bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of electron traps in carbon-60 field-effect transistors by a thermally stimulated current technique
Authors: Matsushima Toshinori , Yahiro Masayuki , Adachi Chihaya
Published: September 2007

The authors investigated the influence of O2 and H2O molecules absorbed in carbon-60 (C60) films on their electron trap and n-type field-effect transistor (FET) characteristics. Electron traps in the C60 films were directly measured using a thermally stimulated current (TSC) technique. The TSC results demonstrate that the absorption of O2 and H2O molecules in the C60 films induced an increase in the electron trap concentration, which degrades C60 FET characteristics. By annealing the C60 films at 100°C for 8h, the electron trap concentrations were markedly lowered, enhancing the C60 FET characteristics. An electron mobility of 0.017cm2∕Vs and a current on/off ratio of 106 were observed from the degassed C60 FETs.
High inverted tunneling magnetoresistance in MgO-based magnetic tunnel junctions
Authors: Feng J. F. , Feng Gen , Coey J. M. D. , Han X. F. , Zhan W. S.
Published: September 2007

Inverted tunneling magnetoresistance, where resistance decreases as the free layer in a magnetic tunnel junction flips its direction of magnetization after saturation, has been observed at zero bias in magnetic tunnel junctions with a thin CoFeB layer in the pinned synthetic antiferromagnetic CoFe∕Ru∕CoFeB stack. Magnetoresistance values as high as −55% at room temperature are measured in MgO-based tunnel junctions when the thickness of the pinned CoFeB layer is 1.5nm. The inverted magnetoresistance is associated with imbalance of the synthetic antiferromagnetic pinned layer. Asymmetric bias dependence with a magnetoresistance sign change is observed for a 0.5nm pinned CoFeB layer.
Reduced free carrier absorption loss in midinfrared double heterostructure diode lasers grown by liquid phase epitaxy
Authors: Yin M. , Krier A. , Jones R. , Carrington P. J.
Published: September 2007

An improved InAsSb∕InAsSbP double heterojunction ridge laser was designed and grown by liquid phase epitaxy. The cladding layer absorption loss was minimized by the introduction of two undoped quaternary layers on either side of the active region to form a five layer epitaxial structure. The inserted layers also helped alleviate interdiffusion of unwanted dopants into the active region and reduced current leakage in the device. The resulting diode lasers operate readily in pulsed mode near 3.5μm at elevated temperatures and with a threshold current density as low as 118Acm−2 at 85K. Compared to the conventional three-layer double heterostructure laser, the modified structure with reduced optical loss increased the maximum lasing temperature by 95–210K.
Ion conduction across nanosized CaF2∕BaF2 multilayer heterostructures
Authors: Guo X. X. , Matei I. , Lee J.-S. , Maier J.
Published: September 2007

The authors investigate the ion conduction of molecular beam epitaxy grown CaF2∕BaF2 multilayers perpendicular to the interfaces. Unlike previous measurements along the heterostructure boundaries, the more resistive contributions dominate here; the detailed analysis allows for a complementary insight into the charge carrier distribution. The features of perpendicular conductivites in both semi-infinite and mesoscopic situations can be qualitatively as well as quantitatively explained by the same defect chemical model used for parallel ion conduction. The authors can distinguish three different size regimes. For large interfacial spacings (ℓ>50nm), the conduction is dominated by bulk parts of the CaF2 layers, showing only a slight increase with decreasing layer thickness. For very small spacings, i.e., ℓ<30nm, the conductivity increases steeply and tends toward a saturation value, corresponding to the space charge overlap situation with the overall value that can be attributed to Fi′ accumulated in CaF2. The intermediate range (30nm<ℓ<50nm) is characterized by markedly lower activation energies in which the transition from Fi′ (depleted near the interface) to VF• (enriched near the interface) in BaF2 plays a significant role.
Tailoring of optical mode profiles of high-power diode lasers evidenced by near-field photocurrent spectroscopy
Authors: Kozlowska Anna , Szymański Michał , Pruszyńska-Karbownik Emilia , Bugajski Maciej , Pomraenke Robert , Lienau Christoph , Renard Julien , Maląg Andrzej
Published: September 2007

Tailoring of optical mode profiles of high-power diode lasers is directly demonstrated by means of near-field photocurrent spectroscopy. Three double barrier separate confinement heterostructures with different confinement geometries are designed and their optical mode profiles are studied both theoretically and experimentally. The near-field spectroscopic results clearly resolve the intended variation in optical mode width. A remaining discrepancy between the designed and experimentally measured mode profiles, manifesting itself in the reduction of their evanescent tails, is attributed to the structure of the antiguiding barrier. The results demonstrate that near-field field photocurrent spectroscopy is a powerful, nondestructive, and quantitative technique for optical waveguide inspection in high-power diode lasers.
Effect of quantum transport on the resistivity of metal nanocrystalline materials in an electric field
Authors: Zhu Linli , Jin Ke , Zheng Xiaojing
Published: September 2007

The resistivities of metal nanocrystalline materials exhibit significant size effect due to the additional scattering sites provided by grain boundaries compared to bulk materials. In this work, the authors investigate the electron ballistic transport in nanocrystalline materials under an applied electric field using the transfer-matrix approach. The theoretical results show that the resistivity increases remarkably due to the quantum effect for the grain size lower than the characteristic parameters such as the electron mean free path, and the predications are in excellent agreement with experimental data. The resistivity is also dependent on the external electric field when the grain size is at several nanometer scale.
Simulation for generation of 15fs laser pulses by Raman backscatter in plasmas
Authors: Hur Min Sup , Kim Jaehoon , Gupta Devki N. , Jang Hyo Jae , Suk Hyyong
Published: September 2007

Pulse compression using the Raman backscatter (RBS) in plasmas was numerically investigated for the strong kinetic regime. It was found that shortening of a seed pulse is more effective when the interaction length is smaller, which is contradictory to the general expectation. In a representative case, compression of up to 14fs could be obtained from the RBS interaction length less than 0.1mm. Behavior of the Raman amplification system for such a short interaction distance was not addressed before. Estimation with realistic parameters indicates that the output power can reach tens of terawatts.
Tailoring of heterostructures in a SnO2∕TiO2 system by the oriented attachment mechanism
Authors: Ribeiro Caue , Longo Elson , Leite Edson R.
Published: September 2007

In order to verify the possibility of forming a heterostructure—i.e., a nanoparticle tailored by the junction of two or more different materials—through the oriented attachment (OA) mechanism, experiments with rutile TiO2 and cassiterite SnO2 as candidate materials were done, since they have similar crystallographic parameters. The experiments were carried out in hydrothermal conditions and in an in situ observation at the high resolution transmission electron microscopy. The results showed the formation of TiO2∕SnO2 heterostructures, confirming the coexistence of rotation-alignment and oriented collision mechanisms, hypothesis of OA behavior proposed in previous theoretical works.
In situ Raman characterization of reversible phase transition in stress-induced amorphous silicon
Authors: Wu Kehui , Yan X. Q. , Chen M. W.
Published: September 2007

The authors report a reversible phase transition of stress-induced amorphous silicon subjected to laser heating. In situ Raman characterization suggested that a metastable crystalline phase precipitates from the amorphous silicon upon annealing at ∼400°C and vanishes after subsequent cooling at room temperature. The unusual reversible phase transition is most likely associated with the unique atomic structure of stress-induced amorphous silicon and high residual stresses within amorphous imprints.
Direct hcp→bcc structural phase transition observed in titanium alloy at high pressure
Authors: Velisavljevic Nenad , Chesnut Gary N.
Published: September 2007

Structural stability of Ti alloy, stabilized as a mixture of bcc (β) and hcp (α) phases, was investigated up to 71GPa. Over this pressure, β phase remains stable, while for α phase, a decrease in c∕a ratio from 1.601 at ambient pressure to 1.568 at 36GPa is observed, followed by an increase to 1.613 at 44GPa. A steady value is then observed up to 67GPa. Above 58GPa, the authors also observe that α phase peak intensity is decreasing. At 67GPa, the authors only observe β phase peaks, which indicates that α→β structural phase transition is complete.
Conduction behavior change responsible for the resistive switching as investigated by complex impedance spectroscopy
Authors: Xia Yidong , Liu Zhiguo , Wang Yang , Shi Lei , Chen Liang , Yin Jiang , Meng Xiangkang
Published: September 2007

Complex impedance spectroscopy has been employed to investigate the conduction behavior of (Ba,Sr)(Zr,Ti)O3 thin films in the low- and high-resistance states for resistive switching applications. The domination of the grain bulk effect on the resistive switching is demonstrated. The analyses of activation energies for the conduction in the low- and high-resistance states have been executed comparatively. It is proposed that the first and the second ionization of oxygen vacancies are responsible for the conduction in the low- and high-resistance states, respectively. The transition of conduction mechanism is also discussed.
Radioimmunoassay of bovine placental lactogen using recombinant and native preparations: determination of fetal concentrations across gestation
Authors: Alvarez-Oxiley A. V. , Sousa N. M. , Hornick J. L. , Touati K. , van der Weijden G. C. , Taverne M. A. M. , Szenci O. , Sulon J. , Debliquy P. , Beckers J. F.
Published: September 2007

Concentrations of bovine placental lactogen (bPL) were determined in fetal plasma samples by twelve double-antibody competitive radioimmunoassay systems (RIA I–XII) based on either recombinant bPL (non-glycosylated) or native bPL (glycosylated). Both preparations were used as standard and tracer, and for primary antisera production. The minimum detection limit measured by these RIA varied from 0.02 to 0.6 ng bPL mL–1. The coefficients of correlation of different bPL RIA systems were up to 90% (P < 0.0001) when each RIA was tested against the average values of all twelve RIA systems. All developed RIA were used to investigate the incidence of different bPL isoforms in bovine fetal serum samples (n = 71). Fetal concentrations ranged from 11.8 to 35.7 ng mL–1 at the third month and from 1.1 to 13.5 ng mL–1 at the ninth month of gestation. They tended to decrease with advancing gestation. In general, those RIA systems that used recombinant bPL as the standard measured higher values than those using the native bPL preparation. These differences decreased toward the end of gestation (P < 0.05), suggesting a lower rate of glycosylation. Our results provide evidence of different glycosylated isoforms of bPL in fetal serum at different gestation periods.
Changes in the testis seminiferous tubules and interstitium in prepubertal bull calves immunised against inhibin at the time of gonadotropin administration
Authors: Schuenemann G. M. , Mendis-Handagama S. M. L. C. , Hopkins F. M. , Kania S. A. , Schrick F. N.
Published: September 2007

The aim of the present study was to evaluate the effects of gonadotropin administration at initiation of inhibin passive immunisation in Jersey bull calves (age 27 � 5 days) on testicular morphology and development. Primary treatments consisted of control (keyhole limpet haemocyanin, KLH; n = 9) or immunisation against inhibin (INH; n = 9). Subsets of calves were randomly assigned within primary treatments (TRT) to receive saline ( n = 3 per TRT), follicle-stimulating hormone (FSH; n = 3 per TRT) or gonadotrophin-releasing hormone (GnRH, n = 3 per TRT). The right testis was removed (age 118 � 5 days) to determine volumes of testicular components and cell numbers per testis using stereology. Data were analysed using the MIXED procedure of the SAS program. Antibody titres against inhibin were increased in INH bulls compared with KLH bulls (P < 0.05). In addition, a significant immunisation � hormone treatment interaction was noted for the number of germ cells. Administration of FSH at the time of initial immunisation against inhibin significantly increased the number of germ cells (92.2 � 9 � 106 cells) compared with INH+saline bulls (54.9 � 10 � 106 cells), with INH+GnRH bulls having an intermediate number of cells (64.5 � 9 � 106 cells; P < 0.05). These results suggest that gonadotropin administration at the time of inhibin immunisation increases the number of germ cells in the testis.
Two high-fertility mouse lines show differences in component fertility traits after long-term selection
Authors: Spitschak Marion , Langhammer Martina , Schneider Falk , Renne Ulla , Vanselow Jens
Published: September 2007

Two selected high-fertility mouse lines, namely FL1 and FL2, and a non-selected control (Fzt:DU), all derived from the same genetic pool, were analysed as an animal model for polytocous species to elucidate the effects of long-term selection and to identify relevant component traits that may be responsible for fertility performance. The index trait used for breeding selection was largely increased by 104% and 142% in the FL1 and FL2 lines, respectively, resulting in an average litter size of 17.3 pups and 18.7 pups per litter in the FL1 and FL2 lines, respectively, compared with a litter size of 11.0 pups per litter in the control (Fzt:DU). In addition, different component fertility traits were analysed in females of all three lines at different stages of the oestrous cycle and pregnancy. In conclusion: (1) early embryonic development was accelerated in the FL1 and FL2 lines compared with control; (2) plasma progesterone levels were not correlated with fertility performance; (3) a largely increased ovulation number (i.e. number of corpora lutea) was responsible for high prolificacy in both lines; however, (4) the number of ova shed, as well as the rate of loss of ova and pre- and postimplantation conceptuses, was very different in the FL1 and FL2 lines, suggesting that different genetic components may be responsible for the high prolificacy in both high-fertility lines.
Effect of embryo source and recipient progesterone environment on embryo development in cattle
Authors: Lonergan P. , Woods A. , Fair T. , Carter F. , Rizos D. , Ward F. , Quinn K. , Evans A.
Published: September 2007

The aim of the present study was to examine the effect of embryo source (in vivo v. in vitro) and the progesterone environment into which it was transferred on Day 7 on embryo survival and size on Day 13. Day 7 blastocysts were produced either in vivo using superovulation, artificial insemination and non-surgical embryo recovery or in vitro using in vitro maturation, fertilisation and culture. In order to produce animals with divergent progesterone concentrations, following synchronisation recipients were either superovulated (High progesterone; n = 10) or not (Control progesterone; n = 10). Ten blastocysts, produced either in vivo or in vitro, were transferred to each recipient on Day 7. Both groups were killed on Day 13. The mean progesterone concentration from Day 7 to Day 13 (the period when the embryos were in the uterus) in the High and Control progesterone recipients was 36.32 ± 1.28 and 10.30 ± 0.51 ng mL–1, respectively. Of the in vivo embryos transferred, the overall recovery rate at Day 13 was 64%, which was higher (P < 0.001) than that of 20% for the in vitro embryos transferred. The mean area of embryos recovered from High progesterone recipients was 3.86 ± 0.45 mm2 (n = 28) compared with 1.66 ± 0.38 mm2 (n = 24) for embryos recovered from Control progesterone recipients (P < 0.001). Similarly, the origin of the embryo used for transfer affected embryo size on Day 13. In summary, the recovery rate of blastocysts was higher for in vivo- than in vitro-derived embryos. Blastocyst size was approximately 2.3-fold greater in recipients with high compared with normal progesterone. The present study lends strong support to the hypothesis that an earlier rise in progesterone after conception stimulates blastocyst growth and the development of competent embryos.
Differential neuroprotective and antiinflammatory effects of estrogen receptor (ER)α and ERβ ligand treatment
Authors: Tiwari-Woodruff Seema , Morales Laurie Beth J. , Lee Ruri , Voskuhl Rhonda R.
Published: September 2007

Treatment with either estradiol or an estrogen receptor (ER)α ligand has been shown to be both antiinflammatory and neuroprotective in a variety of neurological disease models, but whether neuroprotective effects could be observed in the absence of an antiinflammatory effect has remained unknown. Here, we have contrasted effects of treatment with an ERα vs. an ERβ ligand in experimental autoimmune encephalomyelitis, the multiple sclerosis model with a known pathogenic role for both inflammation and neurodegeneration. Clinically, ERα ligand treatment abrogated disease at the onset and throughout the disease course. In contrast, ERβ ligand treatment had no effect at disease onset but promoted recovery during the chronic phase of the disease. ERα ligand treatment was antiinflammatory in the systemic immune system, whereas ERβ ligand treatment was not. Also, ERα ligand treatment reduced CNS inflammation, whereas ERβ ligand treatment did not. Interestingly, treatment with either the ERα or the ERβ ligand was neuroprotective, as evidenced by reduced demyelination and preservation of axon numbers in white matter, as well as decreased neuronal abnormalities in gray matter. Thus, by using the ERβ selective ligand, we have dissociated the antiinflammatory effect from the neuroprotective effect of estrogen treatment and have shown that neuroprotective effects of estrogen treatment do not necessarily depend on antiinflammatory properties. Together, these findings suggest that ERβ ligand treatment should be explored as a potential neuroprotective strategy in multiple sclerosis and other neurodegenerative diseases, particularly because estrogen-related toxicities such as breast and uterine cancer are mediated through ERα.
Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template
Authors: Tsai Ching-Hsuan , Chen Jingyang , Szostak Jack W.
Published: September 2007

Glycerol nucleic acid (GNA) is an interesting alternative base-pairing system based on an acyclic, glycerol-phosphate backbone repeat unit. The question of whether DNA polymerases can catalyze efficient template-dependent synthesis using GNA as the template is of particular interest because GNA is unable to form a stable duplex with DNA. In the present study, we screened a variety of DNA polymerases for GNA-dependent DNA synthesis. We find that Bst DNA polymerase can catalyze full-length DNA synthesis on a dodecamer GNA template. The efficiency of DNA synthesis is increased by replacing adenine with diaminopurine in both the GNA template and the DNA monomers and by the presence of manganese ions. We suggest that the BstDNA polymerase maintains a short, transient region of base-pairing between the DNA product strand and the GNA template, but that stable duplex formation between product and template strands is not required for template-dependent polymerization.
Light signaling to the zebrafish circadian clock by
Cryptochrome 1a
Authors: Tamai T. Katherine , Young Lucy C. , Whitmore David
Published: September 2007

Zebrafish tissues and cells have the unusual feature of not only containing a circadian clock, but also being directly light-responsive. Several zebrafish genes are induced by light, but little is known about their role in clock resetting or the mechanism by which this might occur. Here we show that
Cryptochrome 1a
(
Cry1a
) plays a key role in light entrainment of the zebrafish clock. Intensity and phase response curves reveal a strong correlation between light induction of
Cry1a
and clock resetting. Overexpression studies show that
Cry1a
acts as a potent repressor of clock function and mimics the effect of constant light to “stop” the circadian oscillator. Yeast two-hybrid analysis demonstrates that the Cry1a protein interacts directly with specific regions of core clock components, CLOCK and BMAL, blocking their ability to fully dimerize and transactivate downstream targets, providing a likely mechanism for clock resetting. A comparison of entrainment of zebrafish cells to complete versus skeleton photoperiods reveals that clock phase is identical under these two conditions. However, the amplitude of the core clock oscillation is much higher on a complete photoperiod, as are the levels of light-induced
Cry1a
. We believe that
Cry1a
acts on the core clock machinery in both a continuous and discrete fashion, leading not only to entrainment, but also to the establishment of a high-amplitude rhythm and even stopping of the clock under long photoperiods.
Antipsychotic drugs reverse the disruption in prefrontal cortex function produced by NMDA receptor blockade with phencyclidine
Authors: Kargieman Lucila , Santana Noemí , Mengod Guadalupe , Celada Pau , Artigas Francesc
Published: September 2007

NMDA receptor (NMDA-R) antagonists are extensively used as schizophrenia models because of their ability to evoke positive and negative symptoms as well as cognitive deficits similar to those of the illness. Cognitive deficits in schizophrenia are associated with prefrontal cortex (PFC) abnormalities. These deficits are of particular interest because an early improvement in cognitive performance predicts a better long-term clinical outcome. Here, we examined the effect of the noncompetitive NMDA-R antagonist phencyclidine (PCP) on PFC function to understand the cellular and network elements involved in its schizomimetic actions. PCP induces a marked disruption of the activity of the PFC in the rat, increasing and decreasing the activity of 45% and 33% of the pyramidal neurons recorded, respectively (22% of the neurons were unaffected). Concurrently, PCP markedly reduced cortical synchrony in the delta frequency range (0.3–4 Hz) as assessed by recording local field potentials. The subsequent administration of the antipsychotic drugs haloperidol and clozapine reversed PCP effects on pyramidal cell firing and cortical synchronization. PCP increased
c-fos
expression in PFC pyramidal neurons, an effect prevented by the administration of clozapine. PCP also enhanced
c-fos
expression in the centromedial and mediodorsal (but not reticular) nuclei of the thalamus, suggesting the participation of enhanced thalamocortical excitatory inputs. These results shed light on the involvement of PFC in the schizomimetic action of NMDA-R antagonists and show that antipsychotic drugs may partly exert their therapeutic effect by normalizing a disrupted PFC activity, an effect that may add to subcortical dopamine receptor blockade.
Nuclear gene silencing directs reception of long-distance mRNA silencing in
Arabidopsis
Authors: Brosnan C. A. , Mitter N. , Christie M. , Smith N. A. , Waterhouse P. M. , Carroll B. J.
Published: September 2007

In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway,
NRPD1a
encoding RNA polymerase IVa,
RNA-dependent RNA polymerase 2
(
RDR2
), and
DICER-like 3
(
DCL3
), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway,
argonaute4
(
ago4
), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant
rdr6
shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several
dcl
genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock.
dcl1–8
and a
dcl2 dcl3 dcl4
triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission.
Axonal netrin-Gs transneuronally determine lamina-specific subdendritic segments
Authors: Nishimura-Akiyoshi Sachiko , Niimi Kimie , Nakashiba Toshiaki , Itohara Shigeyoshi
Published: September 2007

Axons from a distinct group of neurons make contact with dendritic trees of target neurons in clearly segregated and laminated patterns, thereby forming functional units for processing multiple inputs of information in the vertebrate central nervous system. Whether and how dendrites acquire lamina-specific properties corresponding to each pathway is not known. We show here that vertebrate-specific membrane-anchored members of the UNC-6/netrin family, netrin-G1 and -G2, organize the lamina/pathway-specific differentiation of dendrites. Netrin-G1 and -G2 distribute on axons of different pathways and specifically interact with receptors NGL-1 and -2, respectively. In the hippocampus, parietal cortex, and piriform cortex, NGL-1 is concentrated in the dendritic segments corresponding to the lamina-specific termination of netrin-G1-positive axons, and NGL-2 is concentrated in distinct dendritic segments corresponding to the termination of netrin-G2-positive axons. In netrin-G1- and -G2-deficient mice, in which axonal path-finding is normal, the segmental distribution of NGL-1 and -2 is selectively disrupted, and the individual receptors are diffused along the dendrites. These findings indicate that transneuronal interactions of netrin-Gs and their specific receptors provide a molecular basis for the axonal innervation-dependent mechanism of postsynaptic membrane organization, and provide insight into the formation of the laminar structure within the dendrites.
UTF1 is a chromatin-associated protein involved in ES cell differentiation
Authors: van den Boom Vincent , Kooistra Susanne M. , Boesjes Marije , Geverts Bart , Houtsmuller Adriaan B. , Monzen Koshiro , Komuro Issei , Essers Jeroen , Drenth-Diephuis Loes J. , Eggen Bart J.L.
Published: September 2007

Embryonic stem (ES) cells are able to grow indefinitely (self-renewal) and have the potential to differentiate into all adult cell types (pluripotency). The regulatory network that controls pluripotency is well characterized, whereas the molecular basis for the transition from self-renewal to the differentiation of ES cells is much less understood, although dynamic epigenetic gene silencing and chromatin compaction are clearly implicated. In this study, we report that UTF1 (undifferentiated embryonic cell transcription factor 1) is involved in ES cell differentiation. Knockdown of UTF1 in ES and carcinoma cells resulted in a substantial delay or block in differentiation. Further analysis using fluorescence recovery after photobleaching assays, subnuclear fractionations, and reporter assays revealed that UTF1 is a stably chromatin-associated transcriptional repressor protein with a dynamic behavior similar to core histones. An N-terminal Myb/SANT domain and a C-terminal domain containing a putative leucine zipper are required for these properties of UTF1. These data demonstrate that UTF1 is a strongly chromatin-associated protein involved in the initiation of ES cell differentiation.
Msk is required for nuclear import of TGF-β/BMP-activated Smads
Authors: Xu Lan , Yao Xiaohao , Chen Xiaochu , Lu Peiyuan , Zhang Biliang , Ip Y. Tony
Published: September 2007

Nuclear translocation of Smad proteins is a critical step in signal transduction of transforming growth factor β (TGF-β) and bone morphogenetic proteins (BMPs). Using nuclear accumulation of the Drosophila Smad Mothers against Decapentaplegic (Mad) as the readout, we carried out a whole-genome RNAi screening in Drosophila cells. The screen identified moleskin (msk) as important for the nuclear import of phosphorylated Mad. Genetic evidence in the developing eye imaginal discs also demonstrates the critical functions of msk in regulating phospho-Mad. Moreover, knockdown of importin 7 and 8 (Imp7 and 8), the mammalian orthologues of Msk, markedly impaired nuclear accumulation of Smad1 in response to BMP2 and of Smad2/3 in response to TGF-β. Biochemical studies further suggest that Smads are novel nuclear import substrates of Imp7 and 8. We have thus identified new evolutionarily conserved proteins that are important in the signal transduction of TGF-β and BMP into the nucleus.
New Tetrahymena basal body protein components identify basal body domain structure
Authors: Kilburn Chandra L. , Pearson Chad G. , Romijn Edwin P. , Meehl Janet B. , Giddings Thomas H. , Culver Brady P. , Yates John R. , Winey Mark
Published: September 2007

Basal bodies organize the nine doublet microtubules found in cilia. Cilia are required for a variety of cellular functions, including motility and sensing stimuli. Understanding this biochemically complex organelle requires an inventory of the molecular components and the contribution each makes to the overall structure. We define a basal body proteome and determine the specific localization of basal body components in the ciliated protozoan Tetrahymena thermophila. Using a biochemical, bioinformatic, and genetic approach, we identify 97 known and candidate basal body proteins. 24 novel T. thermophila basal body proteins were identified, 19 of which were localized to the ultrastructural level, as seen by immunoelectron microscopy. Importantly, we find proteins from several structural domains within the basal body, allowing us to reveal how each component contributes to the overall organization. Thus, we present a high resolution localization map of basal body structure highlighting important new components for future functional studies.
Cdc42-interacting protein–4 functionally links actin and microtubule networks at the cytolytic NK cell immunological synapse
Authors: Banerjee Pinaki P. , Pandey Rahul , Zheng Rena , Suhoski Megan M. , Monaco-Shawver Linda , Orange Jordan S.
Published: September 2007

An essential function of the immunological synapse (IS) is directed secretion. NK cells are especially adept at this activity, as they direct lytic granules to the synapse for secretion, which enables cytotoxicity and facilitates host defense. This initially requires rearrangement of the actin cytoskeleton and, subsequently, microtubule-dependent trafficking of the lytic granules. As these two steps are sequential, specific linkages between them are likely to serve as critical regulators of cytotoxicity. We studied Cdc42-interacting protein–4 (CIP4), which constitutively interacts with tubulin and microtubules but focuses to the microtubule organizing center (MTOC) after NK cell activation, when it is able to associate with Wiskott-Aldrich syndrome protein (WASp) and the actin filament–rich IS. WASp deficiency, overexpression of CIP4, or parts of CIP4 interfere with this union and block normal CIP4 localization, MTOC polarization to the IS, and cytotoxicity. Reduction of endogenous CIP4 expression using small interfering RNA similarly inhibits MTOC polarization and cytotoxic activity but does not impair actin filament accumulation at the IS, or Cdc42 activation. Thus, CIP4 is an important cytoskeletal adaptor that functions after filamentous actin accumulation and Cdc42 activation to enable MTOC polarization and NK cell cytotoxicity.
Programmed death-1 (PD-1) defines a transient and dysfunctional oligoclonal T cell population in acute homeostatic proliferation
Authors: Lin Sue-Jane , Peacock Craig D. , Bahl Kapil , Welsh Raymond M.
Published: September 2007

The host responds to lymphopenic environments by acute homeostatic proliferation, which is a cytokine- and endogenous peptide-driven expansion of lymphocytes that restores the numbers and diversity of T cells. It is unknown how these homeostatically proliferating (HP) cells are ultimately controlled. Using a system where lymphocytic choriomeningitis virus–immune C57BL/6 splenocytes were transferred into lymphopenic T cell–deficient hosts and allowed to reconstitute the environment, we defined the following three populations of T cells: slowly dividing Ly6C+ cells, which contained bona fide virus-specific memory cells, and more rapidly dividing Ly6C− cells segregating into programmed death (PD)-1+ and PD-1− fractions. The PD-1+ HP cell population, which peaked in frequency at day 21, was dysfunctional in that it failed to produce interferon γ or tumor necrosis factor α on T cell receptor (TCR) stimulation, had down-regulated expression of interleukin (IL)-7Rα, IL-15Rβ, and Bcl-2, and reacted with Annexin V, which is indicative of a preapoptotic state. The PD-1+ HP cells, in contrast to other HP cell fractions, displayed highly skewed TCR repertoires, which is indicative of oligoclonal expansion; these skewed repertoires and the PD-1+ population disappeared by day 70 from the host, presumably because of apoptosis. These results suggest that PD-1 may play a negative regulatory role to control rapidly proliferating and potentially pathogenic autoreactive CD8+ T cells during homeostatic reconstitution of lymphopenic environments.
Chromosomal reinsertion of broken RSS ends during T cell development
Authors: Curry John D. , Schulz Danae , Guidos Cynthia J. , Danska Jayne S. , Nutter Lauryl , Nussenzweig Andre , Schlissel Mark S.
Published: September 2007

The V(D)J recombinase catalyzes DNA transposition and translocation both in vitro and in vivo. Because lymphoid malignancies contain chromosomal translocations involving antigen receptor and protooncogene loci, it is critical to understand the types of “mistakes” made by the recombinase. Using a newly devised assay, we characterized 48 unique TCRβ recombination signal sequence (RSS) end insertions in murine thymocyte and splenocyte genomic DNA samples. Nearly half of these events targeted “cryptic” RSS-like elements. In no instance did we detect target-site duplications, which is a hallmark of recombinase-mediated transposition in vitro. Rather, these insertions were most likely caused by either V(D)J recombination between a bona fide RSS and a cryptic RSS or the insertion of signal circles into chromosomal loci via a V(D)J recombination-like mechanism. Although wild-type, p53, p53 x scid, H2Ax, and ATM mutant thymocytes all showed similar levels of RSS end insertions, core-RAG2 mutant thymocytes showed a sevenfold greater frequency of such events. Thus, the noncore domain of RAG2 serves to limit the extent to which the integrity of the genome is threatened by mistargeting of V(D)J recombination.
An Alternative Scoring System to Predict Risk for Surgical Site Infection Complicating Coronary Artery Bypass Graft Surgery
Authors: Friedman N. Deborah , Bull Ann L. , Russo Philip L. , Leder Karin , Reid Christopher , Billah Baki , Marasco Silvana , McBryde Emma , Richards Michael J.
Published: September 2007

Objective.

To analyze the risk factors for surgical site infection (SSI) complicating coronary artery bypass graft (CABG) surgery and to create an alternative SSI risk score based on the results of multivariate analysis.

Methods.

A prospective cohort study involving inpatient and laboratory-based surveillance of patients who underwent CABG surgery over a 27-month period from January 1, 2003 through March 31, 2005. Data were obtained from 6 acute care hospitals in Victoria, Australia, that contributed surveillance data for SSI complicating CABG surgery to the Victorian Hospital Acquired Infection Surveillance System Coordinating Centre and the Australasian Society of Cardiac and Thoracic Surgeons, also in Victoria.

Results.

A total of 4,633 (93%) of the 4,987 patients who underwent CABG surgery during this period were matched in the 2 systems databases. There were 286 SSIs and 62 deep or organ space sternal SSIs (deep or organ space sternal SSI rate, 1.33%). Univariate analysis revealed that diabetes mellitus, body mass index (BMI) greater than 35, and receipt of blood transfusion were risk factors for all types of SSI complicating CABG surgery. Six multivariate analysis models were created to examine either preoperative factors alone or preoperative factors combined with operative factors. All models revealed diabetes and BMI of 30 or greater as risk factors for SSI complicating CABG surgery. A new preoperative scoring system was devised to predict sternal SSI, which assigned 1 point for diabetes, 1 point for BMI of 30 or greater but less than 35, and 2 points for BMI of 35 or greater. Each point in the scoring system represented approximately a doubling of risk of SSI. The new scoring system performed better than the National Nosocomial Infections Surveillance System (NNIS) risk index at predicting SSI.

Conclusion.

A new weighted scoring system based on preoperative risk factors was created to predict sternal SSI risk following CABG surgery. The new scoring system outperformed the NNIS risk index. Future studies are needed to validate this scoring system.
Outbreak ofAcinetobacter baumanniiBacteremia Related to Contaminated Morphine Used for Patient-Controlled Analgesia
Authors: Lee Hsin-Chun , Lee Nan-Yao , Chang Chia-Ming , Chou Cheng-Yang , Wu Yi-Hui , Wang Li-Rong , Ko Nai-Ying , Liu Ching-Chuan , Ko Wen-Chien
Published: September 2007

We investigated a cluster of postoperative febrile episodes and episodes ofAcinetobacter baumanniibacteremia in obstetrics and gynecology wards after an electrical blackout and loss of the water supply. The use of patient-controlled analgesia was the only independent risk factor associated with postoperative fever, andA. baumanniiisolates recovered from the blood of patients who had received patient-controlled analgesia were genetically related to an isolate recovered from the diluted morphine solution used for this procedure. After inappropriate preparation of the morphine solution was identified and stopped, the outbreak ended.
Surveillance of Occupational Blood and Body Fluid Exposures Among French Healthcare Workers in 2004
Authors: Venier A. G. , Vincent A. , L'Hériteau F. , Floret N. , Sénéchal H. , Abiteboul D. , Reyreaud E. , Coignard B. , Parneix P.
Published: September 2007

Objective.

To estimate the incidence rate of reported occupational blood and body fluid exposures among French healthcare workers (HCWs).

Design.

Prospective national follow-up of HCWs from January 1 to December 31, 2004.

Setting.

University hospitals, hospitals, clinics, local medical centers, and specialized psychiatric centers were included in the study on a voluntary basis.

Participants.

At participating medical centers, every reported blood and body fluid exposure was documented by the occupational practitioner in charge of the exposed HCW by use of an anonymous, standardized questionnaire.

Results.

A total of 375 medical centers (15% of French medical centers, accounting for 29% of hospital beds) reported 13,041 blood and body fluid exposures; of these, 9,396 (72.0%) were needlestick injuries. Blood and body fluid exposures were avoidable in 39.1% of cases (5,091 of 13,020), and 52.2% of percutaneous injuries (4,986 of 9,552) were avoidable (5.9% due to needle recapping). Of 10,656 percutaneous injuries, 22.6% occurred during an injection, 17.9% during blood sampling, and 16.6% during surgery. Of 2,065 splashes, 22.6% occurred during nursing activities, 19.1% during surgery, 14.1% during placement or removal of an intravenous line, and 12.0% during manipulation of a tracheotomy tube. The incidence rates of exposures were 8.9 per 100 hospital beds (95% confidence interval [CI], 8.7-9.0 exposures), 2.2 per 100 full-time—equivalent physicians (95% CI, 2.4-2.6 exposures), and 7.0 per 100 full-time—equivalent nurses (95% CI, 6.8-7.2 exposures). Human immunodeficiency virus serological status was unknown for 2,789 (21.4%) of 13,041 patients who were the source of the blood and body fluid exposures.

Conclusion.

National surveillance networks for blood and body fluid exposures help to better document their characteristics and risk factors and can enhance prevention at participating medical centers.
Surgical Site Infection After Surgery to Repair Femoral Neck Fracture: A French Multicenter Retrospective Study
Authors: Merrer Jacques , Girou Emmanuelle , Lortat-Jacob Alain , Montravers Philippe , Lucet Jean-Christophe ,   Groupe de Recherche sur l'Antibioprophylaxie en Chirurgie
Published: September 2007

Objective.

Femoral neck fracture is the most frequent orthopedic emergency among elderly persons. Despite a high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage in this population, no multicenter study of antibiotic prophylaxis practices and the rate and microbiological characteristics of surgical site infection (SSI) has been performed in France.

Design.

Retrospective, multicenter cohort study.

Setting.

Twenty-two university and community hospitals in France.

Patients.

Each center provided data on 25 consecutive patients who underwent surgery for femoral neck fracture during the first quarter of 2005. Demographic, clinical, and follow-up characteristics were recorded, and most patients had a follow-up office visit or were involved in a telephone survey 1 year after surgery.

Results.

These 22 centers provided data on 541 patients, 396 (73%) of whom were followed up 1 year after surgery. Of 504 (93%) patients for whom antibiotic prophylaxis was recorded, 433 (86%) received a cephalosporin. Twenty-two patients had an SSI, for a rate of 5.6% (95% confidence interval, 3.7-8.0). SSI was reported for 15 (6.9%) of patients who had a prosthesis placed and for 7 (3.9%) who underwent osteosynthesis (P = .27). SSI was diagnosed a median of 30 days after surgery (interquartile range, 21-41 days); 7 (32%) of these SSIs were superficial infections, and 15 (68%) were deep or organ-space infections. MRSA caused 7 SSIs (32%), Pseudomonas aeruginosa caused 5 (23%), other staphylococci caused 4 (18%), and other bacteria caused 2 (9%); the etiologic pathogen was unknown in 4 cases (18%). Reoperation was performed for 14 patients with deep or organ-space SSI, including 6 of 7 patients with MRSA SSI. The mortality rate 1 year after surgery was 20% overall but 50% among patients with SSI. In univariate analysis, only the National Nosocomial Infections Surveillance System risk index score was significantly associated with SSI (P = .006).

Conclusions.

SSI after surgery for femoral neck fracture is severe, and MRSA is the most frequently encountered etiologic pathogen. A large, multicenter prospective trial is necessary to determine whether the use of antibiotic prophylaxis effective against MRSA would decrease the SSI rate in this population.
Emergence of Staphylococcal Cassette ChromosomemecType IV Methicillin-ResistantStaphylococcus aureusas a Cause of Ventilator-Associated Pneumonia
Authors: Neofytos D. , Kuhn B. , Shen S. , Zhu X. Hua , Jungkind D. , Flomenberg P.
Published: September 2007

Staphylococcal cassette chromosomemec(SCCmec) type IV methicillin-resistantStaphylococcus aureus(MRSA) strains were identified in 8 (19.5%) of 41 consecutive patients with MRSA ventilator-associated pneumonia (VAP) in this retrospective, observational study. There were no significant differences in VAP severity and crude mortality rates between patients with SCCmectype II strains and patients with SCCmectype IV strains.
Meningitis Following Spinal Anesthesia: 6 Cases in 5 Years
Authors: Rubin Lisa , Sprecher Hannah , Kabaha Ahmed , Weber Gabriel , Teitler Nava , Rishpon Shmuel
Published: September 2007

We describe 6 cases of meningitis after spinal anesthesia associated with a single anesthesiologist over the course of 5 years. The earliest case occurred in 2000, and the other 5 cases occurred over the course of 14 months in 2004-2005. The case identified in 2000 was culture-positive for Streptococcus salivarius. The other 5 cases were culture-negative for this organism but in 2 cases, the cerebrospinal fluid was found to be positive for bacterial DNA that was identified as belonging to S. salivarius by sequencing of the 16S rRNA gene. The association with a single anesthesiologist and a single hospital during a relatively short interval, however, lead us to believe that these occurrences are part of a series associated with possible violations of aseptic technique.
Raising Standards While Watching the Bottom Line Making a Business Case for Infection Control
Authors: Perencevich Eli N. , Stone Patricia W. , Wright Sharon B. , Carmeli Yehuda , Fisman David N. , Cosgrove Sara E.
Published: September 2007

While society would benefit from a reduced incidence of nosocomial infections, there is currently no direct reimbursement to hospitals for the purpose of infection control, which forces healthcare institutions to make economic decisions about funding infection control activities. Demonstrating value to administrators is an increasingly important function of the hospital epidemiologist because healthcare executives are faced with many demands and shrinking budgets. Aware of the difficulties that face local infection control programs, the Society for Healthcare Epidemiology of America (SHEA) Board of Directors appointed a task force to draft this evidence-based guideline to assist hospital epidemiologists in justifying and expanding their programs. In Part 1, we describe the basic steps needed to complete a business-case analysis for an individual institution. A case study based on a representative infection control intervention is provided. In Part 2, we review important basic economic concepts and describe approaches that can be used to assess the financial impact of infection prevention, surveillance, and control interventions, as well as the attributable costs of specific healthcare-associated infections. Both parts of the guideline aim to provide the hospital epidemiologist, infection control professional, administrator, and researcher with the tools necessary to complete a thorough business-case analysis and to undertake an outcome study of a nosocomial infection or an infection control intervention.
MSQT for choosing SNP assays from multiple DNA alignments
Authors: Warthmann Norman , Fitz Joffrey , Weigel Detlef
Published: September 2007

Motivation: One challenging aspect of genotyping and association mapping projects is often the identification of markers that are informative between groups of individuals and to convert these into genotyping assays.

Results: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design. MSQT was applied to Arabidopsis thaliana sequence data to develop SNP genotyping assays that distinguish a recurrent parent (Col-0) from five other strains. SNPs with intermediate allele frequencies were also identified and developed into markers suitable for efficient genetic mapping among random pairs of wild strains.

Availability: The source code for MSQT is available at http://msqt.weigelworld.org, together with an online instance of MSQT containing data on 1214 sequenced fragments from 96 ecotypes (wild inbred strains) of the reference plant A.thaliana. All SNP genotyping assays are available in several formats for broad community use.

Contact:  weigel@weigelworld.org

Supplementary information: Supplementary data are available at Bioinformatics online.