bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrical detection of pathogenic bacteria via immobilized antimicrobial peptides
Authors: Mannoor Manu S. , Zhang Siyan , Link A. James , McAlpine Michael C. 
Published: October 2010

The development of a robust and portable biosensor for the detection of pathogenic bacteria could impact areas ranging from water-quality monitoring to testing of pharmaceutical products for bacterial contamination. Of particular interest are detectors that combine the natural specificity of biological recognition with sensitive, label-free sensors providing electronic readout. Evolution has tailored antimicrobial peptides to exhibit broad-spectrum activity against pathogenic bacteria, while retaining a high degree of robustness. Here, we report selective and sensitive detection of infectious agents via electronic detection based on antimicrobial peptide-functionalized microcapacitive electrode arrays. The semiselective antimicrobial peptide magainin I—which occurs naturally on the skin of African clawed frogs—was immobilized on gold microelectrodes via a C-terminal cysteine residue. Significantly, exposing the sensor to various concentrations of pathogenic
Escherichia coli
revealed detection limits of approximately 1 bacterium/μL, a clinically useful detection range. The peptide-microcapacitive hybrid device was further able to demonstrate both Gram-selective detection as well as interbacterial strain differentiation, while maintaining recognition capabilities toward pathogenic strains of
E. coli
and
Salmonella
. Finally, we report a simulated “water-sampling” chip, consisting of a microfluidic flow cell integrated onto the hybrid sensor, which demonstrates real-time on-chip monitoring of the interaction of
E. coli
cells with the antimicrobial peptides. The combination of robust, evolutionarily tailored peptides with electronic read-out monitoring electrodes may open exciting avenues in both fundamental studies of the interactions of bacteria with antimicrobial peptides, as well as the practical use of these devices as portable pathogen detectors.
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions
Authors: Rahrig Ryan R. , Leontis Neocles B. , Zirbel Craig L. 
Published: October 2010

AbstractMotivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph.Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments.Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: r-rahrig@onu.edu
MEDELLER: homology-based coordinate generation for membrane proteins
Authors: Kelm Sebastian , Shi Jiye , Deane Charlotte M. 
Published: October 2010

Abstract
Motivation: Membrane proteins (MPs) are important drug targets but knowledge of their exact structure is limited to relatively few examples. Existing homology-based structure prediction methods are designed for globular, water-soluble proteins. However, we are now beginning to have enough MP structures to justify the development of a homology-based approach specifically for them.
Results: We present a MP-specific homology-based coordinate generation method, MEDELLER, which is optimized to build highly reliable core models. The method outperforms the popular structure prediction programme Modeller on MPs. The comparison of the two methods was performed on 616 target–template pairs of MPs, which were classified into four test sets by their sequence identity. Across all targets, MEDELLER gave an average backbone root mean square deviation (RMSD) of 2.62 Å versus 3.16 Å for Modeller. On our ‘easy’ test set, MEDELLER achieves an average accuracy of 0.93 Å backbone RMSD versus 1.56 Å for Modeller.
Availability and Implementation: http://medeller.info; Implemented in Python, Bash and Perl CGI for use on Linux systems; Supplementary data are available at http://www.stats.ox.ac.uk/proteins/resources.
Contact: kelm@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes
Authors: Lua Rhonald C. , Lichtarge Olivier 
Published: October 2010

Abstract
Summary: PyETV is a PyMOL plugin for viewing, analyzing and manipulating predictions of evolutionarily important residues and sites in protein structures and their complexes. It seamlessly captures the output of the Evolutionary Trace server, namely ranked importance of residues, for multiple chains of a complex. It then yields a high resolution graphical interface showing their distribution and clustering throughout a quaternary structure, including at interfaces. Together with other tools in the popular PyMOL viewer, PyETV thus provides a novel tool to integrate evolutionary forces into the design of experiments targeting the most functionally relevant sites of a protein.
Availability: The PyETV module is written in Python. Installation instructions and video demonstrations may be found at the URL http://mammoth.bcm.tmc.edu/traceview/HelpDocs/PyETVHelp/pyInstructions.html.
Contact: lichtarge@bcm.tmc.edu
OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data
Authors: Xia Tian , Hemert John V. , Dickerson Julie A. 
Published: October 2010

Abstract
Summary: OmicsAnalyzer is a Cytoscape plug-in for visual omics-based network analysis that (i) integrates hetero-omics data for one or more species; (ii) performs statistical tests on the integrated datasets; and (iii) visualizes results in a network context.
Availability: Implemented in Java, OmicsAnalyzer runs with Cytoscape 2.6 and 2.7. Binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv/omicsanalyzer/
Contact: julied@iastate.edu; netscape@iastate.edu
Dizziness and the genetic influences on subjective experiences to initial cigarette use
Authors: Haberstick Brett C. , Ehringer Marissa A. , Lessem Jeffrey M. , Hopfer Christian J. , Hewitt John K. 
Published: October 2010

ABSTRACTAim  To examine individual differences in positive and negative subjective experiences to initial cigarette use.Design  Retrospective self‐reports of initial subjective experiences were examined to estimate the genetic and environmental influences and the extent of their covariation across different effects.Participants  Data was drawn from 2482 young adult same‐and opposite sex twins‐ and siblings participating in the National Longitudinal Study of Adolescent Health.Measurement  Subjective experiences were retrospectively collected using the Early Smoking Experience (ESE) questionnaire.Findings  Positive experiences evidenced moderate heritable contributions (40%, 95% CI: 0.22 to 0.56), as did an overall hedonic measure (34%, 95% CI: 0.22 to 0.46) and dizziness (34%, 95% CI: 0.15 to 0.52). Negative experiences evidenced small heritable contributions (13%, 95% CI: 0.00 to 0.36). Individual specific environmental influences were strong and accounted for the remaining proportion of observed variation in these experiences. Multivariate genetic modeling identified a moderately heritable underlying factor (37%, 95% CI: 0.22 to 0.52) that influenced the covariation of diverse subjective experiences and loaded most heavily on dizziness. Positive experiences also evidence residual genetic influences that were uncorrelated with other subjective experiences.Conclusions  How a person experiences their initial few cigarettes is due to both heritable contributions and environmental experiences unique to the person. The covariation of diverse subjective experiences appears to be due to a heritable latent sensitivity to the chemicals contained in an average cigarette and is best indexed by dizziness.
Alcohol marketing research: the need for a new agenda
Authors: Meier Petra S. 
Published: October 2010

ABSTRACTAims  This paper aims to contribute to a rethink of marketing research priorities to address policy makers' evidence needs in relation to alcohol marketing.Method  Discussion paper reviewing evidence gaps identified during an appraisal of policy options to restrict alcohol marketing.Findings  Evidence requirements can be categorized as follows: (i) the size of marketing effects for the whole population and for policy‐relevant population subgroups, (ii) the balance between immediate and long‐term effects and the time lag, duration and cumulative build‐up of effects and (iii) comparative effects of partial versus comprehensive marketing restrictions on consumption and harm. These knowledge gaps impede the appraisal and evaluation of existing and new interventions, because without understanding the size and timing of expected effects, researchers may choose inadequate time‐frames, samples or sample sizes. To date, research has tended to rely on simplified models of marketing and has focused disproportionately on youth populations. The effects of cumulative exposure across multiple marketing channels, targeting of messages at certain population groups and indirect effects of advertising on consumption remain unclear.Conclusion  It is essential that studies into marketing effect sizes are geared towards informing policy decision‐makers, anchored strongly in theory, use measures of effect that are well‐justified and recognize fully the complexities of alcohol marketing efforts.
Cessation of groin injecting behaviour among patients on oral opioid substitution treatment
Authors: Senbanjo Richard , Hunt Neil , Strang John 
Published: October 2010

ABSTRACTAims  To identify factors that might influence cessation of groin injecting (GI) among patients receiving oral opioid substitution treatment (OST).Design  A cross‐sectional survey.Setting  Drug treatment centres in South East England.Participants  Groin injectors (GIs) attending an ultrasound ‘health‐check’ clinic.Measurements  Clinical data and ultrasound images; comparing 65 patients who had injected drugs in the femoral vein (fv) in the previous month (current GIs) with 49 former groin injectors (former GIs).Findings  Most of the 114 clinic attendees were men (69.3%) and white European (95.6%). Mean age, duration of GI and time in treatment were 36.4 years, 54.8 months and 20.5 months, respectively. Former GIs were significantly older (P < 0.001) and had been injecting (P < 0.05) and in treatment (P < 0.05) for longer than current GIs. History of deep vein thrombosis (DVT, P < 0.05) and septicaemia (P < 0.05); moderate/severe chronic venous disease (CVD, P < 0.01); and ‘very severe’ fv damage on ultrasonography (P < 0.05) were more common among former GIs. A logistic regression model correcting for the effects of covariants revealed age (B 0.08; Wald 7.1; P < 0.01) and severity of venous disease (B 1.1; Wald 4.1; P < 0.05) as the strongest predictors of behaviour change.Conclusions  GI cessation is associated with longer time in treatment, increasing age and the presence of CVD and severely damaged fv. GI appears to be an intractable behaviour that often persists despite OST and severe health complications. Persistent GI should prompt a review of whether OST is optimized and whether other interventions are needed to promote behaviour change prior to the development of serious harm.
Use of thromboelastometry in the assessment of coagulation before epidural insertion after massive transfusion
Authors: Walker C. , Ingram M. , Edwards D. , Wood P. 
Published: October 2010

SummaryA British soldier presented to the UK Field Hospital, Afghanistan with bilateral traumatic lower limb amputations. Resuscitation and surgery followed accepted damage control principles. Blood component therapy was in keeping with UK military guidelines and included platelets and cryoprecipitate. The patient’s trachea was extubated following insertion of an effective epidural. Ten days later, in the UK, he developed neurological symptoms and the presence of a subdural haematoma was confirmed on magnetic resonance imaging. Conventional laboratory coagulation results in this patient were above accepted limits for epidural insertion; however, thromboelastometry before insertion was suggestive of reduced platelet function. This case highlights the risk of relying solely on platelet count as a marker of platelet function following massive transfusion. Thromboelastometry provides additional information for the assessment of coagulation and should form part of the assessment of coagulation following massive transfusion before epidural insertion.
Different clinical severity of first episodes and recurrences of thrombotic thrombocytopenic purpura
Authors: Lotta Luca A. , Mariani Mariagabriella , Consonni Dario , Mancini Ilaria , Palla Roberta , Maino Alberto , Vucelic Dragica , Pizzuti Michele , Mannucci Pier M. , Peyvandi Flora 
Published: October 2010

SummaryThe clinical course of thrombotic thrombocytopenic purpura (TTP) is characterized by recurrent disease episodes in up to 50% of cases. The clinical presentation and severity of different TTP episodes have not been systematically compared. Laboratory and clinical information from 51 patients with recurrent disease, derived from 136 patients with TTP included in the Milan TTP registry (URL: http://www.ttpdatabase.org), were used to compare mortality, symptoms and disease‐related laboratory measurements in different disease episodes. The prevalence of severe neurological symptoms (coma, seizures, and focal neurological defects) was significantly lower in recurrences than in the first episode. Platelet counts and haemoglobin levels at presentation were higher in recurrences than in the first disease episode, and lactate dehydrogenase levels were lower. Also, mortality tended to be lower in the second and third disease episodes than in the first. Recurrences of TTP are generally milder than first episodes. These differences in severity should be taken into account in clinical research on TTP and in patient management.
Early and treatment‐related deaths in childhood acute myeloid leukaemia in the Nordic countries: 1984–2003
Authors: Molgaard‐Hansen Lene , Möttönen Merja , Glosli Heidi , Jónmundsson Guðmundur K. , Abrahamsson Jonas , Hasle Henrik ,   On behalf of the Nordic Society of Paediatric Haematology and Oncology (NOPHO)
Published: October 2010

SummaryDespite major improvements in the cure rate of childhood acute myeloid leukaemia (AML), 5–15% of patients still die from treatment‐related complications. In a historical prospective cohort study, we analysed the frequency, clinical features and risk factors for early deaths (ED) and treatment‐related deaths (TRD) in 525 children included in the Nordic Society of Paediatric Haematology and Oncology (NOPHO)‐AML‐84, ‐88 and ‐93 trials. Seventy patients (13%) died before starting treatment or from treatment‐related complications. The death rate rose from 11% in NOPHO‐AML‐84 to 29% in ‐88, but then fell to 8% in ‐93. Sixteen patients (3%) died within the first 2 weeks, mainly from bleeding or leucostasis. Hyperleucocytosis, age <2 or ≥10 years were risk factors. After day 15, 10% of patients died from treatment‐related complications with infection as the main cause of death. Risk factors were age <2 or ≥10 years and treatment according to the NOPHO‐AML‐88 protocol. The number of EDs and TRDs in AML is high. Therefore optimal antifungal prophylaxis is essential, and studies on the benefit of antibacterial prophylaxis and individual risk factors for ED and TRD are needed.
One hundred years of sickle cell disease
Authors: Serjeant Graham R. 
Published: October 2010

SummaryThe first formal report of sickle cell disease occurred 100 years ago. This review traces the early historical reports, the evolution of understanding of the genetics, the molecular and chemical basis of sickle haemoglobin, and the advances made over the last 30–40 years in improving the management. Newborn screening and close follow‐up, especially early in life, has significantly improved survival but these advances require resources and sophisticated infrastructure. In sub‐Saharan Africa over 250 000 births annually suggest that these advances are unlikely to be implemented within the foreseeable future. Prevention of the disease where possible, could reduce the numbers of new patients allowing better facilities for the care of others. As the disease results from the inheritance of abnormal haemoglobin genes from both parents, it is eminently preventable. The unanswered question, whether genotype detection and counselling will influence reproductive decisions, is currently being addressed by a project in central Jamaica.
Expression of prostate stem cell antigen in high‐grade prostatic intraepithelial neoplasia and prostate cancer
Authors: Barbisan Francesca , Mazzucchelli Roberta , Santinelli Alfredo , Scarpelli Marina , Lopez‐Beltran Antonio , Cheng Liang , Montironi Rodolfo 
Published: October 2010

Barbisan F, Mazzucchelli R, Santinelli A, Scarpelli M, Lopez‐Beltran A, Cheng L & Montironi R (2010) Histopathology57, 572–579 Expression of prostate stem cell antigen in high‐grade prostatic intraepithelial neoplasia and prostate cancerAims:  To investigate prostate stem cell antigen (PSCA) and Ki‐67 expression in normal‐looking epithelium (NEp), atrophy, high‐grade prostatic intraepithelial neoplasia (HGPIN) and prostatic adenocarcinoma (PCa).Methods and results:  PSCA and Ki‐67 were evaluated immunohistochemically in NEp, atrophy, HGPIN and PCa in 20 radical prostatectomies (RPs) and 20 cystoprostatectomies (CyPs). The proportions of PSCA positive cells and of cases with PSCA expression increased from NEp through atrophy and HGPIN to PCa. The differences between NEp and HGPIN and PCa and between atrophy and HGPIN and PCa were statistically significant for the away and adjacent locations, in both the RP and CyP groups. The differences between HGPIN and PCa were statistically significant in the RP group when it was away from PCa and in the CyP group when it was adjacent to and away from PCa. The values in the RPs were slightly greater than in the CyPs, the differences being not statistically significant. The proportions of Ki‐67 positive nuclei increased from atrophy and NEp to HGPIN and PCa. The correlation between the proportion of Ki‐67 positive nuclei and that of PSCA‐positive cells was statistically significant.Conclusions:  PSCA expression, deregulated in atrophy and HGPIN, is a marker associated with neoplastic transformation of prostate cells, both in RPs and CyPs.
Histological changes in patients with chronic upper gastrointestinal ischaemia
Authors: Van Noord Désirée , Biermann Katharina , Moons Leon MG , Pattynama Peter MT , Verhagen Hence JM , Kuipers Ernst J , Mensink Peter BF 
Published: October 2010

van Noord D, Biermann K, Moons L M G, Pattynama P M T, Verhagen H J M, Kuipers E J & Mensink P B F (2010) Histopathology57, 615–621 Histological changes in patients with chronic upper gastrointestinal ischaemiaAims:  Diagnosing chronic upper gastrointestinal ischaemia (CUGI) remains a challenge in clinical practice. Histological examination of biopsy material currently plays no role in the diagnosis of transient CUGI, as little is known about gastrointestinal histology in these patients. The aim of this study was to investigate upper gastrointestinal histology in patients with well‐defined CUGI.Methods and results:  Consecutive patients suspected of CUGI were included prospectively and underwent a diagnostic work‐up existing of upper endoscopy, gastrointestinal tonometry and computed tomography (CT) or magnetic resonance (MR) angiography. Results were discussed in a multidisciplinary team and a consensus diagnosis was made. Endoscopic biopsy samples were taken from the descending duodenum, gastric antrum and corpus, and scored using the Sydney, Vienna, Chiu, Marsh and Operative Link for Gastritis Assessment (OLGA) classifications. Gastropathy was scored present or absent. Seventy‐nine patients were analysed in 8 months. CUGI was diagnosed in 41 patients (52%): 36 males, mean age 60 (17–86) years. Prevalence of gastropathy was significantly higher in patients with ischaemia (P = 0.025). No other differences were found between patients with and without ischaemia.Conclusions:  Histological examination of biopsy samples plays no definitive role in diagnosing CUGI, but the presence of histological signs of reactive gastropathy can be used to support the clinical diagnosis of ischaemia.
Immunohistochemical expression of p16INK4A protein as a helpful marker of a subset of potentially malignant oral epithelial lesions: study on a series with long‐term follow‐up
Authors: Montebugnoli Lucio , Cervellati Fabio , Cocchi Roberto , Farnedi Anna , Pennesi Maria Gabriella , Flamminio Federica , Foschini Maria Pia 
Published: October 2010

Montebugnoli L, Cervellati F, Cocchi R, Farnedi A, Pennesi M G, Flamminio F & Foschini M P (2010) Histopathology57, 528–534 Immunohistochemical expression of p16INK4A protein as a helpful marker of a subset of potentially malignant oral epithelial lesions: study on a series with long‐term follow‐upAim:  To examine a group of lesions that progressed to oral squamous cell carcinoma (OSCC) to determine whether p16INK4A expression is an early finding during malignant transformation, and whether immunohistochemical evaluation of p16INK4A is an appropriate prognostic marker.Methods and results:  Twenty cases of OSCC were investigated. All cases had had a biopsy on the same site as OSCC performed at least 1 year before OSCC (range 1–11 years; mean 3.15 ± 3.1 years). Twenty specimens from normal oral mucosa served as controls. p16INK4A expression was evaluated by immunohistochemical analysis and cases showing >5% of stained cells were defined as ‘positive’. All 20 control cases were negative for p16INK4A. Oral lesions were p16INK4A‐positive in nine cases and negative in 11. No significant relationship was found between p16INK4A positivity and the presence/absence of dysplasia. Among OSCC, nine tumours showed p16INK4A positivity and 11 showed negativity. A significant relationship (χ2 = 7.1; P < 0.01) was found between the presence/absence of p16INK4A staining in OSCC and the presence/absence of p16INK4A staining in lesions preceding OSCC.Conclusions:  p16INK4A immunohistochemistry has a potential role in detecting a subset of p16INK4A‐positive lesions with malignant potential.