bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectral analyses of sabkha sediments with implications for remote sensing on Mars
Authors: Howari F.M.
Published: July 2006

Spectroscopic investigations of surface mineral components, expected to exist on the surface of Mars, using multiple spectral ranges and techniques, are vital to obtain the ground truth information or reference data for Mars exploration missions. This paper presents visible, near-infrared, thermal infrared reflectance and thermal infrared transmission spectra, as well as X-ray diffraction and scanning electron microscope/energy dispersive X-ray analyses of salt crusts and sediments interleaved with cyanobacterial materials from a coastal zone of the United Arab Emirates, where sabkhas exist. The samples obtained from sabkhas were characterized because they contain minerals requiring the water for formation and they provide a possible environment for some of the earliest organisms on Earth. The surface minerals identified include gypsum, calcite, halite, aragonite and dolomite. These sediments were found to be mixed with each other and intermingled with an algal mat, which consisted of cyanobacteria. If such materials formed in similar environments on Mars, their identification would be important for understanding the geobiological conditions of the planet and the potential habitability for life.
New Directions in Pediatric Neuro-Oncology Practice: Impact of the Children's Cancer Group Study 9933, a Phase II Study of High-Dose Chemotherapy Before Radiation in Children with Newly Diagnosed High-Grade Astrocytoma
Authors: MacDonald Tobey J.
Published: July 2006

ABSTRACT

Background: Despite the use of surgery, radiotherapy (RT) and standard chemotherapy, childhood high-grade astrocytoma (HGA) continues to carry a dismal prognosis. In an attempt to identify effective drug combinations and an alternative treatment strategy, the Children's Cancer Group (CCG) conducted a nationwide clinical trial that prospectively evaluated 102 children with HGA and post-operative residual disease for efficacy and toxicity of four courses of high-dose chemotherapy (HDCT) before RT. Design and methods: Patients were randomly assigned to one of three couplets of drugs: carboplatin/etoposide (Regimen A); ifosfamide/etoposide (Regimen B); or cyclophosphamide/etoposide (Regimen C). After HDCT, all patients received local RT followed by lomustine and vincristine. Results: Of 76 evaluable patients (median age 11.95 years, range 3–20 years), 30 patients relapsed during HDCT and 11 others did not complete HDCT due to toxicity. Non-hematologic serious toxicities were common (29%) and 21% of patients did not receive RT. Objective response rates were not associated with amount of residual disease and did not statistically differ between regimens: 27% (Regimen A), 8% (Regimen B), and 29% (Regimen C). Overall survival (OS) was 24 ± 5% at 5 years and did not differ between groups. The 5-year, event-free survival (EFS) for all patients was 8 ± 3% and 14 ± 7% for Regimen A (p = 0.07). Patients who responded to HDCT had a nominally higher survival rate (p = 0.03 for trend). Interpretation: HDCT prior to RT provides no additional clinical benefit to conventional treatment in HGA, regardless of the amount of measurable residual tumor, and adversely effects ability to complete RT. Strong consideration should be given to investigating alternative strategies and novel biologic agents for this disease.
A Double-Blind, Randomized Clinical Trial to Assess the Augmentation with Nimodipine of Antidepressant Therapy in the Treatment of “Vascular Depression”
Authors: Taragano F.E. , Bagnati P.M. , Allegri R.F.
Published: July 2006

ABSTRACT

There is evidence for an association between vascular disease and depression, and in particular between cerebrovascular disease and depression, especially that occurring later in life. Among the diverse psychiatric diseases, the one which is most widely studied concerning the relationship with the vascular system, is depression. The risk relationship between depression and vascular events is a two-way road: the presence of depression increases the cerebrovascular and cardiovascular event risk (worsening its evolution and prognosis, as well) and a patient evidencing cerebrovascular or heart disease, will also show an increase in the risk of suffering depression (Taragano et al., 2005). Depression is a common cause of disability in the elderly. It reduces quality of life and represents a serious public health problem (Beekman et al., 2001; Steffens et al., 2000). Its prevalence in late life is 2–3% for major depression and 12–15% for all depressive syndromes (Beekman et al., 1999).
An Event-Related Potential Investigation of Varieties of Negative Priming
Authors: Gibbons Henning
Published: July 2006

In an event-related potential (ERP) study of varieties of negative priming (NP), 20 participants performed two basic tasks, identification and localization. NP was established in response times (RTs) for two different conditions employed in the literature, DT (distractor-target shifts between subsequent displays), and DTTD (distractor-target reversals). With identification, there were two findings specific to DTTD: reduced amplitude of frontocentral P200 and earlier onset of response-locked lateralized readiness potential (R-LRP). The pattern suggests that DTTD probes were perceived as highly similar to the prime, causing a tendency to repeat the prime response. Identity-based DT had no significant ERP correlate but was accompanied by wrong preactivation in the stimulus-locked LRP (S-LRP). Regarding localization, P300 seemed reduced with the DTTD condition. However, current-source density (CSD) analysis suggested additional frontal and occipital N2 components, indicating inhibition of a tendency to repeat the prime response and persisting inhibition of the prime distractor location, respectively. A larger frontopolar N440 accompanying spatial NP suggested attempts to resolve conflicts occurring at late stages of processing. Data support the view of NP effects being caused by different subprocesses. Furthermore, distinct brain processes seem to underlie NP obtained from DT and DTTD conditions.
Effects of a volcanic plume on thermal imaging data
Authors: Sawyer Georgina M. , Burton Michael R.
Published: July 2006

Ground‐based thermal imaging is becoming an increasingly important tool for volcano surveillance, however the impact of volcanic plumes on quantitative measurements of surface temperature has not been previously evaluated. Here we use a radiative transfer model to simulate gas (primarily H2O and SO2) and aerosol absorptions over the path between a thermal camera and a heat source on Stromboli volcano, Italy. A FTIR spectrometer was used to quantify path amounts of gases likely to be encountered when making thermal measurements of the active craters. We find that when using a camera sensitive from 7.5 to 13 μm, underestimates of ∼400 K may be produced when viewing a source with an actual temperature of 1200 K. Cameras that operate between 3 and 5 μm are somewhat less susceptible to these errors.
Differences between CME‐driven storms and CIR‐driven storms
Authors: Borovsky Joseph E. , Denton Michael H.
Published: July 2006

Twenty one differences between CME‐driven geomagnetic storms and CIR‐driven geomagnetic storms are tabulated. (CME‐driven includes driving by CME sheaths, by magnetic clouds, and by ejecta; CIR‐driven includes driving by the associated recurring high‐speed streams.) These differences involve the bow shock, the magnetosheath, the radiation belts, the ring current, the aurora, the Earth's plasma sheet, magnetospheric convection, ULF pulsations, spacecraft charging in the magnetosphere, and the saturation of the polar cap potential. CME‐driven storms are brief, have denser plasma sheets, have strong ring currents and Dst, have solar energetic particle events, and can produce great auroras and dangerous geomagnetically induced currents; CIR‐driven storms are of longer duration, have hotter plasmas and stronger spacecraft charging, and produce high fluxes of relativistic electrons. Further, the magnetosphere is more likely to be preconditioned with dense plasmas prior to CIR‐driven storms than it is prior to CME‐driven storms. CME‐driven storms pose more of a problem for Earth‐based electrical systems; CIR‐driven storms pose more of a problem for space‐based assets.
A statistical comparison of hot‐ion properties at geosynchronous orbit during intense and moderate geomagnetic storms at solar maximum and minimum
Authors: Zhang Jichun , Liemohn Michael W. , Thomsen Michelle F. , Kozyra Janet U. , Denton Michael H. , Borovsky Joseph E.
Published: July 2006

Hot‐ion measurements at geosynchronous orbit from the Los Alamos Magnetospheric Plasma Analyzer (MPA) instrument during geomagnetic storms at solar maximum (July 1999–June 2002) and at solar minimum (July 1994–June 1997) are collected, categorized, and analyzed through the superposed epoch technique. To investigate this source of the storm‐time ring current, the local time (LT) and universal time (UT) dependence of the average variations of hot‐ion fluxes (at the energies of ∼30, ∼17, ∼8, and ∼1 keV), density, temperature, entropy, and temperature anisotropy are examined and compared among four storm categories, i.e., 44 intense storms and 120 moderate storms, defined by the pressure corrected Dst (Dst*), at the two solar extrema. All the hot‐ion parameters are highly disturbed around Dst*min; they show distinct peaks or minima and display obvious increase or decrease regions, whose locations do not change much with levels of geomagnetic activity and solar activity. It is also found that intense storms at solar minimum always have the highest (lowest) average peak value (minimum) in each hot‐ion parameter. Around Dst*min in each storm category, hot ions are clearly denser near dawn than those near dusk. On the nightside and in the afternoon sector, temperature and entropy during solar minimum storms are usually higher than those during solar maximum storms; there is actually no clear temperature and entropy enhancement during solar maximum storms. During each type of storm, hot ions are isotropic on the nightside but anisotropic (Tper/Tpar > 1) close to noon.
Airborne measurements of spectral direct aerosol radiative forcing in the Intercontinental chemical Transport Experiment/Intercontinental Transport and Chemical Transformation of anthropogenic pollution, 2004
Authors: Redemann Jens , Pilewskie Peter , Russell Philip B. , Livingston John M. , Howard Steve , Schmid Beat , Pommier John , Gore Warren , Eilers James , Wendisch Manfred
Published: July 2006

As part of the INTEX‐NA (Intercontinental chemical Transport Experiment–North America) and ITCT (Intercontinental Transport and Chemical Transformation of anthropogenic pollution) field studies, the NASA Ames 14‐channel Airborne Tracking Sunphotometer (AATS‐14) and a pair of Solar Spectral Flux Radiometers (SSFR) took measurements from aboard a Sky Research Jet stream 31 (J31) aircraft during 19 science flights over the Gulf of Maine during 12 July to 8 August 2004. The combination of coincident AATS‐14 and SSFR measurements yields plots of net (downwelling minus upwelling) spectral irradiance as a function of aerosol optical depth (AOD) as measured along horizontal flight legs. By definition, the slope of these plots yields the instantaneous change in net irradiance per unit AOD change and is referred to as the instantaneous spectral aerosol radiative forcing efficiency, Ei (W m−2 nm−1). Numerical integration over a given spectral range yields the instantaneous broadband aerosol radiative forcing efficiency (W m−2). This technique for deriving Ei is called the aerosol gradient method. Within 10 case studies considered suitable for our analysis we found a high variability in the derived instantaneous aerosol forcing efficiencies for the visible wavelength range (350–700 nm), with a mean of −79.6 W m−2 and a standard deviation of 21.8 W m−2 (27%). An analytical conversion of the instantaneous forcing efficiencies to 24‐hour‐average values yielded −45.8 ± 13.1 W m−2 (mean ± std). We present spectrally resolved aerosol forcing efficiencies between 350 and 1670 nm, estimates of the midvisible aerosol single scattering albedo and a comparison of observed broadband forcing efficiencies to previously reported values.
On the role of the GRACE mission in the joint assimilation of altimetric and TAO data in a tropical Pacific Ocean model
Authors: Castruccio F. , Verron J. , Gourdeau L. , Brankart J. M. , Brasseur P.
Published: July 2006

Recent advances in our knowledge of the earth geoid have made it possible to exploit absolute sea surface height measurements in realistic numerical modelling studies of the ocean. This letter provides evidence of the benefit of the GRACE referenced mean dynamic topography (MDT) for the simulation of the tropical Pacific ocean through the joint assimilation of altimetric data and of vertical temperature profiles from the TAO/TRITON array. Results are considered in relation to those obtained using a classical model MDT, based on the model itself, and are validated against independent XBT data. The use of the GRACE MDT leads to significantly improved results with respect to these independent data. If the compatibility between the altimetric sea surface height and the TAO/TRITON temperature improves the model simulation, some limitations exist, especially in the Warm Pool where a part of the sea surface height signature is associated to a salinity signal.
Evidence for specific regional patterns of responses to different vasoconstrictors and vasodilators in sheep isolated pulmonary arteries and veins
Authors: Kemp B. K. , Smolich J. J. , Cocks T. M.
Published: July 2006

Responses of large (5–7 mm in diameter) and medium sized (3–4 mm in diameter) branches of sheep isolated intrapulmonary arteries and veins and three groups of small pulmonary arteries (200, 500 and 1000 μm diameter) to the vasoconstrictors endothelin‐1, 5‐hydroxytryptamine (5‐HT), noradrenaline and the thromboxane A2 mimetic, U46619, were examined. Also, relaxation responses to the endothelium‐dependent vasodilators, acetylcholine (ACh), bradykinin and ionomycin and the endothelium‐independent vasodilator, sodium nitroprusside (SNP), were studied to determine their predominant site of action within the pulmonary vasculature.

Endothelin‐1 was the most potent vasoconstrictor tested in all vessels. The maximum response to endothelin‐1, expressed as a percentage of the maximum contraction to KCl depolarization, did not differ significantly between the different vessels. By contrast, pulmonary arteries greater than 200 μm in diameter failed to contract to U46619, whereas U46619 was a potent constrictor of large and medium‐sized veins.

5‐HT caused similar contractions in all arteries >200 μm in diameter, but the maximum response was significantly diminished in smaller arteries. By contrast, the maximum response to noradrenaline was progressively attenuated with decreasing arterial diameter. Both 5‐HT and noradrenaline caused poor contractions in veins. Pulmonary veins were less sensitive to 5‐HT than arteries and at low concentrations 5‐HT caused relaxation. No change in sensitivity to noradrenaline was noted between the arteries and veins.

Relaxation responses to bradykinin and ionomycin decreased progressively along the pulmonary vascular tree and were nearly absent in large veins. Also, ACh was a poor relaxing agent of large and medium‐sized arteries and failed to mediate any relaxation response in other vessel segments. Surprisingly the smallest arteries examined (∼200 μm in diameter) failed to relax to ionomycin, bradykinin and SNP. However, both the sensitivity and maximum relaxation to SNP were similar in all other arterial and venous segments.

In conclusion, marked regional differences in reactivity to both vasoconstrictors and vasodilators occur in arterial and venous segments of the sheep isolated pulmonary vasculature. Such specialization may have important implications for the regulation of resistance in this low tone vascular bed.
Evidence that NO acts as a redundant NANC inhibitory neurotransmitter in the guinea‐pig isolated taenia coli
Authors: Selemidis S. , Satchell D. G. , Cocks T. M.
Published: July 2006

The relative contribution of the putative transmitters, nitric oxide (NO) and an apamin‐sensitive factor, possibly ATP, to inhibitory responses evoked by electrical field stimulation (EFS; 0.2–5 Hz, 0.2 ms duration, supra‐maximal voltage for 10 s) of non‐adrenergic, non‐cholinergic (NANC) nerves was investigated in the guinea‐pig isolated taenia coli contracted with histamine (1 μM).

Peak relaxations to EFS (0.2–5 Hz) were tetrodotoxin (1 μM)‐sensitive, maximal at 0.2 Hz and completely resistant to the nitric oxide synthase inhibitor, NG‐nitro‐L‐arginine (L‐NOARG; 100 μM) in either the presence or absence of atropine (1 μM). Furthermore, the specific inhibitor of soluble guanylyl cyclase, 1H‐[1,2,4] oxadiazolo [4,3‐a] quinoxaline‐1‐one (ODQ; 10 μM), the cytochrome P450 inhibitor and free radical generator, 7‐ethoxyresorufin (7‐ER; 10 μM) and the NO scavenger, oxyhaemoglobin (HbO; 30 μM) had no effect on EFS‐induced relaxations alone and in combination with L‐NOARG (100 μM).

Maximum relaxation to the NO donor, sodium nitroprusside (SNP; 1 μM) was significantly reduced by HbO (30 μM), abolished by 7‐ER (10 μM) and ODQ (10 μM) but was unaffected by apamin (0.1 μM), an inhibitor of small conductance Ca2+‐activated K+ channels.

The relaxation to EFS at 0.2 Hz was resistant to apamin but those to 0.5 and 5 Hz were significantly reduced. EFS (0.2–5 Hz)‐evoked relaxations that persisted in the presence of apamin were further significantly inhibited by L‐NOARG (100 μM) or ODQ (10 μM), but not by HbO (30 μM) or 7‐ER (10 μM).

ATP (1–30 μM) produced concentration‐dependent relaxations that were abolished by apamin (0.1 μM), unaffected by ODQ (10 μM) but only significantly reduced by L‐NOARG (100 μM) at the lowest concentration of ATP (1 μM) used.

Nifedipine (0.3 μM), abolished contractions to 67 mM KCl, histamine (10 μM), endothelin‐1 (0.03 μM), 5‐hydroxytryptamine (5‐HT; 10 μM) and the thromboxane‐mimetic, 9‐11‐dideoxy‐9α, 11α‐methano‐epoxy‐prostaglandin F2α (U46619; 0.1 μM).

The findings of the present study suggest that NO is released during NANC nerve stimulation, but plays no role in NANC relaxations in the guinea‐pig taenia coli unless the effects of another apamin‐sensitive, nerve‐derived hyperpolarizing factor (NDHF) are blocked. Thus, we propose that in this tissue, NO acts as a ‘backup’ or redundant NANC nerve inhibitory transmitter and like NDHF mediates relaxation via hyperpolarization.
Effect of interleukin‐1β, tumour necrosis factor‐α and interferon‐γ on the induction of cyclo‐oxygenase‐2 in cultured human airway smooth muscle cells
Authors: Pang Linhua , Knox Alan J.
Published: July 2006

Increased levels of several pro‐inflammatory cytokines including interleukin‐1β (IL‐1β) and tumour necrosis factor‐α (TNFα) have been found in bronchoalveolar lavage fluid from symptomatic asthmatic patients. IL‐1β, TNFα and interferon‐γ (IFNγ) are known to stimulate a number of cells to produce inflammatory mediators such as prostaglandins. Although airway smooth muscle (ASM) is known to be a rich source of prostaglandins, the regulation of cyclo‐oxygenase (COX) isoforms and prostanoid production by proinflammatory cytokines have not been studied in human airway smooth muscle.

We studied the effects of IL‐1β, TNFα and IFNγ on the induction of two isoforms of cyclo‐oxygenase and its relation to prostaglandin E2 (PGE2) release and COX activity (reflected by PGE2 synthesis from exogenous arachidonic acid) in human cultured airway smooth muscle cells.

IL‐1β, but not TNFα or IFNγ, caused a time‐ and concentration‐dependent enhancement in PGE2 and other prostanoid (6‐keto‐PGF1α, PGF2α, thromboxane B2 (TXB2) and PGD2) production, with PGE2 and 6‐keto‐PGF1α as the principal products. This stimulation was accompanied by a corresponding increase in COX activity.

COX‐2 protein measured by Western blot analysis was not detectable in untreated cells, but was increased in a time‐ and concentration‐dependent manner by IL‐1β, but not TNFα or IFNγ. In contrast, no variation in the expression of COX‐1 protein was observed.

Pretreatment with the conventional non‐steroidal anti‐inflammatory drugs (NSAIDs), indomethacin and ibuprofen, and the selective COX‐2 inhibitors, NS‐398 and nimesulide, completely blocked IL‐1β‐induced PGE2 release and COX activity. The glucocorticosteroid dexamethasone and protein synthesis inhibitors, cycloheximide and actinomycin D, not only markedly inhibited IL‐1β‐stimulated PGE2 release and COX activity but also suppressed IL‐1β‐induced COX‐2 induction.

This study demonstrates that human cultured ASM cells release prostanoids in response to IL‐1β stimulation and that the response is mostly mediated by the induction of COX‐2 rather than COX‐1 isoenzyme, implying that airway smooth muscle may be an important source of prostaglandins in human airways and that COX‐2 may play an important role in the regulation of the inflammatory process in asthma.
Effects of delayed treatment with nebracetam on neurotransmitters in brain regions after microsphere embolism in rats
Authors: Takeo Satoshi , Hayashi Hideki , Miyake Keiko , Takagi Kaori , Tadokoro Mina , Takagi Norio , Oshikawa Sayuri
Published: July 2006

The effects of delayed treatment with nebracetam, a novel nootropic drug, on neurotransmitters of brain regions were examined in rats with microsphere embolism‐induced cerebral ischaemia.

Cerebral ischaemia was induced by administration of 900 microspheres (48 μm) into the internal carotid artery. The rats with stroke‐like symptoms were treated p.o. with 30 mg kg−1 nebracetam twice daily. The levels of acetylcholine, dopamine, noradrenaline, 5‐hydroxytryptamine (5‐HT) and their metabolites in the cerebral cortex, striatum and hippocampus of animals with microsphere embolism were determined by high performance liquid chromatography (h.p.l.c.) on the 3rd and 7th days after the operation.

Although the microsphere embolism induced significant changes in most of the neurotransmitters and some of their metabolites in the brain regions, the delayed treatment with nebracetam partially restored only the hippocampal 5‐HT and the striatal dopamine metabolite contents on the 3rd day.

The hippocampal in vivo 5‐HT synthesis, but not the striatal dopamine synthesis, was attenuated in rats with microsphere embolism on the 3rd day, but was restored by treatment with nebracetam. In vivo striatal dopamine turnover rate of the rats with microsphere embolism was inhibited on the 3rd day irrespective of treatment with nebracetam.

The present study provides evidence for a possible action of nebracetam on 5‐HT metabolism in the ischaemic brain.
The effect of continuous versus intermittent treatment with transdermal nitroglycerin on pacing‐induced preconditioning in conscious rabbits
Authors: Szilvassy Z. , Ferdinandy P. , Nagy I. , Jakab I. , Koltai M.
Published: July 2006

Tolerance to the hypotensive effect of nitroglycerin (NG) blocks preconditioning induced by rapid ventricular pacing (RVP) in rabbits. In the present work the effect of continuous versus intermittent treatment with transdermal nitroglycerin on the pacing‐induced preconditioning phenomenon was studied in conscious rabbits.

RVP (500 beats min−1 over 5 min) increased left ventricular end‐diastolic pressure (LVEDP) from baseline 4.1±0.9 to postpacing 13.8±2.9 mmHg (P<0.001) with a right intraventricular ST‐segment elevation of 1.25±0.13 mV, two indicators of myocardial ischaemia. These changes were significantly attenuated when the RVP period was preceded by a preconditioning pacing of the same rate and duration with an interpacing interval of 5 min.

Protection by preconditioning was abolished when the animals had been made tolerant to the vasodilator effect of 30 μg kg−1 NG by the application of transdermal NG (approx. 0.07 mg kg−1 h−1) over 7 days. Furthermore, transdermal NG per se attenuated both RVP‐induced ST‐segment elevation and LVEDP‐increase over the 7 day period.

With intermittent transdermal NG treatment (12 h ‘patch on’ vs ‘patch off’), neither development of vascular tolerance nor attenuation of the NG‐ or preconditioning‐induced anti‐ischaemic effects were observed. However, the severity of pacing‐induced myocardial ischaemia was significantly increased during the ‘patch off’ periods.

In a second set of experiments, postpacing changes in cardiac cyclic GMP and cyclic AMP levels were determined by means of radioimmunoassay in chronically instrumented anaesthetized open‐chest rabbits with the same NG‐treatment protocols. Preconditioning reduced postpacing increase in cyclic AMP with an increase in cyclic GMP concentrations in hearts of the untreated animals and in those given patches intermittently during both ‘patch on’ and ‘patch off’ periods. However, the preconditioning effect on either cyclic nucleotide was blocked in the tolerant animals.

Transdermal NG increased resting levels of both cardiac cyclic nucleotides in the non‐tolerant but not in the tolerant state. The postpacing increase in cyclic AMP content was inhibited by transdermal NG, independent of vascular tolerance development, whereas, an increase in cyclic GMP content was exclusively seen in the non‐tolerant animals.

We conclude that the anti‐ischaemic effect of NG is independent of the cyclic GMP mechanism in the tolerant state. While intermittent NG therapy prevents development of vascular tolerance and preserves preconditioning, the nitrate‐free periods yield an increased susceptibility of the heart to ischaemic challenges.
X-ray diffraction peaks at glancing incidence and glancing exit from highly mismatched epitaxial layers
Authors: Kaganer V. M. , Shalimov A. , Bak-Misiuk J. , Ploog K. H.
Published: July 2006

We find that the widths of double-crystal x-ray diffraction peaks in asymmetric reflections of relaxed GaAs∕Si(001) heteroepitaxial layers in reciprocal diffraction geometries (glancing incidence and glancing exit) are notably different. This observation is in agreement with previous measurements on other heteroepitaxial systems but apparently contradicts the reciprocity principle of electrodynamics. We show that the apparent contradiction originates from the summation of the scattered waves that are collected by the detector in a double-crystal setup and resolve it by giving an appropriate description of the peak widths.
Band-gap opening in metallic carbon nanotubes adsorbed on H∕Si(001)
Authors: Lee Jung-Yup , Cho Jun-Hyung
Published: July 2006

A recent scanning tunneling microscope nanolithography technique can fabricate one-dimensional “dangling-bond (DB) wire” by the selective removal of H atoms from a H-passivated Si(001) surface along the Si dimer row. We here theoretically investigate the bonding geometry, band structure, and binding mechanism of an armchair (3,3) single-walled carbon nanotube (CNT) adsorbed on the DB wire. We find that the formation of C–Si bonds between the CNT and the DB wire gives rise to hybridization between the carbon π-bond states and the Si dangling-bond states. This hybridization breaks the rotational symmetry of the (3,3) CNT whose π-bonding and π-antibonding bands cross at the Fermi level. As a result, the adsorbed CNT opens an energy gap of ∼0.1eV, yielding a metal-to-semiconductor transition.
Scaling and saturation laws for the expansion of concrete exposed to sulfate attack
Authors: Monteiro Paulo J. M.
Published: July 2006

Reinforced concrete structures exposed to aggressive environments often require repair or retrofit even though they were designed to last >50 years. This statement is especially true for structures subjected to sulfate attack. It is critical that fundamental models of life prediction be developed for durability of concrete. Based on experimental results obtained over a 40-year period, scaling and saturation laws were formulated for concrete exposed to sulfate solution. These features have not been considered in current models used to predict life cycle of concrete exposed to aggressive environment. The mathematical analysis shows that porous concrete made with high and moderate water-to-cement ratios develops a definite scaling law after an initiation time. The scaling coefficient depends on the cement composition but does not depend on the original water-to-cement ratio. Dense concrete made with low water-to-cement ratios develops a cyclic saturation curve. An index for “potential of damage” is created to allow engineers to design concrete structures with better precision and cement chemists to develop portland cements with optimized composition.
CDC7 kinase phosphorylates serine residues adjacent to acidic amino acids in the minichromosome maintenance 2 protein
Authors: Cho Won-Ho , Lee Young-Joo , Kong Soo-Im , Hurwitz Jerard , Lee Joon-Kyu
Published: July 2006

Cdc7 is an essential kinase required for the initiation of eukaryotic DNA replication. Previous studies in many species showed that the minichromosome maintenance complex is a major physiological target of this kinase. In this study, we have mapped the sites in human Mcm2 protein that are phosphorylated by Cdc7. The
in vitro
phosphorylation of several Mcm2 truncated proteins and peptides revealed that Mcm2 contains two major (
5
S and
53
S) and at least three minor phosphorylation sites (
4
S,
7
S, and
59
T) located at the N-terminal region. Alanine substitution experiments with Mcm2 peptides showed that the phosphorylation of
5
S and
53
S by Cdc7 required the presence of an acidic amino acid adjacent to a serine residue. Furthermore, although Cdc7 was unable to phosphorylate a Mcm2 peptide (spanning amino acids 19–30 and containing
26
S and
27
S), it phosphorylated
26
S efficiently when this peptide contained a chemically synthesized phospho-
27
S modification. Hence, additional Cdc7 phosphorylation sites could be generated in Mcm2 by its prior phosphorylation by a cyclin-dependent kinase. This finding may explain why the sequential action of cyclin-dependent and Cdc7 kinases is essential for the initiation of DNA replication.
Spirituality and Addiction: A Research and Clinical Perspective
Authors: Galanter Marc
Published: July 2006

Spirituality is a construct that has recently gained currency among clinicians because of its close association with twelve‐step modalities and its perceived role in the promotion of meaningfulness in recovery from addiction. This article draws on studies from physiology, psychology, and cross‐cultural sources to examine its nature and its relationship to substance use disorders. Illustrations of its potential and limitations as a component of treatment in spiritually oriented recovery movements like Alcoholics Anonymous, meditative practices, and treatment systems for the dually diagnosed are given.
Properties regulating the nature of the plasmacytoid dendritic cell response to Toll-like receptor 9 activation
Authors: Guiducci Cristiana , Ott Gary , Chan Jean H. , Damon Emily , Calacsan Carlo , Matray Tracy , Lee Kyung-Dall , Coffman Robert L. , Barrat Franck J.
Published: July 2006

Human plasmacytoid dendritic cells (PDCs) can produce interferon (IFN)-α and/or mature and participate in the adaptive immune response. Three classes of CpG oligonucleotide ligands for Toll-like receptor (TLR)9 can be distinguished by different sequence motifs and different abilities to stimulate IFN-α production and maturation of PDCs. We show that the nature of the PDC response is determined by the higher order structure and endosomal location of the CpG oligonucleotide. Activation of TLR9 by the multimeric CpG-A occurs in transferrin receptor (TfR)-positive endosomes and leads exclusively to IFN-α production, whereas monomeric CpG-B oligonucleotides localize to lysosome-associated membrane protein (LAMP)-1–positive endosomes and promote maturation of PDCs. However, CpG-B, when complexed into microparticles, localizes in TfR-positive endosomes and induces IFN-α from PDCs, whereas monomeric forms of CpG-A localize to LAMP-1–positive endosomes accompanied by the loss of IFN-α production and a gain in PDC maturation activity. CpG-C sequences, which induce both IFN-α and maturation of PDCs, are distributed in both type of endosomes. Encapsulation of CpG-C in liposomes stable above pH 5.75 completely abrogated the IFN-α response while increasing PDC maturation. This establishes that the primary determinant of TLR9 signaling is not valency but endosomal location and demonstrates a strict compartmentalization of the biological response to TLR9 activation in PDCs.
NK cells promote transplant tolerance by killing donor antigen-presenting cells
Authors: Yu Guang , Xu Xuemin , Vu Minh Diem , Kilpatrick Elizabeth D. , Li Xian Chang
Published: July 2006

Natural killer (NK) cells are programmed to kill target cells without prior antigen priming. Because of their potent cytolytic activities, NK cells are one of the key cell types involved in dismantling allografts. However, in certain transplant models, NK cells also express potent immunoregulatory properties that promote tolerance induction. The precise mechanism for such striking dichotomy remains unknown. In the present study, we showed in a skin transplant model that the skin allografts contain a subset of antigen-presenting cells (APCs) that can home to the recipient mice. We also showed that such graft-derived APCs are usually destroyed by the host NK cells. But in the absence of NK cells, donor APCs can survive and then migrate to the host lymphoid and extralymphoid sites where they directly stimulate the activation of alloreactive T cells. T cells activated in the absence of NK cells are more resistant to costimulatory blockade treatment, and under such conditions stable skin allograft survival is difficult to achieve. Our study identified a novel role for NK cells in regulating T cell priming in transplant models, and may have important clinical implications in tolerance induction.
Inferring gene regulatory networks from multiple microarray datasets
Authors: Wang Yong , Joshi Trupti , Zhang Xiang-Sun , Xu Dong , Chen Luonan
Published: July 2006

Motivation: Microarray gene expression data has increasingly become the common data source that can provide insights into biological processes at a system-wide level. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to a large number of genes, which makes the problem of inferring gene regulatory network an ill-posed one. On the other hand, gene expression data generated by different groups worldwide are increasingly accumulated on many species and can be accessed from public databases or individual websites, although each experiment has only a limited number of time-points.

Results: This paper proposes a novel method to combine multiple time-course microarray datasets from different conditions for inferring gene regulatory networks. The proposed method is called GNR (Gene Network Reconstruction tool) which is based on linear programming and a decomposition procedure. The method theoretically ensures the derivation of the most consistent network structure with respect to all of the datasets, thereby not only significantly alleviating the problem of data scarcity but also remarkably improving the prediction reliability. We tested GNR using both simulated data and experimental data in yeast and Arabidopsis. The result demonstrates the effectiveness of GNR in terms of predicting new gene regulatory relationship in yeast and Arabidopsis.

Availability: The software is available from , and or upon request from the authors.

Contact:  chen@eic.osaka-sandai.ac.jp, xudong@missouri.edu, zxs@amt.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Postoperative Infusion of Amino Acids Induces a Positive Protein Balance Independently of the Type of Analgesia Used
Authors: Donatelli Francesco , Schricker Thomas , Mistraletti Giovanni , Asenjo Francisco , Parrella Piervirgilio , Wykes Linda , Carli Franco
Published: July 2006

Background

Net loss of body protein is a prominent feature of the catabolic response to surgical tissue trauma. Epidural analgesia with hypocaloric dextrose has been demonstrated to attenuate leucine oxidation but was unable to make protein balance positive. The current study was set to determine whether an infusion of amino acids on the second day after colon surgery would revert the catabolic state and promote protein synthesis while maintaining glucose homeostasis in patients receiving epidural analgesia as compared with patient-controlled analgesia with morphine (PCA).

Methods

Sixteen patients undergoing colorectal surgery were randomly assigned to receive epidural blockade or PCA as analgesic techniques and underwent a 6-h stable isotope infusion study (3 h fasted, 3 h fed) on the second postoperative day. Whole body glucose kinetics and protein turnover were measured using [6,6-2H2]glucose and l-[1-13C]leucine as tracer.

Results

The infusion of amino acids caused a decrease in endogenous glucose rate of appearance in both groups (P < 0.05), with greater changes in the PCA group (P < 0.05). Administration of amino acids suppressed the appearance of leucine from protein breakdown in both groups (P < 0.05), although the decrease was greater in the PCA group (P < 0.05). Leucine oxidation increased in both groups (P < 0.05), with greater change in the epidural group (P < 0.05). Protein synthesis increased to the same extent in both groups (P < 0.05). Protein balance became positive after the infusion of amino acids, and the effect was greater in the PCA group (P < 0.05).

Conclusions

Infusion of amino acids decreased the endogenous glucose production and induced a positive protein balance independent of the type of anesthesia provided, although such effects were greater in the PCA group.
Impaired neutrophil chemotaxis in Crohn's disease relates to reduced production of chemokines and can be augmented by granulocyte‐colony stimulating factor
Authors: HARBORD M. W. N. , MARKS D. J. B. , FORBES A. , BLOOM S. L. , DAY R. M. , SEGAL A. W.
Published: July 2006

Background

Defective neutrophil recruitment has been described as a primary pathogenic abnormality in Crohn’s disease. Cantharidin‐induced blisters provide a novel investigative tool to assess cellular influx and inflammatory mediator production during acute inflammation and allows the effects of therapy on these parameters to be measured.

Aims

To determine whether reduced neutrophil tissue penetration in Crohn's disease relates to impaired production of inflammatory mediators, and whether it can be reversed by granulocyte‐colony stimulating factor (G‐CSF).

Methods

Neutrophil and monocyte/macrophage populations and inflammatory mediators were measured in cantharidin blisters at 24 h. Neutrophil chemotaxis was assessed in vitro using blister fluid as the chemoattractant. The effect of s.c. G‐CSF on blister phenotype was determined.

Results

Significantly fewer neutrophils migrated into blisters in Crohn's patients. The production of neutrophil chemokines, but not other inflammatory mediators, was reduced. This significantly correlated with reduced chemotaxis in vitro. Differences were unrelated to caspase‐recruitment domain 15 genotype. G‐CSF significantly increased blister neutrophil concentrations in control subjects and Crohn's patients.

Conclusions

Reduced neutrophil migration during acute inflammation in Crohn's disease is associated with impaired production of appropriate chemoattractants. G‐CSF therapy increases neutrophil tissue migration, which may partially account for its observed therapeutic effect.
A case study of acenocoumarol sensitivity and genotype‐phenotype discordancy explained by combinations of polymorphisms in VKORC1 and CYP2C9
Authors: Rettie Allan E. , Farin Frederico M. , Beri Nitasha G. , Srinouanprachanh Sengkeo L. , Rieder Mark J. , Thijssen Henk H.
Published: July 2006

Aims

To determine the cause of a genotype‐phenotype discordancy for acenocoumarol sensitivity.

Methods

A patient, highly sensitive to acenocoumarol, and previously determined to carry only a single CYP2C9 *3 allele, was genotyped for additional functionally defective alleles in the CYP2C9 and VKORC1 genes. Family members were also analyzed to trace the pedigree.

Results

The acenocoumarol‐sensitive patient was found to possess, in addition to CYP2C9 *3 allele, a CYP2C9 *11 allele and the VKORC1 AA diplotype which were all traced back through the parental lines.

Conclusions

Acenocoumarol sensitivity in this subject is the consequence of inheritance of multiple functionally defective alleles in both the CYP2C9 and VKORC1 genes. The study provides additional data in support of diminished CYP2C9 activity due to the presence of the rare *11 allele.
Prevalence and prediction of malignancy in cytologically indeterminate thyroid nodules
Authors: Sahin M. , Gursoy A. , Tutuncu N. B. , Guvener D. N.
Published: July 2006

Objective Controversy surrounds the evaluation of nodules with indeterminate cytology results. Malignancy rates in these nodules are not low. We examined the malignancy rates in nodules that showed follicular neoplasm or atypical cells on cytology and attempted to predict malignancy based on ultrasonographic features.

Design and patients We retrospectively analysed 5 years’ cytopathology results of fine‐needle aspiration biopsy (FNAB) specimens of indeterminate follicular thyroid lesions prior to thyroidectomy. The prevalence of malignancy on final histology was determined. The sonographic features of the thyroid nodules with respect to size, echogenicity, echo structure, border shape and presence of calcification were analysed.

Results A total of 86 patients (15 men, 61 women; mean age 52·1 ± 12·5 years) with indeterminate cytology underwent thyroidectomy and had histopathological diagnoses. The average nodule was 18·9 ± 12·3 mm. The prevalence of malignancy in patients with atypical cell cytology was 51·7% (30 of 59), and the prevalence of malignancy in patients with follicular neoplasm cytology was 15% (4 of 27). Malignancy prevalence was higher in patients who had follicular neoplasm cytology with atypical cells than in those without atypical cells (2 of 7 and 2 of 20, respectively).

We found no significant correlations between sonographic or clinical features and malignancy in this patient group. Sonographic features and nodule size are not useful predictors of malignancy.

Conclusion Until better molecular markers for malignancy are developed, surgical consultation remains necessary after examination of cytologically indeterminate FNAB specimens in patients with follicular thyroid lesions. But in follicular lesions without atypical cells the malignancy rate is low and reassessment later on could be an alternative approach.
Local environmental effects and spatial effects in macroecological studies using mapped abundance classes: the case of the rookCorvus frugilegusin Scotland
Authors: GIMONA A. , BREWER M. J.
Published: July 2006

The study of the spatial pattern of species abundance is complicated by statistical problems, such as spatial autocorrelation of the abundance data, which lead to the confusion of environmental effects and dispersal.

Atlas‐derived data for the rook in Scotland are used as a case study to propose an approach for assessing the likely contribution of dispersal and local environmental effects, based on a Bayesian Conditional Autoregressive (CAR) approach.

The availability of moist grasslands is a key factor explaining the spatial pattern of abundance. This is influenced by a combination of climatic and soil‐related factors. A direct link to soil properties is for the first time reported for the wide‐scale distribution of a bird species. In addition, for this species, dispersal seems to contribute significantly to the spatial pattern and produces a smoother than expected decline in abundance at the north‐western edge of its distribution range. Areas where dispersal is most likely to be important are highlighted.

The approach described can help ecologists make more efficient use of atlas data for the investigation of the structure of species abundance, and can highlight potential sink areas at the landscape and regional scale.

Bayesian spatial models can deal with data autocorrelation in atlas‐type data, while clearly communicating uncertainty through the estimation of the full posterior probability distribution of all parameters.
Reductionist inference‐based medicine, i.e. EBM
Authors: De Simone John
Published: July 2006

Rationale, aims and objectives  Unbeknown to many, reductionist and postmodern worldviews competitively coexist in science and society. The debate on evidence‐based medicine (EBM) is at the tip of this ‘iceberg’. Via systems thinking and complexity science EBM reveals crucial flaws and its reductionism entails an inability to appreciate (even tolerate) contrasting ideas and/or ‘see a bigger picture’. An interdisciplinary approach provides insight into novel explanations. Thereafter, the conceptual barrier shifts to communication, a challenge which mandates attempts to steer the discourse by reframing the debate.

Method  Interdisciplinary perspectives serve to illustrate a ‘bigger picture’. Also, ‘wicked’ questions stimulate reflection, discern leverage points and dismantle resilient defences. Lastly, a proposal: exploring the value of ‘glasses half full’.

Conclusion  Some may realize that postmodern concepts behind compelling criticisms to EBM have already taken root, being shared by policymakers, practitioners and patients as well.
Oestradiol Up‐Regulates Glutamine Synthetase mRNA and Protein Expression in the Hypothalamus and Hippocampus: Implications for a Role of Hormonally Responsive Glia in Amino Acid Neurotransmission
Authors: Blutstein T. , Devidze N. , Choleris E. , Jasnow A. M. , Pfaff D. W. , Mong J. A.
Published: July 2006

Rapidly emerging evidence suggests that glial cells in the central nervous system are sensitive to oestrogen actions. However, the functional consequences of the cellular mechanisms of these cells have proven difficult to study in vivo because of the intimate relationships between neurones and glia. Microarray technology offers the potential to uncover steroid hormone regulation of glial‐specific genes that may play a role in hormone‐dependent neuronal–glial interactions. Analysis of transcriptomes from the medial basal hypothalamus (MBH) of oestradiol and vehicle‐treated adult ovariectomised mice revealed an up‐regulation of several glial specific genes by oestradiol, including glutamine synthetase (GS), which facilitates the conversion of glutamate to glutamine and plays an integral role in amino acid neurotransmission. In situ hybridisation confirmed that oestradiol treatment resulted in an up‐regulation of GS gene expression in the arcuate and ventromedial nuclei of the MBH, as well as the medial amygdala and hippocampus. Moreover, oestradiol increased protein expression of GS in both the MBH and hippocampus. Neurones are incapable of de novo net synthesis of glutamate from glucose and are dependent on glial‐provided precursors such as glutamine to renew their amino acid transmitter pools. Thus, oestradiol induced expression of GS suggests a significant role for glial cells in hormonal modulation of glutamatergic neurotransmission important to female reproductive behaviours, neuroendocrine physiology and cognitive functions.