early life parameters and migration routes to their recruitment areas.
Sediment and nutrient accumulation rates in sediments of twelve New Zealand lakes: influence of lake morphology, catchment characteristics and trophic state
Authors: Trolle Dennis , Hamilton David P. , Hendy Chris , Pilditch Conrad
Published: December 2008

Intact sediment cores were collected from the deepest basins of 12 lakes in the Rotorua District, New Zealand, to test for effects of morphological features, catchment characteristics and lake trophic state on net sedimentation rates and sediment nutrient concentrations. Multiple linear regression was used to show that 68% of the variation in net sedimentation rates across the lakes could be explained by lake trophic state and catchment area. Comparison of 2006 data with results from a survey in 1995 showed that surficial sediment (0–2 cm) total phosphorus concentrations (TP) have increased in three of the 12 lakes, at rates ranging from 27.5 to 114.4 mg P kg–1 dry wt y–1. Total nitrogen (TN) concentrations in surficial sediments have increased in nine of the 12 lakes at rates ranging from 51.8 to 869.2 mg N kg–1 dry wt y–1. Temporal changes in sediment TP and TN concentrations were not significantly linearly related (P = 0.12–0.88) to catchment area or different water column indices considered to reflect lake trophic state, including annual mean water column concentrations of TP, TN or chlorophyll a. It is concluded that between-lake variations in sediment TP and TN concentrations are influenced by a range of complex interacting factors, such as sediment redox conditions (and periodic anoxia in the hypolimnion of some lakes) as well as variations in sediment mineral composition (which influences retention and release of various sediment phosphorus and nitrogen species). Subsequently, these factors cause sediment TP and TN concentrations across the 12 lakes to respond differently to temporal changes in water column TP and TN concentrations.
Essential function of Chk1 can be uncoupled from DNA damage checkpoint and replication control
Authors: Wilsker Deborah , Petermann Eva , Helleday Thomas , Bunz Fred
Published: December 2008

Chk1 is widely known as a DNA damage checkpoint signaling protein. Unlike many other checkpoint proteins, Chk1 also plays an essential but poorly defined role in the proliferation of unperturbed cells. Activation of Chk1 after DNA damage is known to require the phosphorylation of several C-terminal residues, including the highly conserved S317 and S345 sites. To evaluate the respective roles of these individual sites and assess their contribution to the functions of Chk1, we used a gene targeting approach to introduce point mutations into the endogenous human
CHK1
locus. We report that the essential and nonessential functions of Chk1 are regulated through distinct phosphorylation events and can be genetically uncoupled. The DNA damage response function of Chk1 was nonessential. Targeted mutation of S317 abrogated G
2
/M checkpoint activation, prevented subsequent phosphorylation of Chk1, impaired efficient progression of DNA replication forks, and increased fork stalling, but did not impact viability. Thus, the nonessential DNA damage response function of Chk1 could be unambiguously linked to its role in DNA replication control. In contrast, a
CHK1
allele with mutated S345 did not support viability, indicating an essential role for this residue during the unperturbed cell cycle. A distinct, physiologic mode of S345 phosphorylation, initiated at the centrosome during unperturbed mitosis was independent of codon 317 status and mechanistically distinct from the ordered and sequential phosphorylation of serine residues on Chk1 induced by DNA damage. Our findings suggest an essential regulatory role for Chk1 phosphorylation during mitotic progression.
Adrenal peripheral clock controls the autonomous circadian rhythm of glucocorticoid by causing rhythmic steroid production
Authors: Son Gi Hoon , Chung Sooyoung , Choe Han Kyoung , Kim Hee-Dae , Baik Sun-Mee , Lee Hankyu , Lee Han-Woong , Choi Sukwoo , Sun Woong , Kim Hyun , Cho Sehyung , Lee Kun Ho , Kim Kyungjin
Published: December 2008

Glucocorticoid (GC) is an adrenal steroid with diverse physiological effects. It undergoes a robust daily oscillation, which has been thought to be driven by the master circadian clock in the suprachiasmatic nucleus of the hypothalamus via the hypothalamus–pituitary–adrenal axis. However, we show that the adrenal gland has its own clock and that the peripheral clockwork is tightly linked to steroidogenesis by the steroidogenic acute regulatory protein. Examination of mice with adrenal-specific knockdown of the canonical clock protein BMAL1 reveals that the adrenal clock machinery is required for circadian GC production. Furthermore, behavioral rhythmicity is drastically affected in these animals, together with altered expression of
Period1
, but not
Period2,
in several peripheral organs. We conclude that the adrenal peripheral clock plays an essential role in harmonizing the mammalian circadian timing system by generating a robust circadian GC rhythm.
A dual-signal regulatory circuit activates transcription of a set of divergent operons in
Salmonella typhimurium
Authors: Zhao Guang , Weatherspoon Natasha , Kong Wei , Curtiss Roy , Shi Yixin
Published: December 2008

We present a molecular mechanism for signal transduction that activates transcription of the SlyA regulon in
Salmonella typhimurium
. We demonstrate that SlyA mediates transcriptional activation in response to guanosine tetraphosphate, ppGpp, according to the following observations: (
i
) in vivo transcription of SlyA-dependent genes is repressed when ppGpp is absent; this transcription can be restored by overproducing SlyA; (
ii
) in vivo dimerization and binding of SlyA to the target promoter are facilitated in the presence of ppGpp; and (
iii
) in vitro SlyA binding to the target promoter is enhanced when ppGpp is supplemented. Thus, ppGpp must be the cytoplasmic component that stimulates SlyA regulatory function by interacting directly with this regulator in
Salmonella
. This signaling domain, integrated by the PhoP/PhoQ 2-component system that activates
slyA
transcription by sensing Mg
2+
, forms feedforward loops that regulate chromosomal loci identified through a motif search over the
S. typhimurium
genome. Many such loci are divergent operons, each formed by 2 neighboring genes in which transcription of these 2 loci proceeds in opposite directions. Both genes, however, are controlled by PhoP and SlyA through a single shared PhoP box and SlyA box present in their intergenic regions. A substitution in either box sequence causes a simultaneous cessation of transcription of a divergent operon,
pagD-pagC
, equivalent to the phenotype in a
phoP
or
slyA
mutant. We also identified several chromosomal loci that possess
pagC
-type genes without the cognate
pagD
-type genes. Therefore, our results provide a molecular basis for the understanding of SlyA-dependent phenotypes associated with
Salmonella
virulence.
Translation performance of beginning, intermediate and proficient Spanish-Catalan bilinguals
Authors: Guasch Marc , Sánchez-Casas Rosa , Ferré Pilar , García-Albea José E.
Published: December 2008

This study explores how proficiency in a second language determines the way that lexical and semantic representations are functionally connected in bilingual memory by testing three groups of participants (beginning and intermediate Spanish-Catalan learners and highly proficient bilinguals). The experiment reported examines how form and semantic manipulations affect the performance of these groups in a translation recognition task using three types of word relations (very close and close semantically related word pairs and form-related pairs). The results reveal that form manipulation affects the performance of the three participant groups, whereas the influence of semantic relations depends on the participants’ level of proficiency. Results are discussed within the framework of the Revised Hierarchical Model (Kroll & Stewart, 1994).
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance
Authors: Xin Fuxiao , Li Meng , Balch Curt , Thomson Michael , Fan Meiyun , Liu Yunlong , Hammond Scott M. , Kim Sun , Nephew Kenneth P.
Published: December 2008

Motivation: Recent evidence shows significant involvement of microRNAs (miRNAs) in the initiation and progression of numerous cancers; however, the role of these in tumor drug resistance remains unknown.

Results: By comparing global miRNA and mRNA expression patterns, we examined the role of miRNAs in resistance to the ‘pure antiestrogen’ fulvestrant, using fulvestrant-resistant MCF7-FR cells and their drug-sensitive parental estrogen receptor (ER)-positive MCF7 cells. We identified 14 miRNAs downregulated in MCF7-FR cells and then used both TargetScan and PITA to predict potential target genes. We found a negative correlation between expression of these miRNAs and their predicted target mRNA transcripts. In genes regulated by multiple miRNAs or having multiple miRNA-targeting sites, an even stronger negative correlation was found. Pathway analyses predicted these miRNAs to regulate specific cancer-associated signal cascades. These results suggest a significant role for miRNA-regulated gene expression in the onset of breast cancer antiestrogen resistance, and an improved understanding of this phenomenon could lead to better therapies for this often fatal condition.

Contact:  knephew@indiana.edu; sunkim2@indiana.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Molecular Cloning and Characterization of a cDNA for Pterocarpan 4-Dimethylallyltransferase Catalyzing the Key Prenylation Step in the Biosynthesis of Glyceollin, a Soybean Phytoalexin
Authors: Akashi Tomoyoshi , Sasaki Kanako , Aoki Toshio , Ayabe Shin-ichi , Yazaki Kazufumi
Published: December 2008

Glyceollins are soybean (Glycine max) phytoalexins possessing pterocarpanoid skeletons with cyclic ether decoration originating from a C5 prenyl moiety. Enzymes involved in glyceollin biosynthesis have been thoroughly characterized during the early era of modern plant biochemistry, and many genes encoding enzymes of isoflavonoid biosynthesis have been cloned, but some genes for later biosynthetic steps are still unidentified. In particular, the prenyltransferase responsible for the addition of the dimethylallyl chain to pterocarpan has drawn a large amount of attention from many researchers due to the crucial coupling process of the polyphenol core and isoprenoid moiety. This study narrowed down the candidate genes to three soybean expressed sequence tag sequences homologous to genes encoding homogentisate phytyltransferase of the tocopherol biosynthetic pathway and identified among them a cDNA encoding dimethylallyl diphosphate: (6aS, 11aS)-3,9,6a-trihydroxypterocarpan [(−)-glycinol] 4-dimethylallyltransferase (G4DT) yielding the direct precursor of glyceollin I. The full-length cDNA encoding a protein led by a plastid targeting signal sequence was isolated from young soybean seedlings, and the catalytic function of the gene product was verified using recombinant yeast microsomes. Expression of the G4DT gene was strongly up-regulated in 5 to 24 h after elicitation of phytoalexin biosynthesis in cultured soybean cells similarly to genes associated with isoflavonoid pathway. The prenyl part of glyceollin I was demonstrated to originate from the methylerythritol pathway by a tracer experiment using [1-13C]Glc and nuclear magnetic resonance measurement, which coincided with the presumed plastid localization of G4DT. The first identification of a pterocarpan-specific prenyltransferase provides new insights into plant secondary metabolism and in particular those reactions involved in the disease resistance mechanism of soybean as the penultimate gene of glyceollin biosynthesis.
Drug abuse and responsible fathering: a comparative study of men enrolled in methadone maintenance treatment
Authors: McMahon Thomas J. , Winkel Justin D. , Rounsaville Bruce J.
Published: December 2008

Aim  Because very little is known about the parenting of drug‐abusing men, this study was designed to document ways that drug abuse contributes to compromise of responsible fathering.

Design, setting, participants  Generalized linear models and data representing different dimensions of responsible fathering were used to clarify ways that the fathering of 106 men receiving methadone maintenance treatment differed from that of 118 men living in the same community with no history of alcohol or drug abuse.

Measurement  Men who enrolled in the study completed two structured interviews and a battery of five self‐report measures selected to document current and historical dimensions of responsible fathering.

Findings  When the opioid‐dependent fathers were compared to the other fathers, there were significant differences in: (i) economic resources to support family formation; (ii) patterns of pair‐bonding; (iii) patterns of procreation; and (iv) parenting behavior. When fathering of the youngest biological child was examined, the opioid‐dependent fathers confirmed few differences in historical dimensions of fathering, but they reported significant differences in current dimensions reflecting: (i) constricted personal definitions of the fathering role; (ii) poorer relationships with biological mothers; (iii) less frequent residence with the child; (iv) less frequent provision of financial support; (v) less involvement in positive parenting; (vi) poorer appraisal of self as a father; and (vii) less satisfaction as a father.

Conclusions  The findings highlight ways that drug abuse contributes to compromise of responsible fathering, and they raise questions about ways that the drug abuse treatment system might better address parenting as a treatment issue for men.
A lateral model parameter correlation procedure for one‐dimensional inverse modelling
Authors: Christensen Niels B. , Tølbøll Rasmus J.
Published: December 2008

We present a new, fast and versatile method, the lateral parameter correlation method, of invoking lateral smoothness in model sections of one‐dimensional (1D) models. Modern, continuous electrical and electromagnetic methods are capable of recording very large data sets and except for a few cases, standard inversion methodology still relies on 1D models. In environments where the lateral rate of change of resistivity is small, 1D inversion can be justified but model sections of concatenated 1D models do not necessarily display the expected lateral smoothness.

The lateral parameter correlation method has three steps. First, all sounding data are inverted individually. Next, a laterally smooth version of each model parameter, one at a time, is found by solving a simple constrained inversion problem. Identity is postulated between the uncorrelated and correlated parameters and the equations are solved including a model covariance matrix. As a last step, all sounding data are inverted again to produce models that better fit the data, now subject to constraints by including the correlated parameter values as a priori values. Because the method separates the inversion from the correlation it is much faster than methods where the inversion and correlation are solved simultaneously, typically with a factor of 200–500.

Theoretical examples show that the method produces laterally smooth model sections where the main influence comes from the well‐determined parameters in such a way that problems with equivalence and poor resolution are alleviated. A field example is presented, demonstrating the improved resolution obtained with the lateral parameter correlation method. The method is very flexible and is capable of coupling models from inversion of different data types and information from boreholes.
Estimating the magnetization direction of sources from southeast Bulgaria through correlation between reduced‐to‐the‐pole and total magnitude anomalies
Authors: Gerovska Daniela , Araúzo‐Bravo Marcos J. , Stavrev Petar
Published: December 2008

We present a new method to estimate the direction of the magnetization vector of geological bodies based upon the correlation between the reduced‐to‐the‐pole field for tentative values of the magnetization direction and the total magnitude anomaly, obtained by a transform of the measured magnetic field. The reduced‐to‐the‐pole and the total magnitude anomaly are centred over the sources in the case of 2D anomalies or well‐centred in the case of compact 3D sources and have similar patterns for the same source. The method has several important advantages over similar transform‐correlation methods for estimation of the magnetization direction. It calculates only one transform for many tentative values of the magnetization direction. The method does not use derivatives of any order and relies on confident isolation of the target anomalies based on one of the compared transforms, the total magnitude anomaly. We studied the performance of the method on five 2.5D and compact 3D sources. We analysed possible inherent to the method errors, as well as errors due to interference from neighbouring sources. Finally, we estimated the magnetization‐vector direction of the main sources causing the magnetic field in the Burgas region and the adjoining southeast Bulgarian Black Sea shelf. The sources in the Black Sea shelf show prevalently reverse magnetization, while the sources on land have normal or reverse magnetization.
Major histocompatibility complex (MHC) class II but not MHC class I molecules are required for efficient control of Strongyloides venezuelensis infection in mice
Authors: Rodrigues Rosângela M. , Silva Neide M. , Gonçalves Ana Lúcia R. , Cardoso Cristina R. , Alves Ronaldo , Gonçalves Flávia A. , Beletti Marcelo E. , Ueta Marlene T. , Silva João S. , Costa‐Cruz Julia M.
Published: December 2008

Strongyloides stercoralis is an intestinal nematode capable of chronic, persistent infection and hyperinfection of the host; this can lead to dissemination, mainly in immunosuppressive states, in which the infection can become severe and result in the death of the host. In this study, we investigated the immune response against Strongyloides venezuelensis infection in major histocompatibility complex (MHC) class I or class II deficient mice. We found that MHC II−/− animals were more susceptible to S. venezuelensis infection as a result of the presence of an elevated number of eggs in the faeces and a delay in the elimination of adult worms compared with wild‐type (WT) and MHC I−/− mice. Histopathological analysis revealed that MHC II−/− mice had a mild inflammatory infiltration in the small intestine with a reduction in tissue eosinophilia. These mice also presented a significantly lower frequency of eosinophils and mononuclear cells in the blood, together with reduced T helper type 2 (Th2) cytokines in small intestine homogenates and sera compared with WT and MHC I−/− animals. Additionally, levels of parasite‐specific immunoglobulin M (IgM), IgA, IgE, total IgG and IgG1 were also significantly reduced in the sera of MHC II−/− infected mice, while a non‐significant increase in the level of IgG2a was found in comparison to WT or MHC I−/− infected mice. Together, these data demonstrate that expression of MHC class II but not class I molecules is required to induce a predominantly Th2 response and to achieve efficient control of S. venezuelensis infection in mice.
Dislocation resistance of ProRoot Endo Sealer, a calcium silicate‐based root canal sealer, from radicular dentine
Authors: Huffman B. P. , Mai S. , Pinna L. , Weller R. N. , Primus C. M. , Gutmann J. L. , Pashley D. H. , Tay F. R.
Published: December 2008

Aim  To examine the dislocation resistance of three root canal sealers from radicular dentine with and without immersion in a simulated body fluid (SBF), using a modified push‐out test design that produced simulated canal spaces of uniform dimensions under identical cleaning and shaping conditions.

Methodology  Sixty single‐rooted caries‐free human canine teeth were used. Standardized simulated canal spaces were created using 0.04 taper ProFile instruments along the coronal, middle and apical thirds of longitudinal tooth slabs. Following NaOCl/ethylenediamine tetra‐acetic acid cleaning, the cavities were filled with ProRoot Endo Sealer, AH Plus Jet or Pulp Canal Sealer. After setting, half of the cavities were tested with a fibre‐optic light‐illuminated push‐out testing device. The rest were immersed in SBF for 4 weeks before push‐out evaluation. Failure modes were examined with stereomicroscopy and field emission (FE)‐scanning electron microscopy.

Results  Location of the sealer‐filled cavities did not affect push‐out strengths. ProRoot Endo Sealer exhibited higher push‐out strengths than the other two sealers particularly after SBF storage (P < 0.001). Failure modes were predominantly adhesive and mixed for Pulp Canal Sealer and AH Plus Jet, and predominantly cohesive for ProRoot Endo Sealer. Spherical amorphous calcium phosphate‐like phases that spontaneously transformed into apatite‐like phases were seen in the fractured specimens of ProRoot Endo Sealer after SBF storage.

Conclusions  When tested in bulk without a main core, both ‘sealer type’ and ‘SBF storage’ were significant in affecting push‐out results. The ProRoot Endo Sealer demonstrated the presence of spherical amorphous calcium phosphate‐like phases and apatite‐like phases (i.e. ex vivo bioactivity) after SBF storage.
Clinical utility of a T cell‐based assay in the diagnosis of extrapulmonary tuberculosis
Authors: KOBASHI Yoshihiro , MOURI Keiji , YAGI Shinichi , OBASE Yasushi , MIYASHITA Naoyuki , OKA Mikio
Published: December 2008

Background and objective:  The aim of this study was to evaluate the QuantiFERON TB‐2G (QFT‐2G) results in patients with active extrapulmonary tuberculosis (E‐TB) to determine whether QFT‐2G test might be a reliable diagnostic method for detecting active E‐TB infection compared with the tuberculin skin test (TST).

Methods:  TST and QFT‐2G tests were performed for 35 patients with confirmed E‐TB, 30 with probable E‐TB and 45 who did not have E‐TB.

Results:  For patients with confirmed E‐TB, the positive rate of the TST was 57% and that of the QFT‐2G test was 86%. For patients with probable E‐TB, the positive rate of the TST was 60%, whereas that of the QFT‐2G test was 80%. However, the positive rate of the TST was 51% and that of QFT‐2G test was 9% for patients that did not have E‐TB. The QFT‐2G test showed a significantly lower percentage of false‐negative results compared with the TST. The sensitivity and specificity of the TST for the diagnosis of active E‐TB were 57% and 49%, respectively. By comparison, the sensitivity and specificity of the QFT‐2G test were 86% and 84%, respectively. When the results of the TST and QFT‐2G tests were separated by the site of E‐TB, the positive rates for both tests in patients with miliary tuberculosis were lower than those in patients with other E‐TB disease, although the difference was not significant.

Conclusions:  The QFT‐2G appears to be a reliable diagnostic test and in the appropriate clinical context QFT‐2G may be more useful than the TST to support a diagnosis of E‐TB. Studies are needed to evaluate its value also in situations of low clinical probability.
Endoscopic ultrasound‐guided fine‐needle aspiration when combined with positron emission tomography improves specificity and overall diagnostic accuracy in unexplained mediastinal lymphadenopathy and staging of non‐small‐cell lung cancer
Authors: Kalade A. V. , Eddie Lau W. F. , Conron M. , Wright G. M. , Desmond P. V. , Hicks R. J. , Chen R.
Published: December 2008

Background:  The aim of this study was to assess the incremental value of endoscopic ultrasound (EUS)‐guided fine‐needle aspiration (FNA) to positron emission tomography (PET) in the diagnosis of unexplained mediastinal lymphadenopathy and staging of non‐small‐cell lung cancer (NSCLC).

Methods:  Patients who had both EUS‐guided FNA and PET were retrospectively identified from an EUS database at a tertiary hospital. All EUS‐guided FNA were carried out by one endoscopist between August 2002 and April 2005, either for the diagnosis of unexplained mediastinal lymphadenopathy or for the staging of NSCLC. Results of PET and EUS were compared with histology. A true histological positive result was defined as histological involvement in either surgery (mediastinoscopy or resection) or EUS‐guided FNA. A true histological negative result was defined as negative involvement at surgery (mediastinoscopy or resection).

Results:  Forty‐nine patients who had both PET scanning and EUS‐guided FNA for diagnosis of unexplained mediastinal lymphadenopathy or staging of NSCLC were identified. Of these, 33 (73% males, n = 24, age range = 44–78 years, mean = 62 years) had surgical confirmation of mediastinal lymph node pathology. In these patients, PET alone showed sensitivity, 95%; specificity, 90%; positive predictive value, 87%; negative predictive value, 90% and accuracy, 88%; whereas the addition of EUS‐guided FNA increased the overall specificity and positive predictive value to 100%, with an overall accuracy of 97%.

Conclusions:  This study suggests that EUS‐guided FNA complements PET by improving the overall specificity and thereby the accuracy for diagnosis of unexplained mediastinal lymphadenopathy. It provides a minimally invasive technique to assess the mediastinum in patients with NSCLC and is particularly valuable in cases in which PET findings are equivocal.
Crossing Invisible Boundaries: the Effectiveness of the Langebaan Lagoon Marine Protected Area as a Harvest Refuge for a Migratory Fish Species in South Africa
Authors: KERWATH SVEN E. , THORSTAD EVA B. , NÆSJE TOR F. , COWLEY PAUL D. , ØKLAND FINN , WILKE CHRIS , ATTWOOD COLIN G.
Published: December 2008

Abstract:  The application of no‐take areas in fisheries remains controversial. Critics argue that many targeted species are too mobile to benefit from area protection and that no‐take areas are only appropriate for resident species. The degree of protection does not depend on the size of the no‐take area but rather on the time fish reside inside its boundaries during key life‐history events (i.e., spawning) and during periods of peak fishing activity. We evaluated the potential of a small no‐take marine protected area (MPA) inside a coastal embayment as a harvest refuge for a mobile, possibly migratory, long‐lived fish species. We used acoustic telemetry to track movements of 30 transmitter‐tagged white stumpnose (Rhabdosargus globiceps) across and on both sides of the boundary of a small (34 km2) no‐take area over a full year. Being landlocked on 3 sides, the location of the MPA inside the lagoon made it practical to detect all boundary crossings and to calculate the time individual fish used the MPA. We detected frequent movements across the boundary, with strong seasonal and individual variations. There were significant differences in MPA use patterns between fish from different release areas. The time spent in the MPA by individual fish during summer (mean 50%; max 98%) was out of proportion with the size of that area (4% of total habitat). Summer coincided with peak recreational fishing activity and with the spawning season of this species. The small MPA provided a refuge for a part of the spawning stock of white stumpnose. Our findings suggest that if strategically placed, a small no‐take area can be effective in protecting mobile species and that models of spillover from no‐take areas should account for seasonal and individual variation in area use and the spatiotemporal distribution of fish and fishers.
Parastrombidinopsis minima n. sp. (Ciliophora: Oligotrichia) from the Coastal Waters of Northeastern Taiwan: Morphology and Small Subunit Ribosomal DNA Sequence
Authors: TSAI SHENG‐FANG , XU DAPENG , CHUNG CHIH‐CHING , CHIANG KUO‐PING
Published: December 2008

ABSTRACT. Parastrombidinopsis minima n. sp. is investigated, using live observations, protargol preparations, and molecular data. In living cells, the ranges of cell length are 85–95 μm, cell width 60–70 μm, and oral diameter 40–50 μm. In protargol‐impregnated specimens, cell length ranges between 43 and 71 μm, cell width between 23 and 42 μm, and oral diameter between 13 and 24 μm. The numbers of external oral polykinetids are 12–16 and of somatic kineties are 11–13. There are always two ovoid macronuclei (9–16 × 4–9 μm). Based on the analysis of morphologic data, the new species can be placed in the family Strombidinopsidae, but based on the small subunit rRNA gene sequence data, the Parastrombidinopsis species are more closely associated with strobilidiids and tintinnids.
How Epigenomics Contributes to the Understanding of Gene Regulation in Toxoplasma gondii1
Authors: GISSOT MATHIEU , KIM KAMI
Published: December 2008

ABSTRACT. How apicomplexan parasites regulate their gene expression is poorly understood. The complex life cycle of these parasites implies tight control of gene expression to orchestrate the appropriate expression pattern at the right moment. Recently, several studies have demonstrated the role of epigenetic mechanisms for control of coordinated expression of genes. In this review, we discuss the contribution of epigenomics to the understanding of gene regulation in Toxoplasma gondii. Studying the distribution of modified histones on the genome links chromatin modifications to gene expression or gene repression. In particular, coincident trimethylated lysine 4 on histone H3 (H3K4me3), acetylated lysine 9 on histone H3 (H3K9ac), and acetylated histone H4 (H4ac) mark promoters of actively transcribed genes. However, the presence of these modified histones at some non‐expressed genes and other histone modifications at only a subset of active promoters implies the presence of other layers of regulation of chromatin structure in T. gondii. Epigenomics analysis provides a powerful tool to characterize the activation state of genomic loci of T. gondii and possibly of other Apicomplexa including Plasmodium or Cryptosporidium. Further, integration of epigenetic data with expression data and other genome‐wide datasets facilitates refinement of genome annotation based upon experimental data.
Factors Affecting Preference Responses of the Freshwater Ciliate Uronema nigricans to Bacterial Prey
Authors: AYO BEGOÑA , LATATU AINHOA , ARTOLOZAGA ITXASO , JÜRGENS KLAUS , IRIBERRI JUAN
Published: December 2008

ABSTRACT. To enhance our understanding of the factors affecting feeding selectivity of bacterivorous protists in aquatic systems, we examined the preference responses of the freshwater ciliate Uronema nigricans towards three bacterial prey taxa, Pseudomonas luteola, Serratia rubidaea, and Aeromonas hydrophila. Potential factors influencing the predator–prey contact rate included the previous feeding history of the ciliate and physiological state of bacteria. Preference indexes were obtained from multiple‐choice mazes in which ciliates moved preferentially towards alternative bacteria or the prey species on which they had been feeding. Uronema nigricans showed differential attraction towards the offered prey types, and these preferences varied as a function of the ciliate feeding history: U. nigricans growing on P. luteola showed lower preference responses towards the offered bacteria than U. nigricans growing on S. rubidaea. The bacteria in stationary phase elicited a higher degree of attraction than bacteria in exponential phase, probably due to a higher concentration of carbohydrates in the former. Therefore, this protist will preferentially swim towards bacteria in stationary growth phase, although the degree of this response will be affected by the recent feeding history of the ciliate.
Detecting compensatory dynamics in competitive communities under environmental forcing
Authors: Ranta Esa , Kaitala Veijo , Fowler Mike S. , Laakso Jouni , Ruokolainen Lasse , O'Hara Robert
Published: December 2008

Competition is assumed to generate compensatory dynamics where an increase in one species is compensated by a decrease in others. Recently, using a community covariance technique, Houlahan et al. found that compensatory dynamics are only visible in 25–30% of natural communities studied. The study was based on scoring the sum of covariances of population densities. In contrast to the theory, and as a cautionary reminder to the interpretation of natural time series data, we show that negative community covariance can be absent even in strongly competitive communities and can be found present in communities without competitive interactions. Precise knowledge of various features of the underlying species’ biology and characteristics of the environmental variation is required before community covariance can be correctly interpreted as a proxy for the importance of competition or environmental forcing in driving community fluctuations. Other tools may therefore be more appropriate, e.g. explicit modelling of competition using modern time series analytical tools.
Summer diet selection of snowshoe hares: a test of nutritional hypotheses
Authors: Seccombe‐Hett Pippa , Turkington Roy
Published: December 2008

We examined summer diet selection by snowshoe hares in the southwestern Yukon, Canada, and attempted to explain how plant qualities such as nutritional content (protein, energy, fiber, water) and defensive compounds affect hare food choice. Male hares were placed in enclosures in natural vegetation areas dominated by shrubs and in both open and closed spruce forests. Each site contained a variety of herbaceous plant species. After 24 h, hares were sacrificed, their stomachs collected, and the contents removed and analyzed. Of the 30 plant species recorded in the enclosures only 10 were identified in the stomach contents of the hares. The summer diet is composed predominantly of five plant species;Lupinus arcticus, Salixspp.Shepherdia canadensis,Betula glandulosaandFestuca altaica.The selection of these species changes between sampling times. Protein, energy and water contents were highest in leaf tissues of most species early in the season, and most species had an increase in fiber through the summer. Protein content consistently explains the largest amount of variation in diet selection, although protein selection is modified by extremely high concentrations of defence compounds. It is likely that hares are not protein limited and are selecting for other plant characteristics correlated with protein content such as energy content. It is significant that hares continue to ingest heavily defended species (e.g.Shepherdia canadensis, B. glandulosaandL. arcticus)when many less defended plants are available to be eaten (e.g.F. altaica, Epilobium latifoliumandAnemone parviflora).Our results support the idea that hares are selecting dietary items on the basis of energy content. No single plant species can satisfy all of the hares’ nutritional requirements and the selection patterns may reflect the need to balance many conflicting plant qualities.
Pesticide exposure strongly enhances parasite virulence in an invertebrate host model
Authors: Coors Anja , Decaestecker Ellen , Jansen Mieke , De Meester Luc
Published: December 2008

Parasites are a common and constant threat to organisms at all levels of phyla. The virulence of a parasite, defined as the impact on survival and reproduction of its host, depends on the specific host–parasite combination and can also be influenced by environmental conditions. Environmental pollution might be an additional factor influencing host–parasite interactions. We here aimed to test whether the combined stress of pollutant exposure and parasite challenge results in stronger impacts on host organisms than expected from the single stressors applied alone. We used the water flea Daphnia magna and two of its endoparasites, the bacterium Pasteuria ramosa and the microsporidium Flabelliforma magnivora, as invertebrate host–parasite models. For each parasite, we tested in a full‐factorial design for interactions between parasitism and pollution using the neurotoxic pesticide carbaryl as a model substance. Sublethal concentrations of the pesticide synergistically enhanced the virulence of both parasites by increasing host mortality. Furthermore, host castration induced by P. ramosa was accelerated by carbaryl exposure. These effects likely reflect decreased host resistance due to direct or indirect immunosuppressive activity of carbaryl. The present study provides experimental evidence that the in vivo development of infectious diseases can be influenced by a pesticide at environmentally realistic concentrations. This implies that host–parasite interactions and subsequently co‐evolution might be influenced by environmental pollution at toxicant concentrations being sublethal to parasite‐free hosts. Standard toxicity testing as employed in the current way of conducting ecological risk assessments for anthropogenic substances does not consider natural antagonists such as infectious diseases, and thereby likely underestimates the impact these substances may pose to natural populations in the environment.
Parental mental health, education, age at childbirth and child development from six to 18 months
Authors: Lung For‐Wey , Shu Bih‐Ching , Chiang Tung‐Liang , Lin Shio‐Jean
Published: December 2008

Aim: To investigate the effect six‐month parental mental health has on children's six and 18‐month development. Parental covariates of age and education were also analysed.

Methods: Through a national random selection, 21 648 babies were selected. Parental self perceived overall mental health was measured using 36‐Item Short Form Health Survey (SF‐36) and children's development using the Taiwan Birth Cohort Study (TBCS) instrument which measures gross motor, fine motor, language and social dimensions of children's development.

Results: Both multiple linear regression and structural equation modeling showed that when the covariates of parental education and age at childbirth were added, the effect parental mental health has on children's development decreases. Additionally, maternal mental health had a more persistent and pervasive effect than paternal mental health. Father's mental health at six months had a delayed effect, in that its influence was seen only with children's development at 18 months. Of the three factors of parental mental health, education and age at childbirth, parental education had the most pervasive and persistent effect on children's development.

Conclusion: Although parental mental health has an effect on children's development, parental education and age at childbirth are vital confounding factors, which should be considered in future studies. Clinical health care providers should provide childcare resources and instructions to younger, less educated and parents with mental symptoms.
Macular appearance after diabetic vitrectomy for fibrovascular proliferation: an optical coherence tomography study
Authors: Yang Chung‐May , Yeh Po‐Ting , Cheng Shuo‐Fang , Yang Chang‐Hao , Chen Muh‐Shy
Published: December 2008

Purpose:  To investigate morphological variations in the macular area with optical coherence tomography (OCT) after vitrectomy for diabetic fibrovascular proliferation.

Methods:  We reviewed 108 cases using OCT 7–15 months after vitrectomy. Of these, 32 received OCT within 3 months postoperatively. Morphological variations were categorized and correlated with visual outcome.

Results:  Only 24 cases (21.4%) had no obvious abnormalities. The most frequent findings were epiretinal membrane (52.8%), macular thickening (37.0%) and macular cysts (28.7%). Multivariate regression showed that diffuse macular thickening, loss of foveal depression and diffuse retinal thinning were significantly associated with poor visual acuity. Sequential OCT (< 3 and ≥ 7 months) revealed that epiretinal membrane and oedema outside of fovea changed significantly between two examinations.

Conclusion:  OCT may identify diverse morphological changes in the macular area after diabetic vitrectomy for fibrovascular proliferation. Macular appearance may change over time, and certain types of morphological changes may be associated with poor visual function.