bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid equilibrium sampling initiated from nonequilibrium data
Authors: Huang Xuhui , Bowman Gregory R. , Bacallado Sergio , Pande Vijay S.
Published: September 2009

Simulating the conformational dynamics of biomolecules is extremely difficult due to the rugged nature of their free energy landscapes and multiple long-lived, or metastable, states. Generalized ensemble (GE) algorithms, which have become popular in recent years, attempt to facilitate crossing between states at low temperatures by inducing a random walk in temperature space. Enthalpic barriers may be crossed more easily at high temperatures; however, entropic barriers will become more significant. This poses a problem because the dominant barriers to conformational change are entropic for many biological systems, such as the short RNA hairpin studied here. We present a new efficient algorithm for conformational sampling, called the adaptive seeding method (ASM), which uses nonequilibrium GE simulations to identify the metastable states, and seeds short simulations at constant temperature from each of them to quantitatively determine their equilibrium populations. Thus, the ASM takes advantage of the broad sampling possible with GE algorithms but generally crosses entropic barriers more efficiently during the seeding simulations at low temperature. We show that only local equilibrium is necessary for ASM, so very short seeding simulations may be used. Moreover, the ASM may be used to recover equilibrium properties from existing datasets that failed to converge, and is well suited to running on modern computer clusters.
Inhibition of KCa2.2 and KCa2.3 channel currents by protonation of outer pore histidine residues
Authors: Goodchild Samuel J. , Lamy Cedric , Seutin Vincent , Marrion Neil V.
Published: September 2009

Ion channels are often modulated by changes in extracellular pH, with most examples resulting from shifts in the ionization state of histidine residue(s) in the channel pore. The application of acidic extracellular solution inhibited expressed KCa2.2 (SK2) and KCa2.3 (SK3) channel currents, with KCa2.3 (pIC50 of ∼6.8) being approximately fourfold more sensitive than KCa2.2 (pIC50 of ∼6.2). Inhibition was found to be voltage dependent, resulting from a shift in the affinity for the rectifying intracellular divalent cation(s) at the inner mouth of the selectivity filter. The inhibition by extracellular protons resulted from a reduction in the single-channel conductance, without significant changes in open-state kinetics or open probability. KCa2.2 and KCa2.3 subunits both possess a histidine residue in their outer pore region between the transmembrane S5 segment and the pore helix, with KCa2.3 also exhibiting an additional histidine residue between the selectivity filter and S6. Mutagenesis revealed that the outer pore histidine common to both channels was critical for inhibition. The greater sensitivity of KCa2.3 currents to protons arose from the additional histidine residue in the pore, which was more proximal to the conduction pathway and in the electrostatic vicinity of the ion conduction pathway. The decrease of channel conductance by extracellular protons was mimicked by mutation of the outer pore histidine in KCa2.2 to an asparagine residue. These data suggest that local interactions involving the outer turret histidine residues are crucial to enable high conductance openings, with protonation inhibiting current by changing pore shape.
Detection of sub-ppm traces of aqueous heavy-metal ions using micro-electro-mechanical beam resonators
Authors: Rahafrooz Amir , Pourkamali Siavash
Published: September 2009

Capacitive silicon micro-mechanical resonators have been utilized in this work as ultra-sensitive mass sensors for the detection of trace amounts of copper ions in water samples. The approach is based on the reduction of aqueous metal ions by the silicon in a resonant structure and consequently deposition of a very thin metal layer on the resonator surface changing its resonant frequency. Measurements demonstrate successful detection of sub-ppm concentrations of copper(II) ions in water. Relatively large frequency shifts (hundreds of ppm) have been measured for resonators exposed to copper concentrations as low as 4 µM (0.26 ppm). An analytical model for the resonant frequency of the resulting complex beams has been derived and used to calculate the thickness of the deposited copper layer based on the measured frequency shifts. The model shows that the measured frequency shifts correspond to only a few atomic layers of copper (as thin as ∼7 Å) deposited on the resonator surfaces. This corresponds to a mass sensitivity of more than 4000 Hz µg−1 cm−2 which is much larger than the highest mass sensitivities measured for quartz crystal microbalances.
VDNA: The virtual DNA plug-in for VMD
Authors: Bishop Thomas C.
Published: September 2009

Summary: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason, we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, bent and circular DNA, and models of the nucleosome superhelix, chromatin, thermal motion and nucleosome unwrapping.

Availability: VDNA is pre-installed in VMD, http://www.ks.uiuc.edu/Research/vmd. Updates are at http://dna.ccs.tulane.edu.

Contact:  bishop@tulane.edu
Withania somnifera Improves Semen Quality in Stress‐Related Male Fertility
Authors: Mahdi Abbas Ali , Shukla Kamla Kant , Ahmad Mohammad Kaleem , Rajender Singh , Shankhwar Satya Narain , Singh Vishwajeet , Dalela Deepansh
Published: September 2009

Stress has been reported to be a causative factor for male infertility. Withania somnifera has been documented in Ayurveda and Unani medicine system for its stress‐combating properties. However, limited scientific literature is available on this aspect of W. somnifera. We undertook the present study to understand the role of stress in male infertility, and to test the ability of W. somnifera to combat stress and treat male infertility. We selected normozoospermic but infertile individuals (N = 60), further categorized in three groups: normozoospermic heavy smokers (N = 20), normozoospermics under psychological stress (N = 20) and normozoospermics with infertility of unknown etiology (N = 20). Normozoospermic fertile men (N = 60) were recruited as controls. The subjects were given root powder of W. somnifera at a rate of 5 g/day for 3 months. Measuring various biochemical and stress parameters before and after treatment, suggested a definite role of stress in male infertility and the ability of W. somnifera to treat stress‐related infertility. Treatment resulted in a decrease in stress, improved the level of anti‐oxidants and improved overall semen quality in a significant number of individuals. The treatment resulted in pregnancy in the partners of 14% of the patients.
Alpinia pricei Rhizome Extracts Induce Cell Cycle Arrest in Human Squamous Carcinoma KB Cells and Suppress Tumor Growth in Nude Mice
Authors: Hseu You-Cheng , Chen Chih-Sheng , Wang Sheng-Yang
Published: September 2009

Alpinia pricei has been shown to induce apoptosis in human squamous carcinoma (KB) cells. In this study, we report the effectiveness of the ethanol (70%) extracts of A. pricei rhizome (AP extracts) in terms of tumor regression as determined using both in vitro cell culture and in vivo athymic nude mice models of KB cells. We found that the AP extract (25–200 μg/mL) treatment decreased the proliferation of KB cells by arresting progression through the G2/M phase of the cell cycle. This cell cycle blockade was associated with reductions in cyclin A and B1, Cdc2, and Cdc25C, and increased p21/WAF1, Wee1, p53 and phospho‐p53 (p‐p53) in a dose‐ and time‐dependent manner. Moreover, we found that AP extract treatment decreased metalloproteinase‐9 (MMP‐9) and urokinase plasminogen activator (u‐PA) expression, while expression of their endogenous inhibitors, tissue inhibitor of MMP‐1 (TIMP‐1) and plasminogen activator inhibitor‐1 (PAI‐1), were increased in KB cells. Furthermore, AP extract treatment effectively delayed tumor incidence in nude mice inoculated with KB cells and reduced the tumor burden. AP extract treatment also induced apoptotic DNA fragmentation, as detected by in situ TUNEL staining. Thus, A. pricei may possess antitumor activity in human squamous carcinoma (KB) cells.
[Retracted] Protective Effects of Rosa damascena and Its Active Constituent on Aβ(25–35)‐Induced Neuritic Atrophy
Authors: Awale Suresh , Tohda Chihiro , Tezuka Yasuhiro , Miyazaki Makoto , Kadota Shigetoshi
Published: September 2009

Dementia is a clinical syndrome characterized by multiple cognitive deficits and causes progressive neurodegeneration leading eventually to death. The incidence of dementia is increasing worldwide with the increase in ageing population. However, no effective treatment is available yet. It has been hypothesized that drugs activating neurite outgrowth might induce neuronal reconstruction and help in the recovery of brain function. Working on this hypothesis, we recently observed that the chloroform extract of the Rosa damascena significantly induced the neurite outgrowth activity and inhibited the Aβ(25–35)‐induced atrophy and cell death. Further workup led the isolation of a very long polyunsaturated fatty acid having molecular formula C37H64O2 as an active constituent. The structure of this compound was established by extensive analysis of fragmentations observed in EI‐MS mode. The isolated compound protected Aβ(25–35)‐induced atrophy and displayed strong neurite outgrowth activity. The length of dendrite in the cells treated with this compound were comparable to those of nerve growth factor (NGF) treated cells.
Independent relationship of left atrial size and mortality in patients with heart failure: an individual patient meta‐analysis of longitudinal data (MeRGE Heart Failure)
Authors: Rossi Andrea , Temporelli Pier Luigi , Quintana Miguel , Dini Frank L. , Ghio Stefano , Hillis Graham S. , Klein Allan L. , Ajmone Marsan Nina , Prior David L. , Yu Cheuk Man , Poppe Katrina K. , Doughty Robert N. , Whalley Gillian A. ,   on behalf of the MeRGE Heart Failure Collaborators
Published: September 2009

Aims

Left atrial (LA) size is considered a marker of poor prognosis in heart failure (HF) patients. Prior studies have recruited relatively few subjects limiting their power to adequately analyse the interaction between LA size, left ventricular (LV) systolic and diastolic function, and prognosis.

Method and results

The MeRGE collaboration combines prospective data from 18 studies in HF patients. In this analysis of data from 1157 patients, the primary endpoint was death or hospitalization for worsening HF. In multivariate analysis (Cox proportion hazard model), LA area was associated with prognosis (HR 1.03 per cm2, 95% CI 1.02, 1.05; P < 0.0001) independently of age, NYHA class, LV ejection fraction, and restrictive filling pattern (RFP). When LA area was used as a categorical variable, the HR associated with larger LA area (above median) was 1.4 (95% CI 1.13, 1.74) and when LA area index was used, the HR was 2.36 (95% CI 1.80, 3.08). When the patients with and without RFP were divided on the basis of either LA area or LA area index, significantly higher event rates were observed in those with larger LA area.

Conclusion

Left atrial area is a powerful predictor of outcome among HF patients with predominantly impaired systolic function, and is independent of, and provides additional prognostic information beyond LV systolic and diastolic function.
Staged heart transplantation and chemotherapy as a treatment option in patients with severe cardiac light‐chain amyloidosis
Authors: Kristen Arnt V. , Sack Falk‐Udo , Schonland Stefan O. , Hegenbart Ute , Helmke Burkhard M. , Koch Achim , Schnabel Philipp A. , Röcken Christoph , Hardt Stefan , Remppis Andrew , Goldschmidt Hartmut , Karck Matthias , Ho Anthony D. , Katus Hugo A. , Dengler Thomas J.
Published: September 2009

Aims

The prognosis of advanced cardiac light‐chain amyloidosis is poor. Heart transplantation might enable causative therapy and ultimately improve prognosis.

Methods and results

Nineteen patients with cardiac amyloidosis but no obvious involvement of other organs were scheduled for heart transplantation. Four to 6 months later, high‐dose melphalan chemotherapy and autologous stem cell transplantation (HDM–ASCT) was planned in patients not in complete remission. Seven of nineteen patients died while waiting for heart transplantation. The remaining 12 patients (complete remission, n = 4) underwent surgery. Chemotherapy in patients not in complete remission consisted of HDM–ASCT (n = 5/12; subsequent complete remission, n = 2; partial remission, n = 3) or melphalan–prednisolone (partial remission, n = 1). Two of twelve patients were ineligible for any chemotherapy. Three of twelve patients died [423.5 (105–2131) days] from progressive disease, relapse, or sepsis. The 1‐ and 3‐year survival rates were 83 and 83%, respectively, similar to those of patients undergoing heart transplantation for standard indications. Corresponding survival rates stratified by haematological response were 100 and 100% for complete remission (partial remission, 100 and 100%; progressive disease, 0 and 0%).

Conclusion

Heart transplantation in advanced cardiac amyloidosis is a promising approach to interrupting the vicious circle of ineligibility for potential curative chemotherapeutic treatment and extremely poor prognosis of cardiac amyloidosis without chemotherapy. Highly urgent heart transplantation combined with subsequent HDM–ASCT appears to offer a successful treatment option to improve the poor outcome of cardiac amyloidosis. However, it should be restricted to highly selected patients in specialized centres.
Regional abnormalities of myocardial deformation in patients with hypertrophic cardiomyopathy: correlations with delayed enhancement in cardiac magnetic resonance
Authors: Ghio Stefano , Revera Miriam , Mori Francesca , Klersy Catherine , Raisaro Arturo , Raineri Claudia , Serio Alessandra , Pasotti Michele , Visconti Luigi Oltrona
Published: September 2009

Aims

Hypertrophic cardiomyopathy (HCM) is a genetic disease histologically characterized by a profound disarray of myocardial fibres and by local fibrosis. We sought to characterize regional left ventricular contractility in HCM patients using deformation analysis and to compare it with the presence or absence of delayed enhancement in cardiac magnetic resonance (CMR).

Methods and results

We studied 58 HCM patients (mean age 41 years, 37 male). The control population comprised 15 normal subjects. Colour tissue‐Doppler imaging was acquired in two‐dimensional mode from apical four‐chamber and two‐chamber views; off‐line analysis was performed in four basal and four middle left ventricular segments. Gadolinium‐enhanced CMR was performed in 36 HCM patients. In HCM patients, peak systolic strain was not uniform across left ventricular segments; differences were not related to site or thickness of the segment analysed. Paradoxically, positive systolic strain values were measured in six middle segments. Delayed CMR enhancement was associated with lower peak systolic strain (P = 0.007). Regional non‐uniformities in peak systolic strain were not observed in normal subjects.

Conclusion

Areas of reduced left ventricular contractility in deformation analysis are associated with delayed CMR enhancement in patients with HCM.
Uncertainty and Operational Considerations in Mass Prophylaxis Workforce Planning
Authors: Hupert Nathaniel , Xiong Wei , King Kathleen , Castorena Michelle , Hawkins Caitlin , Wu Cindie , Muckstadt John A.
Published: September 2009

Background: The public health response to an influenza pandemic or other large-scale health emergency may include mass prophylaxis using multiple points of dispensing (PODs) to deliver countermeasures rapidly to affected populations. Computer models created to date to determine “optimal” staffing levels at PODs typically assume stable patient demand for service. The authors investigated POD function under dynamic and uncertain operational environments.

Methods: The authors constructed a Monte Carlo simulation model of mass prophylaxis (the Dynamic POD Simulator, or D-PODS) to assess the consequences of nonstationary patient arrival patterns on POD function under a variety of POD layouts and staffing plans. Compared are the performance of a standard POD layout under steady-state and variable patient arrival rates that may mimic real-life variation in patient demand.

Results: To achieve similar performance, PODs functioning under nonstationary patient arrival rates require higher staffing levels than would be predicted using the assumption of stationary arrival rates. Furthermore, PODs may develop severe bottlenecks unless staffing levels vary over time to meet changing patient arrival patterns. Efficient POD networks therefore require command and control systems capable of dynamically adjusting intra- and inter-POD staff levels to meet demand. In addition, under real-world operating conditions of heightened uncertainty, fewer large PODs will require a smaller total staff than many small PODs to achieve comparable performance.

Conclusions: Modeling environments that capture the effects of fundamental uncertainties in public health disasters are essential for the realistic evaluation of response mechanisms and policies. D-PODS quantifies POD operational efficiency under more realistic conditions than have been modeled previously. The authors’ experiments demonstrate that effective POD staffing plans must be responsive to variation and uncertainty in POD arrival patterns. These experiments highlight the need for command and control systems to be created to manage emergency response successfully. (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S121–S131)
Systematic methods, fossils, and relationships within Heteroptera (Insecta)
Authors: Cassis Gerasimos , Schuh Randall T.
Published: September 2009

Three recent papers dealing with phylogenetic relationships within the Heteroptera are discussed and analysed. A character set representing 43 taxa and 78 characters is used to test theories presented in those papers. The conclusions of Grimaldi and Engel concerning the placement of the Cretaceous fossil taxonCretopiesmain the Piesmatidae are rejected in favour of placement in the Aradidae. The placement by Nel et al. ofProtodorisfrom Eocene amber of the Paris Basin in the Thaumastocoridae is considered ambiguous because it has none of the diagnostic characters of that family group and is therefore regarded asincertae sedis. The arguments of Sweet concerning the elevation of the Aradoidea to infraordinal status on the basis of autapomorphies are also treated as invalid. General arguments against the use of phenetic methods in palaeontology, andad hocapproaches under the guise of cladistics, are offered, with the conclusion that rigorous cladistic analyses are a prerequisite to testable conclusions concerning the placement of fossil and Recent taxa.

 © The Willi Hennig Society 2009.
Soy product and isoflavone intake and breast cancer risk defined by hormone receptor status
Authors: Zhang Caixia , Ho Suzanne C. , Lin Fangyu , Cheng Shouzhen , Fu Jianhua , Chen Yuming
Published: September 2009

The association between soy food consumption and breast cancer risk has been inconsistent. A hospital‐based case–control study was conducted to assess the relationship between soy food intake and breast cancer risk according to the estrogen receptor (ER) and/or progesterone receptor (PR) status of breast cancer in Chinese women residing in Guangdong province from June 2007 to August 2008. A total of 438 consecutively recruited cases with primary breast cancer were frequency matched to 438 controls by age (5‐year interval) and residence (rural/urban). Dietary intake was assessed by face‐to‐face interviews using a validated food frequency questionnaire. Odds ratios (OR) and 95% confidence intervals (CI) were obtained by using multiple unconditional logistic regression adjusted for the potential confounders. We observed a statistically significant inverse association between soy isoflavone and soy protein intake with breast cancer risk. The multivariate ORs (95% CIs) of breast cancer risk for the highest quartile compared with the lowest quartile were 0.54 (0.34–0.84) for soy isoflavone and 0.62 (0.40–0.96) for soy protein, respectively. A preventive effect of soy food was found for all subtypes of ER and/or PR status of breast cancer. The inverse association was more evident among premenopausal women. This study suggests that consumption of soy food, soy isoflavone, is inversely associated with the risk of breast cancer. The protective effects of soy did not seem to differ by ER and PR breast cancer status. (Cancer Sci 2009)
The evolution of Pseudomonas syringae host specificity and type III effector repertoires
Authors: LINDEBERG MAGDALEN , CUNNAC SÉBASTIEN , COLLMER ALAN
Published: September 2009

The discovery 45 years ago that many Pseudomonas syringae pathovars elicit the hypersensitive response in plant species other than their hosts fostered the use of these bacteria as experimental models. However, the basis for host specificity and the corresponding resistance of nonhosts remain unclear. Pseudomonas syringae is now known to inject into the host cytoplasm, via the type III secretion system, effector proteins that suppress basal innate immunity, but may be recognized by cognate resistance (R) proteins in a second level of defence. The identification and manipulation of complete repertoires of type III effectors have revealed the highly polymorphic nature of effector repertoires and their potential to limit the host range. However, the maintenance of compatible effector repertoires may be driven by adaptations to life in a given plant species involving many factors. Tools are now available to test several hypotheses for the nature and evolution of P. syringae host specificity and nonhost resistance.
Influence of temperature and salinity on the germination of Lotus creticus (L.) from the arid land of Tunisia
Authors: Rejili Mokhtar , Vadel Ahmedou M. , Guetet Arbi , Mahdhi Mosbah , Lachiheb Belgacem , Ferchichi Ali , Mars Mohamed
Published: September 2009

Effects of salinity, temperature and their interactions on the rate and final percentage of germination were evaluated for two populations (Msarref, Oued dkouk) of the invasive glycophyte Lotus creticus Linné, grown under arid environmental conditions of the Tunisia. Seeds that were not treated with NaCl germinated well in a wide range of temperatures. For both populations, maximum germination occurred in distilled water at 25°C and lowest germination for all salinities was at 35°C. Germination was substantially delayed and significantly reduced with an increase in NaCl to levels above 300 mm. Compared to the Oued dkouk population, final germination and germination rate of the Msarref population was completely inhibited at 300 mm NaCl. The interactive effect of temperature and NaCl concentration on final germination and germination rate was significant (P < 0.01), indicating that the germination response to salinity depended on temperature. The inhibition of Oued dkouk population seed germination at high salt concentration was mostly due to osmotic effects while ionic effects were noted at Msarref population. The germination behaviour of the Oued dkouk population would therefore imply adaptive mechanisms to saline environments, while in the Msarref population such mechanisms seem to be absent. Since seed germination is more sensitive to salinity stress than the growth of established plants, the greater tolerance to salinity of Oued dkouk population would be an adaptive feature of this population to saline environment.
An ecological study of the relationship between two living fossils in Malawi: the Mulanje Tiger Moth (Callioratis grandis) and the Mulanje Cycad (Encephalartos gratus)
Authors: Bayliss Julian , Burrow Camilla , Martell Sara , Staude Hermann
Published: September 2009

The Mulanje tiger moth (Callioratis grandis) has recently been discovered feeding solely on the Mulanje Cycad, Encephalartos gratus. In its type locality Encephalartos gratus is severely threatened through habitat destruction and human population growth. As a result the first detailed demographic survey of Encephalartos gratus on Mount Mulanje was undertaken with particular emphasis on the relationship between E. gratus and Callioratis grandis. What is unusual about C. grandis is that the males exhibit lekking behaviour, for which aposematism may be a prerequisite. Cycads were surveyed in a systematic manner. Both the biotic and abiotic parameters were recorded from 532 wild Encephalartos gratus. Results showed the morphological range of measurements differed from that of previously published literature on this species. Results also showed that the incidence of Callioratis larval damage was related to the maturity of the wild cycads – moth damage was greater on more mature plants. Approximately 50% of surveyed cycads showed evidence of Callioratis moth damage, however, there was no apparent preference from the moth to select either male or female cycads as food plants for the larvae. In some cases there was severe damage to cycad fronds, but this did not seem to affect the production of reproductive cones or even the survival of individual cycads.
The importance of post‐fire regrowth for sable antelope in a Southern African savanna
Authors: Parrini Francesca , Owen‐Smith Norman
Published: September 2009

Burning is commonly used in savannas to stimulate grass regrowth for grazing ungulates. We recorded the relative use of burns occurring at different stages in the seasonal cycle, as well as in different regions of the landscape by two herds of sable. We also recorded behavioural measures of foraging efficiency and faecal nutrient contents as an indication of nutrient gains. Sable consistently concentrated their grazing on burned areas provided there was sufficient green regrowth during the dry season. In these circumstances they grazed for longer per feeding station, showed a slower step rate while foraging, and shorter between‐patch moves, and a higher probability of encountering acceptable food per step taken while foraging than on unburnt areas. In the year when only a burn with insufficient regrowth was available, sable continued to forage in the area that had been burned during the previous year. Faecal crude protein was substantially higher at the end of the dry season in the year when burned areas were utilized. Accordingly early dry season fires can be important in helping sable bridge the nutritional limitations posed by the dry season, provided sufficient soil moisture remains to promote adequate grass regrowth.
Diversity, dynamics and reproduction in a community of small mammals in Upper Guinea, with emphasis on pygmy mice ecology
Authors: Fichet‐Calvet Elisabeth , Audenaert Leen , Barrière Patrick , Verheyen Erik
Published: September 2009

As part of a large survey on reservoirs of Lassa fever in Guinea, three villages were investigated in high endemic zone, close to Sierra Leone border. Biodiversity of the small mammal community is presented in this study through a standardized trapping in houses, cultivations and forest. Identification of the small mammals was based on morphology and by molecular technique for sibling species. Of the 1123 specimens collected in 2003–2005, we identified seventeen species (thirteen Muridae, four Soricidae), leading to high diversity (Shannon index = 1.6–1.8) and high equitability (evenness index = 0.7–0.8) in cultivations and forest. In houses conversely, the rodent community was dominated by Mastomys natalensis (95–98%), leading to low diversity and equitability. Dynamics and reproduction were investigated in two species of pygmy mice, Mus mattheyi and Mus minutoides, two species of Praomys, P. daltoni and P. rostratus, and in Mastomys erythroleucus. The pygmy mice were abundant in cultivations in early rainy season, and reproduced from rainy to dry season. Praomys daltoni was also found more abundant in cultivations and seemed to reproduce between rainy and dry season, whereas P. rostratus preferred forest and cultivations in late rainy season, and reproduced throughout the year. Finally, M. erythroleucus was more abundant in forest in dry season, and seemed to reproduce from late rainy to dry season. This species had a low occurrence (6.5%) in the Faranah’s zone, and probably lived at its southern limit in Guinea. The presence of other Murinae, such as M. natalensis, Praomys spp as possible competitors in the same habitats, is discussed. For the first time, this study relates population biology of pygmy mice with molecular identification.
Characterization of the porcine AMPK alpha 2 catalytic subunitgene (PRKAA2): genomic structure, polymorphism detection and association study
Authors: Lin L. , Flisikowski K. , Schwarzenbacher H. , Scharfe M. , Severitt S. , Blöcker H. , Fries R.
Published: September 2009

AMP‐activated protein kinase (AMPK), known as a key regulator of cellular energy homeostasis, plays an important role in regulation of glucose and lipid metabolism, and protein synthesis in mammals. The characterization of porcine PRKAA2 encoding the alpha 2 catalytic subunit of AMPK is reported in this study. PRKAA2 was assigned to porcine chromosome 6q by analysis of radiation hybrids (IMpRH panel), and its genomic structure was determined by BAC sequencing. PRKAA2 spans more than 62 kb and consists of nine exons and eight introns. A total of 25 polymorphisms were identified by re‐sequencing approximately 7 kb, including all the exons, exon–intron boundaries and 5′ and 3′ gene flanking regions using twelve founder animals of a Mangalitsa × Piétrain intercross. Neither of two single nucleotide polymorphisms (SNPs) found in the coding region caused an amino acid substitution. Two SNPs (NM_214266.1: c.236+142A>G and NM_214266.1: c.630C>T) in PRKAA2 were genotyped in the Mangalitsa × Piétrain F2 cross (n = 589) and two commercial populations [Piétrain (n = 1173) and German Landrace (n = 536)] and evaluated for association with traits of interest (muscle development and fat deposition). Single SNP and haplotype analyses revealed weak associations between the PRKAA2 genotypes and loin muscle area in the investigated populations.
Volatile organic compounds in exhaled breath as a diagnostic tool for asthma in children
Authors: Dallinga J. W. , Robroeks C. M. H. H. T. , Van Berkel J. J. B. N. , Moonen E. J. C. , Godschalk R. W. L. , Jöbsis Q. , Dompeling E. , Wouters E. F. M. , Van Schooten F. J.
Published: September 2009

Background
The correct diagnosis of asthma in young children is often hard to achieve, resulting in undertreatment of asthmatic children and overtreatment in transient wheezers.

Objectives
To develop a new diagnostic tool that better discriminates between asthma and transient wheezing and that leads to a more accurate diagnosis and hence less undertreatment and overtreatment. A first stage in the development of such a tool is the ability to discriminate between asthmatic children and healthy controls. The integrative analysis of large numbers of volatile organic compounds (VOC) in exhaled breath has the potential to discriminate between various inflammatory conditions of the respiratory tract.

Methods
Breath samples were obtained and analysed for VOC by gas chromatography–mass spectrometry from asthmatic children (n=63) and healthy controls (n=57). A total of 945 determined compounds were subjected to discriminant analysis to find those that could discriminate diseased from healthy children. A set of samples from both asthmatic and healthy children was selected to construct a model that was subsequently used to predict the asthma or the healthy status of a test group. In this way, the predictive value of the model could be tested.

Measurements and main results
The discriminant analyses demonstrated that asthma and healthy groups are distinct from one another. A total of eight components discriminated between asthmatic and healthy children with a 92% correct classification, achieving a sensitivity of 89% and a specificity of 95%.

Conclusion
The results show that a limited number of VOC in exhaled air can well be used to distinguish children with asthma from healthy children.

Cite this as: J. W. Dallinga, C. M. H. H. T. Robroeks, J. J. B. N. van Berkel, E. J. C. Moonen, R. W. L. Godschalk, Q. Jöbsis, E. Dompeling, E. F. M. Wouters and F. J. van Schooten, Clinical & Experimental Allergy, 2010 (40) 68–76.
Mitogen activated protein kinases: a role in inflammatory bowel disease?
Authors: Broom O J , Widjaya B , Troelsen J , Olsen J , Nielsen O H
Published: September 2009

Since their discovery more than 15 years ago, the mitogen activated protein kinases (MAPK) have been implicated in an ever-increasingly diverse array of pathways, including inflammatory signalling cascades. Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are characterized by the perpetual production of inflammatory mediators. Research into the transduction pathway behind this over-production has highlighted the potential mediating role for the MAPKs and their related signalling components. This review highlights some of the research into the role for the MAPKs and their related signalling proteins in influencing the progression of IBD.
Association of the −31C/T functional polymorphism in the interleukin-1β gene with the intractability of Graves' disease and the proportion of T helper type 17 cells
Authors: Hayashi F , Watanabe M , Nanba T , Inoue N , Akamizu T , Iwatani Y
Published: September 2009

Interleukin (IL)-1β is a proinflammatory cytokine and has been implicated in the pathogenesis of several autoimmune diseases. To evaluate the hypothesis that the functional −31C/T polymorphism (rs1143627) in the gene encoding IL-1β is associated with the intractability and the severity of autoimmune thyroid diseases, we genotyped this polymorphism in 64 patients with intractable Graves' disease (GD), 28 GD patients in remission, 49 patients with Hashimoto's disease (HD) who developed hypothyroidism (severe HD), 28 untreated euthyroid HD patients (mild HD) and 59 healthy volunteers. The −31T allele, which is related to the high producibility of IL-1β, was significantly more frequent in patients with intractable GD than in those with GD in remission (P = 0·0017; odds ratio 2·8; 95% confidence interval 1·5-5·3), although there was no difference in this frequency between two groups of HD patients. We showed additionally that the proportion of IL-17-producing T helper type 17 (Th17) cells, whose differentiation and proliferation are promoted by IL-1β, was higher in autoimmune thyroid disease patients with the T allele than in those with CC genotypes. In conclusion, our data indicated that the T allele of −31C/T polymorphism in the IL1B gene was involved in the intractability of GD, and this involvement may arise through the differentiation and proliferation of Th17 cells.
Modelling intercrop management impact on runoff and erosion in a continuous maize cropping system: Part I. Model description, global sensitivity analysis and Bayesian estimation of parameter identifiability
Authors: LALOY E. , BIELDERS C. L.
Published: September 2009

In order to evaluate the long‐term impact of intercrop management on runoff and erosion in a continuous maize cropping system a new model was developed, based on the continuous plot‐scale runoff model of Laloy & Bielders (2008). This model is called the Continuous Runoff and Erosion Hillslope model with DYnamic soil Surface properties (CREHDYS). This paper details the erosion and crop growth and decay model components and presents a thorough global variance‐based sensitivity analysis (GSA) with regard to the erosion prediction, followed by a Bayesian parameter identifiability assessment. As compared with the classical local univariate sensitivity analysis, a GSA is able to deal with the typical non‐linearity of process‐based hydrological and erosion models. The most influential parameters were the Manning's roughness coefficient followed by the saturated hydraulic conductivity of wheel track cells and the median particle size of the material. The soil aggregate stability and soil‐cohesion parameters were found to be almost non‐influential. Most of the results of the parameter identifiability procedure were in close agreement with the GSA. Indeed, the parameter uncertainty seemed to be proportional to the degree of influence, with Manning's coefficient being the most precisely identified, whereas soil and wheel track cohesion parameters showed the largest uncertainty. Exceptions were the soil aggregate stability and the Green‐Ampt soil matric potential. The uncertainty associated with the former was surprisingly low given its low level of influence whereas the uncertainty associated with the latter is partially explained by its negative correlation with the soil saturated hydraulic conductivities of overland flow and wheel track cells.
Barriers to Research Utilization Scale: psychometric properties of the Turkish version
Authors: Temel Ayla Bayik , Uysal Aynur , Ardahan Melek , Ozkahraman Sukran
Published: September 2009

Bayik T.A., uysal a., ardahan m. & ozkahraman s. (2010) Barriers to Research Utilization Scale: psychometric properties of the turkish version. Journal of Advanced Nursing 66(2), 456–464.

Title.  Barriers to Research Utilization Scale: psychometric properties of the Turkish version.

Aim.  This paper is report of a study designed to assess the psychometric properties of the Turkish version of the Barriers to Research Utilization Scale.

Background.  The original Barriers to Research Utilization Scale was developed by Funk et al. in the United States of America. Many researchers in various countries have used this scale to identify barriers to research utilization.

Methods.  A methodological study was carried out at four hospitals. The sample consisted of 300 nurses. Data were collected in 2005 using a socio‐demographic form (12 questions) and the Turkish version of the Barriers to Research Utilization Scale. A Likert‐type scale composed of four sub‐factors and 29 items was used. Means and standard deviations were calculated for interval level data. A P value of <0·05 was considered statistically significant.

Findings.  Language equivalence and content validity were assessed by eight experts. Confirmatory factor analysis revealed that the Turkish version was made up of four subscales. Internal consistency reliability coefficient was 0·92 for the total scale and ranged from 0·73 to 0·80 for the subscales. Total‐item correlation coefficients ranged from 0·37 to 0·60.

Conclusion.  The Turkish version of the scale is similar in structure to the original English language scale.
Colour compatibility between teeth and dental shade guides in Quinquagenarians and Septuagenarians
Authors: COCKING C. , CEVIRGEN E. , HELLING S. , OSWALD M. , CORCODEL N. , RAMMELSBERG P. , REINELT G. , HASSEL A. J.
Published: September 2009

Summary  The aim of this investigation was to determine colour compatibility between dental shade guides, namely, VITA Classical (VC) and VITA 3D‐Master (3D), and human teeth in quinquagenarians and septuagenarians. Tooth colour, described in terms of L*a*b* values of the middle third of facial tooth surface of 1391 teeth, was measured using VITA Easyshade in 195 subjects (48% female). These were compared with the colours (L*a*b* values) of the shade tabs of VC and 3D. The mean coverage error and the percentage of tooth colours being within a given colour difference (ΔEab) from the tabs of VC and 3D were calculated. For comparison, hypothetical, optimized, population‐specific shade guides were additionally calculated based on discrete optimization techniques for optimizing coverage. Mean coverage error was ΔEab = 3·51 for VC and ΔEab = 2·96 for 3D. Coverage of tooth colours by the tabs of VC and 3D within ΔEab = 2 was 23% and 24%, respectively, (ΔEab ≤ 2 as clinically acceptable match). The hypothetical guides performed better and would only need seven to eight tabs to reach the same results as VC and 3D. Both guides had a mean coverage error that was too high and coverage that was too low according to an acceptable colour difference of tooth colour for these subjects. The optimized hypothetical, population‐specific guides performed better indicating the possibility for improvement in colour compatibility of the guides with tooth colour in future shade guide development, allowing acceptable shade matching for most of the patients in clinical routine.
Review: To What Extent are T Cells Tolerant to Immunoglobulin Variable Regions?
Authors: Bogen B. , Ruffini P.
Published: September 2009

During the last 25 years it has become increasingly clear that short peptides derived from Ig V‐regions are displayed on MHC class II molecules. Recognition of such idiotypic(Id)‐peptide/MHC class II complexes by Id‐specific CD4+ T cells plays a role in (1) Id‐driven T‐B collaboration, (2) immunosurveillance of B cell cancers and (3) Id‐vaccination. A crucial question is then: to what extent are T cells tolerized to Ig V‐region sequences? Or rephrased: how large is the T‐cell repertoire for Ig V‐region sequences presented by MHC class II molecules? We argue that T cells are to a large extent tolerant to germline‐encoded V‐region sequences but that there is a T‐cell repertoire for rare Id‐sequences that arise as a consequence of somatic hyper mutation or N‐region diversity. Moreover, when otherwise rare Id‐sequences increase in concentration, T‐cell tolerance is induced (Fig. 1). For these reasons, T cells that recognize rare Id‐peptides, arising as a consequence of somatic genetic events unique to each B cell, may play a special importance in Id‐driven T–B collaboration, immunosurveillance of B‐cell malignancies, and Id‐vaccination.

 Ig V‐region Id‐peptides and T‐cell tolerance. Germline‐encoded Id‐peptides are expressed by relatively many B cells and Ig molecules in the body and are therefore considered “frequent”. Experimental evidence reviewed in the text suggests that T cells are tolerant such frequent Id‐peptides. By contrast, V‐region Id‐peptides that express either somatic mutations or N‐region diversity are restricted to only few B cells and Ig molecules and are therefore considered ‘rare’. T cells apparently are not tolerant and can respond to such rare Id‐peptides. Note that an otherwise rare Id‐peptide may upon clonal expansion, like e.g. in multiple myeloma, become frequent and induce T‐cell tolerance.

image
Eosinophil activity in infants hospitalized for wheezing and risk of persistent childhood asthma
Authors: Hyvärinen Mari K. , Kotaniemi‐Syrjänen Anne , Reijonen Tiina M. , Piippo‐Savolainen Eija , Korppi Matti
Published: September 2009

Hyvärinen MK, Kotaniemi‐Syrjänen A, Reijonen TM, Piippo‐Savolainen E, Korppi M. Eosinophil activity in infants hospitalized for wheezing and risk of persistent childhood asthma. Pediatr Allergy Immunol 2010: 21: 96–103. © 2009 John Wiley & Sons A/S

Eosinophilic inflammation has a central role in the pathogenesis of asthma. We aimed to elucidate whether elevated blood eosinophil count (B‐EOS), eosinophil cationic protein in serum (S‐ECP) or in nasopharyngeal aspirate (NPA‐ECP) predict later asthma after hospitalization for wheezing in infancy. In 1992–1993, 100 infants aged <24 months were hospitalized for wheezing associated with respiratory infection. B‐EOS, S‐ECP and NPA‐ECP were measured on admission. Asthma status was evaluated at the follow‐up visits at the median ages of 4.0, 7.2 and 12.3 yr. Twenty (25%) of 81 children had asthma at all three visits and were considered to have persistent childhood asthma (PCA). Children with B‐EOS ≥ 0.450 × 109 cells/l had a 2.9‐fold PCA risk compared with other children. The risk was 6.1‐fold when S‐ECP was ≥20.0 μg/l and 6.7‐fold when NPA‐ECP was ≥815.0 ng/g. By these cut‐off limits, all these markers were specific (75–93%), but not very sensitive (30–58%) in predicting PCA. At least one marker was elevated in 75% of the children with PCA. The respective figure for NPA‐ECP alone was 58%. In adjusted analyses, only elevated NPA‐ECP was an independent risk factor for PCA (OR 4.09). In conclusion, eosinophil activity in early life predicts the development of childhood asthma after hospitalization for wheezing in infancy. The results highlight NPA‐ECP as an independent predictor of the persistence of asthma at school age.
Analysis of 3′‐end variable region of the cagA gene in Helicobacter pylori isolated from Iranian population
Authors: Shokrzadeh Leila , Baghaei Kaveh , Yamaoka Yoshio , Dabiri Hossein , Jafari Fereshteh , Sahebekhtiari Navid , Tahami Ali , Sugimoto Mitsushige , Zojaji Homayon , Zali Mohammad Reza
Published: September 2009

Background and Aims:  The 3′ region of the cagA gene, the most well‐known virulence factor of Helicobacter pylori, contains Glu‐Pro‐Ile‐Tyr‐Ala (EPIYA) motifs. Four segments flanking the EPIYA motifs, EPIYA‐A, ‐B, ‐C, or ‐D, were reported to play important roles in H. pylori‐related gastroduodenal pathogenesis. The aim was to determine the roles of EPIYA segments in gastroduodenal pathogenesis in an Iranian population.

Methods:  A total of 92 cagA‐positive Iranian strains isolated from dyspepsia patients with non‐ulcer dyspepsia (n = 77), peptic ulcer (n = 11) and gastric cancer (n = 4) were studied. The EPIYA motif genotyping was determined by polymerase chain reaction and sequencing.

Results:  A total of 86 (93.5%) strains had three copies of EPIYA (ABC type), three (3.3%) had four copies (ABCC type) and three (3.3%) had two copies (AB type). The alignment of the deduced protein sequences confirmed that there were no East Asian type EPIYA‐D sequences (EPIYATIDFDEANQAG) in Iranian strains. When the prevalence of strains with multiple EPIYA‐C segments in Iran was compared with previously published data, it was much lower than that in Colombia and Italy, but was higher than that of Iraq, and the patterns were parallel to the incidence of gastric cancer in these countries.

Conclusion:  The structure of the 3′ region of the cagA gene in Iranian strains was Western type. Although we could not find differences between EPIYA types and clinical outcomes, low prevalence of strains with multiple EPIYA‐C segments might be reasons for low incidence of gastric cancer in Iran.
Late onset Pneumocystis pneumonia in patients receiving rituximab for humoral renal transplant rejection
Authors: SHELTON EDWARD , YONG MICHELLE , COHNEY SOLOMON
Published: September 2009

Rituximab has been used increasingly in the treatment of antibody‐mediated rejection (AbMR) in solid organ transplantation despite the absence of clinical trials demonstrating efficacy. A contributor to the growing use of rituximab is an apparent lack of morbidity; and there are no reports of specific opportunistic infections associated with its use in renal transplant recipients. Two cases of Pneumocystis pneumonia (PCP) occurring nearly 3 years after administration of rituximab for refractory AbMR are reported herein. These cases emphasize the need for ongoing vigilant observation in patients who have received rituximab, and highlight the importance of clinical trials to establish the role of rituximab in prevention and treatment of AbMR.