bluuebunny/crossref_metadata_2025 huggingface dataset:
Contributing Factors to Aggressive Behaviors in High School Students in Turkey
Authors: Kaya Fadime , Bilgin Hulya , Singer Mark I.
Published: August 2011

Violence among young people is an important public health topic as a universal problem. One of the recent issues concerning both the media and parents is the aggressive behavior among the high school students in Istanbul and the worldwide. The aim of this study was to investigate the types and rates of aggressive behavior and the contributing factors to this behavior among high school students. Sample was composed of 805 students of 14–18 ages attending five high schools in Istanbul. The most common aggressive behavior among the students was found to be “beating others,” 34.5% ( n = 278). Past experiences of violence of high school students (direct exposure to violence/witnessing violence/exposure to/witnessing attack with knife/gun) were determined as the most contributing factor to aggressive behavior. The present study investigated the nature of violent behaviors and associations between violent behaviors and contributing factors among high school students from Turkey.
Vibration control of Timoshenko beam traversed by moving vehicle using optimized tuned mass damper
Authors: Moghaddas Mahsa , Esmailzadeh Ebrahim , Sedaghati Ramin , Khosravi Peyman
Published: August 2011

The dynamic behavior of a combined bridge–vehicle system in which the bridge is modeled as a Timoshenko beam and the vehicle as a half-car planar model is investigated using the finite element method. The governing equations of motion of the Timoshenko beam with the attached tuned mass damper (TMD) traversed by a moving vehicle are obtained. Adesign optimization algorithm is developed in which the analysis module based on the derived finite element formulation has been combined with the optimization module using the sequential programming technique. The objective is to determine the optimum values of the parameters (frequency and damping ratios) of a TMD, in order to minimize the maximum frequency response of the beam midspan when traversed by a moving vehicle. Results obtained illustrate that by attaching an optimally TMD to the Timoshenko beam a significantly faster vibration control can be achieved.
Analysing the dynamic response of a rotor system under uncertain parameters by polynomial chaos expansion
Authors: Didier Jérôme , Faverjon Béatrice , Sinou Jean-Jacques
Published: August 2011

In this paper, the quantification of uncertainty effects on response variability in rotor systems is investigated. To avoid the use of Monte Carlo simulation (MCS), one of the most straightforward but computationally expensive tools, an alternative procedure is proposed. MCS builds statistics from responses obtained from sampling uncertain inputs by using a large number of runs. However, the method proposed here is based on the stochastic finite element method using polynomial chaos expansion. The efficiency and robustness of the method proposed is demonstrated through different numerical simulations in order to analyse the random response against uncertain parameters and random excitation to assess its accuracy and calculation time.
Molecular characterization and regulation of the angiotensin-converting enzyme type 2/Angiotensin-(1-7)/MAS receptor axis during the ovulation process in cattle
Authors: Tonellotto dos Santos Joabel , Ferreira Rogério , Gasperin Bernardo Garziera , Siqueira Lucas Carvalho , de Oliveira João Francisco , Santos Robson AS , Reis Adelina M , Gonçalves Paulo Bayard
Published: August 2011

The objective of this study was to characterize the profiles of Ang-(1-7), MAS receptor, ACE2, NEP and PEP during the ovulatory process in cattle. For this study, 40 synchronized cows with follicular diameter ≥ 12 mm were ovariectomized at different time-points (0, 3, 6, 12 and 24 h) after i.m. application of gonadotropin-releasing hormone (GnRH) to induce a luteinizing hormone surge. Follicular fluid was collected for measuring Ang-(1-7) by radioimmunoassay. Theca and granulosa cells were isolated from the preovulatory follicles to evaluate the gene expression of MAS receptor, ACE2, NEP and PEP by qRT-PCR assay. Cross-contamination between theca and granulosa cells was tested by RT-PCR to detect cytochrome P450 aromatase (CYP19A1) and 17α-hydroxylase (CYP17A1) mRNA. Ang-(1-7) levels were constant until 12 h and then increased ( p < 0.05) at 24 h after GnRH. Messenger RNA expression of MAS, ACE2, NEP and PEP was detected in theca and granulosa cells at all time-points after GnRH. In granulosa cells, ACE2, NEP and PEP were differentially expressed after GnRH treatment ( p < 0.05). In conclusion, the Ang-(1-7), MAS receptor, ACE2, NEP and PEP profiles in preovulatory follicles indicate that Ang-(1-7) plays a role in the regulation of the ovulatory process in cattle.
Is there a role of the local tissue RAS in the regulation of physiologic and pathophysiologic conditions in the reproductive tract?
Authors: Schwentner Lukas , Wöckel Achim , Herr Daniel , Wulff Christine
Published: August 2011

The renin–angiotensin system is well known as a systemic endocrine pathway that regulates blood pressure and salt–water metabolism. In addition to the systemic renin–angiotensin system there is evidence in different species for the presence of a local tissue renin–angiotensin system, which allows local production of the bioactive peptides angiotensin II and angiotensin (1-7). The local renin–angiotensin system has been found in a variety of tissues including tissue of the human reproductive tract. Thus, it was suspected that it may have important functions in the local hormonal microenvironment. Here, a systematic literature search was undertaken to review whether there is evidence for regulatory functions of the local tissue renin–angiotensin system in the human reproductive tract under physiological and pathological conditions.
The Mediumship of Listening: Notes on Sound in the Silent Arts
Authors: Toop David
Published: August 2011

This article is a series of excerpts from the author’s most recent book Sinister Resonance. It begins with the premise that sound is a haunting, a ghost, a presence whose location in space is ambiguous and whose existence in time is transitory. The intangibility of sound is uncanny – a phenomenal presence both in the head, at its point of source and all around, and never entirely distinct from auditory hallucinations. The close listener is like a medium who draws out substance from that which is not entirely there. The history of listening must be constructed from narratives of myth and fiction, silent arts such as painting, the resonance of architecture, auditory artefacts and nature. In such contexts, sound often functions as a metaphor for mystical revelation, instability, forbidden desires, disorder, formlessness, the unknown, unconscious and extra-human, a representation of immaterial worlds. Threaded through is Marcel Duchamp’s curious observation – ‘One can look at seeing but one can’t hear hearing’ – and his concept of the infra-thin, those human experiences so fugitive that they exist only in the imaginative absences of perception.
The Sound of Old Media
Authors: Shin Seongah
Published: August 2011

In the field of hand-made film, sound and music are a limited part of the media due to the character of the medium; there are only a few sound tracks with poor quality. Hand-made film may be considered ‘old media’ or ‘traditional media’ that are not as popular today due to the spread of digital technologies. However, the limited character of this medium and the low quality of the sound tracks become a very attractive and creative limitation for the author’s recent works. She discusses two recent works for experimental film and sound, The Thin Black Line (2007) and flowing_water (2008) which explore how the limitation of media allows expansion of the sonic and visual arts.
Do matters of concern matter? Bringing issues back to participation
Authors: Leino Helena , Laine Markus
Published: August 2011

The objective of our article is twofold. First, we claim that the theoretical planning discussion dealing with public participation has forgotten one basic principle, namely that the people are taking part in the planning process because they are interested in a particular issue. There is a need for new conceptual approaches in participatory research which carry the discussion first towards the issues, then to the structures of participation. For this reason, we have combined practice-oriented policy analysis with the recent discussion of issue politics. Second, we implement the key propositions of the theoretical debate in an empirical case. The aim is to indicate how the trajectory of the issue, as well as its continuities and discontinuities, develop in diverse ways in different civic forums. We claim that this perspective provides more information for researchers, civil servants and citizens about the logic of participatory practice.
Linear Models with Outliers: Choosing between Conditional-Mean and Conditional-Median Methods
Authors: Harden Jeffrey J. , Desmarais Bruce A.
Published: August 2011

State politics researchers commonly employ ordinary least squares (OLS) regression or one of its variants to test linear hypotheses. However, OLS is easily influenced by outliers and thus can produce misleading results when the error term distribution has heavy tails. Here we demonstrate that median regression (MR), an alternative to OLS that conditions the median of the dependent variable (rather than the mean) on the independent variables, can be a solution to this problem. Then we propose and validate a hypothesis test that applied researchers can use to select between OLS and MR in a given sample of data. Finally, we present two examples from state politics research in which (1) the test selects MR over OLS and (2) differences in results between the two methods could lead to different substantive inferences. We conclude that MR and the test we propose can improve linear models in state politics research.
Lung Cancer Survival With Herbal Medicine and Vitamins in a Whole-Systems Approach
Authors: McCulloch Michael , Broffman Michael , van der Laan Mark , Hubbard Alan , Kushi Lawrence , Kramer Alan , Gao Jin , Colford John M.
Published: August 2011

Complementary and alternative medicines are used by up to 48% of lung cancer patients but have seen little formal assessment of survival efficacy. In this 10-year retrospective survival study, the authors investigated Pan-Asian medicine + vitamins (PAM+V) therapy in a consecutive case series of all non-small-cell lung cancer patients (n = 239) presenting at a San Francisco Bay Area Chinese medicine center (Pine Street Clinic). They compared short-term treatment lasting the duration of chemotherapy/radiotherapy with long-term therapy continuing beyond conventional therapy. They also compared PAM+V plus conventional therapy with conventional therapy alone, using concurrent controls from the Kaiser Permanente Northern California and California Cancer Registries. They adjusted for confounding with Kaplan-Meier, Cox regression, and newer methods – propensity score and marginal structural models (MSMs), which when analyzing data from observational studies or clinical practice records can provide results comparable with randomized trials. Long-term use of PAM+V beyond completion of chemotherapy reduced stage IIIB deaths by 83% and stage IV by 72% compared with short-term use only for the duration of chemotherapy. Long-term PAM+V combined with conventional therapy reduced stage IIIA deaths by 46%, stage IIIB by 62%, and stage IV by 69% compared with conventional therapy alone. Survival rates for stage IV patients treated with PAM+V were 82% at 1 year, 68% at 2 years, and 14% at 5 years. PAM+V combined with conventional therapy improved survival in stages IIIA, IIIB, and IV, compared with conventional therapy alone. Prospective trials using PAM+V with conventional therapy for lung cancer patients are justified.
Being a Good Daughter and Sister
Authors: Leverentz Andrea
Published: August 2011

Family has long been central to our understandings of offending and desistance. However, in research on adult offenders or prisoners, the focus is more often on romantic partners, children, and peers than on families of origin. This article underscores the continuing importance of families of origin in the reentry and desistance processes of urban female African American former prisoners and probationers. The author demonstrates that these relationships play an important part in women’s identities, even when they often come into direct conflict with desistance efforts. Thus, these women must learn to balance sometimes-contradictory messages of their obligations within their family and their emerging identities as desisting former offenders.
Morphological study of the proximal boundary of the flexor retinaculum and of its constituent parts
Authors: Won H.-S. , Han S.-H. , Oh C.-S. , Chung I.-H. , Suh J.-S. , Lim S. Y.
Published: August 2011

The proximal boundary of the flexor retinaculum is not readily demarcated, and previous reports of three distinct regions of the flexor retinaculum were not consistent with the authors’ experience. This study was undertaken to clarify the proximal boundary and the constituent parts of the flexor retinaculum. A total of 56 cadaveric wrists were used in the study. The proximal boundary of the flexor retinaculum was identified by a change in thickness and colour of the longitudinally sectioned surface of the continuous membranous sheet of the flexor retinaculum and antebrachial fascia. Steel wires were placed on the proximal and distal boundaries, and anteroposterior radiographic images were taken. MRI was carried out before dissection or serial section. The locations of the proximal and distal boundaries of the flexor retinaculum varied. The flexor retinaculum was comprised of two parts, which were distinguishable by thickness and transparency. These two parts were also identified on MR images and by light microscopy.
Extracellular matrix structure and nano-mechanics determine megakaryocyte function
Authors: Malara Alessandro , Gruppi Cristian , Pallotta Isabella , Spedden Elise , Tenni Ruggero , Raspanti Mario , Kaplan David , Tira Maria Enrica , Staii Cristian , Balduini Alessandra
Published: August 2011

Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1–dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.
A randomized trial comparing standard versus high-dose daunorubicin induction in patients with acute myeloid leukemia
Authors: Lee Je-Hwan , Joo Young-Don , Kim Hawk , Bae Sung Hwa , Kim Min Kyoung , Zang Dae Young , Lee Jung-Lim , Lee Gyeong Won , Lee Jung-Hee , Park Jae-Hoo , Kim Dae-Young , Lee Won-Sik , Ryoo Hun Mo , Hyun Myung Soo , Kim Hyo Jung , Min Young Joo , Jang Yae-Eun , Lee Kyoo-Hyung ,   for the Cooperative Study Group A for Hematology
Published: August 2011

We conducted a phase 3 randomized trial comparing 2 different doses of daunorubicin as induction chemotherapy in young adults (60 years of age or younger) with acute myeloid leukemia (AML). Of 383 patients who were analyzed, 189 received standard-dose daunorubicin (SD-DN, 45 mg/m2 per day times 3 days) and 194 received high-dose daunorubicin (HD-DN, 90 mg/m2 per day times 3 days) in addition to cytarabine (200 mg/m2 per day times 7 days) to induce complete remission (CR). The CR rates were 72.0% in the SD-DN arm and 82.5% in the HD-DN arm (P = .014). At a median follow-up of 52.6 months, overall (OS) and event-free (EFS) survival were higher in the HD-DN arm than in the SD-DN arm (OS, 46.8% vs 34.6%, P = .030; EFS, 40.8% vs 28.4%, P = .030). Differences in CR rate and both OS and EFS remained significant after adjusting for other variables (CR, hazard ratio [HR], 1.802, P = .024; OS, HR, 0.739, P = .032; EFS, HR, 0.774, P = .048). The survival benefits of HD-DN therapy were evident principally in patients with intermediate-risk cytogenetic features. The toxicity profiles were similar in the 2 arms. In conclusion, HD-DN improved both the CR rate and survival duration compared with SD-DN in young adults with AML. This study is registered at www.clinicaltrials.gov as #NCT00474006.
The emphysematous lung is abnormally sensitive to TRAIL-mediated apoptosis
Authors: Morissette Mathieu C , Parent Julie , Milot Julie
Published: August 2011

Background

Alveolar apoptosis is increased in the emphysematous lung. However, mechanisms involved are not fully understood. Recently, we demonstrated that levels of TRAIL receptor 1 and 2, levels of p53, and Bax/Bcl-xL ratio were elevated in the lung of subjects with emphysema, despite smoking cessation. Thus, we postulate that due to chronic pulmonary oxidative stress, the emphysematous lung would be abnormally sensitive to TRAIL-mediated apoptosis.

Methodology

A549 cells were exposed to rTRAIL, cigarette smoke extract, and/or H2O2 prior to caspase-3 activity measurement and annexin V staining assessment. In addition, freshly resected lung samples were obtained from non-emphysematous and emphysematous subjects and exposed ex vivo to rTRAIL for up to 18 hours. Lung samples were harvested and levels of active caspase-3 and caspase-8 were measured from tissue lysates.

Results

Both cigarette smoke extract and H2O2 were able to sensitize A549 cells to TRAIL-mediated apoptosis. Moreover, following exposure to rTRAIL, caspase-3 and -8 were activated in lung explants from emphysematous subjects while being decreased in lung explants from non-emphysematous subjects.

Significance of the study

Alveolar sensitivity to TRAIL-mediated apoptosis is strongly increased in the emphysematous lung due to the presence of oxidative stress. This might be a new mechanism leading to increased alveolar apoptosis and persistent alveolar destruction following smoking cessation.
In vitro activation and enzyme kinetic analysis of recombinant midgut serine proteases from the Dengue vector mosquito Aedes aegypti
Authors: Rascón Alberto A , Gearin Johnathon , Isoe Jun , Miesfeld Roger L
Published: August 2011

Background

The major Dengue virus vector Aedes aegypti requires nutrients obtained from blood meal proteins to complete the gonotrophic cycle. Although bioinformatic analyses of Ae. aegypti midgut serine proteases have provided evolutionary insights, very little is known about the biochemical activity of these digestive enzymes.

Results

We used peptide specific antibodies to show that midgut serine proteases are expressed as zymogen precursors, which are cleaved to the mature form after blood feeding. Since midgut protein levels are insufficient to purify active proteases directly from blood fed mosquitoes, we engineered recombinant proteins encoding a heterologous enterokinase cleavage site to permit generation of the bona fide mature form of four midgut serine proteases (AaET, AaLT, AaSPVI, AaSPVII) for enzyme kinetic analysis. Cleavage of the chromogenic trypsin substrate BApNA showed that AaET has a catalytic efficiency (kcat/KM) that is ~30 times higher than bovine trypsin, and ~2-3 times higher than AaSPVI and AaSPVII, however, AaLT does not cleave BApNA. To measure the enzyme activities of the mosquito midgut proteases using natural substrates, we developed a quantitative cleavage assay based on cleavage of albumin and hemoglobin proteins. These studies revealed that the recombinant AaLT enzyme was indeed catalytically active, and cleaved albumin and hemoglobin with equivalent efficiency to that of AaET, AaSPVI, and AaSPVII. Structural modeling of the AaLT and AaSPVI mature forms indicated that AaLT is most similar to serine collagenases, whereas AaSPVI appears to be a classic trypsin.

Conclusions

These data show that in vitro activation of recombinant serine proteases containing a heterologous enterokinase cleavage site can be used to investigate enzyme kinetics and substrate cleavage properties of biologically important mosquito proteases.
Classifying short genomic fragments from novel lineages using composition and homology
Authors: Parks Donovan H , MacDonald Norman J , Beiko Robert G
Published: August 2011

Background

The assignment of taxonomic attributions to DNA fragments recovered directly from the environment is a vital step in metagenomic data analysis. Assignments can be made using rank-specific classifiers, which assign reads to taxonomic labels from a predetermined level such as named species or strain, or rank-flexible classifiers, which choose an appropriate taxonomic rank for each sequence in a data set. The choice of rank typically depends on the optimal model for a given sequence and on the breadth of taxonomic groups seen in a set of close-to-optimal models. Homology-based (e.g., LCA) and composition-based (e.g., PhyloPythia, TACOA) rank-flexible classifiers have been proposed, but there is at present no hybrid approach that utilizes both homology and composition.

Results

We first develop a hybrid, rank-specific classifier based on BLAST and Naïve Bayes (NB) that has comparable accuracy and a faster running time than the current best approach, PhymmBL. By substituting LCA for BLAST or allowing the inclusion of suboptimal NB models, we obtain a rank-flexible classifier. This hybrid classifier outperforms established rank-flexible approaches on simulated metagenomic fragments of length 200 bp to 1000 bp and is able to assign taxonomic attributions to a subset of sequences with few misclassifications. We then demonstrate the performance of different classifiers on an enhanced biological phosphorous removal metagenome, illustrating the advantages of rank-flexible classifiers when representative genomes are absent from the set of reference genomes. Application to a glacier ice metagenome demonstrates that similar taxonomic profiles are obtained across a set of classifiers which are increasingly conservative in their classification.

Conclusions

Our NB-based classification scheme is faster than the current best composition-based algorithm, Phymm, while providing equally accurate predictions. The rank-flexible variant of NB, which we term ε-NB, is complementary to LCA and can be combined with it to yield conservative prediction sets of very high confidence. The simple parameterization of LCA and ε-NB allows for tuning of the balance between more predictions and increased precision, allowing the user to account for the sensitivity of downstream analyses to misclassified or unclassified sequences.
Development of a classification scheme for disease-related enzyme information
Authors: Söhngen Carola , Chang Antje , Schomburg Dietmar
Published: August 2011

Background

BRENDA (BR aunschweig EN zyme DA tabase, http://www.brenda-enzymes.org) is a major resource for enzyme related information. First and foremost, it provides data which are manually curated from the primary literature. DRENDA (D isease RE lated EN zyme information DA tabase) complements BRENDA with a focus on the automatic search and categorization of enzyme and disease related information from title and abstracts of primary publications. In a two-step procedure DRENDA makes use of text mining and machine learning methods.

Results

Currently enzyme and disease related references are biannually updated as part of the standard BRENDA update. 910,897 relations of EC-numbers and diseases were extracted from titles or abstracts and are included in the second release in 2010. The enzyme and disease entity recognition has been successfully enhanced by a further relation classification via machine learning. The classification step has been evaluated by a 5-fold cross validation and achieves an F1 score between 0.802 ± 0.032 and 0.738 ± 0.033 depending on the categories and pre-processing procedures. In the eventual DRENDA content every category reaches a classification specificity of at least 96.7% and a precision that ranges from 86-98% in the highest confidence level, and 64-83% for the smallest confidence level associated with higher recall.

Conclusions

The DRENDA processing chain analyses PubMed, locates references with disease-related information on enzymes and categorises their focus according to the categories
causal interaction
,
therapeutic application
,
diagnostic usage
and
ongoing research
. The categorisation gives an impression on the focus of the located references. Thus, the relation categorisation can facilitate orientation within the rapidly growing number of references with impact on diseases and enzymes. The DRENDA information is available as additional information in BRENDA.
Deploying mutation impact text-mining software with the SADI Semantic Web Services framework
Authors: Riazanov Alexandre , Laurila Jonas Bergman , Baker Christopher JO
Published: August 2011

Background

Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining for mutation impacts resulted in (i) the development of a GATE-based pipeline that mines texts for information about impacts of mutations on proteins, (ii) the population of this information into our OWL DL mutation impact ontology, and (iii) establishing an experimental semantic database for storing the results of text mining.

Results

This article explores the possibility of using the SADI framework as a medium for publishing our mutation impact software and data. SADI is a set of conventions for creating web services with semantic descriptions that facilitate automatic discovery and orchestration. We describe a case study exploring and demonstrating the utility of the SADI approach in our context. We describe several SADI services we created based on our text mining API and data, and demonstrate how they can be used in a number of biologically meaningful scenarios through a SPARQL interface (SHARE) to SADI services. In all cases we pay special attention to the integration of mutation impact services with external SADI services providing information about related biological entities, such as proteins, pathways, and drugs.

Conclusion

We have identified that SADI provides an effective way of exposing our mutation impact data such that it can be leveraged by a variety of stakeholders in multiple use cases. The solutions we provide for our use cases can serve as examples to potential SADI adopters trying to solve similar integration problems.
Transcription analysis on response of swine lung to H1N1 swine influenza virus
Authors: Li Yongtao , Zhou Hongbo , Wen Zhibin , Wu Shujuan , Huang Canhui , Jia Guangmin , Chen Huanchun , Jin Meilin
Published: August 2011

Background

As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mortality in pigs. Nevertheless, the systematical host response of pigs to swine influenza virus infection remains largely unknown. To explore it, a time-course gene expression profiling was performed for comprehensive analysis of the global host response induced by H1N1 swine influenza virus in pigs.

Results

At the early stage of H1N1 swine virus infection, pigs were suffering mild respiratory symptoms and pathological changes. A total of 268 porcine genes showing differential expression (DE) after inoculation were identified to compare with the controls on day 3 post infection (PID) (Fold change ≥ 2, p < 0.05). The DE genes were involved in many vital functional classes, mainly including signal transduction, immune response, inflammatory response, cell adhesion and cell-cell signalling. Noticeably, the genes associated with immune and inflammatory response showed highly overexpressed. Through the pathway analysis, the significant pathways mainly concerned with Cell adhesion molecules, Cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway and MAPK signaling pathway, suggesting that the host took different strategies to activate these pathways so as to prevent virus infections at the early stage. However, on PID 7, the predominant function classes of DE genes included signal transduction, metabolism, transcription, development and transport. Furthermore, the most significant pathways switched to PPAR signaling pathway and complement and coagulation cascades, showing that the host might start to repair excessive tissue damage by anti-inflammatory functions. These results on PID 7 demonstrated beneficial turnover for host to prevent excessive inflammatory damage and recover the normal state by activating these clusters of genes.

Conclusions

This study shows how the target organ responds to H1N1 swine influenza virus infection in pigs. The observed gene expression profile could help to screen the potential host agents for reducing the prevalence of swine influenza virus and further understand the molecular pathogenesis associated with H1N1 infection in pigs.
Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis
Authors: Hinse Dennis , Vollmer Tanja , Rückert Christian , Blom Jochen , Kalinowski Jörn , Knabbe Cornelius , Dreier Jens
Published: August 2011

Background

Streptococcus gallolyticus subsp. gallolyticus is an important causative agent of infectious endocarditis, while the pathogenicity of this species is widely unclear. To gain insight into the pathomechanisms and the underlying genetic elements for lateral gene transfer, we sequenced the entire genome of this pathogen.

Results

We sequenced the whole genome of S. gallolyticus subsp. gallolyticus strain ATCC BAA-2069, consisting of a 2,356,444 bp circular DNA molecule with a G+C-content of 37.65% and a novel 20,765 bp plasmid designated as pSGG1. Bioinformatic analysis predicted 2,309 ORFs and the presence of 80 tRNAs and 21 rRNAs in the chromosome. Furthermore, 21 ORFs were detected on the plasmid pSGG1, including tetracycline resistance genes telL and tet(O/W/32/O). Screening of 41 S. gallolyticus subsp. gallolyticus isolates revealed one plasmid (pSGG2) homologous to pSGG1. We further predicted 21 surface proteins containing the cell wall-sorting motif LPxTG, which were shown to play a functional role in the adhesion of bacteria to host cells. In addition, we performed a whole genome comparison to the recently sequenced S. gallolyticus subsp. gallolyticus strain UCN34, revealing significant differences.

Conclusions

The analysis of the whole genome sequence of S. gallolyticus subsp. gallolyticus promotes understanding of genetic factors concerning the pathogenesis and adhesion to ECM of this pathogen. For the first time we detected the presence of the mobilizable pSGG1 plasmid, which may play a functional role in lateral gene transfer and promote a selective advantage due to a tetracycline resistance.
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Authors: Alikhan Nabil-Fareed , Petty Nicola K , Ben Zakour Nouri L , Beatson Scott A
Published: August 2011

Background

Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.

Results

BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically.

Conclusions

There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.
Filtering "genic" open reading frames from genomic DNA samples for advanced annotation
Authors: D'Angelo Sara , Velappan Nileena , Mignone Flavio , Santoro Claudio , Sblattero Daniele , Kiss Csaba , Bradbury Andrew RM
Published: August 2011

Background

In order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolation of genic DNA for functional annotation can be carried out by PCR. However, not all genes are correctly assigned, and even when correctly assigned, gene products are often incorrectly folded when expressed in heterologous hosts. This is a problem that can sometimes be overcome by the expression of protein fragments encoding domains, rather than full-length proteins. One possible method to isolate DNA encoding such domains would to "filter" complex DNA (cDNA libraries, genomic and metagenomic DNA) for gene fragments that confer a selectable phenotype relying on correct folding, with all such domains present in a complex DNA sample, termed the “domainome”.

Results

In this paper we discuss the preparation of diverse genic ORF libraries from randomly fragmented genomic DNA using ß-lactamase to filter out the open reading frames. By cloning DNA fragments between leader sequences and the mature ß-lactamase gene, colonies can be selected for resistance to ampicillin, conferred by correct folding of the lactamase gene. Our experiments demonstrate that the majority of surviving colonies contain genic open reading frames, suggesting that ß-lactamase is acting as a selectable folding reporter. Furthermore, different leaders (Sec, TAT and SRP), normally translocating different protein classes, filter different genic fragment subsets, indicating that their use increases the fraction of the “domainone” that is accessible.

Conclusions

The availability of ORF libraries, obtained with the filtering method described here, combined with screening methods such as phage display and protein-protein interaction studies, or with protein structure determination projects, can lead to the identification and structural determination of functional genic ORFs. ORF libraries represent, moreover, a useful tool to proceed towards high-throughput functional annotation of newly sequenced genomes.
A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans
Authors: Chen Yihong , Apolinario Ethel , Brachova Libuse , Kelman Zvi , Li Zhuo , Nikolau Basil J , Showman Lucas , Sowers Kevin , Orban John
Published: August 2011

Background

Correct annotation of function is essential if one is to take full advantage of the vast amounts of genomic sequence data. The accuracy of sequence-based functional annotations is often variable, particularly if the sequence homology to a known function is low. Indeed recent work has shown that even proteins with very high sequence identity can have different folds and functions, and therefore caution is needed in assigning functions by sequence homology in the absence of experimental validation. Experimental methods are therefore needed to efficiently evaluate annotations in a way that complements current high throughput technologies. Here, we describe the use of nuclear magnetic resonance (NMR)-based ligand screening as a tool for testing functional assignments of putative enzymes that may be of variable reliability.

Results

The target genes for this study are putative enzymes from the methanogenic archaeon Methanosarcina acetivorans (MA) that have been selected after manual genome re-annotation and demonstrate detectable in vivo expression at the level of the transcriptome. The experimental approach begins with heterologous E. coli expression and purification of individual MA gene products. An NMR-based ligand screen of the purified protein then identifies possible substrates or products from a library of candidate compounds chosen from the putative pathway and other related pathways. These data are used to determine if the current sequence-based annotation is likely to be correct. For a number of case studies, additional experiments (such as in vivo genetic complementation) were performed to determine function so that the reliability of the NMR screen could be independently assessed.

Conclusions

In all examples studied, the NMR screen was indicative of whether the functional annotation was correct. Thus, the case studies described demonstrate that NMR-based ligand screening is an effective and rapid tool for confirming or negating the annotated gene function of putative enzymes. In particular, no protein-specific assay needs to be developed, which makes the approach broadly applicable for validating putative functions using an automated pipeline strategy.
Analysis of MEFV exon methylation and expression patterns in familial Mediterranean fever
Authors: Kirectepe Asli K , Kasapcopur Ozgur , Arisoy Nil , Celikyapi Erdem Gokce , Hatemi Gulen , Ozdogan Huri , Tahir Turanli Eda
Published: August 2011

Background

MEFV mutations and decreased expression level of the gene are related to FMF pathology. DNA methylation at CpG islands is a well-known mechanism for transcriptional silencing. MEFV has a CpG island, spanning a part of the first intron and the whole of the second exon of the gene covering 998 bp region. Here, we tested the hypothesis that the MEFV transcript level in FMF patients correlates with its methylation level, and methylation, by allowing transcription silencing, has a role in FMF ethiopathogenesis.

Methods

The study group was composed of pediatric FMF patients (N = 51) and age-gender matched healthy controls (N = 21). The relative expression level of MEFV was assessed via quantitative real-time PCR (qRT-PCR) and bisulfite sequencing (BS) was performed to analyse the methylation level quantitatively.

Results

MEFV expression in FMF patients were decreased compared to healthy controls (P = 0.031). Methylation level of exon 2 of MEFV was found to be slightly higher in FMF patients compared to healthy controls (76% versus 74%) (P = 0.049). The expression level of the MEFV was negatively correlated with the methylation level of the CpG island in both FMF and healthy controls groups (cor = -0.29, P = 0.041) but more so in the FMF only group (cor = -0.36, P = 0.035).

Conclusions

In this study, the relation between reduced MEFV expression level and FMF was confirmed. Observed slight increase in methylation in FMF patients, and correlation of methylation with expression might be indicative of its role in FMF, however a larger dataset is needed to confirm our preliminary findings.
Prescribing patterns in dementia: a multicentre observational study in a German network of CAM physicians
Authors: Jeschke Elke , Ostermann Thomas , Vollmar Horst C , Tabali Manuela , Schad Friedemann , Matthes Harald
Published: August 2011

Background

Dementia is a major and increasing health problem worldwide. This study aims to investigate dementia treatment strategies among physicians specialised in complementary and alternative medicine (CAM) by analysing prescribing patterns and comparing them to current treatment guidelines in Germany.

Methods

Twenty-two primary care physicians in Germany participated in this prospective, multicentre observational study. Prescriptions and diagnoses were reported for each consecutive patient. Data were included if patients had at least one diagnosis of dementia according to the 10th revision of the International Classification of Diseases during the study period. Multiple logistic regression was used to determine factors associated with a prescription of any anti-dementia drug including Ginkgo biloba.

Results

During the 5-year study period (2004-2008), 577 patients with dementia were included (median age: 81 years (IQR: 74-87); 69% female). Dementia was classified as unspecified dementia (57.2%), vascular dementia (25.1%), dementia in Alzheimer's disease (10.4%), and dementia in Parkinson's disease (7.3%). The prevalence of anti-dementia drugs was 25.6%. The phytopharmaceutical Ginkgo biloba was the most frequently prescribed anti-dementia drug overall (67.6% of all) followed by cholinesterase inhibitors (17.6%). The adjusted odds ratio (AOR) for receiving any anti-dementia drug was greater than 1 for neurologists (AOR = 2.34; CI: 1.59-3.47), the diagnosis of Alzheimer's disease (AOR = 3.28; CI: 1.96-5.50), neuroleptic therapy (AOR = 1.87; CI: 1.22-2.88), co-morbidities hypertension (AOR = 2.03; CI: 1.41-2.90), and heart failure (AOR = 4.85; CI: 3.42-6.88). The chance for a prescription of any anti-dementia drug decreased with the diagnosis of vascular dementia (AOR = 0.64; CI: 0.43-0.95) and diabetes mellitus (AOR = 0.55; CI: 0.36-0.86). The prescription of Ginkgo biloba was associated with sex (female: AOR = 0.41; CI: 0.19-0.89), patient age (AOR = 1.06; CI: 1.02-1.10), treatment by a neurologist (AOR = 0.09; CI: 0.03-0.23), and the diagnosis of Alzheimer's disease (AOR = 0.07; CI: 0.04-0.16).

Conclusions

This study provides a comprehensive analysis of everyday practice for treatment of dementia in primary care in physicians with a focus on CAM. The prescribing frequency for anti-dementia drugs is equivalent to those found in other German studies, while the administration of Ginkgo biloba is significantly higher.
Prognostic significance of CD44s expression in resected non-small cell lung cancer
Authors: Ko Yoon Ho , Won Hye Sung , Jeon Eun Kyoung , Hong Sook Hee , Roh Sang Young , Hong Young Seon , Byun Jae Ho , Jung Chan-Kwon , Kang Jin Hyoung
Published: August 2011

Background

CD44s is a cell adhesion molecule known to mediate cellular adhesion to the extracellular matrix, a prerequisite for tumor cell migration. CD44s plays an important role in invasion and metastasis of various cancers. In the present study, we sought to determine whether CD44s is involved in clinical outcomes of patients with resected non-small cell lung cancer (NSCLC).

Methods

Using immunohistochemical staining, we investigated CD44s protein expression using tissue array specimens from 159 patients with resected NSCLC (adenocarcinoma (AC; n = 82) and squamous cell carcinoma (SCC; n = 77). Additionally, the immunoreactivity of cyclooxygenase (COX)-2 was also studied. The clinicopathological implications of these molecules were analyzed statistically.

Results

High CD44s expression was detected more frequently in NSCLC patients with SCC (66/72; 91.7%) than in those with AC histology (P < 0.001). Additionally, high CD44s expression was significant correlated with more advanced regional lymph node metastasis (P = 0.021). In multivariate analysis of survival in NSCLC patients with AC histology, significant predictors were lymph node metastasis status (P < 0.001), high-grade tumor differentiation (P = 0.046), and high CD44s expression (P = 0.014). For NSCLC patients with SCC histology, the significant predictor was a more advanced tumor stage (P = 0.015). No significant association was found between CD44s and clinical outcome (P = 0.311).

Conclusions

High CD44s expression was a negative prognostic marker with significance in patients with resected NSCLC, particularly those with AC histology, and was independent of tumor stage.
Ki67 proliferation in core biopsies versus surgical samples - a model for neo-adjuvant breast cancer studies
Authors: Romero Quinci , Bendahl Pär-Ola , Klintman Marie , Loman Niklas , Ingvar Christian , Rydén Lisa , Rose Carsten , Grabau Dorthe , Borgquist Signe
Published: August 2011

Background

An increasing number of neo-adjuvant breast cancer studies are being conducted and a novel model for tumor biological studies, the "window-of-opportunity" model, has revealed several advantages. Change in tumor cell proliferation, estimated by Ki67-expression in pre-therapeutic core biopsies versus post-therapeutic surgical samples is often the primary end-point. The aim of the present study was to investigate potential differences in proliferation scores between core biopsies and surgical samples when patients have not received any intervening anti-cancer treatment. Also, a lack of consensus concerning Ki67 assessment may raise problems in the comparison of neo-adjuvant studies. Thus, the secondary aim was to present a novel model for Ki67 assessment.

Methods

Fifty consecutive breast cancer cases with both a core biopsy and a surgical sample available, without intervening neo-adjuvant therapy, were collected and tumor proliferation (Ki67, MIB1 antibody) was assessed immunohistochemically. A theoretical model for the assessment of Ki67 was constructed based on sequential testing of the null hypothesis 20% Ki67-positive cells versus the two-sided alternative more or less than 20% positive cells..

Results

Assessment of Ki67 in 200 tumor cells showed an absolute average proliferation difference of 3.9% between core biopsies and surgical samples (p = 0.046, paired t-test) with the core biopsies being the more proliferative sample type. A corresponding analysis on the log-scale showed the average relative decrease from the biopsy to the surgical specimen to be 19% (p = 0.063, paired t-test on the log-scale). The difference was significant when using the more robust Wilcoxon matched-pairs signed-ranks test (p = 0.029). After dichotomization at 20%, 12 of the 50 sample pairs had discrepant proliferation status, 10 showed high Ki67 in the core biopsy compared to two in the surgical specimen (p = 0.039, McNemar's test). None of the corresponding results for 1000 tumor cells were significant - average absolute difference 2.2% and geometric mean of the ratios 0.85 (p = 0.19 and p = 0.18, respectively, paired t-tests, p = 0.057, Wilcoxon's test) and an equal number of discordant cases after dichotomization. Comparing proliferation values for the initial 200 versus the final 800 cancer cells showed significant absolute differences for both core biopsies and surgical samples 5.3% and 3.2%, respectively (p < 0.0001, paired t-test).

Conclusions

A significant difference between core biopsy and surgical sample proliferation values was observed despite no intervening therapy. Future neo-adjuvant breast cancer studies may have to take this into consideration.