bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Abnormalities of Peripheral Blood Distinct T, B, and Natural Killer Cell Subsets and Clinical Findings in Obstetric Antiphospholipid Syndrome
Authors: CARBONE JAVIER , GALLEGO ANTONIO , LANIO NALLIBE , NAVARRO JOAQUIN , ORERA MARIA , AGUARON ANGEL , FERNANDEZ-CRUZ EDUARDO , SARMIENTO ELIZABETH
Published: March 2009

Objetive.

Few studies have assessed immunophenotypic abnormalities on lymphocyte subsets in patients with antiphospholipid syndrome (APS). We performed an extended immunological study to define alterations of distinct T, B, and natural killer (NK) cell subsets in obstetric patients with APS and their relationship with APS–associated complications.

Methods.

Patients and controls: 36 women with APS [Sydney criteria, Group A1 without thrombosis (n = 26), Group A2 with thrombosis (n = 10)]; and 36 age matched women with recurrent abortion without antiphospholipid antibodies (disease controls; Group B), 36 healthy parous women (healthy controls; Group C), and 36 healthy nonparous women (healthy controls; Group D). Thrombotic events occurred after history of abortions in all A2 women. Three-color whole-blood flow cytometry was used to characterize the distinct immunophenotypes.

Results.

A1 patients had significantly higher percentages of CD4+CD45RA–CCR7+ central memory cells (A1 vs D), higher percentages of activated CD4+CD25+ T cells (A1 vs D), and lower percentages and absolute counts of CD4+CD45RA–CCR7– effector memory cells (A1 vs D). GroupA2 patients had higher percentages and absolute numbers of CD19+CD27–IgD+ naive B cells (A2 vs A1 vs all controls), lower percentages and absolute numbers of CD3–CD56+CD16+ NK cells (A2 vs all controls), and higher percentages of activated CD4+DR+ (A2 vs all controls), CD8+DR+ (A2 vs A1 vs C vs D), CD4+CD38+DR+ (A2 vs D), and CD4+CD25+DR+ T cells (A2 vs all controls). Increased percentages of CD8+DR+ T cells [relative risk (RR) 2.43, 95% CI 1.09–5.44, p = 0.02] and of naive B cells (RR 3.05, 95% CI 1.30–7.11, p = 0.009) were associated with development of thrombosis.

Conclusion.

In obstetric patients with APS we documented significant changes in T, B, and NK cell homeostasis. Increased levels of CD8+DR+ and CD19+CD27–IgD+ cells might identify obstetric patients with APS at risk of having thrombosis.
Conversion of Carbon Dioxide into Methanol with Silanes over N‐Heterocyclic Carbene Catalysts
Authors: Riduan Siti Nurhanna , Zhang Yugen , Ying Jackie Y.
Published: March 2009

Aktivieren und reduzieren: Kohlendioxid wurde unter milden Bedingungen in Gegenwart eines stabilen N‐heterocyclischen Carbens mit einem Silan zu Methanol reduziert. Als Ausgangsmaterial kann auch trockene Luft dienen. Der Organokatalysator ist in diesem Prozess zur chemischen CO2‐Aktivierung und ‐Fixierung viel effizienter als Übergangsmetallkatalysatoren.

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Schooling Behavior of Light‐Powered Autonomous Micromotors in Water
Authors: Ibele Michael , Mallouk Thomas E. , Sen Ayusman
Published: March 2009

A new school of thought: Micrometer‐sized silver chloride (AgCl) particles (red) in deionized water move under UV illumination by self‐diffusiophoresis (see picture). Each AgCl particle secretes ions to which the other particles respond, and they are observed to “school” into regions with higher concentrations of particles. Photo‐inactive silica particles (blue) also respond to the chemical secretion by swimming towards and surrounding individual AgCl particles.

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Inside Cover: Perfluoropentaphenylborole (Angew. Chem. Int. Ed. 16/2009)
Authors: Fan Cheng , Piers Warren E. , Parvez Masood
Published: March 2009

Perfluoroaryl boranes are an important class of organometallic Lewis acids. The synthesis of perfluorinated compounds brings special challenges to tried‐and‐true synthetic methodologies. In their Communication on page 2955 ff., W. E. Piers and co‐workers present the synthesis of a new, fully fluorinated heterocyclic borane that is also a member of the rare antiaromatic borole class of compounds. The route relies on normally facile transmetallation reactions made more difficult by the electron‐withdrawing C6F5 groups of the target product.

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Occurrence of killer whales in Scottish inshore waters: temporal and spatial patterns relative to the distribution of declining harbour seal populations
Authors: Bolt Harriet E. , Harvey Paul V. , Mandleberg Laura , Foote Andrew. D.
Published: March 2009

Sightings of killer whales around Shetland were recorded between 1991 and 2006 and for the whole of Scotland for 2007. The data were used to investigate temporal patterns in killer whale occurrence around Shetland and spatial patterns in occurrence around Scotland.

There was a strong seasonal peak in sightings around Shetland during June–July, coinciding with the harbour seal pupping season.

There was no clear trend in annual sightings around Shetland between 1991 and 2006.

Killer whales were sighted most frequently around Shetland and the Pentland Firth as well as around Mull and the Treshnish Isles.

These findings are discussed in terms of potential impacts upon local declining harbour seal populations and future research requirements.

Copyright © 2009 John Wiley & Sons, Ltd.
Juvenile dermatomyositis calcifications selectively displayed markers of bone formation
Authors: Urganus Annette L. , Zhao Yong‐dong , Pachman Lauren M.
Published: March 2009

Objective

To determine the presence of small integrin‐binding ligand N‐linked glycoprotein (SIBLING) and bone components in juvenile dermatomyositis (DM) pathologic calcifications.

Methods

Calcifications were removed from 4 girls with juvenile DM symptoms for mean ± SD 36.9 ± 48.3 months and were stained for SIBLING proteins: full‐length osteopontin (OPN), bone sialoprotein (BSP), dentin matrix protein 1 (DMP1), dentin phosphoprotein (DPP), and matrix extracellular phosphoglycoprotein (MEPE); bone markers: osteocalcin (OC), core‐binding factor α 1 (CBFα1), and alkaline phosphatase (AP) for osteoblasts; tartrate‐resistant acid phosphatase (TRAP) for osteoclasts; and the mineral regulators osteonectin (ON) and matrix Gla protein (MGP). The deposit center, periphery, adjacent connective tissue, and vascular endothelial cells were examined.

Results

Alizarin red stained calcified deposits that did not localize with collagen, like bone, under polarized light. Hematoxylin and eosin stain revealed a paucity of connective tissue and absence of bone‐like structures. The deposits, connective tissue, and vascular endothelial cells were positive for BSP, DPP, DMP1, and AP; MEPE was not detected. OC, ON, and MGP were present in the deposits and vascular endothelial cells; OPN and CBFα1 were present in deposits and connective tissue. TRAP‐positive osteoclasts were localized to the calcification periphery.

Conclusion

The disorganized juvenile DM calcifications differ in structure, composition, and protein content from bone, suggesting that they may not form through an osteogenic pathway. Osteoclasts at the deposit surface represent an attempt to initiate its resolution.
Absence of a classically activated macrophage cytokine signature in peripheral spondylarthritis, including psoriatic arthritis
Authors: Vandooren Bernard , Noordenbos Troy , Ambarus Carmen , Krausz Sarah , Cantaert Tineke , Yeremenko Nataliya , Boumans Maartje , Lutter Rene , Tak Paul P. , Baeten Dominique
Published: March 2009

Objective

Peripheral spondylarthritis (SpA) is characterized by macrophages that express CD163, a marker of alternative activation (M2). The purpose of this study was to assess whether this differential infiltration with macrophage subsets was associated with a different local inflammatory milieu in SpA as compared with rheumatoid arthritis (RA).

Methods

The effect of SpA and RA synovial fluid (SF) on macrophage polarization was tested in vitro on normal peripheral blood monocytes. SF levels of classically activated macrophage (M1)–derived and alternatively activated macrophage (M2)–derived mediators were analyzed by enzyme‐linked immunosorbent assay and multiparameter Luminex bead assay in 47 patients with non‐psoriatic SpA, 55 with RA, and 15 with psoriatic arthritis (PsA). Paired synovial biopsy samples were analyzed histologically.

Results

SF from SpA patients promoted preferential expression of the M2 markers CD163 and CD200R in vitro, even if SF levels of the prototypical M2‐polarizing factors (interleukin‐4 [IL‐4], IL‐13, and IL‐10) were not increased as compared with those in RA SF. Despite a similar degree of overall joint inflammation in SpA and RA, SpA synovitis displayed strongly reduced SF levels of M1‐derived, but not M2‐derived, mediators, such as tumor necrosis factor α (TNFα), IL‐1β, IL‐12p70, and interferon‐γ–inducible protein 10. SF levels of M1‐derived mediators correlated well with peripheral joint inflammation in RA, but neither these mediators nor IL‐1α and IL‐17 did so in SpA. Of interest, the SF cytokine profile in PsA, a more destructive subtype of SpA, was similar to that in non‐psoriatic SpA.

Conclusion

The local inflammatory milieu is clearly different in SpA as compared with RA peripheral arthritis. Synovitis in SpA, including that in PsA, is characterized by a selective decrease in M1‐derived proinflammatory mediators, such as TNFα and IL‐1β.
The incidence of primary hip osteoarthritis in active duty US military servicemembers
Authors: Scher Danielle L. , Belmont Philip J. , Mountcastle Sally , Owens Brett D.
Published: March 2009

Objective

Although multiple studies have reported the prevalence of primary hip osteoarthritis (OA), little has been reported on incidence rates of hip OA. We sought to determine the incidence rate and demographic risk factors of hip OA in an ethnically diverse and physically active population of US military servicemembers.

Methods

A query was performed using the US Defense Medical Epidemiology Database for the International Classification of Diseases, Ninth Revision, Clinical Modification code for hip OA (715.95). Multivariate Poisson regression analysis was used to estimate the rate of hip OA per 100,000 person‐years, controlling for sex, race, age, rank, and service.

Results

The overall unadjusted incidence rate of hip OA was 35 per 100,000 person‐years. Women, compared with men, had a significantly increased adjusted incidence rate ratio for hip OA of 1.87 (95% confidence interval [95% CI] 1.73–2.01). The adjusted incidence rate ratio for black servicemembers when compared with white servicemembers was 1.32 (95% CI 1.23–1.41). The adjusted incidence rate ratio for the ≥40‐year‐old age group compared with the 20‐year‐old group was 22.21 (95% CI 17.54–28.14). With junior officers as the referent category, junior enlisted, senior enlisted, and senior officers rank groups had a significantly increased adjusted incidence rate ratio for hip OA. With the Air Force as the referent category, each service had a significantly increased adjusted incidence rate ratio for hip OA.

Conclusion

Female sex; black race; age ≥40 years; junior enlisted, senior enlisted, and senior officer rank groups; and military service in the Navy, Army, or Marines were all risk factors for hip OA.
Effector CD8+ T cells in systemic sclerosis patients produce abnormally high levels of interleukin‐13 associated with increased skin fibrosis
Authors: Fuschiotti Patrizia , Medsger Thomas A. , Morel Penelope A.
Published: March 2009

Objective

T lymphocytes play an important role in systemic sclerosis (SSc), a connective tissue disease characterized by inflammation, fibrosis, and vascular damage. While their precise role and antigen specificity are unclear, T cell–derived cytokines likely contribute to the induction of fibrosis. The aim of this study was to establish the role of cytokine dysregulation by T cells in the pathogenesis of SSc.

Methods

To identify relationships between a specific cytokine, T cell subset, and the disease course, we studied a large cohort of patients with diffuse cutaneous SSc (dcSSc) or limited cutaneous SSc (lcSSc). Using Luminex analysis and intracellular cytokine staining, we analyzed the intrinsic ability of CD4+ and CD8+ T cell subsets to produce cytokines following in vitro activation.

Results

High levels of the profibrotic type 2 cytokine interleukin‐13 (IL‐13) were produced following activation of peripheral blood effector CD8+ T cells from SSc patients as compared with normal controls or with patients with rheumatoid arthritis. In contrast, CD4+ T cells showed a lower and more variable level of IL‐13 production. This abnormality correlated with the extent of fibrosis and was more pronounced in dcSSc patients than in lcSSc patients.

Conclusion

Dysregulated IL‐13 production by effector CD8+ T cells is important in the pathogenesis of SSc and is critical in the predisposition to more severe forms of cutaneous disease. Our study is the first to identify a specific T cell phenotype that correlates with disease severity in SSc and can be used as a marker of immune dysfunction in SSc and as a novel therapeutic target.
Development and evaluation of web service‐based interactive and simulated learning environment for computer numerical control
Authors: Wu Wen‐Hsiung , Chen Wei‐Fan , Fang Lung‐Ching , Lu Chao‐Wei
Published: March 2009

Multimedia technology and Internet applications are important tools for teaching and learning in engineering education. Nowadays online simulative environments are indispensable tools for teaching computer numerical control (CNC) course in mechanical engineering. Nevertheless, past studies seldom designed CNC code or program error handling mechanisms, and failed to use new emergent technologies and applications. This study proposed a design for a WSISLE‐CNC (web service‐based interactive and simulated learning environment for CNC) based on Web service technology. A questionnaire survey from vocational school instructors and students revealed a high degree of enthusiasm for this proposed approach. In summary, the main contributions of this study to engineering education are: (1) development of several types of CNC code or program error handling mechanisms and applications, and (2) use of Web service concepts and technology to develop various kinds of CNC simulation services. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 407–422, 2010; View this article online at wileyonlinelibrary.com; DOI 10.1002/cae.20147
Randomized gossip algorithms for maintaining a distributed bulletin board with guaranteed age properties
Authors: Amar Lior , Barak Amnon , Drezner Zvi , Okun Michael
Published: March 2009

Scalable computer systems, including clusters and multi‐cluster grids, require routine exchange of information about the state of system‐wide resources among their nodes. Gossip‐based algorithms are popular for providing such information services due to their simplicity, fault tolerance and low communication overhead. This paper presents a randomized gossip algorithm for maintaining a distributed bulletin board among the nodes of a scalable computer system. In this algorithm each node routinely disseminates its most recently acquired information while maintaining a snapshot of the other nodes' states. The paper provides analytical approximations for the expected average age, the age distribution and the expected maximal age for the acquired information at each node. We confirm our results by measurements of the performance of the algorithm on a multi‐cluster campus grid with 256 nodes and by simulations of configurations with up to 2048 nodes. The paper then presents practical enhancements of the algorithm, which makes it more suitable for a real system. Such enhancements include using fixed‐size messages, reducing the number of messages sent to inactive nodes and supporting urgent information. The enhanced algorithm guarantees the age properties of the information at each node in the configurations with an arbitrary number of inactive nodes. It is being used in our campus grid for resource discovery, for dynamic assignment of processes to the best available nodes, for load‐balancing and for on‐line monitoring. Copyright © 2009 John Wiley & Sons, Ltd.
Electron Transfer Dynamics in Dye‐Sensitized Solar Cells Utilizing Oligothienylvinylene Derivates as Organic Sensitizers
Authors: Clifford John N. , Forneli Amparo , López‐Arroyo Leticia , Caballero Rubén , de la Cruz Pilar , Langa Fernando , Palomares Emilio
Published: March 2009

Many dyes make light work: Molecular photovoltaic devices based on nanocrystalline TiO2 are prepared by using two dye sensitizers (see figure). Their relative efficiencies are greatly dependent on the molecular structures of the dyes.

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Two new organic dyes have been synthesized and used as efficient light‐harvesting materials in molecular photovoltaic devices. These dyes are based on conjugated thienylvinylene units, with FL‐4 consisting of a four‐unit thienylvinylene oligomer and its homologue FL‐7 which additionally incorporates the electron‐donating triphenylamine unit (TPA) into its structure. Upon light excitation both dyes show efficient electron injection into the TiO2 conduction band and slow back electron transfer to the oxidized dye. In fact, for FL‐7, the back electron transfer dynamics are slower owing to efficient hole transfer to the TPA moiety situated further from the semiconductor surface. However, the electron recombination kinetics with the oxidized electrolyte for both FL‐4 and FL‐7 in dye‐sensitized solar cells are faster than for devices made using the ruthenium dye N719. We believe that this is a serious limiting factor for devices based on oligothiophenes which, despite showing higher molecular extinction coefficients in the vis‐NIR region of the solar spectrum, still cannot challenge the light‐to‐energy conversion efficiency of N719 or other ruthenium polypyridyl complexes.
Use of adenovirus for ectopic gene expression in Xenopus
Authors: Dutton James R. , Daughters Randy S. , Chen Ying , O'Neill Kathy E. , Slack J.M.W.
Published: March 2009

We show that replication defective adenovirus can be used for localized overexpression of a chosen gene in Xenopus tadpoles. Xenopus contains two homologs of the Coxsackie and Adenovirus Receptor (xCAR1 and 2), both of which can confer sensitivity for adenovirus infection. xCAR1 mRNA is present from the late gastrula stage and xCAR2 throughout development, both being widely expressed in the embryo and tadpole. Consistent with the expression of the receptors, adenovirus will infect a wide range of Xenopus tissues cultured in vitro. It will also infect early embryos when injected into the blastocoel or archenteron cavities. Furthermore, adenovirus can be delivered by localized injection to tadpoles and will infect a patch of cells around the injection site. The expression of green fluorescent protein in infected cells persists for several weeks. This new gene delivery method complements the others that are already available. Developmental Dynamics 238:1412–1421, 2009. © 2009 Wiley‐Liss, Inc.
In vitro investigations related to the hypothesis that Lipoatrophia semicircularis finds its origin in electro‐stimulation
Authors: Verschaeve Luc , Maes Annemarie
Published: March 2009

Lipoatrophia semicircularis (L.s.) is an idiopathic condition characterized by semicircular impressions of the skin, usually at the front and sides of both thighs. It is characterized by atrophy of the subcutaneous adipocytes whereas the skin and muscles remain normal. L.s. was originally considered to be very rare but over the past 13 years an outburst of L.s. has been observed in companies in Belgium and later on also in companies in other countries (e.g., Spain) where several hundred individuals were diagnosed with L.s. All these subjects belonged to the administrative personnel and worked in renovated or new offices. Different hypotheses have been put forward to explain the appearance of Lipoatrophia semicircularis but the hypothesis of an ‘electric’ origin of L.s. is probably the best documented and plausible. The present study was aimed to further investigate the likelihood of this hypothesis. The alkaline comet assay was used to investigate DNA damage in cells of different origin following exposure to a (strong) electric current. It was found that adipocytes showed more DNA damage than the other cells and hence that they are more vulnerable to such a current than macrophages and white blood cells. It was also found that DNA damage is significantly induced by an electric current in the blood from L.s. subjects whereas this is not so in blood from subjects without L.s. This may indicate that L.s. subjects are more responsive to an induced electric current and supports the hypothesis of an ‘electric’ origin of L.s. Copyright © 2009 John Wiley & Sons, Ltd.
Systematic study of the performance of a reverse flow reactor for the treatment of lean hydrocarbon emissions
Authors: Marín Pablo , Ordóñez Salvador , Díez Fernando V.
Published: March 2009

BACKGROUND: Reverse flow reactors are widely used for the treatment of gaseous emissions containing different hydrocarbons. However, most of the reported studies are focused on the combustion of a given hydrocarbon over a given catalyst. Consequently, any conclusions are difficult to extrapolate to other systems due to the wide range of variation of the chemical properties in these systems (reactivity, concentrations, combustion enthalpy, etc.).

RESULTS: A new generalized approach for the design of reverse flow reactors (RFR) for the catalytic combustion of lean hydrocarbon‐air mixtures is proposed in this work. This approach allows the preliminary design of RFR for the combustion of a given hydrocarbon on a given catalyst, in terms of intrinsic kinetics (kinetic constant and activation energy) and adiabatic temperature rise (a function of concentration and combustion enthalpy). The combined effect of the adiabatic temperature rise, Damköhler number, dimensionless activation energy and space velocity (GHSV) on typical RFR performance (switching time of 300 s) has been determined, building different charts for determining the stable operating regions in terms of these variables. A one‐dimensional heterogeneous model, experimentally validated for the combustion of hexane and toluene over a Pt/Al2O3 catalyst, was used.

CONCLUSIONS: Results obtained allow a preliminary design (i.e. determination of the required space velocity) for the effective abatement (99.99% conversion) of a given hydrocarbon in a RFR, if its concentration, reaction enthalpy and kinetic parameters are known. Copyright © 2009 Society of Chemical Industry
Early detection (9+6 weeks) of cardiac failure in a fetus diagnosed as Turner syndrome by 2D transvaginal ultrasound‐guided coelocentesis
Authors: Tonni Gabriele , Azzoni Daniela , Ventura Alessandro , De Felice Claudio , Marinelli Maria
Published: March 2009

A 28‐year‐old woman was diagnosed by transvaginal ultrasound at 9+6 weeks with early fetal cardiac failure (hydrothorax and bradycardia). Doppler analysis of ductus venosus showed a negative A‐wave pattern. The follow‐up sonogram obtained at 11+6 weeks documented a missed abortion. A transvaginal ultrasound‐guided coelocentesis was performed under local cervical anesthesia before uterine suction and 8 mL of clear extracoelomic fluid were successfully aspirated. Cytogenetic analysis demonstrated a 45,X karyotype. Ultrasound and Doppler waveform analysis of ductus venosus allowed early diagnosis of fetal cardiac failure. Coelocentesis may be the method of choice for early fetal karyotyping and may be used in the future to induce immunologic tolerance. © 2009 Wiley Periodicals, Inc. J Clin Ultrasound, 2009.
Raman spectroscopic study of the uranyl mineral pseudojohannite Cu6.5[(UO2)4O4(SO4)2]2(OH)5·25H2O
Authors: Frost Ray L. , Plášil Jakub , Čejka Jiří , Sejkora Jiří , Keeffe Eloise C. , Bahfenne Silmarilly
Published: March 2009

Raman spectra of pseudojohannite were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (SO4)2− units and of water molecules. The published formula of pseudojohannite is Cu6.5(UO2)8[O8](OH)5[(SO4)4]·25H2O. Raman bands at 805 and 810 cm−1 are assigned to (UO2)2+ stretching modes. The Raman bands at 1017 and 1100 cm−1 are assigned to the (SO4)2− symmetric and antisymmetric stretching vibrations. The three Raman bands at 423, 465 and 496 cm−1 are assigned to the (SO4)2−ν2 bending modes. The bands at 210 and 279 cm−1 are assigned to the doubly degenerate ν2 bending vibration of the (UO2)2+ units. UO bond lengths in uranyl and OH···O hydrogen bond lengths were calculated from the Raman and infrared spectra. Copyright © 2009 John Wiley & Sons, Ltd.
Substrate binding modifies the hinge bending characteristics of human 3‐phosphoglycerate kinase: A molecular dynamics study
Authors: Palmai Zoltan , Chaloin Laurent , Lionne Corinne , Fidy Judit , Perahia David , Balog Erika
Published: March 2009

3‐Phosphogycerate kinase (PGK) is a two domain enzyme, with a binding site of the 1,3‐bisphosphoglycerate on the N‐domain and of the ADP on the C‐domain. To transfer a phosphate group the enzyme has to undergo a hinge bending motion from open to closed conformation to bring the substrates to close proximity. Molecular dynamics simulation was used to elucidate the effect of ligand binding onto the domain motions of this enzyme. The simulation results of the apo form indicate a hinge bending motion in the ns timescale while the time period of the hinge bending motion of the complex form is clearly over the 20 ns simulation time. The apo form exhibits several hinge points that contribute to the hinge bending motion while upon binding the ligands, the hinge bending becomes strictly restrained with one dominant hinge point in the vicinity of the substrates. At the same time, ligand binding results in an enhanced correlation of internal domain motions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Quantitative analysis and prediction of curvature in leucine‐rich repeat proteins
Authors: Hindle K. Lauren , Bella Jordi , Lovell Simon C.
Published: March 2009

Leucine‐rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein–protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large‐scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine‐rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain‐like thiol protease fold
Authors: Pei Jimin , Grishin Nick V.
Published: March 2009

A Rho GTPase inactivation domain (RID) has been discovered in the multifunctional, autoprocessing RTX toxin RtxA from Vibrio cholerae. The RID domain causes actin depolymerization and rounding of host cells through inactivation of the small Rho GTPases Rho, Rac, and Cdc42. With only a few toxin proteins containing RID domains in the current sequence database, the structure and molecular mechanisms of this domain are unknown. Using comparative sequence and structural analyses, we report homology inference, fold recognition, and active site prediction for RID domains. Remote homologs of RID domains were identified in two other experimentally characterized bacterial virulence factors: IcsB of Shigella flexneri and BopA of Burkholderia pseudomallei, as well as in a group of uncharacterized bacterial membrane proteins. IcsB plays an important role in helping Shigella to evade the host autophagy defense system. RID domain homologs share a conserved diad of cysteine and histidine residues, and are predicted to adopt a circularly permuted papain‐like thiol protease fold. RID domains from MARTX toxins and virulence factors IcsB and BopA thus could function as proteases or acyltransferases acting on host molecules. Our results provide structural and mechanistic insights into several important proteins functioning in bacterial pathogenesis. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Examination of the distribution of nicosulfuron in sunflower plants by matrix‐assisted laser desorption/ionisation mass spectrometry imaging
Authors: Anderson David M. G. , Carolan Vikki A. , Crosland Susan , Sharples Kate R. , Clench Malcolm R.
Published: March 2009

Matrix‐assisted laser desorption/ionisation mass spectrometry imaging (MALDI‐MSI) has been used to image the distribution of the pesticide nicosulfuron (2‐[[(4,6‐dimethoxypyrimidin‐2‐yl)aminocarbonyl]aminosulfonyl]‐N,N‐dimethyl‐3‐pyridinecarboxamide) in plant tissue using direct tissue imaging following root and foliar uptake. Sunflower plants inoculated with nicosulfuron were horizontally sectioned at varying distances along the stem in order to asses the extent of translocation; uptake via the leaves following foliar application to the leaves and uptake via the roots from a hydroponics system were compared. An improved sample preparation methodology, encasing samples in ice, allowed sections from along the whole of the plant stem from the root bundle to the growing tip to be taken. Images of fragment ions and alkali metal adducts have been generated that show the distribution of the parent compound and a phase 1 metabolite in the plant. Positive and negative controls have been included in the images to confirm ion origin and prevent false‐positive results which could originate from endogenous compounds present within the plant tissue. Copyright © 2009 John Wiley & Sons, Ltd.
Semi‐automated tandem mass spectrometric (MS/MS) triple quadrupole operating parameter optimization for high‐throughput MS/MS detection workflows
Authors: Geddes Kristin , Adamson Gary , Dube Neal , Crathern Susan , King Richard C.
Published: March 2009

This paper describes an automated workflow for the determination of selected reaction monitoring (SRM) transitions and optimum mass spectrometric (MS) instrument parameters. The approach uses a Nanomate from Advion Biosciences for automated infusion of small amounts of sample in combination with Automaton optimization software from Sciex. The results are stored in the Analyst software Compound Database for automated acquisition method building. Comparisons are presented between the more traditional optimization methods of manual flow injection optimization, Autotune infusion optimization, Automaton flow injection optimization and the Nanomate–Automaton optimization approach. Data is also presented to show that acquisition methods developed on the Sciex model API3000 instrument can be effectively transferred to the Sceix API4000 and API5000 model instruments. Copyright © 2009 John Wiley & Sons, Ltd.
Hydrophilic interaction liquid chromatography/tandem mass spectrometry for the simultaneous determination of dasatinib, imatinib and nilotinib in mouse plasma
Authors: Hsieh Yunsheng , Galviz Gerica , Zhou Qiao , Duncan Christine
Published: March 2009

Hydrophilic interaction liquid chromatography (HILIC) interfaced with atmospheric pressure ionization (API) sources and a tandem mass spectrometer (MS/MS) was developed for the simultaneous determination of dasatinib, imatinib and nilotinib in mouse plasma samples. The retention profiles of all analytes on several silica stationary phases under HILIC conditions were explored. The influences of experimental factors such as the compositions of mobile phases on the chromatographic performance and the ionization efficiency of all analytes in positive ion mode were investigated. The applicability of the proposed HILIC/MS/MS approach following a protein precipitation procedure for the quantitative determination of dasatinib, imatinib and nilotinib at low nano‐mole levels was examined with respect to assay specificity and linearity. The analytical results obtained by various HILIC/MS/MS approaches were found to be in good agreement with those obtained by reversed‐phase liquid chromatography/tandem mass spectrometry (RPLC/MS/MS) methods in terms of assay sample throughputs, sensitivity and accuracy. Furthermore, the potential of matrix ionization suppression on the proposed HILIC/MS/MS systems was investigated using the post‐column infusion technique. Copyright © 2009 John Wiley & Sons, Ltd.
Lymphocytic mitochondrial DNA deletions, biochemical folate status and hepatocellular carcinoma susceptibility in a case–control study
Authors: Wu Meng-Ying , Kuo Chang-Sheng , Lin Ching-Yih , Lu Chin-Li , Syu Huang Rwei-Fen
Published: March 2009

Mitochondrial (mt) DNA deletions and low folate status, proposed characteristics of carcinogenesis, in relation to human hepatocellular carcinoma (HCC) susceptibility are not clearly understood. We hypothesised that low folate status may modify frequencies of mtDNA deletions in humans, both of which could predispose individuals to HCC development. Biochemical folate status of serum and lymphocytes, and frequencies of mtDNA deletions in lymphocytes were determined in ninety HCC cases and ninety cancer-free healthy controls, individually matched by age and sex. The data revealed that HCC patients had lower levels of serum folate (P = 0·0002), lymphocytic folate (P = 0·040) and accumulated higher frequency of lymphocytic mtDNA deletions (P < 0·0001) than the controls. In the total studied subjects, frequencies of lymphocytic mtDNA deletions were associated with hepatitic B infection (P = 0·004) and HCC incidents (P = 0·001), and were correlated with serum folate (r− 0·155;P = 0·041), lymphocyte folate (r− 0·314;P = 0·0001), levels of glutamate-oxaloacetate transaminase (GOT) (r0·206;P = 0·006), glutamate-pyruvate transaminase (GPT) (r0·163;P = 0·037) and α-fetal protein concentrations (r0·212;P = 0·005). After adjustment for age, sex, lifestyle and one-carbon metabolite factors, individuals with low blood folate ( < 11·5 nmol/l) or high mtDNA deletions (Δ threshold cycle number (Ct)>5·3) had increased risks for HCC (OR 7·7, 95 % CI 1·9, 29·9,P = 0·003; OR 5·4; 95 % CI 1·7, 16·8,P = 0·003, respectively). When combined with folate deficiency (serum folate < 14 nmol/l), the OR of HCC in individuals with high levels of lymphocytic mtDNA deletions was enhanced (OR 13·3; 95 % CI 1·45, 122;P = 0·008). Further controlling for GOT and GPT levels, however, negated those effects on HCC risk. Taken together, the data suggest that biochemical folate status and liver injuries are important modulators to lymphocytic mtDNA deletions. The mt genetic instability that results from a high rate of mtDNA deletions and/or low folate status increased the risk for HCC, which is mediated by clinical hepatic lesions.
Tolerance and safety ofLactobacillus paracaseissp.paracaseiin combination withBifidobacterium animalisssp.lactisin a prebiotic-containing infant formula: a randomised controlled trial
Authors: Vlieger Arine M. , Robroch Afke , van Buuren Stef , Kiers Jeroen , Rijkers Ger , Benninga Marc A. , te Biesebeke Rob
Published: March 2009

The addition of probiotics to infant formula has been shown to be an efficient way to increase the number of beneficial bacteria in the intestine in order to promote a gut flora resembling that of breast-fed infants. The objective of the present study was to evaluate the safety and tolerance of a combination of two probiotic strains in early infancy. A group of 126 newborns were randomised to receive a prebiotic-containing starter formula supplemented withLactobacillus paracaseissp.paracaseiandBifidobacterium animalisssp.lactisor the same formula without probiotics for the first 3 months of life. A total of eighty infants continued the study until they were aged 6 months. Growth measurements were taken monthly at healthy baby clinics. Diaries were used to monitor behaviour, infections, use of antibiotics, as well as stool characteristics. Normal growth occurred in all infants and no statistically significant differences were detected between the probiotics group and the control group for gain in weight, length and head circumference. Infants in the probiotics group produced softer and more frequent stools during the first 3 months of life. No differences were found in crying and sleeping hours, number of parent-diagnosed infections, antibiotic use, visits to the general practitioner and number of adverse events. The use of a prebiotic-containing starter formula supplemented withL. paracaseissp.paracaseiandB. animalisssp.lactisin early infancy is safe, well tolerated and has no adverse effects on growth and infant behaviour.
The determination of the number of bacteria in soil. (Preliminary communication)
Authors: Whittles C. L.
Published: March 2009

1. The usual shaking methods have been examined and found unsatisfactory.

2. A method has been evolved for the estimation of the number of soil organisms by a direct count, and the numbers found to be very much higher than any previously reported.

3. A method for the disintegration and dispersion of the soil particles and bacteria has been devised, by means of which plate counts were made which were comparable with direct counts.

4. The dispersive actions of shaking and of vibrating have been compared. The former was found to give results which depended on the moisture content of the soil, whereas the trembling motion gave results in which the effect due to the moisture content was not apparent.

5. High counts made by previous observers can usually be correlated with one or more of the following factors:

(i) Greater dispersion of the soil as a result of the action of frost, etc.

(ii) An alkaline reaction,e.g.presence of ammonia, magnesia, etc.

(iii) Presence of a protective colloid,e.g.the effect of the addition of large quantities of straw, or traces of gelatine.

(iv) Absence of a flocculating agent, especially calcium compounds.

In conclusion the author wishes to express his gratitude to Dr G. S. Graham-Smith, F.R.S. at whose suggestion the investigation was started and under whose guidance and direction the bacteriological work was carried out in the Pathological Laboratory, Medical Schools, Cambridge; to Professor T. B. Wood, C.B.E., M.A., F.I.C., F.R.S., for facilities for carrying out the physico-chemical investigation at the School of Agriculture; to Messrs L. F. Newman, M.A., F.I.C., W. B. Hardy, M.A., F.R.S., W. H. Harvey, M.D., E. K. Rideal, M.B.E., M.A., G. Udny Yule, M.A., F.R.S., F. W. Foreman, M.A., F.I.C., and to the late Professor Sir German Sims Woodhead for their kindly advice and encouragement; to Messrs E. G. Staples, B.A., W. M. Davies, B.A., B.Sc, A.I.C. and A. W. R. Joachim, B.Sc. for assistance in the execution of the physico-chemical experiment; and to Mr W. A. Mitchell of the Medical School for his assistance in fitting up apparatus.
Estimation of nitric nitrogen and total nitrogen in plant tissue extracts
Authors: Gallagher Patrick Hugh
Published: March 2009

Several methods for estimating nitrates by reduction to ammonia were examined. The error involved in the use of acid reducing agents in presence of amino groups was emphasised.

A method based on the use of Devarda's alloy and magnesia is recommended.

In the estimation of nitrates in plant extracts, etc., by this method an equal volume of rectified spirit is first added to the solution to precipitate colloidal matter. The precipitate is filtered off and an aliquot part of the filtrate containing the equivalent in nitrate nitrogen of about 0.1 gm. of KNO3 is distilled with steam for 45 minutes with 1 gm. of Devarda's alloy and ½ gm. of freshly ignited magnesia. A blank determination is essential, in which the same volume of filtrate is distilled for the same length of time with ½ gm. of magnesia.

In Kjeldahl estimations in presence of nitrates, where the separate estimation of nitrates is not required, 2 c.c. of 25 per cent. NaOH may be substituted for the magnesia. Relatively this is very much less soda than Devarda recommends. The mixture in this case may be distilled directly for half-an-hour. The nitrates are thus reduced and the ammonia produced is collected before beginning the digestion with sulphuric acid.

This work was carried out under the supervision of Mr F. W. Foreman to whom the author's best thanks are due for much valuable criticism and advice.
The intensive production of herbage for crop-drying: Part II. A study of the effect of massive dressings of nitrogenous fertilizer and of the time of their application on the yield, chemical and botanical composition of two grass leys.
Authors: Holmes W.
Published: March 2009

1. Two experiments are described in which nine manurial treatments were applied ranging from no application to an application of 312 lb. N, 135 lb. P2O5and 168 lb. K2O per acre in one season. Some treatments included one or more massive dressings of nitrogen (104 lb./acre), while others received several light dressings spread over the season. The applications were made at differing periods of the season. In one experiment (Series 3) the treatments were applied to a 1-year Italian ryegrass ley, in the other (Series 4) to an established ryegrass pasture.
The determination of cellulose in nutritional studies: Part II. A comparison of the applicability of three methods for the determination of cellulose
Authors: Druce Edward , Willcox James Stuart
Published: March 2009

Three methods for the determination of cellulose have been compared for their value in nutritional studies, and have indicated the applicability of the procedure of Druce &Willcox (1949) in this connexion.

The use of the method of Crampton & Maynard (1938) has been shown to give an erroneous picture of the extent of cellulose digestibility, and it has been concluded that the procedure is not satisfactory.
Experiments on the ventilation of cattle byres
Authors: Findlay J. D.
Published: March 2009

1. The ventilation of two byres, one of large (1248 cu.ft.) and one of small (567 cu.ft.) cubic capacity per cow, was studied. The CO2 concentration in the atmosphere was used as a measure of the rate of air change and the dry katathermometer to determine the cooling power of the atmosphere. Temperatures and relative humidities were recorded and the actual air movements were studied by using smoke trails. The investigations were made under a variety of weather conditions and with a wide range of outlet and inlet areas.

2. It was shown that the atmospheric conditions in the large byre were almost always superior to those in the small byre, and this was undoubtedly due to the greater cubic space per cow in the large byre. Adequate ventilation was, however, readily attained in the small byre provided the outlet area was sufficiently large.
Loss of mineral nitrogen from soil
Authors: Shaw K.
Published: March 2009

1. The pattern of downward movement of nitrate in light soil is different from that in heavy clay soil of the kind used in this work.

2. In light sandy soils, where vertical structural fissures are absent, nitrate becomes distributed down the profile on leaching.

3. In heavy soils, which are well fissured and possess a gleyed horizon of partially decomposed plant debris at cultivation depth, most of the nitrate disappears from the profile after removal, by leaching or denitrification, from the cultivation layer.

4. There is little difference in the amount of rain required to remove nitrate from the surface layers of light or heavy soil.

5. Heavy and continuous rain is required to remove nitrate completely from either light or heavy soils.

6. Nitrification of ammonium sulphate is more rapid in summer than winter, but nitrification does proceed slowly during winter.

7. Ammonium nitrogen is not leached from the surface layer of either light or heavy soil.
The utilization of Hyparrhenia veld for the nutrition of cattle in the dry season III. Studies on the digestibility of the produce of mature veld and veld hay, and the effect of feeding supplementary protein and urea
Authors: Smith C. A.
Published: March 2009

Indigenous (Bos indicus) oxen fed ad lib. were used to measure the changes in the apparent digestibility of mature Hyparrhenia veld during the dry season, and also the apparent digestibility of late-cut veld hay and nitrogen-fertilized veld hay. The forages were those used in a field trial, and the present results complement previous work.

1. Mature Hyparrhenia veld harvested at the end of the rains as veld hay or green forage, contains approximately 50% digestible o.m. and 0·6% digestible c.p. The low level of approx. 3% c.p. resulted in a low apparent c.p. digestibility and consequent protein deficiency.

2. The nutritive value of the mature Hyparrhenia grassland as ‘standing hay’ progressively dropped to 38% digestible o.m. and negative c.p. digestibility by mid-dry-season in July.

3. There was an accompanying decline in voluntary intake of forage from approximately 12 lb. d.m./1000 lb. animal/day at the end of the rains to 8 lb. d.m./1000 lb. animal/day in mid dry season.

4. The seasonal drop in digestibility values is accentuated by the drop in dry-matter intake so that a diet of mature veld herbage in mid dry season is grossly deficient in both energy and protein.

5. The feeding of supplementary protein or urea resulted in a 40–60% increase in the intake of mature Hyparrhenia forage. Urea and groundnut meal were of equal value in their effect on herbage intake at the level of feeding used in this trial.

6. The main factor limiting the utilization of the mature Hyparrhenia veld appears to be a dietary protein deficiency. Increasing the dietary protein level, either by using nitrogen fertilizers to raise the herbage crude protein, per cent, or by supplementary feeding of protein or urea, not only relieved the dietary protein deficiency, but, due to the resultant increase in forage intake, also corrected the deficiency in dietary energy. The nutritive value of mature Hyparrhenia forage was thus raised from a submaintenance to a supra-maintenance level.