bluuebunny/crossref_metadata_2025_split huggingface dataset:
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination
Authors: Lee Woonghee , Kim Jin Hae , Westler William M. , Markley John L. 
Published: April 2011

AbstractSummary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means.Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Reaching out towards cannabis: approach‐bias in heavy cannabis users predicts changes in cannabis use
Authors: Cousijn Janna , Goudriaan Anna E. , Wiers Reinout W. 
Published: April 2011

ABSTRACTAims  Repeated drug exposure can lead to an approach‐bias, i.e. the relatively automatically triggered tendencies to approach rather that avoid drug‐related stimuli. Our main aim was to study this approach‐bias in heavy cannabis users with the newly developed cannabis Approach Avoidance Task (cannabis‐AAT) and to investigate the predictive relationship between an approach‐bias for cannabis‐related materials and levels of cannabis use, craving, and the course of cannabis use.Design, settings and participants  Cross‐sectional assessment and six‐month follow‐up in 32 heavy cannabis users and 39 non‐using controls.Measurements  Approach and avoidance action‐tendencies towards cannabis and neutral images were assessed with the cannabis AAT. During the AAT, participants pulled or pushed a joystick in response to image orientation. To generate additional sense of approach or avoidance, pulling the joystick increased picture size while pushing decreased it. Craving was measured pre‐ and post‐test with the multi‐factorial Marijuana Craving Questionnaire (MCQ). Cannabis use frequencies and levels of dependence were measured at baseline and after a six‐month follow‐up.Findings  Heavy cannabis users demonstrated an approach‐bias for cannabis images, as compared to controls. The approach‐bias predicted changes in cannabis use at six‐month follow‐up. The pre‐test MCQ emotionality and expectancy factor were associated negatively with the approach‐bias. No effects were found on levels of cannabis dependence.Conclusions  Heavy cannabis users with a strong approach‐bias for cannabis are more likely to increase their cannabis use. This approach‐bias could be used as a predictor of the course of cannabis use to identify individuals at risk from increasing cannabis use.
Low-dose 5-fluorouracil in combination with salicylic acid as a new lesion-directed option to treat topically actinic keratoses: histological and clinical study results
Authors: Stockfleth E. , Kerl H. , Zwingers T. , Willers C. 
Published: April 2011

Summary
Background Actinic keratoses (AKs) arise after chronic sun exposure. Because long-term ultraviolet (UV) damage may induce proliferation of atypical keratinocytes, treatment of AKs is recommended.
Objectives To compare 5-fluorouracil 0·5%/salicylic acid 10·0% [low-dose 5-FU/SA (Actikerall®)] with diclofenac 3% in hyaluronic acid (diclofenac HA) and vehicle for the treatment of AKs.
Methods This was a randomized, placebo-controlled, double-blind, parallel-group, multicentre trial. Patients received topical low-dose 5-FU/SA once daily, its vehicle or diclofenac HA twice daily for a maximum of 12 weeks. The final evaluation was at week 20. The primary objectives were to demonstrate the histological clearance rate of one predefined lesion. The secondary objectives were the improvement of treated lesions, tolerability and safety.
Results There were 470 patients with 4–10 AK lesions each (grade I or II) on the face/forehead or bald scalp included in the study. Low-dose 5-FU/SA was superior to diclofenac HA (P &lt;0·01) and vehicle (P &lt;0·0001) for histological clearance of one representative lesion 8 weeks post-treatment. In 72·0%, 59·1% and 44·8% of patients in the low-dose 5-FU/SA, diclofenac HA and vehicle groups, respectively, the week-20 biopsy revealed no AKs. Significantly more lesions were cleared with low-dose 5-FU/SA (74·5%) compared with diclofenac HA (54·6%; P &lt;0·001) or vehicle (35·5%; P &lt;0·001). Low-dose 5-FU/SA was superior in terms of complete clinical clearance: 55·4%, vs. diclofenac HA (32·0%, P &lt;0·001) and vehicle (15·1%P &lt;0·001). Application-site disorders (mainly burning and inflammation) were more frequent with low-dose 5-FU/SA but mainly of mild to moderate intensity.
Conclusions Topical low-dose 5-FU/SA demonstrated higher histological and clinical clearance rates vs. diclofenac HA or vehicle. Low-dose 5-FU/SA is an effective lesion-directed treatment for AKs.
Inducing apoptosis in chemotherapy‐resistant B‐lineage acute lymphoblastic leukaemia cells by targeting HSPA5, a master regulator of the anti‐apoptotic unfolded protein response signalling network
Authors: Uckun Fatih M. , Qazi Sanjive , Ozer Zahide , Garner Amanda L. , Pitt Jason , Ma Hong , Janda Kim D. 
Published: April 2011

SummaryWe present previously unknown evidence that the immunoglobulin heavy chain binding protein BIP/HSPA5, also known as glucose regulated protein (GRP)78, serving as a pivotal component of the pro‐survival axis of the unfolded protein response (UPR) signalling network, is abundantly expressed in relapsed B‐lineage acute lymphoblastic leukaemia (ALL) and contributes to chemotherapy resistance of leukaemic B‐cell precursors. The resistance of B‐lineage ALL cells to the standard anti‐leukaemic drug vincristine was overcome by the HSPA5 inhibitor epigallocatechin gallate, which inhibits the anti‐apoptotic function of HSPA5 by targeting its ATP‐binding domain. Notably, chemotherapy‐resistant B‐lineage ALL cells underwent apoptosis within 48 h of exposure to a doxorubicin‐conjugated cell‐penetrating cyclic anti‐HSPA5 peptide targeting surface‐expressed HSPA5 molecules on leukaemia cells. The identification of the HSPA5 as a chemoresistance biomarker and molecular target for B‐lineage ALL may lead to new anti‐leukaemic treatment strategies that are much needed.
Evaluation of two new recombinant guinea‐pig lipocalins, Cav p 2 and Cav p 3, in the diagnosis of guinea‐pig allergy
Authors: Hilger C. , Swiontek K. , Kler S. , Diederich C. , Lehners C. , Vogel L. , Vieths S. , Hentges F. 
Published: April 2011

Cite this as: C. Hilger, K. Swiontek, S. Kler, C. Diederich, C. Lehners, L. Vogel, S. Vieths and F. Hentges, Clinical & Experimental Allergy, 2011 (41) 899–908.SummaryBackground
Guinea‐pigs, classical laboratory animals now often kept as pets, regularly elicit important allergic reactions. Two guinea‐pig allergens have been described previously to some extent; however, biomolecular and immunological data are lacking.Objective
To identify major guinea‐pig allergens, produce them as recombinant proteins and define their allergenic potential and clinical importance in allergic patients.Methods
Protein extracts were prepared from various guinea‐pig tissues and allergens were purified by ion exchange chromatography. The N‐termini of two immunoglobulin E (IgE)‐reactive proteins were determined and degenerate primers were designed for cDNA amplification by RT‐PCR. Allergenic properties of recombinant proteins were assayed by immunoblotting, ELISA and mediator release assays. Specific IgE were quantified in the sera of 26 guinea‐pig‐allergic patients.Results
Major IgE‐reactive proteins were detected in submaxillary and harderian gland extracts. Two proteins were identified and the cDNAs were cloned. The 17 kDa protein expressed in the harderian gland corresponds to the previously described Cav p 2. The 19 kDa protein, Cav p 3, is a new allergen expressed in the submaxillary gland. Recombinant Cav p 2 and Cav p 3 were recognized by IgE antibodies from 65% and 54% of guinea‐pig‐allergic patients, respectively. Both proteins demonstrated equivalent allergenic activity in the mediator release assays.Conclusion and Clinical Relevance
Two major guinea‐pig allergens, Cav p 2 and Cav p 3, have been characterized and produced as recombinant proteins. Combined to guinea‐pig serum albumin, the new allergens proved to be valuable in the component‐resolved diagnosis of guinea‐pig allergy.
Specific immunotherapy in children
Authors: Bufe A. , Roberts G. 
Published: April 2011

SummarySubcutaneous immunotherapy (SCIT) with allergen extracts in children with allergic rhinitis, with or without co‐seasonal asthma, has developed into a routine treatment although the scientific evidence for its efficacy is not as strong as for adults. In the hands of experienced allergists, this treatment has been proven to be safe. The development of allergen tablets for sublingual immunotherapy (SLIT) may open a new age of more convenient, safer SIT. In children, in particular, the evidence for the long‐term efficacy of SLIT, its ability to prevent the development of asthma and polysensitization and its comparability to SCIT will be required before it will replace the traditional subcutaneous route. Issues of compliance represent an important drawback of SLIT. We need ways of improving this. Treatment of asthma by immunotherapy is still restricted to clearly defined patients with mild to moderate asthma with symptoms that are related to the specific allergen sensitization. In these patients, symptoms and use of anti‐inflammatory therapy can be reduced by SIT. Cite this as: A. Bufe and G. Roberts, Clinical & Experimental Allergy, 2011 (41) 1256–1262.
The utilization of knowledge of and interest in research and development among primary care staff by means of strategic communication – a staff cohort study
Authors: Morténius Helena , Marklund Bertil , Palm Lars , Fridlund Bengt , Baigi Amir 
Published: April 2011

AbstractObjective  The obvious gap between evidence and practice in health care is unfavourable for patient care and requires the promotion of a scientific attitude among health care professionals. The aim of the present study was to determine the utilization of knowledge of and interest in research and development among primary care staff by means of a strategic communication process.Method  A cohort consisting of primary care staff (n = 1276) was designed and strategic communication was utilized as a platform over a 7‐year period. Quantitative and qualitative methods were taken in account.Results  We found that 97% of the staff had gained knowledge of research and development, 60% of whom remained interested in the subject. The oral communication channel was the most powerful for creating research interest. Organizational culture was a barrier to interest in science.Conclusion  The study demonstrates a significant increase in knowledge and interest among primary care staff as a result of a strategic communication process.Practice implications  Strategic communication should lead to a more evenly distributed research commitment among all health care professionals, thus facilitating communication between them and patients in order to clarify, for example, the causes of disease.
Psychometric properties of the Turkish version of the Perception of Aggression Scale
Authors: BILGIN H. , TULEK Z. , OZCAN N. 
Published: April 2011

Accessible summary
There is a distinct lack of studies that explore the perceptions of aggressive behaviour in health care at the national and international levels.
There is also a lack of tools to evaluate the perceptions of aggression in the Turkish language.
This study examines psychometric validation of the Perception of Aggression Scale to gain an insight into aggression in different cultures.
AbstractThe aim of this study was to investigate the psychometric properties of the Turkish version of the Perception of Aggression Scale. Cross‐sectional data were collected by the completion of questionnaires by 350 nursing students from two nursing schools in Istanbul, Turkey. The psychometric properties of the Turkish version of the scale were analysed by using factor analysis (principal component analysis), assessment of internal consistency and reliability, and Spearman's rank correlation coefficients. The two‐factor structure was confirmed by principal component analysis: the first factor treated aggression as functional and the second as dysfunctional. The correlation between the means of the items and dimensions was moderate (r for factor 1: 0.47–0.73; r for factor 2: 0.29–0.70). The coefficient of internal consistency of the scale was 0.85 for factor 1 and 0.81 for factor 2. Thus, Turkish version of Perception of Aggression Scale is a valid and reliable tool. It is essential to understand perceptions of aggressive behaviour in order to establish effective management strategies to tackle untoward events in clinical settings.
Changes in health professionals' knowledge, attitudes and practice following provision of educational resources about prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder
Authors: Payne Janet , France Kathryn , Henley Nadine , D'Antoine Heather , Bartu Anne , O'Leary Colleen , Elliott Elizabeth , Bower Carol 
Published: April 2011

SummaryPayne J, France K, Henley N, d'Antoine H, Bartu A, O'Leary C, Elliott E, Bower C. Changes in health professionals' knowledge, attitudes and practice following provision of educational resources about prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder. Paediatric and Perinatal Epidemiology 2011; 25: 316–327.We provided health professionals in Western Australia (WA) with educational resources about prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder and assessed changes in their knowledge, attitudes and practice concerning fetal alcohol syndrome (FAS) and alcohol consumption in pregnancy. Following our 2002 survey of health professionals in WA, we developed and distributed educational resources to 3348 health professionals in WA in 2007. Six months later we surveyed 1483 of these health professionals. Prevalence rate ratios [PRR] and 95% confidence intervals [CI] were calculated to compare 2007 results with results from the 2002 survey. Of the 1001 responding health professionals, 69.8% had seen the educational resources; of these 77.1% have used them and 48.5% said the resources had assisted them to change their practice or their intention to change their practice. Compared with 2002, there was an increase in the proportion who knew all the essential features of FAS from 11.7% to 15.8% [PRR 1.35; 95% CI 1.09, 1.67] and had diagnosed FAS, from 4.8% to 7.3% [PRR 1.52; 95% CI 1.08, 2.13]. In 2007, 98.1% of health professionals stated they would advise pregnant women to consider not drinking at all or advise them that no alcohol in pregnancy is the safest choice. Health professionals surveyed in 2007 have increased their knowledge, changed their attitudes and practice about FAS, and altered the advice they give to pregnant women about alcohol consumption since our survey in 2002. It is essential that we build on this change and continue to support health professionals' knowledge, attitudes and practice about the prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder. The educational resources for health professionals may be ordered as hard copies and downloaded from the internet http://www.ichr.uwa.edu.au/alcoholandpregnancy
Maternal dietary glycaemic intake during pregnancy and the risk of birth defects
Authors: Yazdy Mahsa M. , Mitchell Allen A. , Liu Simin , Werler Martha M. 
Published: April 2011

SummaryYazdy MM, Mitchell AA, Liu S, Werler MM. Maternal dietary glycaemic intake during pregnancy and the risk of birth defects. Paediatric and Perinatal Epidemiology 2011; 25: 340–346.High sugar intake has been linked to fetal anomalies in the presence and absence of insulin resistance. Using dietary data collected in the Boston University Slone Epidemiology Birth Defects Study, we examined whether high dietary glycaemic index (dGI) or load (dGL) increased the risk of birth defects. Non‐diabetic mothers of 1921 cases and 704 controls were interviewed within 6 months of delivery (1988–98) about pregnancy events and exposures, including a 99‐item food frequency questionnaire. Case groups included amniotic bands, craniosynostosis, gastroschisis, hypospadias, small intestinal defects, anorectal defects, limb reductions, omphalocele, cleft lip and/or palate, renal agenesis, and tracheoesophageal fistula. Cubic splines were used to determine cut‐point values for high dGI and dGL in relation to the risk of each birth defect. The cut‐points were used in logistic regression models to calculate odds ratios (OR) and 95% confidence intervals [CI]. Control mothers in the lowest quartile of glycaemic intake were more likely to be non‐Hispanic White, ≥30 years of age, have higher family income, have a normal body mass index and reside in Boston. Findings were null for most case groups. The anorectal defect case group was found to have elevated risks for dGL [adjusted OR: 2.4; 95% CI: 1.1, 4.9], while estimates for dGI were elevated for the amniotic band case group [adjusted OR: 3.0; 95% CI: 1.1, 8.1]. Because this is the first paper (to our knowledge) to explore dGI and dGL in relation to a spectrum of birth defects, additional studies are needed.
The effect of RBC transfusions on cytokine gene expression after cardiac surgery in patients developing post‐operative multiple organ failure
Authors: Sitniakowsky L. S. , Later A. F. L. , van de Watering L. M. G. , Bogaerts M. , Brand A. , Klautz R. J. M. , Smit N. P. M. , van Hilten J. A. 
Published: April 2011

Aim: To determine the effect of red blood cell (RBC) transfusions during cardiac surgery on cytokine gene expression (GE) in relation to multiple organ failure (MOF) development after systemic inflammatory response syndrome (SIRS). Background: RBC transfusion in cardiac surgery patients is dose‐dependently associated with post‐operative MOF, possibly acting as a second hit after cardiopulmonary bypass. Methods: For this observational study, 29 patients divided into four groups of cardiac surgery patients were selected from a randomised controlled trial (RCT). Group 1: no‐RBC, no‐MOF (N = 8); group 2: MOF, no‐RBC (N = 7); group 3: RBC, no‐MOF (N = 6); group 4: RBC and MOF (N = 8). Selection was based on age, gender, number of (leukocyte‐depleted) RBC transfusions, type and duration of surgery.A 114 cytokine GE array was applied to blood samples withdrawn before and 24 h after surgery. Expression of selected genes was confirmed with reverse transcriptase real time‐polymerase chain reaction (RT‐PCR). Results: Nineteen of the 39 detectable genes showed a significant change in GE after surgery. Confirmed by RT‐PCR, transfused MOF patients exhibit significantly less downregulation of CD40 ligand than control patients. Patients who would develop MOF show significantly larger increases in GE of transforming growth factor‐α (TGF‐α), tumour necrosis factor (TNF)‐superfamily members 10 and 13B (TNFsf10/13B). Conclusions: When tested at 24 h after surgery, cytokine GE in peripheral blood leucocytes showed no significant differences between those transfused and those not transfused. Some alterations were seen in those developing MOF compared to those who did not, but the findings offer no role of leukocyte depleted (LD) RBC transfusion in the development of MOF.
Tolerance of Auditory Disturbance by an Avian Urban Adapter, the Noisy Miner
Authors: Lowry Hélène , Lill Alan , Wong Bob B. M. 
Published: April 2011

AbstractUrbanization creates challenges for wildlife, most notably through changes in resource availability and the frequent occurrence of sensory disturbance. Some native species, however, have been able to exploit and thrive in urban environments. Research, in this regard, has mostly focused on the ecological conditions that have allowed such species to prosper. In contrast, less attention has been devoted to evaluating how they cope with human proximity and disturbance. In a field experiment on a successful Australian ‘urban adapter’, the Noisy miner, Manorina melanocephala, we compared tolerance of a loud, startling sound stimulus by urban and rural individuals. We found group size differences between birds occupying urban and rural sites: more urban birds came into the testing area in response to the initial alarm‐call playback compared with rural birds. Urban and rural birds also differed significantly in their behavioural response profile to the test sound stimulus. Nearly half (47.5%) of the rural, but only 22.5% of the urban birds took flight and of those that did, only 1 of 9 urban individuals retreated >5 m, compared with 13 of 19 rural birds. About one‐third of urban, but only 5% of rural individuals responded to the sound stimulus with aggressive displays. The most frequent response to the stimulus, irrespective of habitat type, was to remain near the sound source and engage in visual surveillance. The high frequency of this response in both urban and rural individuals suggested that most noisy miners were quite ‘bold’, a temperament trait that is likely to be important in successful urban colonization by birds.
Recombination frequency variation in maize as revealed by genomewide single‐nucleotide polymorphisms
Authors: Farkhari Mohammad , Lu Yanli , Shah Trushar , Zhang Shihuang , Naghavi Mohammad R. , Rong Tingzhao , Xu Yunbi 
Published: April 2011

With 2 tablesAbstractRecombination frequency greatly affects selection efficiency in plant breeding. A high‐density single‐nucleotide polymorphism (SNP) map integrated with physical map and other molecular maps is very useful for characterizing genetic recombination variation. In this study, recombination frequency in maize was investigated through SNP linkage maps constructed with three recombinant inbred line populations. The integrated map consisted of 1443 molecular markers, including 1155 SNPs, spanning 1346 cM. A 100‐fold difference in recombination frequency was observed between different chromosomal regions, ranging from an average of 0.09 cM/Mb for pericentromeric regions to 7.08 cM/Mb for telomeric regions. Recombination suppression in non‐centromeric regions identified nine recombination‐suppressed regions, one of which likely contained condensed heterochromatin (knobs). Recombination variation along chromosomes was highly predictable for pericentromeric and telomeric regions, but population‐specific with 4.5‐fold difference for the same marker interval across the three populations or specific chromosome regions because of the presence of knobs. As recombination variation can be identified and well characterized as shown in this study, the related information will facilitate future genetic studies, gene cloning and marker‐assisted plant breeding.