bluuebunny/crossref_metadata_2025 huggingface dataset:
A study of gas‐phase cationization in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Erb William J. , Hanton Scott D. , Owens Kevin G.
Published: June 2006

A specially constructed split sample probe was used to unequivocally demonstrate that gas‐phase cationization occurs within the desorption plume during a matrix‐assisted laser desorption/ionization experiment. Two separate samples were prepared for analysis: on side A, a mixture of poly(ethylene glycol) (PEG) 1500 analyte and 2,5‐dihydroxybenzoic acid (DHB) matrix, and on side B a mixture of DHB matrix and lithium hydroxide (LiOH), the cationization reagent. Analysis of the data showed that when the ionization laser was focused on the split (so that both sides were illuminated), Li+‐cationized PEG peaks were observed. Since the PEG analyte did not come into contact with Li+ in either the solution or solid phase, the only possibility for the observed cationization was a reaction in the gas phase. Due to the difficulty in completely removing the adventitious cations (Na+ and K+) present in DHB and on sample surfaces, gas‐phase cationization could not be demonstrated to be either the only or most important mechanism operating in the MALDI experiment. Copyright © 2006 John Wiley & Sons, Ltd.
A matrix‐assisted laser desorption/ionization mass spectrometry approach to the lipid A from Mesorhizobium loti
Authors: Casabuono Adriana C. , D'Antuono Alejandra , Sato Yasuto , Nonami Hiroshi , Ugalde Rodolfo , Lepek Viviana , Erra‐Balsells Rosa , Couto Alicia S.
Published: June 2006

The isolation, purification and analysis of the lipid A obtained from Mesorhizobium loti Ayac 1 BII strain is presented. Analysis of the carbohydrate moiety after acid hydrolysis by high‐pH anion‐exchange chromatography with pulse amperometric detection (HPAEC‐PAD) showed the presence of glucosamine and galacturonic acid as the only sugar components. Gas chromatographic (GC) and GC/mass spectrometric (MS) analysis of the fatty acids revealed the presence of 3‐OH‐C12:0; 3‐OH‐C13:0; 3‐OH‐C20:0 and 27‐OH‐C28:0 among the major hydroxylated species. In addition, C16:0, C17:0, C18:0 and C 20:0 were shown as main saturated fatty acids. Different polyacylated species were evidenced by thin layer chromatography of lipid A, allowing the purification of two fractions. Ultraviolet matrix‐assisted laser desorption/ionization time‐of‐flight (UV‐MALDI‐TOF) MS analysis with different matrices, in the positive‐ and negative‐ion mode, was performed. The fast moving component revealed the presence of hexa‐acylated species, varying in the fatty acid composition. Species containing three 3‐OH fatty acids and a 27‐OH‐C28:0 fatty acid were observed. Individual ions within this family differ by ±14 mass units. The slow moving component was enriched mainly in penta‐acylated species. Among them, three subgroups were detected: the major one compatible with the sugar core bearing two 3‐OH 20:0 fatty acids, a 3‐OH 13:0 or a 3‐OH 12:0 fatty acid, a 27‐OH 28:0 fatty acid and one saturated fatty acid. Each signal differs in a C18:0 acyl unit from the corresponding hexa‐acylated family. On the other hand, a subgroup bearing one 3‐OH 20:0 fatty acid, one 27‐OH 28:0 fatty acid and two non‐polar fatty acids was shown. A minor subgroup compatible with structures containing two hydroxylated and three non‐polar fatty acids was also detected. The results obtained showed that nor‐harmane was an excellent matrix for charged lipid A structural studies in both, positive and negative ion modes. Copyright © 2006 John Wiley & Sons, Ltd.
Determination of paclitaxel in human plasma following the administration of Genaxol or Genetaxyl by liquid chromatography/tandem mass spectrometry
Authors: Gardner Erin R. , Liau Chi‐Ting , Chu Zyting E. , Figg William D. , Sparreboom Alex
Published: June 2006

A sensitive and specific assay for paclitaxel in plasma has been developed to overcome limitations in previously published assays, using liquid chromatography with tandem mass spectrometric detection. Plasma samples (100 µL) were subjected to liquid‐liquid extraction with 1‐chlorobutane/acetonitrile (4:1, v/v), with [2H5]paclitaxel employed as the internal standard. Chromatography was carried out with a Waters SymmetryShield C8 column (50 × 2.1 mm, 3.5 µm). The total run time, including equilibration, was 8 min, using a gradient of acetonitrile and 10 mM ammonium formate, pH 4.0. The assay is accurate and precise over the range of 2–2500 ng/mL and has been successfully applied to study the clinical pharmacokinetics of two formulations of paclitaxel, Genaxol and Genetaxyl, given orally and intravenously. Copyright © 2006 John Wiley & Sons, Ltd.
Classification of some species, genera and families of plants by x‐ray spectrometry
Authors: Alexandre Thais Levatti , Bueno Maria Izabel M. S.
Published: June 2006

The Linnaean systematic classification of plants has been used for many years but eventually it caused great discord among taxonomists, since it is still based on visual inspection, without the necessary accuracy. Chemical classification methods are also applied, but are destructive and time and reagent consuming, which makes them expensive, and requiring also treatment of the liquid and solid residues. The latter are based on the determination of the proteins in a species that is not encountered in others. In the present work, a new, reliable method for the classification of vegetables without destroying samples is proposed using x‐ray spectrometry combined with chemometrics, using both the PCA and HCA tools. Conventional EDXRF equipment is used to obtain the spectra and classification is achieved by processing them using multivariate analysis. Seeds of species and varieties of carnations and species of bananas were used to demonstrate the applicability of the method. Copyright © 2006 John Wiley & Sons, Ltd.
Reconstruction technique for umbilical endometriosis
Authors: Kokuba E.M. , Sabino N.M. , Sato H. , Aihara A.Y. , Schor E. , Ferreira L.M.
Published: June 2006

Objective: To present a technique for immediate umbilical reconstruction in women undergoing resection of umbilical endometriosis. Methods: Umbilical reconstruction using 2 semicircular defatted skin flaps was performed in 7 patients surgically treated for umbilical endometriosis from October 2000 to June 2004. The patients were followed up for at least 6 months. Results: Anatomical aspect, depression, and abdominal wall scar were considered satisfactory, although hypertrophic umbilical scars developed in 2 patients. Conclusion: This technique using 2 semicircular defatted flaps is efficient in creating a new umbilicus with a natural appearance while leaving a minimal scar. Moreover, it allows for laparoscopic inspection of the abdominal cavity.
A theoretical model of bursty bulk flows
Authors: Machida S.
Published: June 2006

Bursty bulk flows (BBFs) are known to exhibit abrupt increases in plasma flow velocity and in the intensity of the northward/southward magnetic fields, occasionally followed by periodic variations in a characteristic time of 1–3 min. In this paper a theoretical model for BBFs is proposed. In this model a region of a dawnward electric field is assumed to propagate earthward, corresponding to the propagation of the variation front associated with magnetic reconnection. The coupling of the magnetosphere and the ionosphere is modeled using an equivalent electric circuit. We conducted a series of test particle simulations with the assumption that each test particle corresponds to a magnetic flux tube. We also obtained an analytic solution that approximates the numerical results and explains the main characteristics of BBFs.
CO2 fluxes in the subtropical and subarctic North Atlantic based on measurements from a volunteer observing ship
Authors: Lüger Heike , Wanninkhof Rik , Wallace Douglas W. R. , Körtzinger Arne
Published: June 2006

Surface seawater pCO2 and related parameters were measured at high frequency onboard the volunteer observing ship M/V Falstaff in the North Atlantic Ocean between 36° and 52°N. Over 90,000 data points were used to produce monthly CO2 fluxes for 2002/2003. The air‐sea CO2 fluxes calculated by two different averaging schemes were compared. The first approach used gas transfer velocity determined from wind speed retrieved at the location of the ship and called colocated winds, while for the second approach a monthly averaged gas transfer velocity was calculated from the wind for each grid pixel including the variability in wind. The colocated wind speeds determined during the time of passage do not capture the monthly wind speed variability of the grid resulting in fluxes that were 47% lower than fluxes using the monthly averaged wind products. The Falstaff CO2 fluxes were in good agreement with a climatology using averaged winds. Over the entire region they differed by 2–5%, depending on the time‐dependent correction scheme to account for the atmospheric in increase in pCO2. However, locally the flux differences between the ship measurements and the climatology were greater, especially in regions north of 45°N, like the eastern sector. A comparison of two wind speed products showed that the annual CO2 sink is 4% less when using 6 hourly NCEP/NCAR wind speeds compared to the QuikSCAT wind speed data.
Insights from simulations with high‐resolution transport and process models on sampling of the atmosphere for constraining midlatitude land carbon sinks
Authors: Karstens U. , Gloor M. , Heimann M. , Rödenbeck C.
Published: June 2006

We analyze the requirements for detecting changes in midlatitude land carbon sources or sinks from sampling the atmospheric CO2 concentration. Programs to sample the continental lower troposphere have only recently started, and it is not yet clear which atmospheric sampling strategy is most adequate. To shed some light on this question, we use simulations of atmospheric CO2 over Eurasia with two regional‐scale atmospheric transport models. Our analysis focuses on the detection of the monthly mean CO2 signal caused by a perturbation of Eurasian summer biospheric fluxes by 20% (0.06 PgC/month). The main results are (1) that several measurements per day, preferably during the afternoon, are necessary to permit the detection of the additional land sink and (2) that the ratio between signal and background variation, corrected for autocorrelation in time, suggests no preferred level in the vertical for sampling. However, (3) the signals in the free troposphere are very small (0.2 ppm per 0.06 PgC/month) given the precision of atmospheric measurements. In contrast, signals in the planetary boundary layer (PBL) are on the order of 1 ppm per 0.06 PgC/month. This suggests that optimal sampling on continents should concentrate on the mixed portion of the PBL during afternoon. (4) Finally, the spatial correlation structure of the atmospheric CO2 concentrations suggests that a horizontal sampling density on the order of a few 100 km is needed.
Ability to quantify coherent turbulent structures in the convective boundary layer using thermodynamic profiling instruments
Authors: Mecikalski J. R. , Bedka K. M. , Turner D. D. , Feltz W. F. , Paech S. J.
Published: June 2006

Water vapor mixing ratio data from the Raman lidar and Atmospheric Emitted Radiance Interferometer (AERI) are analyzed toward inferring the presence of organized, three‐dimensional, turbulent features within convective boundary layers (CBLs). The Raman lidar and AERI instruments provide unique, high‐quality data sets, from 200‐m to ∼3‐km altitude at ≤1‐min temporal resolution profiles of water vapor. CBLs under the influence of solar heating for two fair‐weather days over the Atmospheric Radiation Measurement (ARM) Central Facility near Lamont, Oklahoma, during the International H20 Project 2002 (IHOP_2002), and 1 day during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers (CRYSTAL)‐Florida Area Cirrus Experiment (FACE) 2002 experiment, are evaluated. This research provides a means of inferring the presence of coherent, convectively driven circulation (momentum) signatures exclusively from high‐temporal resolution water vapor profiles. Spectral and statistical analysis of Raman lidar water vapor‐time series reveal the passage of coherent turbulent structures, including horizontal convective rolls (HCRs), within the CBL over the ARM site at ∼8 and 12 min intervals for 2 days during IHOP_2002. AERI data collected during CRYSTAL‐FACE also indicate similar structures, with meteorological conditions on this day also dictating the presence of cloud streets over the AERI (every 12 and 28 min). Radiosonde, satellite, and ceilometer analyses provide information about the favored stability and CBL cloud patterns, as well as a check on our spectral analysis. Evidence within the perturbation water vapor time series from these two instruments is well correlated with HCRs and other cumulus patterns seen in 1 km resolution GOES visible satellite imagery.
Heterogeneous nucleation of ice on surrogates of mineral dust
Authors: Knopf Daniel A. , Koop Thomas
Published: June 2006

Field studies have shown that mineral dust particles can act as ice nuclei in cirrus clouds. Here, we present a laboratory investigation of heterogeneous ice nucleation on surrogates of mineral dust particles, in particular pure Arizona test dust (ATD) particles, and ATD particles coated with sulfuric acid. The experiments have been performed using a new apparatus in which ice formation on the particles is determined by optical microscopy at temperatures between 197 and 260 K and relative humidities up to water saturation. The experiments reveal that pure and sulfuric acid coated ATD particles nucleate ice at considerably lower relative humidities than required for homogeneous ice nucleation in liquid aerosols. Nucleation occurred over a broad relative humidity range indicating that the different minerals contained in ATD have different ice nucleation thresholds. No significant difference in the ice nucleation ability of pure and H2SO4 coated ATD particles was observed. Below 240 K, ice nucleated on ATD particles apparently by deposition nucleation. Preactivation of ATD particles, that is, a reduction in supersaturation, required for heterogeneous ice nucleation after a previous ice nucleation event on the same particle, has been observed for temperatures as low as 200 K. Differences of 10–30% in the onset RHice values were obtained for particles with or without preactivation. The results indicate that pure and sulfuric acid coated mineral dust particles may act as efficient ice nuclei in the atmosphere. Preactivation of the particles should be considered when modeling long‐range transport of mineral dust particles and their impact on cloud formation.
Remote sensing studies of the Dionysius region of the Moon
Authors: Giguere T. A. , Hawke B. Ray , Gaddis L. R. , Blewett D. T. , Gillis‐Davis J. J. , Lucey P. G. , Smith G. A. , Spudis P. D. , Taylor G. J.
Published: June 2006

The Dionysius region is located near the western edge of Mare Tranquillitatis and is centered on Dionysius crater, which exhibits a well‐developed dark ray system. Proposed origins for these dark rays included impact melt deposits and dark primary ejecta. The region also contains extensive deposits of Cayley‐type light plains. Clementine multispectral images and a variety of spacecraft photography were utilized to investigate the composition and origin of geologic units in the Dionysius region. The portions of the dark rays for which spectral and chemical data were obtained are composed of mare debris contaminated with minor amounts of highland material. Both five‐point spectra and values of the optical maturity (OMAT) parameter indicate that the dark rays are dominated by mare basalts, not glassy impact melts. The high‐albedo rays associated with Dionysius exhibit FeO and TiO2 values that are lower than those of the adjacent dark ray surfaces and OMAT values that indicate that bright ray surfaces are not fully mature. The high‐albedo rays are bright largely because of the contrast in albedo between ray material containing highlands‐rich ejecta and the adjacent mare‐rich surfaces. The mafic debris ejected by Dionysius was derived from a dark, iron‐rich unit exposed high on the inner wall of the crater. This layer probably represents a mare deposit that was present at the surface of the preimpact target site. With one possible exception, there is no evidence for buried mare basalts associated with Cayley plains in the region.
Role of MAP1B in axonal retrograde transport of mitochondria
Authors: Jiménez-Mateos Eva-María , González-Billault Christian , Dawson Hana N. , Vitek Michael P. , Avila Jesús
Published: June 2006

The MAPs (microtubule-associated proteins) MAP1B and tau are well known for binding to microtubules and stabilizing these structures. An additional role for MAPs has emerged recently where they appear to participate in the regulation of transport of cargos on the microtubules found in axons. In this role, tau has been associated with the regulation of anterograde axonal transport. We now report that MAP1B is associated with the regulation of retrograde axonal transport of mitochondria. This finding potentially provides precise control of axonal transport by MAPs at several levels: controlling the anterograde or retrograde direction of transport depending on the type of MAP involved, controlling the speed of transport and controlling the stability of the microtubule tracks upon which transport occurs.
Tumour necrosis factor α causes hypoferraemia and reduced intestinal iron absorption in mice
Authors: Laftah Abas H. , Sharma Naveen , Brookes Matthew J. , McKie Andrew T. , Simpson Robert J. , Iqbal Tariq H. , Tselepis Chris
Published: June 2006

Cytokines are implicated in the anaemia of chronic disease by reducing erythropoiesis and increasing iron sequestration in the reticuloendotheial system. However, the effect of cytokines, in particular TNFα (tumour necrosis factor α), on small bowel iron uptake and iron-transporter expression remains unclear. In the present study, we subjected CD1 male mice to intraperitoneal injection with TNFα (10 ng/mouse) and then examined the expression and localization of DMT1 (divalent metal transporter 1), IREG1 (iron-regulated protein 1) and ferritin in duodenum. Liver and spleen samples were used to determine hepcidin mRNA expression. Changes in serum iron and iron loading of duodenum, spleen and liver were also determined. We found a significant (P<0.05) fall in serum iron 3 h post-TNFα exposure. This was coincident with increased iron deposition in the spleen. After 24 h of exposure, there was a significant decrease in duodenal iron transfer (P<0.05) coincident with increased enterocyte ferritin expression (P<0.05) and re-localization of IREG1 from the basolateral enterocyte membrane. Hepatic hepcidin mRNA levels remained unchanged, whereas splenic hepcidin mRNA expression was reduced at 24 h. In conclusion, we provide evidence that TNFα may contribute to anaemia of chronic disease by iron sequestration in the spleen and by reduced duodenal iron transfer, which seems to be due to increased enterocyte iron binding by ferritin and a loss of IREG1 function. These observations were independent of hepcidin mRNA levels.
Need a single-mode red laser, cheap? Check your pockets!
Authors: Tellinghuisen Joel
Published: June 2006

An inexpensive (<$5) key-chain model of red laser pointer (RLP) operates with typically 98% of its total emission in a single longitudinal cavity mode. The laser self-tunes with time, interpreted as due to thermal effects. The laser can also be tuned by varying its operating current and voltage. These properties permit one to quickly and easily record absorption spectral segments spanning ranges of 1–6cm−1, with high quantitative reliability, resolution, and accuracy. As examples, spectra of I2 are recorded in the 650nm region as a function of pressure for several RLP wavelengths and are used to estimate the strength of the underlying continuum (due to A←X absorption) with relative standard error less than 1%. Similarly, measurements of the integrated line absorption on selected lines in the B←X transition yield estimates of the electronic transition strength with unprecedented precision.
Selective utilization of nonhomologous end-joining and homologous recombination DNA repair pathways during nervous system development
Authors: Orii Kenji E. , Lee Youngsoo , Kondo Naomi , McKinnon Peter J.
Published: June 2006

The repair of DNA double-strand breaks (DSBs) occurs via nonhomologous end-joining (NHEJ) or homologous recombination (HR). These mechanistically distinct pathways are critical for maintenance of genomic integrity and organismal survival. Although inactivation of either pathway leads to embryonic lethality, here we show selective requirements for each DNA DSB repair pathway at different stages of mammalian nervous system development. DNA damage-induced apoptosis resulting from inactivation of HR (Xrcc2 deficiency) only occurred in proliferating neural precursor cells, whereas disruption of NHEJ (DNA ligase IV deficiency) mainly affected differentiating cells at later developmental stages. Therefore, these data suggest that NHEJ is dispensable for a substantial portion of early development because DSB repair during this period utilizes HR. Moreover, DNA damage-induced apoptosis required the ataxia telangiectasia mutated (Atm) kinase after disruption of NHEJ, but not HR, during neurogenesis. However, embryonic lethality arising from disruption of either repair pathway was rescued by loss of p53 and resulted in specific tumor types reflective of the particular DSB repair pathway inactivated. Thus, these data reveal distinct tissue- and cell-type requirements for each DNA DSB repair pathway during neural development and provide insights for understanding the contributions of DNA DSB responses to disease.
Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity
Authors: Koropatkin Nicole M. , Pakrasi Himadri B. , Smith Thomas J.
Published: June 2006

Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of all aquatic food chains by fixing carbon and nitrogen into cellular biomass. The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments particularly the open ocean. It is therefore not surprising that NrtA, the solute-binding component of the high-affinity nitrate ABC transporter, is the single-most abundant protein in the plasma membrane of these bacteria. Here, we describe the structure of a nitrate-specific receptor, NrtA from
Synechocystis
sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5 Å. NrtA is significantly larger than other oxyanion-binding proteins, representing a previously uncharacterized class of transport proteins. From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonate-binding protein. Therefore, these organisms created a solute-binding protein for two of the most important nutrients: inorganic nitrogen and carbon. The electrostatic charge distribution of NrtA appears to force the protein off the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore. The structure not only details the determinants for nitrate selectivity in NrtA but also the bicarbonate specificity in CmpA. Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively. Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate. This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.
Estimates on the dimension of an attractor for a nonclassical hyperbolic equation
Authors: Wu Delin , Zhong Chengkui
Published: June 2006

In this paper, we estimate the dimension of a global attractor for a nonclassical hyperbolic equation with a viscoelastic damping term in Hilbert spaces

H

0

2

×

L

2

H_{0}^{2}\times L^{2}

and

D
(
A
)
×

H

0

2

D(A)\times H_{0}^{2}

, where

D
(
A
)
=
{
v
∈

H

0

2

∣
A
v
∈

L

2

}

D(A)=\{v\in H_{0}^{2}\mid Av\in L^{2}\}

and

A
=

Δ

2

A=\Delta ^{2}

. We obtain an explicit formula of the upper bound of the dimension of the attractor. The obtained dimension decreases as damping grows and is uniformly bounded for large damping, which conforms to physical intuition.
Roundup: a multi-genome repository of orthologs and evolutionary distances
Authors: DeLuca Todd F. , Wu I-Hsien , Pu Jian , Monaghan Thomas , Peshkin Leonid , Singh Saurav , Wall Dennis P.
Published: June 2006

SUMMARY: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that has been shown to improve upon alternative approaches of ortholog detection, such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data.

Availability:  

Contact:  dpwall@hms.harvard.edu
Cold Therapy in Migraine Patients: Open‐label, Non‐controlled, Pilot Study
Authors: Ucler Serap , Coskun Ozlem , Inan Levent E. , Kanatli Yonca
Published: June 2006

Some patients with headache report that they have frequently used physical therapies such as application of cold to relieve their headache. There are only a few reported studies related to cold therapies in patients with migraine. In this study, we investigated the effect of cold application on migraine patients. Twenty‐eight migraine patients were included. Cold therapy was administered to them by gel cap. Patients used this cap during their two migraine attacks. Before and after the cold therapy, headache severity was recorded by using visual analogue scale (VAS). Patients used this cap for 25 min in each application. They recorded their VAS score just after the therapy and 25 min, 1 h, 2 h and 3 h later. Two patients could not use this therapy due to side effects (one due to cold intolerance and one due to vertigo) in both applications. Therefore, therapeutic efficacy was evaluated in 26 patients. Twenty‐five minutes after treatment of the first attack, VAS score was decreased from 7.89 ± 1.93 to 5.54 ± 2.96 (P < 0.01). Twenty‐five minutes after treatment of the second attack, VAS score was decreased from 7.7 ± 1.8 to 5.4 ± 3.55 (P < 0.01). Cold application alone may be effective in some patients suffering from migraine attacks. Its combination with conventional drugs should be investigated in future studies.
Smelly feet are not always a bad thing: the relationship between cyprid footprint protein and the barnacle settlement pheromone
Authors: Dreanno Catherine , Kirby Richard R , Clare Anthony S
Published: June 2006

A critical phase in the life cycle of sessile benthic marine invertebrates is locating a suitable substratum for settlement. For barnacles, it is the lecithotrophic cypris larva that makes this plankto–benthic transition. In exploring possible substrata for settlement, the cyprid leaves behind ‘footprints’ of a proteinaceous secretion that reportedly functions as a temporary adhesive, and also acts as a secondary cue in larval–larval interactions at settlement. Here, we show that two polyclonal antibodies raised against peptides localized at the N- and C-terminal regions of the adult settlement cue—the settlement-inducing protein complex (SIPC)—could both detect ‘temporary adhesive’ indicating that the SIPC is either a component of this secretion or that they are the same protein.
Automated tracking of gene expression in individual cells and cell compartments
Authors: Shen Hailin , Nelson Glyn , Nelson David E , Kennedy Stephnie , Spiller David G , Griffiths Tony , Paton Norman , Oliver Stephen G , White Michael R.H , Kell Douglas B
Published: June 2006

Many intracellular signal transduction processes involve the reversible translocation from the cytoplasm to the nucleus of transcription factors. The advent of fluorescently tagged protein derivatives has revolutionized cell biology, such that it is now possible to follow the location of such protein molecules in individual cells in real time. However, the quantitative analysis of the location of such proteins in microscopic images is very time consuming. We describe CellTracker, a software tool designed for the automated measurement of the cellular location and intensity of fluorescently tagged proteins. CellTracker runs in the MS Windows environment, is freely available (athttp://www.dbkgroup.org/celltracker/), and combines automated cell tracking methods with powerful image-processing algorithms that are optimized for these applications. When tested in an application involving the nuclear transcription factor NF-κB, CellTracker is competitive in accuracy with the manual human analysis of such images but is more than 20 times faster, even on a small task where human fatigue is not an issue. This will lead to substantial benefits for time-lapse-based high-content screening.
The Comfort of Denial: External Assistance in Southern Sudan
Authors: Marriage Zoe
Published: June 2006

Aid organizations profess universalist objectives, such as humanitarian principles and human rights, whilst operating in areas in which these objectives cannot be fulfilled. How do they deal with the disparity between the claims they make and what actually happens? How are parts of the story covered up, and what do the stated objectives achieve? This article argues that denial — at a personal, organizational and institutional level — is crucial for sustaining assistance, and is facilitated by the language of rights and principles. Drawing on research from southern Sudan, it explores how aid organizations construct an official version of events that fabricates clarity whilst maintaining a degree of tactical confusion. This establishes a political morality, a seemingly ethical position that has political and psychological returns.
Targeting Research for Poverty Reduction in Marginal Areas of Rural Syria
Authors: Rovere Roberto La , Aw‐Hassan Aden , Turkelboom Francis , Thomas Richard
Published: June 2006

Agricultural research in marginal dry areas can contribute to reducing poverty through the development of technological, institutional and policy options for poor farmers. Such research should address diversified opportunities and development pathways. This article analyses the diversity of livelihood strategies of rural people living in the Khanasser Valley in northwestern Syria, an area that is typical of marginal drylands. It proposes an operational classification of households based on their different livelihood strategies, applying an integrated methodology within a Sustainable Livelihoods framework. Households are classified into three clusters: agriculturists, labourers and pastoralists. The article examines the diversity of livelihoods involved, and considers where and how research should be directed to have greatest impact on poverty. Given that rural households are not homogeneous but dynamic entities, with diverse assets, capabilities and opportunities, the definition of household typologies can help to target development research. The article concludes that while agriculturists benefit most, poor labourers with enough land can also gain from pro‐poor agricultural research. The poorest households with little land, and pastoralists, benefit little or only indirectly.
Utility of red flag symptom exclusions in the diagnosis of irritable bowel syndrome
Authors: WHITEHEAD W. E. , PALSSON O. S. , FELD A. D. , LEVY R. L. , VON KORFF M. , TURNER M. J. , DROSSMAN D. A.
Published: June 2006

Background

Studies suggest that the positive predictive value of the Rome II criteria for diagnosing irritable bowel syndrome can be enhanced by excluding red flag symptoms suggestive of organic diseases.

Aim

We assessed the utility of red flags for detecting organic diseases in patients diagnosed irritable bowel syndrome by their physicians.

Methods

Systematic chart reviews were completed in 1434 patients with clinical diagnoses of irritable bowel syndrome, abdominal pain, diarrhoea or constipation, who also completed questionnaires to identify Rome II criteria for irritable bowel syndrome and red flag symptoms.

Results

The overall incidence of gastrointestinal cancer was 2.5% (but 1.0% in those with irritable bowel syndrome), for inflammatory bowel disease 2.0% (1.2% in irritable bowel syndrome), and for malabsorption 1.3% (0.7% in irritable bowel syndrome). Red flags were reported by 84% of the sample. The positive predictive value of individual red flags for identifying organic disease was 7–9%. Excluding any patient with a red flag improved the agreement between Rome II and clinical diagnosis by a modest 5%, but left 84% of patients who were diagnosed with irritable bowel syndrome by their physicians, without a diagnosis.

Conclusions

Red flags may be useful for identifying patients who require additional diagnostic evaluation, but incorporating them into the Rome criteria would not improve sensitivity and would result in too many missed irritable bowel syndrome diagnoses.
Patterns of gastritis and the effect of eradicating Helicobacter pylori on gastro‐oesophageal reflux disease in Western patients with non‐ulcer dyspepsia
Authors: VAKIL N. , TALLEY N. J. , STOLTE M. , SUNDIN M. , JUNGHARD O. , BOLLING‐STERNEVALD E.
Published: June 2006

Background

The effect of Helicobacter pylori eradication on the development of gastro‐oesophageal reflux disease is controversial.

Aim

To determine the incidence of symptoms of reflux disease and of erosive oesophagitis, and the relationship to changes in histological gastritis, in patients with non‐ulcer dyspepsia over 12 months.

Methods

Six hundred and ninety‐three patients in two similar randomized placebo controlled trials of H. pylori eradication in non‐ulcer dyspepsia were studied. Symptoms were assessed using the validated Gastrointestinal Symptom Rating Scale during a 1‐week run‐in period, at 6 months and 12 months. Endoscopy was performed at baseline to exclude patients with pathology and at 3 months and 12 months to determine if oesophagitis was present. Gastric biopsies were scored using the modified Sydney Classification.

Results

Patients without predominant heartburn, oesophagitis or ulcers at endoscopy were randomized to active (n = 297, omeprazole, amoxicillin and clarithromycin) treatment or to placebo/omeprazole (n = 306) for 1 week. The eradication rate was 82% in the active treatment group. Antrum‐predominant gastritis (55%) was more frequently found than corpus‐predominant gastritis (6%). In patients with antrum‐predominant gastritis, heartburn and regurgitation scores improved significantly 12 months after eradication. Erosive oesophagitis developed in 15/232 patients in the eradication group (7%) compared with 2/227 (2%) in the control group, but there was no significant difference when adjusted for oesophagitis present at baseline.

Conclusions

Antrum‐predominant gastritis is the most common pattern of gastritis seen in non‐ulcer dyspepsia in Western populations. Heartburn and regurgitation improve after eradication therapy or placebo in patients with non‐ulcer dyspepsia; the development of oesophagitis is uncommon.
Gene expression of cytokines and cytokine receptors is modulated by the common variability of the mitochondrial DNA in cybrid cell lines
Authors: Bellizzi Dina , Cavalcante Paola , Taverna Daniela , Rose Giuseppina , Passarino Giuseppe , Salvioli Stefano , Franceschi Claudio , De Benedictis Giovanna
Published: June 2006

Some lines of evidence indicate that common polymorphisms of mitochondrial DNA (mtDNA) act as susceptibility factors in complex traits, such as age‐related common diseases. There is also evidence that the cell capability to compensate ravages caused by intrinsic or extrinsic stress factors could contribute to some of these diseases. The cross‐talk between nuclear and mitochondrial genome may link the above observations if we assume that the transcription of stress‐responder nuclear genes is modulated according to the mtDNA common variability. Cytokines and cytokine receptors are key molecules in stress response. We could, therefore, check the above hypothesis by analyzing expression patterns of cytokine and cytokine receptor genes in response to stress in cell lines sharing the same nuclear genome but different mtDNA. By using a cybrid model (143B.TK− osteosarcoma cells depleted of their own mtDNA and repopulated with foreign mitochondria) we show that the transcription patterns of some of such genes are specifically modulated by the variability of the mitochondrial genome not only under stress conditions (interleukin‐6) but also at basal conditions (interleukin‐1β and tumor necrosis factor receptor 2). These findings provide a first experimental evidence of a relationship between mtDNA common variability and expression pattern of stress responder nuclear genes in human cells.
Literacy achievement of children with intellectual disabilities and differing linguistic backgrounds
Authors: Verhoeven L. , Vermeer A.
Published: June 2006

Background  The aim of the present study was to examine the literacy achievement of 10‐ to 12‐year‐old native and non‐native children with intellectual disabilities (ID) living in the Netherlands. An intriguing question within this context was whether the second language learning non‐native children with ID would show a double disadvantage when compared with their monolingual Dutch peers with no ID.

Methods  Dutch literacy scores in the domains of word decoding, vocabulary, syntax and text were therefore compared for: (1) intellectually disabled native Dutch children; (2) intellectually disabled non‐native children; (3) normally developing native Dutch children; and (4) normally developing non‐native children. The interrelations between literacy subskills were also compared for native vs. non‐native children with ID.

Results  The native and non‐native students diagnosed as intellectually disabled produced substantially lower literacy scores than their non‐disabled peers. The differences between the native (L1) and non‐native (L2) children in regular vs. special education were found to depend on the aspect of literacy considered. Word decoding and language skills turned out to significantly predict the children’s reading comprehension, although some differences in the strength of relationships could also be evidenced.

Conclusions  The literacy achievement of intellectually disabled children with differing linguistic backgrounds generally falls behind that of their non‐disabled peers. For word decoding, the non‐native children in regular and special education were generally able to keep up with their native peers. For higher‐order literacy abilities closely related to the mental lexicon, sentence processing and text processing, however, significant differences in the performances of the native (L1) and non‐native (L2) children in regular vs. special education were found, suggesting a double disadvantage for the non‐native children in special education.
Social climate within secure inpatient services for people with intellectual disabilities
Authors: Langdon P. E. , Swift A. , Budd R.
Published: June 2006

Background The social climate of inpatient facilities is thought to be an important contributor to treatment outcome. However, little research has focused on this construct within secure forensic services for people with intellectual disabilities (ID). Therefore, the objective of this study was to investigate the social climate of two different types of secure units (‘low’ secure vs. ‘medium’ secure) contained within the same facility for offenders with ID. Two hypotheses were generated: (1) residents would rate the social climate of the whole facility in a more negative direction than staff, and (2) residents and staff would rate the social climate of the ‘low’ secure unit in a more positive direction than that of the ‘medium’ secure unit.

Method Using a 2 (factor ‘Participant’ = Staff or Resident) × 2 (factor ‘Unit’ = ‘Low’ or ‘Medium’ Secure Unit) between‐subjects design, 18 residents and 37 staff members were recruited and completed the Correctional Institutions Environment Scale (CIES), a measure of social climate.

Results Residents tended to rate the units in a more positive direction than staff on some sub‐scales. Participants rated the ‘low’ secure unit in a more positive direction than the ‘medium’ secure unit on two sub‐scales of the CIES. However, on selected sub‐scales there were differences. The findings of this study suggest that the CIES may be a valid instrument for use within forensic services for people with ID, and further suggests that residents and staff have different perceptions of the shared social climate, which may have implications for service development.
Induction of Interleukin‐6 Release from Monocytes by Serine Proteinases and its Potential Mechanisms
Authors: Li T. , Wang H. , He S.
Published: June 2006

Serine proteinases have been recognized playing an important role in inflammation via proteinase‐activated receptors (PAR). However, little is known of the influence of serine proteinases and PAR on interleukin‐6 (IL‐6) secretion from highly purified monocytes. We challenged monocytes from human peripheral blood with serine proteinases and agonist peptides of PAR and measured the levels of IL‐6, IL‐1β and IL‐12 in culture supernatants by enzyme‐linked immunosorbent assay. The results showed that thrombin, trypsin, tryptase and elastase stimulated approximately up to 2.9‐, 2.0‐, 1.8‐ and 2.1‐fold increase in IL‐6 release from monocytes following 16 h of incubation, respectively. Proteinase inhibitors inhibited the actions of proteinases on monocytes. Agonist peptides of PAR‐1 (SFLLR‐NH3) and PAR‐4 (GYPGQV‐NH2), but not PAR‐3 (TFRGAP‐NH2), also induced IL‐6 release from monocytes. The proteinases and agonists of PAR failed to stimulate IL‐1β and IL‐12 secretion. In conclusion, the induction of IL‐6 secretion by serine proteinases may be through the activation of PAR.
The preservation potential of some recent stromatolites
Authors: PARK ROBERT K.
Published: June 2006

Stromatolites are laminated organo‐sedimentary structures, generally compared to present day blue‐green algal mats. Their morphology, species composition and overall extent are largely governed by the amount of wetting, although other factors such as competition, predation and desiccation, also contribute.

The Trucial Coast mats are essentially intertidal. Stromatolite accretion rates in this area are of the order of 0·2 mm p.a. but lamina growth is far from regular. The area is also characterized by the development of evaporites, especially gypsum which proves to be an important agent of mat destruction. The growth of crystals causes disruption within the upper portions of the stromatolite section with the result that none of the upper intertidal mat forms are preserved. Other agencies of destruction include bacterial decay, desiccation and dehydration, and compaction under burial which may depress and deform the original mat relief. Decay results in the almost total loss of cellular contents, only a few empty sheaths and the pigment surviving into the fossil record.

Preservation may be effected via (a) burial or (b) lithification. However, few modern algal mat structures bear any resemblance to fossil stromatolite heads with the exception of those from Shark Bay. From this, one might infer that pene‐contemporaneous lithification is a prerequisite for their preservation.
A Histochemical Investigation of Different Distribution of TSH Cells in Adenohypophsis of Female and Male Rats
Authors: Kum S. , Eren U. , Sandikci M. , Musal B.
Published: June 2006

The aim of the present study was to investigate histochemically the localization of thyroid‐stimulating hormone (TSH) cells and the number of TSH cells in adenohypophysis of ovariectomized adult females, intact females at estrous and diestrous phase of sexual cycles and castrated and non‐castrated adult male rats. TSH cells, distributed throughout the pars distalis in all groups, were observed more frequent in areas near to the pars intermedia than other regions. The cells were round, ovoid, stellar‐shaped and had contacts with sinusoids. Their nuclei were large and round‐shaped. The cells were found mostly single or occasionally in groups of double and triple. The number of TSH cells was higher in estrous than diestrous phase in intact rats. In adenohypophysis of ovariectomized rats, their numbers were less than that of intacts in estrous, but higher than that of found in diestrous phases. Furthermore, the numbers of TSH cells in intact females during estrous phase was higher than those found in intact and castrated male rats. On the other hand, castration reduced the number of TSH cells while ovariectomy had no effect in this respect.
In vitro efficacy of 75 essential oils against Aspergillus niger
Authors: Pawar V. C. , Thaker V. S.
Published: June 2006

Aspergillus niger is an opportunistic human pathogen and a strong air pollutant. A study was conducted with 75 different essential oils for the inhibition of hyphal growth and spore formation in Aspergillus niger. Cinnamomum zeylanicum (bark), Cinnamomum zeylanicum (leaf), Cinnamomum cassia, Syzygium aromaticum and Cymbopogon citratus were the top five essential oils which demonstrated marked inhibitory effect against hyphal growth and spore formation of A. niger. The chemical composition of these five most active essential oils was investigated by gas chromatography–mass spectra (GC–MS). Most of the other essential oils were found challenging to combat A. niger, suggesting their use as strong aroma therapeutic agents.
Incidence and odds ratio of appendicitis as first manifestation of colon cancer: A retrospective analysis of 1873 patients
Authors: Lai Hung‐Wen , Loong Che‐Chuan , Tai Ling‐Chen , Wu Chew‐Wun , Lui Wing‐Yiu
Published: June 2006

Background and Aim:  Obstruction of the lumen of the appendix is the major cause of appendicitis. Tumors could obstruct this lumen and cause appendicitis in the elderly. The association between appendicitis and colon cancer has not been sufficiently investigated, and this study was designed to clarify this association.

Methods:  This was a retrospective study. Patients diagnosed with acute appendicitis from January 1998 to December 2003 at the Taipei Veterans General Hospital were surveyed. Patients found to have colon cancers immediately or subsequently after appendectomy were included and analyzed.

Results:  A total of 1873 patients were diagnosed as having appendicitis of whom 16 were found to have colon cancer. The incidence of appendicitis associated with colon cancer was 0.85%. The time from appendectomy to the recognition of colonic cancer was at a median delay of 5.8 months. From the Taiwan Cancer Research Annual Report, the incidence of colon cancer was 31.91/100 000 in the year 2000. The odds ratio of colon cancer incidence had a 38.5‐fold increase among patients older than 40 with acute appendicitis.

Conclusions:  In patients over 40 years who present with symptoms of acute appendicitis the possibility of a coexistent colonic neoplasm should always be kept in mind. These patients should undergo colonoscopy 6 weeks after surgery to exclude the possibility of a coexistent colorectal cancer.