bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data
Authors: Wang Penghao , Yang Pengyi , Arthur Jonathan , Yang Jean Yee Hwa 
Published: July 2010

Abstract
Motivation: Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identification of a protein is the critical first step in elucidating its biological function. Successful protein identification depends on various interrelated factors, including effective analysis of MS data generated in a proteomic experiment. This analysis comprises several stages, often combined in a pipeline or workflow. The first component of the analysis is known as spectra pre-processing. In this component, the raw data generated by the mass spectrometer is processed to eliminate noise and identify the mass-to-charge ratio (m/z) and intensity for the peaks in the spectrum corresponding to the presence of certain peptides or peptide fragments. Since all downstream analyses depend on the pre-processed data, effective pre-processing is critical to protein identification and characterization. There is a critical need for more robust pre-processing algorithms that perform well on tandem mass spectra under a variety of different conditions and can be easily integrated into sophisticated data analysis pipelines for practical wet-lab applications.
Result: We have developed a new pre-processing algorithm. Based on wavelet theory, our method uses a dynamic peak model to identify peaks. It is designed to be easily integrated into a complete proteomic analysis workflow. We compared the method with other available algorithms using a reference library of raw MS and tandem MS spectra with known protein composition information. Our pre-processing algorithm results in the identification of significantly more peptides and proteins in the downstream analysis for a given false discovery rate.
Availability: Software available at: http://www.maths.usyd.edu.au/u/penghao/index.html
Contact: penghao.wang@sydney.edu.au
Editing, validating and translating of SBGN maps
Authors: Czauderna Tobias , Klukas Christian , Schreiber Falk 
Published: July 2010

Abstract
Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable.
Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats.
Availability: SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files.
Contact: schreibe@ipk-gatersleben.de
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
Authors: Rialle Stéphanie , Felicori Liza , Dias-Lopes Camila , Pérès Sabine , El Atia Sanaâ , Thierry Alain R. , Amar Patrick , Molina Franck 
Published: July 2010

Abstract
Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks.
Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network.
Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/
Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Differentiating Arabidopsis Shoots from Leaves by Combined YABBY Activities
Authors: Sarojam Rajani , Sappl Pia G. , Goldshmidt Alexander , Efroni Idan , Floyd Sandra K. , Eshed Yuval , Bowman John L. 
Published: July 2010

AbstractIn seed plants, leaves are born on radial shoots, but unlike shoots, they are determinate dorsiventral organs made of flat lamina. YABBY genes are found only in seed plants and in all cases studied are expressed primarily in lateral organs and in a polar manner. Despite their simple expression, Arabidopsis thaliana plants lacking all YABBY gene activities have a wide range of morphological defects in all lateral organs as well as the shoot apical meristem (SAM). Here, we show that leaves lacking all YABBY activities are initiated as dorsiventral appendages but fail to properly activate lamina programs. In particular, the activation of most CINCINNATA-class TCP genes does not commence, SAM-specific programs are reactivated, and a marginal leaf domain is not established. Altered distribution of auxin signaling and the auxin efflux carrier PIN1, highly reduced venation, initiation of multiple cotyledons, and gradual loss of the SAM accompany these defects. We suggest that YABBY functions were recruited to mold modified shoot systems into flat plant appendages by translating organ polarity into lamina-specific programs that include marginal auxin flow and activation of a maturation schedule directing determinate growth.
The pharmacokinetics and safety of porfimer after repeated administration 30–45 days apart to patients undergoing photodynamic therapy
Authors: Pereira S. P. , Ayaru L. , Ackroyd R. , Mitton D. , Fullarton G. , Zammit M. , Grzebieniak Z. , Messmann H. , Ortner M.‐A. , Gao L. , Trinh M. M. , Spénard J. 
Published: July 2010

SummaryBackground  Porfimer is an intravenous (i.v.) injectable photosensitizing agent used in the photodynamic treatment of tumours and of high‐grade dysplasia in Barrett’s oesophagus.Aim  To assess the pharmacokinetics as well as the safety profiles of porfimer after a first and a second dose administered 30–45 days apart in patients undergoing photodynamic therapy.Methods  Nineteen patients (16 with cholangiocarcinoma) were enrolled. Porfimer sodium was administered by i.v. injection over 3–5 min. Blood samples were collected prior to starting i.v. drug injection and postdose at different time points after the first and second administrations.Results  Porfimer exposure values after the second administration were statistically higher than those observed after the first administration, suggesting a slight accumulation of porfimer following repeated administration. The apparent mean elimination half‐life of porfimer increased from 410 h after the first administration to 725 h after the second administration. The safety profiles of porfimer after a first and a second administration were similar and did not raise additional concern. Eight patients experienced nine serious adverse events. Only photosensitivity was deemed study‐drug related.Conclusion  Porfimer appears to display a safe and tolerable profile when used in patients requiring a second photodynamic therapy within 45 days.
The Patient Health Questionnaire 12 Somatic Symptom scale as a predictor of symptom severity and consulting behaviour in patients with irritable bowel syndrome and symptomatic diverticular disease
Authors: Spiller R. C. , Humes D. J. , Campbell E. , Hastings M. , Neal K. R. , Dukes G. E. , Whorwell P. J. 
Published: July 2010

SummaryBackground  Anxiety, depression and nongastrointestinal symptoms are often prominent in irritable bowel syndrome (IBS), but their relative value in patient management has not been quantitatively assessed. We modified the Patient Health Questionnaire 15 (PHQ‐15) by excluding three gastrointestinal items to create the PHQ‐12 Somatic Symptom (PHQ‐12 SS) scale.Aims  To compare the value of the PHQ‐12 SS scale with the Hospital Anxiety and Depression (HAD) scale in predicting symptoms and patient behaviour in IBS and diverticular disease.Methods  We compared 151 healthy volunteers (HV), 319 IBS patients and 296 patients with diverticular disease (DD), 113 asymptomatic [ASYMPDD] and 173 symptomatic DD (SYMPDD).Results  Patient Health Questionnaire 12 SS scores for IBS and SYMPDD were significantly higher than HV. Receiver–operator curves showed a PHQ‐12 SS >6, gave a sensitivity for IBS of 66.4% with a specificity of 94.7% and a positive likelihood ratio (PLR) = 13.2, significantly better than that associated with an HAD anxiety score >7, PLR = 3.0 and depression score >7 PLR = 6.5. PHQ‐12 SS correlated strongly with IBS severity scale and GP visits in both IBS and DD.Conclusion  The PHQ‐12 SS scale is a useful clinical tool which correlates with patient behaviour in both IBS and symptomatic DD.
ORIGINAL ARTICLE: Ultrasonographic evaluation of the femoral vein in anaesthetised infants and young children
Authors: Suk E. H. , Lee K.‐Y. , Kweon T. D. , Jang Y.‐H. , Bai S. J. 
Published: July 2010

SummaryWe investigated the cross‐sectional area of the femoral vein and its relationship to the femoral artery at two anatomical levels, in infants and children. Sixty‐six subjects were allocated to one of two groups: infants (< 1 year, n = 31) or children (1–6 years, n = 35). After induction of general anaesthesia, the femoral vein was evaluated by ultrasound with the patients’ legs at 30° and 60° of abduction and their hips externally rotated. In each position, measurements were taken at the level of the inguinal crease and 1 cm below the crease. Hip rotation with 60° leg abduction decreased femoral artery overlap at the level of the inguinal crease in both infants (p = 0.013) and children (p = 0.003). Thus, the optimal place for femoral vein cannulation in paediatric patients seems to be at the level of the inguinal crease with 60° leg abduction and external hip rotation.
ORIGINAL ARTICLE: Comparison of guided insertion of the LMA ProSeal™ vs the i‐gel™
Authors: Gasteiger L. , Brimacombe J. , Perkhofer D. , Kaufmann M. , Keller C. 
Published: July 2010

SummaryIn a randomised, non‐crossover study, we tested the hypothesis that the ease of insertion using a duodenal tube guided insertion technique and the oropharyngeal leak pressure differ between the LMA ProSeal™ and the i‐gel™ in non‐paralysed, anesthetised female subjects. One hundred and fifty‐two females aged 19–70 years were studied. Insertion success rate, insertion time and oropharyngeal leak pressure were measured. First attempt and overall insertion success were similar (LMA ProSeal, 75/76 (99%) and 76/76 (100%); i‐gel 73/75 (97%) and 75 (100%), respectively). Mean (SD) insertion times were similar (LMA ProSeal, 40 (16) s; i‐gel 43 (21) s). Mean oropharyngeal leak pressure was 7 cmH2O higher with the LMA ProSeal (p < 0.0001). Insertion of the LMA ProSeal and i‐gel is similarly easy using a duodenal tube guided technique, but the LMA ProSeal forms a more effective seal for ventilation.
Advances in understanding the aetiology of atypical Haemolytic Uraemic Syndrome
Authors: Sánchez‐Corral Pilar , Melgosa Marta 
Published: July 2010

SummaryAtypical Haemolytic Uraemic Syndrome (aHUS) is a thrombotic microangiopathy that often provokes irreversible renal damage and post‐transplantation recurrence. Studies performed during the last decade have shown that 50–60% of aHUS patients present genetic or acquired defects in the complement system that enhance the initial endothelial damage and favour disease development. This review analyses the complement proteins and processes that are disturbed in aHUS patients, and outlines the relevance of a prompt genetic/molecular diagnosis for improving clinical management and prognosis.
Phase II trial of zanolimumab (HuMax‐CD4) in relapsed or refractory non‐cutaneous peripheral T cell lymphoma
Authors: D’Amore Francesco , Radford John , Relander Thomas , Jerkeman Mats , Tilly Hervé , Österborg Anders , Morschhauser Franck , Gramatzki Martin , Dreyling Martin , Bang Bo , Hagberg Hans 
Published: July 2010

SummaryThe efficacy and safety of zanolimumab (HuMax‐CD4) in patients with relapsed or refractory peripheral T Cell lymphoma (PTCL) was evaluated. Twenty‐one adult patients with relapsed or refractory CD4+ PTCL of non‐cutaneous type (angioimmunoblastic T cell lymphoma (AITL) n = 9, PTCL‐not otherwise specified (NOS) n = 7, anaplastic large cell lymphoma (ALCL) n = 4 and enteropathy type T cell lymphoma n = 1) were treated in a single‐arm multi‐centre study, with weekly intravenous infusions of zanolimumab 980 mg for 12 weeks. Median age was 69 years (range 26–85). Seventeen of the patients had advanced stage disease (Ann Arbor stages III–IV). Objective tumour responses were obtained in 24% of the patients with two complete responses unconfirmed (CRu) and three partial responses (PR). One of the CRus lasted more than 252 d. Responses were obtained in different PTCL entities: AITL (n = 3), ALCL (n = 1) and PTCL‐NOS (n = 1). In general, the trial drug was well tolerated with no major toxicity. Zanolimumab at a dose of 980 mg weekly demonstrated clinical activity and an acceptable safety profile in this poor‐prognosis patient population, suggesting that the potential benefit combining zanolimumab with standard chemotherapy in the treatment of PTCL should be investigated.
Sleep problems and daytime tiredness in Finnish preschool‐aged children‐a community survey
Authors: Simola P. , Niskakangas M. , Liukkonen K. , Virkkula P. , Pitkäranta A. , Kirjavainen T. , Aronen E. T. 
Published: July 2010

AbstractBackground  Sleep is important to the well‐being and development of children. Specially, small children are vulnerable to the effects of inadequate sleep. However, not much is known about the frequency of all types of sleep problems and daytime tiredness in preschool‐aged children.Objective  To evaluate the prevalence of a wide spectrum of sleep problems, daytime tiredness and associations between these in 3‐ to 6‐year‐old Finnish children.Methods  A population‐based study where parents of 3‐ to 6‐year‐old children (n= 904) living in Helsinki filled in the Sleep Disturbance Scale for Children (SDSC).Results  Of the children, 45% had at least one sleep‐related problem occurring at least three times a week: 14.1% were unwilling to go to bed, 10.2% had difficulties in falling asleep, 10.2% had bruxism, 6.4% sleep talking, 2.1% sleep terrors, 8.2% had sleep‐related breathing problem, 11.2% had excessive sweating while falling asleep and 12.9% excessive sweating during sleep. Age and gender were related to phenotype of the sleeping problems. In multiple regression analysis, the difficulties in initiating and maintaining sleep were most strongly associated with tiredness in the morning and during the day.Conclusions  Different types of sleep problems are frequent in preschool‐aged children. Poor sleep quality is associated with morning and daytime tiredness. In screening for sleep problems in children, attention should be paid not only to sleep amount but also to sleep quality.
The impact of eating habits on anthropometric characteristics in French primary school children
Authors: Isacco L. , Lazaar N. , Ratel S. , Thivel D. , Aucouturier J. , Doré E. , Meyer M. , Duché P. 
Published: July 2010

AbstractBackground  Obesity is increasing worldwide, reaching alarming proportions. Eating habits have changed over time and nowadays children and adolescents' environment favours the adoption of unhealthy eating behaviours leading to metabolic impairment.Objective  To explore the impact of eating risk factors and their cumulative effect on anthropometric characteristics in French primary school children.Methods  A total of 278 healthy French children (7.50 ± 0.67 years old) and their legal representatives agreed to take part in this study. Parents were asked to fill in an eating habits clinical questionnaire with questions about skipping breakfast, snacking between meals, eating in front of the TV and sugar‐sweetened beverage consumption. On the basis of the answers, children were classified into four categories as a function of the number of eating risk factors they presented. Body mass index (BMI), the sum of four skinfolds (Σ4 skinfolds: tricipital, bicipital, sub‐scapular and supra‐iliac) and waist circumference (WC) were measured. BMI was transformed into z‐BMI for each child.Results  anova and unpaired t‐test provided significantly higher z‐BMI, Σ4 skinfolds and WC in children who were used to skipping breakfast, snacking, watching TV while eating and consuming sugar‐sweetened beverages. The more children accumulated eating risk factors, the higher were their z‐BMI, Σ4 skinfolds and WC (manova: P < 0.001).Conclusions  Eating habits appear to be associated with anthropometric characteristics in French primary school children. Anthropometric values (z‐BMI, Σ4 skinfolds and WC) increased with the number of eating risk factors they presented.
Involvement of T helper type 17 and regulatory T cell activity in tumour immunology of bladder carcinoma
Authors: Chi L J , Lu H T , Li G L , Wang X M , Su Y , Xu W H , Shen B Z 
Published: July 2010

Summary
T helper type 17 (Th17) and regulatory T cells (Treg) play an important role in the pathogenesis of inflammation and autoimmune disorders. Recent studies have suggested that they also had an impact on tumour immunology. However, the relationship between Th17 and Treg cells in the pathogenesis of bladder carcinoma is still unclear. Flow cytometry was used to analyse the numbers, phenotype and cytokine production of Th17 cells in peripheral blood and tumour tissue from bladder carcinoma patients, in parallel with analysis of Treg cells. The suppressor capacity of Treg and the potential effects of interleukin (IL)-2 on the differentiation of Th17 and Treg cells in vitro were studied in a T cell stimulation and suppression assays. The results were as follows: Th17 cells were enriched in the tumours of patients with bladder carcinoma compared with the peripheral blood of patients and controls; patients with bladder carcinoma had a higher proportion of Treg cells in peripheral blood compared with healthy controls and nearly all patients examined showed a relative enrichment of tumour-infiltrating Treg with respect to peripheral blood; there appeared to be an inverse relationship between tumour-infiltrating Th17 and Treg cells; IL-2 could convert tumour-infiltrating Treg cells cultured in the presence of the autologous irradiated CD3– fraction into Th17 cells, down-regulate forkhead box P2 expression and suppressive capacity of Treg cells. This study is the first to define the frequency and characteristics of Th17 cells in bladder carcinoma. We suggest that the balance between Th17 and Treg cells may be involved in the development or progression of bladder carcinoma.
NOD2polymorphisms in clinical phenotypes of common variable immunodeficiency disorders
Authors: Packwood K , Drewe E , Staples E , Webster D , Witte T , Litzman J , Egner W , Sargur R , Sewell W , Lopez-Granados E , Seneviratne S L , Powell R J , Ferry B L , Chapel H M 
Published: July 2010

SummaryCommon variable immunodeficiency disorders (CVIDs) are a heterogeneous group of diseases characterized by hypogammaglobulinaemia and consequent susceptibility to infection. CVID patients commonly develop a variety of additional manifestations for which the causative factors are not fully understood. Two such manifestations are granulomatous disease and enteropathy. Because the ability to predict complications would aid clinical management, we continue to search for possible disease modifier genes. NOD2 acts a microbial sensor and is involved in proinflammatory signalling. Particular mutations of the NOD2 gene are associated with Crohn's disease including gly908arg, leu1007finsc and arg702trp polymorphisms. We hypothesized that NOD2 polymorphisms may be a disease modifier gene towards an enteropathic or granulomatous phenotype within CVIDs. Sequence-specific primers returned genotypes for 285 CVID patients from centres across the United Kingdom and Europe. We present the frequencies of the different phenotypes of patients within our international cohort. Arg702trp polymorphisms were significantly less frequent than wild-type (WT) (P = 0·038) among international CVID patients with splenomegaly. Gly908arg polymorphisms were more prevalent than WT in UK patients with autoimmune disorders (P = 0·049) or enteropathy (P = 0·049). NOD2 polymorphisms were not more prevalent than WT in CVID patients with clinical phenotypes of granulomata. UK allele frequencies of 0·014, 0·056 and 0·026 were found for gly908arg, arg702trp and leu1007finsc NOD2 polymorphisms, respectively. These do not differ significantly from UK immunocompetent controls confirming, as expected, that in addition these NOD2 polymorphisms do not confer susceptibility to CVIDs per se.
Increased programmed death-ligand-1 expression in human gastric epithelial cells inHelicobacter pyloriinfection
Authors: Wu Y-Y , Lin C-W , Cheng K-S , Lin C , Wang Y-M , Lin I-T , Chou Y-H , Hsu P-N 
Published: July 2010

SummaryB7-H1 [programmed death-ligand-1 (PD-L1)] is a B7-family member that binds to programmed death-1 (PD-1). Recently, deficiency of PD-L1 has been demonstrated to result in accelerated gastric epithelial cell damage in gastritis, and PD-L1 is suggested to play a critical role in regulating T cell homeostasis. Here, we aimed to gain more insight into gastric PD-L1 expression, regulation and function during Helicobacter pylori infection. PD-L1 expression in human gastric epithelial cells was analysed using Western blotting, quantitative polymerase chain reaction and fluorescence activated cell sorter analysis. Furthermore, co-culture experiments of human gastric epithelial cells with primary human T cells or Jurkat T cells were conducted. PD-L1 expression in primary human gastric epithelial cells was strongly enhanced by H. pylori infection and activated T cells, and augmented markedly by further stimulation with interferon-γ or tumour necrosis factor-α. Moreover, PD-L1 expression in gastric epithelial cells significantly induced apoptosis of T cells. Our results indicate that a novel bidirectional interaction between human gastric epithelial cells and lymphocytes modulates PD-L1 expression in human gastric epithelial cells, contributing to the unique immunological properties of the stomach.