bluuebunny/crossref_metadata_2025 huggingface dataset:
Isotopic criteria for predicting the phase composition of hydrocarbons in Riphean and Vendian deposits of the Lena–Tunguska petroleum province
Authors: Dakhnova M.V. , Bazhenova T.K. , Lebedev V.S. , Kiselev S.M.
Published: August 2011

The isotopic criteria used to predict the hydrocarbon phase composition were justified by a comparison of regional trends in the δ13C values for hydrocarbon liquids and gases from Riphean and Vendian–Cambrian deposits of the Lena–Tunguska petroleum province. The δ13C ratios for liquid hydrocarbons and gases, which are defined by kinetic isotope effects due to kerogen cracking during petroleum generation, were used as a criterion for establishing a genetic relationship between different hydrocarbon phases.

The study has revealed that oil-versus gas-prone areas exhibit significant differences in the δ13C values and the reverse isotope distributions in the liquids and gases. In the oil-prone areas, methane becomes progressively enriched in 12C compared to oils and condensates, which is the normal trend of carbon isotopic compositions of liquid hydrocarbons and gases generated by organic matter of the same type and same maturity level. In the gas-prone areas, the δ13C values for methane either overlap with those of liquids or methane may show a general trend of enrichment in 13C relative to liquids. This relationship suggests that gases were probably generated and migrated later than oils, which may provide explanation for predominant gas accumulation in the study areas.

The results of the isotopic studies and analysis of the geologic history of the region allowed the recognition of hydrocarbon kitchen areas that were potentially expelling late-stage gas to mostly gas-prone areas.

The proposed isotopic method, i.e., a comparison of variations in carbon isotopic compositions of hydrocarbon liquids and gases, allowed us to establish a genetic relationship and discriminate between different hydrocarbon phases on the basis of the δ13C ratios. This can provide additional information about the timing of liquid hydrocarbons and gases generation and help to establish the likely locations of hydrocarbon kitchen areas and the history of hydrocarbon accumulations, thus improving the reliability of predictions for the hydrocarbon resource potential in the study areas and the phase composition of accumulated hydrocarbons.
Longitudinal changes in body composition associated with healthy ageing: men, aged 20–96 years
Authors: Jackson Andrew S. , Janssen Ian , Sui Xuemei , Church Timothy S. , Blair Steven N.
Published: August 2011

Obesity and sarcopenia are health problems associated with ageing. The present study modelled the longitudinal changes in body composition of healthy men, aged from 20 to 96 years, and evaluated the fidelity of BMI to identify age-dependent changes in fat mass and fat-free mass. The data from 7265 men with multiple body composition determinations (total observations 38 328) were used to model the age-related changes in body mass, fat mass, fat-free mass, BMI and percentage of body fat. Changes in fat mass and fat-free mass were used to evaluate the fidelity of BMI and to detect body composition changes with ageing. Linear mixed regression models showed that all trajectories of body composition with healthy ageing were quadratic. Fat mass, BMI and percentage of body fat increased from age 20 years and levelled off at approximately 80 years. Fat-free mass increased slightly from age 20 to 47 years and then declined at a non-linear rate with ageing. Levels of aerobic exercise had a positive influence on fat mass and a slight negative effect on fat-free mass. BMI and percentage of body fat were sensitive in detecting the increase in fat mass that occurred with healthy ageing, but failed to identify the loss of fat-free mass that started at age 47 years.
Tuberculosis presenting as bilateral vocal fold palsy: case report and review of otolaryngological manifestations of tuberculosis
Authors: Rennie C E , Pai I , Selvadurai D
Published: August 2011

Objective:

We report a rare case of tuberculosis presenting with bilateral vocal fold palsy.

Method:

Case report and discussion of ENT manifestations of tuberculosis.

Case report:

A 39-year-old man presented with stridor and bilateral vocal fold palsies, and underwent an emergency tracheostomy. Intra-operatively, a mass was identified overlying the thyroid cartilage. Fine needle aspiration cytology of this mass showed well formed granulomas but negative Ziehl–Nielsen staining. Computed tomography showed the mass to be surrounding the thyroid cartilage, causing airway occlusion; pulmonary infiltrates were also seen. The patient was commenced on tuberculosis treatment. Subsequent sputum samples from the tracheostomy confirmed the diagnosis. The patient responded very well to treatment, and was successfully decannulated after one week.

Conclusion:

The incidence of tuberculosis in the UK is increasing, particularly in urban areas. The otolaryngologist may encounter a wide variety of presentations. Diagnosis requires a high index of clinical suspicion.
Fibro-hyaline extensions from the bony nasal aperture, causing nasal obstruction
Authors: Haye R , Jebsen P , Dingsør B
Published: August 2011

Objective:

We report a rare case of fibro-hyaline anterior extensions of the bony nasal pyramid.

Method:

The clinical, radiological, intra-operative and histological findings are presented.

Results:

A 34-year-old man presented with bilateral nasal obstruction due to enlarged lateral walls of the nasal vestibule. Radiology showed normal bony structures. Surgery revealed three histologically identical, non-malignant, fibrous masses, one in the nasal septum and one in each of the vestibular walls. The latter were attached to the bony pyramid, protruding anteriorly and converging medially.

Conclusion:

The location and symmetry of the fibro-hyaline projections indicated that they constituted a malformation mimicking congenital bony nasal pyriform aperture stenosis. Histological analysis showed that the masses were not neoplastic.
Bilateral, spontaneous cerebrospinal fluid rhinorrhoea: endoscopic, uninasal, trans-septal approach for simultaneous closure
Authors: Kurien M , Mathew G A , Abraham S L , Irodi A
Published: August 2011

Background:

Bilateral, spontaneous cerebrospinal fluid rhinorrhoea is extremely rare, with only one previous case report (this patient developed contralateral cerebrospinal fluid leakage four years after successful endoscopic repair). We present the first English-language report of simultaneous, bilateral, spontaneous cerebrospinal fluid rhinorrhoea.

Objective:

To recommend a simple alternative endoscopic technique for simultaneous closure of bilateral, spontaneous cerebrospinal fluid rhinorrhoea.

Case report:

A 47-year-old woman presented with recent onset of bilateral, spontaneous cerebrospinal fluid rhinorrhoea, a recent history suggestive of meningitis, and a past history of pneumococcal meningitis. Bony defects on both sides of the cribriform plate were closed endoscopically in the same anaesthetic session, via a uninasal, trans-septal approach, enabling both leakage sites to be sealed simultaneously.

Conclusion:

In cases of bilateral, spontaneous cerebrospinal fluid rhinorrhoea, uninasal, trans-septal endoscopic repair is a simple and effective technique for simultaneous closure of cerebrospinal fluid leakage.
Differential effectiveness of berry polyphenols as anti-giardial agents
Authors: ANTHONY J.-P. , FYFE L. , STEWART D. , McDOUGALL G. J.
Published: August 2011

Following previous work on the anti-giardial effect of blueberry polyphenols, a range of polyphenol-rich extracts from berries and other fruits was screened for their ability to kill Giardia duodenalis, an intestinal parasite of humans. Polyphenol-rich extracts were prepared from berries using solid-phase extraction and applied to trophozoites of Giardia duodenalis grown in vitro. All berry extracts caused inhibition at 166 μg gallic acid equivalents (GAE)/ml phenol content but extracts from strawberry, arctic bramble, blackberry and cloudberry were as effective as the currently used drug, metronidazole, causing complete trophozoite mortality in vitro. Cloudberry extracts were found to be the most effective causing effectively complete trophozoite mortality at 66 μg GAE/ml. The polyphenol composition of the more effective berry extracts suggested that the presence of ellagitannins could be an important factor. However, the potency of cloudberry could be related to high ellagitannin content but also to the presence of substantial amounts of unconjugated p-coumaric acid and benzoic acid. These in vitro effects occur at concentrations easily achievable in the gut after berry ingestion and we discuss the likelihood that berry extracts could be effective anti-giardial agents in vivo.
Leishmania donovani: proteasome-mediated down-regulation of methionine adenosyltransferase
Authors: PÉREZ-PERTEJO YOLANDA , ÁLVAREZ-VELILLA RAQUEL , ESTRADA CARLOS GARCÍA , BALAÑA-FOUCE RAFAEL , REGUERA ROSA M.
Published: August 2011

Methionine adenosyltransferase (MAT) is an important enzyme for metabolic processes, to the extent that its product, S-adenosylmethionine (AdoMet), plays a key role intrans-methylation,trans-sulphuration and polyamine synthesis. Previous studies have shown that a MAT-overexpressing strain ofLeishmania donovanicontrols AdoMet production, keeping the intracellular AdoMet concentration at levels that are compatible with cell survival. This unexpected result, together with the fact that MAT activity and abundance changed with time in culture, suggests that different regulatory mechanisms acting beyond the post-transcriptional level are controlling this protein. In order to gain an insight into these mechanisms, several experiments were carried out to explain the MAT abundance during promastigote cell growth. Determination of MAT turnover in cycloheximide (CHX)-treated cultures resulted in a surprising 5-fold increase in MAT turnover compared to CHX-untreated cultures. This increase agrees with a stabilization of the MAT protein, whose integrity was maintained during culture. The presence of proteasome inhibitors, namely MG-132, MG-115, epoxomycin and lactacystin in the culture medium prevented MAT degradation in both MAT-overexpressing and ‘mock-transfected’ leishmanial strains. The role of the ubiquitin (Ub) pathway in MAT down-regulation was supported using immunoprecipitation experiments. Immunoprecipitated MAT cross-reacted with anti-Ub antibodies, which provides evidence of a proteasome-mediated down-regulation of the leishmanial MAT abundance.
Rational deployment of antimalarial drugs in Africa: should first-line combination drugs be reserved for paediatric malaria cases?
Authors: SUTHERLAND COLIN J. , BABIKER HAMZA , MACKINNON MARGARET J. , RANFORD-CARTWRIGHT LISA , SAYED BADRIA BABIKER EL
Published: August 2011

Artemisinin-based combination therapy is exerting novel selective pressure upon populations ofPlasmodium falciparumacross Africa. Levels of resistance to non-artemisinin partner drugs differ among parasite populations, and so the artemisinins are not uniformly protected from developing resistance, already present in South East Asia. Here, we consider strategies for prolonging the period of high level efficacy of combination therapy for two particular endemicities common in Africa. Under high intensity transmission, two alternating first-line combinations, ideally with antagonistic selective effects on the parasite genome, are advocated for paediatric malaria cases. This leaves second-line and other therapies for adult cases, and for intermittent preventive therapy. The drug portfolio would be selected to protect the ‘premier’ combination regimen from selection for resistance, while maximising impact on severe disease and mortality in children. In endemic areas subject to low, seasonal transmission ofPlasmodium falciparum, such a strategy may deliver little benefit, as children represent a minority of cases. Nevertheless, the deployment of other drug-based interventions in low transmission and highly seasonal areas, such as mass drug administration aimed to interrupt malaria transmission, or intermittent preventive therapy, does provide an opportunity to diversify drug pressure. We thus propose an integrated approach to drug deployment, which minimises direct selective pressure on parasite populations from any one drug component. This approach is suitable for qualitatively and quantitatively different burdens of malaria, and should be supported by a programme of routine surveillance for emerging resistance.
Comparative efficacy of immunization with inactivated whole tachyzoites versus a tachyzoite-bradyzoite mixture against neosporosis in mice
Authors: ROJO-MONTEJO S. , COLLANTES-FERNÁNDEZ E. , RODRÍGUEZ-MARCOS S. , PÉREZ-ZABALLOS F. , LÓPEZ-PÉREZ I. , PRENAFETA A. , ORTEGA-MORA L. M.
Published: August 2011

The worldwide economic impact ofNeospora caninuminfection has caused the development of effective vaccines to become one of the main goals in the field of neosporosis research. In this study, the protection conferred by antigens from inactivated whole tachyzoites (TZ) and a tachyzoite-bradyzoite mixture (TZ-BZ) ofN. caninum(Nc-Spain7 isolate) incorporated into a water-in-oil emulsion (W/O) and aluminium hydroxide-ginseng extract (Al/G) was evaluated in mouse models of congenital and cerebralN. caninuminfection. Immunization with TZ-BZ induced congenital and cerebral neosporosis exacerbation that was mainly characterized by reduced neonatal median survival time and increased parasite presence in adult mouse brains. The immune response of mice immunized with TZ-BZ was characterized by an increase in IFN-γexpression prior to challenge and an increase in IL-4 expression accompanied with significantly higher levels of antibodies against 2 recombinant bradyzoite-specific proteins (rNcSAG4 and rNcBSR4) after challenge. Immunization with TZ in W/O significantly reduced neonatal mortality, vertical transmission as well as parasite presence in adult mouse brains and induced a strong humoral immune response. The current study demonstrates the critical role of stage-specific antigens and adjuvants on the development of effective inactivated vaccines for the prevention ofN. caninuminfection.
Rating reliability for life events and difficulties in the elderly
Authors: Wilkinson Susan J. , Downes John , James Owen , Davies Morris G. , Davies Ann D. M.
Published: August 2011

Synopsis

The inter-rater reliability of Brown's measure of ongoing difficulties (‘severity’) is shown to be comparable with that of the measure of life events (‘long-term threat’) when using data from an elderly subject pool. Test–retest reliabilities for both the life event and difficulty measures are shown to be adequate if based on ‘consensus’ ratings. The question is raised of generalizability of the concepts of ‘threat’ and ‘severity’ across the lifespan.
Self-incineration: a controlled comparison of in-patient suicide attempts. Clinical features and history of self-harm
Authors: Jacobson R. , Jackson M. , Berelowitz M.
Published: August 2011

Synopsis

A systematic survey of in-patient accidents and injuries in an inner London hospital over 9 years established that, after incisions and overdoses, self-incineration was one of the commoner methods of violent self-harm. A case-controlled study of in-patient suicide attempts compared a series of 12 self-incinerators with 12 patients using other methods. Irrespective of method, the suicide attempt was predominantly a psychotic act of young single people with chronic, severe disorders and considerable past parasuicide, in a setting of escalating self-harm. Younger age, greater psychiatric morbidity, absence of alcoholism, a history of childhood arson, past and current self-burning were the features specific to self-incineration, which had a 25% mortality rate.
A Bite of BITE at the Barbican
Authors: Shevtsova Maria
Published: August 2011

Report on the BITE season at the Barbican, 2010–2011.
Implementing and evaluating the effectiveness of a payment scheme for environmental services from agricultural land
Authors: ULBER LENA , KLIMEK SEBASTIAN , STEINMANN HORST-HENNING , ISSELSTEIN JOHANNES , GROTH MARKUS
Published: August 2011

The current rapid decline in biodiversity in human-dominated agricultural landscapes, both in Europe and worldwide, impacts on the provision of environmental services essential to human well-being. There is, therefore, a pressing need to develop and implement incentive-based conservation policies to counteract the ongoing loss of biodiversity. This paper presents results of a regionally-scaled conservation procurement auction, a type of incentive-based payments for environmental services (PES), targeted at the conservation of arable plant diversity. By matching arable fields that were participating in the PES scheme to control fields that were not enrolled in the PES scheme, two critical key characteristics were addressed, namely additionality and bid prices. Additionality was addressed by evaluating whether fields for which PES were issued had significantly higher arable plant diversity than the matched control fields. The cost-effectiveness of a conservation auction increases if payments compensate just farmers’ opportunity costs (in terms of forgone production); bid prices of participating farmers were thus also evaluated to determine whether they were related to their individual opportunity costs. The PES scheme proved to be highly effective in ensuring environmental services delivery through enhanced arable plant diversity on participating fields. In contrast, the potential of the proposed conservation auction design to raise cost-effectiveness has to be questioned, because bid prices submitted in this scheme substantially exceeded individual farmers’ opportunity costs. Therefore, bid prices were most likely influenced by socioeconomic factors other than opportunity costs. This case study illustrates potentials and pitfalls associated with the implementation of a PES scheme and, by evaluating the effectiveness of the scheme, contributes to an improved understanding of incentive-based mechanisms for both policymakers and practitioners involved in PES scheme design and implementation.
CONTACT PROBLEMS FOR NONLINEARLY ELASTIC MATERIALS: WEAK SOLVABILITY INVOLVING DUAL LAGRANGE MULTIPLIERS
Authors: MATEI A. , CIURCEA R.
Published: August 2011

A class of problems modelling the contact between nonlinearly elastic materials and rigid foundations is analysed for static processes under the small deformation hypothesis. In the present paper, the contact between the body and the foundation can be frictional bilateral or frictionless unilateral. For every mechanical problem in the class considered, we derive a weak formulation consisting of a nonlinear variational equation and a variational inequality involving dual Lagrange multipliers. The weak solvability of the models is established by using saddle-point theory and a fixed-point technique. This approach is useful for the development of efficient algorithms for approximating weak solutions.
Image-Derived Input Function for Brain PET Studies: Many Challenges and Few Opportunities
Authors: Zanotti-Fregonara Paolo , Chen Kewei , Liow Jeih-San , Fujita Masahiro , Innis Robert B
Published: August 2011

Quantitative positron emission tomography (PET) brain studies often require that the input function be measured, typically via arterial cannulation. Image-derived input function (IDIF) is an elegant and attractive noninvasive alternative to arterial sampling. However, IDIF is also a very challenging technique associated with several problems that must be overcome before it can be successfully implemented in clinical practice. As a result, IDIF is rarely used as a tool to reduce invasiveness in patients. The aim of the present review was to identify the methodological problems that hinder widespread use of IDIF in PET brain studies. We conclude that IDIF can be successfully implemented only with a minority of PET tracers. Even in those cases, it only rarely translates into a less-invasive procedure for the patient. Finally, we discuss some possible alternative methods for obtaining less-invasive input function.
Quantification of Ligand PET Studies using a Reference Region with a Displaceable Fraction: Application to Occupancy Studies with [11C]-DASB as an Example
Authors: Turkheimer Federico E , Selvaraj Sudhakar , Hinz Rainer , Murthy Venkatesha , Bhagwagar Zubin , Grasby Paul , Howes Oliver , Rosso Lula , Bose Subrata K
Published: August 2011

This paper aims to build novel methodology for the use of a reference region with specific binding for the quantification of brain studies with radioligands and positron emission tomography (PET). In particular: (1) we introduce a definition of binding potential BPD = DVR–1 where DVR is the volume of distribution relative to a reference tissue that contains ligand in specifically bound form, (2) we validate a numerical methodology, rank-shaping regularization of exponential spectral analysis (RS-ESA), for the calculation of BPD that can cope with a reference region with specific bound ligand, (3) we demonstrate the use of RS-ESA for the accurate estimation of drug occupancies with the use of correction factors to account for the specific binding in the reference. [11C]-DASB with cerebellum as a reference was chosen as an example to validate the methodology. Two data sets were used; four normal subjects scanned after infusion of citalopram or placebo and further six test—retest data sets. In the drug occupancy study, the use of RS-ESA with cerebellar input plus corrections produced estimates of occupancy very close the ones obtained with plasma input. Test-retest results demonstrated a tight linear relationship between BPD calculated either with plasma or with a reference input and high reproducibility.
Low Prevalence of Clinically High-Risk Women and Pathological Thyroid Ultrasound among Pregnant Women Positive in Universal Screening for Thyroid Disorders
Authors: Jiskra J. , Bartáková J. , Holinka Š. , Límanová Z. , Springer D. , Antošová M. , Telička Z. , Potluková E.
Published: August 2011

It is controversial whether screening program for thyroid disorders in pregnancy should be universal or targeted case-finding.

To evaluate the relationship between history, laboratory parameters and thyroid ultrasound (TUS) in pregnant women positive in universal screening.

The screening included investigation of serum TSH (thyroid stimulating hormone) and TPOAb (antithyroperoxidase antibodies) in 5 520 unselected pregnant women in the 9–11th gestational week. In 822 the screening was positive: abnormal TSH (> 3.67 or < 0.06 mIU/l) and/or positive TPOAb (> 143 kIU/l). 200 consecutive women with positive screening were included it the study.

41 women (21%) had transient gestational hyperthyroidism (TGH) and 159 (79%) had a thyroid pathology: 10 (5%) overt hypothyroidism; 76 (38%) subclinical hypothyroidism, 7 (3.5%) overt hyperthyroidism and 66 (33%) euthyroid TPOAb positivity. After exclusion of TGH, only 74/159 (47%) women were classified as high-risk for thyroid disease according to their history. There were no significant clinical and laboratory differences between the high- vs. low-risk women, except for higher proportion of FT4<75th percentile (P=0.008) and larger thyroid volume in the high-risk group (P=0.04). Finally, only 66/126 (52%) of TPOAb-positive pregnant women had autoimmune pattern in TUS in comparison with 41/49 (84%) TPOAb-positive non-pregnant control women of comparable age (P<0.001).

Less than half of the positively screened pregnant women can be classified as high-risk and almost half of them had not autoimmune pattern in TUS. High- and low-risk pregnant women have similar clinical and laboratory characteristics.
Placental protection of the fetal brain during short-term food deprivation
Authors: Broad Kevin D. , Keverne Eric B.
Published: August 2011

The fetal genome regulates maternal physiology and behavior via its placenta, which produces hormones that act on the maternal hypothalamus. At the same time, the fetus itself develops a hypothalamus. In this study we show that many of the genes that regulate placental development also regulate the developing hypothalamus, and in mouse the coexpression of these genes is particularly high on embryonic days 12 and 13 (days E12–13). Such synchronized expression is regulated, in part, by the maternally imprinted gene, paternally expressed gene 3 (
Peg3
), which also is developmentally coexpressed in the hypothalamus and placenta at days E12–13. We further show that challenging this genomic linkage of hypothalamus and placenta with 24-h food deprivation results in disruption to coexpressed genes, primarily by affecting placental gene expression. Food deprivation also produces a significant decrease in
Peg3
gene expression in the placenta, with consequences similar to many of the placental gene changes induced by
Peg3
mutation. Such genomic dysregulation does not occur in the hypothalamus, where
Peg3
expression increases with food deprivation. Thus, changes in gene expression brought about by food deprivation are consistent with the fetal genome's maintaining hypothalamic development at a cost to its placenta. This biased change to gene dysregulation in the placenta is linked to autophagy and ribosomal turnover, which sustain, in the short term, nutrient supply for the developing hypothalamus. Thus, the fetus controls its own destiny in times of acute starvation by short-term sacrifice of the placenta to preserve brain development.
Size dependence of the magnetization reversal process in microfabricated L10-FePt nano dots
Authors: Seki Takeshi , Iwama Hiroki , Shima Toshiyuki , Takanashi Koki
Published: August 2011

We investigated the dot size dependence of the magnetization reversal process in microfabricated L10-FePt (0 0 1) circular dots with perpendicular magnetization. Both the as-patterned and the post-annealed dots showed the gradual increase in coercivities (H
c) as the dot diameter (D) was reduced from 1 µm to 30 nm. The dots with D ⩾ 500 nm formed a multiple domain structure at the remanent magnetization state whereas a single domain structure was observed for D ⩽ 100 nm. H
c as a function of the angle between the applied magnetic field and the out-of-plane direction suggested that the magnetization reversal for D ⩽ 100 nm occurred through incoherent magnetization rotation while domain wall propagation was the dominant magnetization reversal process for D ⩾ 500 nm. The present results imply that local structural defects, e.g. the inhomogeneity of L10 ordering, the microfabrication damage and the distribution of the c-axis orientation of L10 ordered structure, act as sites where the magnetization vectors start to rotate, which gives rise to the incoherent magnetization rotation even in the case of small dots with D = 30 nm.
Transfer maps in Hochschild (co)homology and applications to stable and derived invariants and to the Auslander–Reiten conjecture
Authors: Koenig Steffen , Liu Yuming , Zhou Guodong
Published: August 2011

Derived equivalences and stable equivalences of Morita type, and new (candidate) invariants thereof, between symmetric algebras will be investigated, using transfer maps as a tool. Close relationships will be established between the new invariants and the validity of the Auslander–Reiten conjecture, which states the invariance of the number of non-projective simple modules under stable equivalence. More precisely, the validity of this conjecture for a given pair of algebras, which are stably equivalent of Morita type, will be characterized in terms of data refining Hochschild homology (via Külshammer ideals) being invariant and also in terms of cyclic homology being invariant. Thus, validity of the Auslander–Reiten conjecture implies a whole set of ring theoretic and cohomological data to be invariant under stable equivalence of Morita type, and hence also under derived equivalence. We shall also prove that the Batalin–Vilkovisky algebra structure of Hochschild cohomology for symmetric algebras is preserved by derived equivalence. The main tools to be developed and used are transfer maps and their properties, in particular a crucial compatibility condition between transfer maps in Hochschild homology and Hochschild cohomology via the duality between them.
A powerful and flexible approach to the analysis of RNA sequence count data
Authors: Zhou Yi-Hui , Xia Kai , Wright Fred A.
Published: August 2011

Motivation: A number of penalization and shrinkage approaches have been proposed for the analysis of microarray gene expression data. Similar techniques are now routinely applied to RNA sequence transcriptional count data, although the value of such shrinkage has not been conclusively established. If penalization is desired, the explicit modeling of mean–variance relationships provides a flexible testing regimen that ‘borrows’ information across genes, while easily incorporating design effects and additional covariates.

Results: We describe BBSeq, which incorporates two approaches: (i) a simple beta-binomial generalized linear model, which has not been extensively tested for RNA-Seq data and (ii) an extension of an expression mean–variance modeling approach to RNA-Seq data, involving modeling of the overdispersion as a function of the mean. Our approaches are flexible, allowing for general handling of discrete experimental factors and continuous covariates. We report comparisons with other alternate methods to handle RNA-Seq data. Although penalized methods have advantages for very small sample sizes, the beta-binomial generalized linear model, combined with simple outlier detection and testing approaches, appears to have favorable characteristics in power and flexibility.

Availability: An R package containing examples and sample datasets is available at http://www.bios.unc.edu/research/genomic_software/BBSeq

Contact:  yzhou@bios.unc.edu; fwright@bios.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mauve Assembly Metrics
Authors: Darling Aaron E. , Tritt Andrew , Eisen Jonathan A. , Facciotti Marc T.
Published: August 2011

Summary: High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high-quality reference genome, and measuring assembly accuracy using some metrics.

We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high-quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms.

Availability: GPL source code and a usage tutorial is at http://ngopt.googlecode.com

Contact:  aarondarling@ucdavis.edu

Supplementary information:  Supplementary data is available at Bioinformatics online.
Influence of Adjuvants and Spray Timing of Movento on Aphid Contamination and Crop Injury in Baby Spinach
Authors: Palumbo John C.
Published: August 2011

Movento (spirotetramat), a new tetramic acid derivative insecticide, has shown to provide excellent activity against sucking insects through acropetal and basipetal systemic activity following foliar application on some vegetable crops. Studies conducted from 2007-2010 clearly showed that the addition of a penetrating adjuvant (i.e., Dyne-Amic) with Movento sprays significantly enhanced its efficacy against green peach aphid in baby spinach and prevented aphid contamination on marketable spinach plants. Aliette, a systemic fungicide, also significantly enhanced aphid control when combined with Movento. In the absence of a penetrating adjuvant, Movento sprays did not provide commercially acceptable control of green peach aphids in spinach, regardless of spray timing. Addition of other spray additives commonly used in spinach production did not significantly enhance Movento's aphicidal activity. Trials in 2009 and 2010 suggested that a single spray application of Movento with Dyne-Amic on older spinach plants (4-leaf stage) provided control comparable with the same mixture applied twice on smaller (2- and 4-leaf stages). Although growers are generally reluctant to apply oil-based chemicals on baby spinach crops due to risk of crop injury, no phytotocixity was observed with application of Movento/Dyne-Amic mixtures in any of the trials.

Accepted for publication 16 May 2011. Published 30 June 2011.
Non-muscle myosin II induces disassembly of actin stress fibres independently of myosin light chain dephosphorylation
Authors: Matsui Tsubasa S. , Kaunas Roland , Kanzaki Makoto , Sato Masaaki , Deguchi Shinji
Published: August 2011

Dynamic remodelling of actin stress fibres (SFs) allows non-muscle cells to adapt to applied forces such as uniaxial cell shortening. However, the mechanism underlying rapid and selective disassembly of SFs oriented in the direction of shortening remains to be elucidated. Here, we investigated how myosin crossbridge cycling induced by MgATP is associated with SF disassembly. Moderate concentrations of MgATP, or [MgATP], induced SF contraction. Meanwhile, at [MgATP] slightly higher than the physiological level, periodic actin patterns emerged along the length of SFs and dispersed within seconds. The actin fragments were diverse in length, but comparable to those in characteristic sarcomeric units of SFs. These results suggest that MgATP-bound non-muscle myosin II dissociates from the individual actin filaments that constitute the sarcomeric units, resulting in unbundling-induced disassembly rather than end-to-end actin depolymerization. This rapid SF disassembly occurred independent of dephosphorylation of myosin light chain. In terms of effects on actin–myosin interactions, a rise in [MgATP] is functionally equivalent to a temporal decrease in the total number of actin–myosin crossbridges. Actin–myosin crossbridges are known to be reduced by an assisting load on myosin. Thus, the present study suggests that reducing the number of actin–myosin crossbridges promotes rapid and orientation-dependent disassembly of SFs after cell shortening.
Experimental and numerical determination of cellular traction force on polymeric hydrogels
Authors: Ng Soon Seng , Li Chuan , Chan Vincent
Published: August 2011

Anchorage-dependent cells such as smooth muscle cells (SMCs) rely on the transmission of actomyosin-generated traction forces to adhere and migrate on the extracellular matrix. The cellular traction forces exerted by SMCs on substrate can be measured from the deformation of substrate with embedded fluorescent markers. With the synchronous use of phase-contrast and fluorescent microscopy, the deformation of polyacrylamide (PAM) gel substrate can be quantitatively determined using particle image velocimetry. This displacement map is then input as boundary conditions for the stress analysis on PAM gel by the finite-element method. In addition to optical microscopy, atomic force microscopy was also used to characterize the PAM substrate using the contact mode, from which the elasticity of PAM can be quantified using Hertzian theory. This provides baseline information for the stress analysis of PAM gel deformation. The material model introduced for the computational part is the Mooney–Rivlin constitutive law because of its long proven usefulness in predicting polymers' mechanical behaviour. Numerical results showed that adhesive stresses are high around the cell edges, which is in accordance with the general phenomena of cellular focal adhesion. Further calculations on the total traction forces indicate a slightly contact-dominated regime for a broad range of Mooney–Rivlin stiffnesses.
Two Mechanosensitive Channel Homologs Influence Division Ring Placement in Arabidopsis Chloroplasts
Authors: Wilson Margaret E. , Jensen Gregory S. , Haswell Elizabeth S.
Published: August 2011

Chloroplasts must divide repeatedly to maintain their population during plant growth and development. A number of proteins required for chloroplast division have been identified, and the functional relationships between them are beginning to be elucidated. In both chloroplasts and bacteria, the future site of division is specified by placement of the Filamentous temperature sensitive Z (FtsZ) ring, and the Min system serves to restrict FtsZ ring formation to mid-chloroplast or mid-cell. How the Min system is regulated in response to environmental and developmental factors is largely unstudied. Here, we investigated the role in chloroplast division played by two Arabidopsis thaliana homologs of the bacterial mechanosensitive (MS) channel MscS: MscS-Like 2 (MSL2) and MSL3. Immunofluorescence microscopy and live imaging approaches demonstrated that msl2 msl3 double mutants have enlarged chloroplasts containing multiple FtsZ rings. Genetic analyses indicate that MSL2, MSL3, and components of the Min system function in the same pathway to regulate chloroplast size and FtsZ ring formation. In addition, an Escherichia coli strain lacking MS channels also showed aberrant FtsZ ring assembly. These results establish MS channels as components of the chloroplast division machinery and suggest that their role is evolutionarily conserved.
Clinical significance of tumor‐infiltrating FOXP3+ T cells in patients with ocular adnexal mucosa‐associated lymphoid tissue lymphoma
Authors: Kim Ki Hwan , Kim Tae Min , Go Heounjeong , Kim Wook Youn , Jeon Yoon Kyung , Lee Se‐Hoon , Kim Dong‐Wan , In Khwarg Sang , Kim Chul‐Woo , Heo Dae Seog
Published: August 2011

We evaluated the association between tumor‐infiltrating FOXP3+ T cells and clinical outcomes in patients with ocular adnexal lymphoma of mucosa‐associated lymphoid tissue type (OAML). Pretreatment formalin‐fixed paraffin‐embedded tissues from 42 patients with OAML were stained with 236A/E7 anti‐FOXP3 murine monoclonal antibody as well as CD3, CD4 and CD8 antibodies. The amount of FOXP3+ T cells was numerically quantified using an image analysis program. Front‐line treatments were as follows: combination chemotherapy (n = 25); radiotherapy (n = 9); doxycycline (n = 6); and wait and see (n = 2). Complete response (CR) was observed in 20 (50%) of 40 evaluable patients. Median progression‐free survival (PFS) was 50 months. A high number of FOXP3+ T cells (n = 21, ≥180/0.58 mm2) showed a higher CR rate (33%vs 71%, P = 0.013) and tendency towards prolonged PFS (48 vs 67 months, P = 0.110). In the combination chemotherapy group, a high number of FOXP3+ T cells was significantly associated with a higher CR rate (29%vs 82%, P = 0.008) and prolonged PFS (17 vs 79 months, P = 0.003). A high number of tumor‐infiltrating FOXP3+ T cells correlates with a favorable clinical outcome in OAML patients. (Cancer Sci 2011; 102: 1972–1976)
Clinical efficacy, safety and pharmacokinetic properties of the plasma‐derived factor IX concentrate Haemonine® in previously treated patients with severe haemophilia B
Authors: SERBAN M. , SKOTNICKI A. B. , COLOVIC M. , JINCA C. , KLUKOWSKA A. , LAGUNA P. , WOLF D. M.
Published: August 2011

Summary.  Plasma‐derived factor IX (FIX) concentrate remains an important choice for replacement therapy in haemophilia B patients. Haemonine® is a high purity double‐virus inactivated human plasma‐derived coagulation FIX concentrate (pdFIX). Aim was to evaluate the clinical efficacy, safety and pharmacokinetic properties of Haemonine in three prospective, open‐label uncontrolled studies and a compassionate use program in previously treated patients with severe haemophilia B. Long‐term efficacy and safety were investigated in 29 patients treated prophylactically and, in addition, treatment on‐demand (TOD) in the case of acute haemorrhage. Pharmacokinetic properties were assessed in 14 patients at baseline and after 3 months of regular treatment. Pharmacokinetic parameters were in accordance with published data and remained nearly unchanged over time, notably recovery and half‐life. Mean terminal elimination half‐life was 27.6 h and 25.0 h, mean incremental recovery (IU dL−1/IU kg−1) was 1.55 and 1.60, at baseline and 3 months, respectively. Haemonine was shown to be effective in preventing and controlling bleeds. 55.2% (16/29) of patients were free of bleeds under prophylaxis. 38 haemorrhages occurred, 42% (16/38) required treatment and 87.5% (14/16) resolved after a single infusion, 12.5% after 2 infusions. All responses reported on haemorrhages were rated as ‘excellent’ or ‘good’. Moreover, ‘excellent’ haemostatic efficacy was demonstrated in 12 surgeries with no complications. Few adverse events (AEs) and no thrombogenic complication, nor induction of FIX inhibitory antibodies were observed. Haemonine is effective, safe and well tolerated in long‐term prophylaxis, TOD and when applied after minor and major surgeries.
The effects of a care map for total knee replacement patients
Authors: Lin Pi‐Chu , Hung Shih‐Hsin , Wu Heng‐Fei , Hsu Hsiu‐Chu , Chu Chan‐Yi , Su Shu‐Juan
Published: August 2011

Aims.  The aim of this study was to establish and evaluate the effectiveness of a care map for total knee replacement patients.

Background.  Bureau of National Health Insurance in Taiwan is about to launch a diagnosis‐related group. This major reform has seriously affected the running of medical institutions, which are facing unprecedented management pressure.

Design.  A quasi‐experimental control group design was carried out.

Methods.  Eighty‐three patients were recruited, with 39 experimental group patients received nursing care based on a care map, while 44 patients who were in control group received routine nursing care. An interdisciplinary team designed the care map, which included items required for patient care from outpatient to postdischarge.

Results.  (1) The mean age of patients was 72·73 (SD 8·42) years. Mean length of stay was 4·92 (SD 0·77) days for the experimental group and 7·09 (SD = 1·09) for the control group. Difference between groups was significant (t = −10·285, p < 0·001). The medical cost for the experimental group was less than that for the control group (t = −6·03, p < 0·001). (2) The self‐care efficacy score before discharge for the experimental group was higher than that for the control group (t = 5·90, p < 0·001). (3) Significant improvements were observed in activities of daily living for both groups with the passage of time after discharge (F = 229·034, p < 0·001), and the experimental group was better than the control group (F = 40·895, p < 0·001). The instrumental activities of daily living abilities of both groups were also significant improvements with the passage of time after discharge (F = 46·568, p < 0·001), and the experimental group was better than the control group (F = 32·163, p < 0·001).

Conclusions.  A care map for total knee replacement patient can shorten length of stay, save medical cost and improve patient’s functional recovery.

Relevance to clinical practice.  Results of this study can be used as a basis for practical implementation of care map in total knee replacement patients.
Critical care nurses’ knowledge, attitudes and practices of oral care for patients with oral endotracheal intubation: a questionnaire survey
Authors: Lin Ying‐Siou , Chang Jung‐Chen , Chang Tsyr‐Huei , Lou Meei‐Fang
Published: August 2011

Aim.  This study investigated intensive care unit nurses’ knowledge, attitudes and practices of oral care for intubated patients together with the associated factors of the same.

Background.  Effective oral care improves patient comfort and prevents oral infection. Although oral care is a common requirement of nursing practice, providing intubated patients with oral care is a challenging task.

Design.  A descriptive, cross‐sectional design.

Methods.  This study applied purposive sampling method at 12 adult intensive care units in one medical centre in northern Taiwan. Two hundred and five nurses were recruited. Data were collected by structured questionnaires which consisted of four sections: knowledge, attitudes and practices of oral care for intubated patients and demographic information for the nurses.

Results.  The average percentages indicating the intensive care unit nurses’ oral care knowledge, attitudes and practices were 58·8, 79·4 and 49·8%, respectively. Higher scores on oral care knowledge were associated with nurses performing oral care more frequently. Nurses learning about oral care from reading related studies and materials of their own accord may increase the frequency with which they provide oral care to intubated patients. The nurses’ age and the type of intensive care unit they work in were significant factors related to the frequency of performing practices related to oral care.

Conclusion.  Findings show that nurses who have more resources for learning about oral care have greater knowledge about it and provide oral care to intubated patients more frequently.

Relevance to clinical practice.  Encouraging nurses to learn more about oral care using diverse educational resources will enhance their knowledge and improve their practice. Nursing administrators are encouraged to establish policies and procedures for oral care of intubated patients based on the type of patients cared for, in addition to holding in‐service training, with a view to enhancing the quality of oral care for critically ill patients.
Killer‐cell immunoglobulin‐like receptor genotyping and HLA killer‐cell immunoglobulin‐like receptor‐ligand identification by real‐time polymerase chain reaction
Authors: Hong H. A. , Loubser A. S. , de Assis Rosa D. , Naranbhai V. , Carr W. , Paximadis M. , Lewis D. A. , Tiemessen C. T. , Gray C. M.
Published: August 2011

The effector function of natural killer (NK) cells is modulated by surface expression of a range of killer‐cell immunoglobulin‐like receptors (KIRs) that interact with human leukocyte antigen (HLA) class I ligands. We describe the use of real‐time polymerase chain reaction (PCR) assays that allow easy and quick detection of 16 KIR genes and the presence/absence of KIR‐ligands based on allelic discrimination at codon 80 in the HLA‐A/B Bw4 and HLA‐C C1/C2 genes. These methods overcome the tedious and expensive nature of conventional KIR genotyping and HLA class I typing using sequence‐specific primer (SSP) PCR, sequence‐specific oligonucleotide (SSO) hybridization or sequence‐based typing (SBT). Using these two cost‐effective assays, we measured the frequencies of KIRs, KIR‐ligands and KIR/KIR‐ligand pairs in a cohort of Black women recruited in South Africa.