bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Covariates of Gang Homicide in Large U.S. Cities
Authors: Pyrooz David C. 
Published: August 2011

Objectives: This study examined the structural covariates of gang homicide in large U.S. cities and whether the structural conditions associated with gang homicide differed from non-gang homicide. Methods: Several national data sources were used to gather information on the structural conditions of the 88 largest U.S. cities, including the U.S. Census Bureau, Law Enforcement Management and Administrative Statistics, Uniform Crime Report, and National Gang Center. Negative binomial regression was used to model the relationship between the structural conditions of cities and homicide rates. Results: Socioeconomic deprivation, official rates of gang membership, and population density explained between-city variability in gang homicide rates. In addition, quadratic associations were observed for socioeconomic deprivation and population density. Equality of coefficients tests revealed that the structural covariates of gang homicide differed in magnitude from non-gang homicide. Conclusions: Prior to this study, the etiology of gang homicide was found to differ from other homicide types in terms of event characteristics and sub-city correlates. This macro-level study extended this line of research to cities, providing evidence that the structural correlates of violence operated differently for gang homicide.
A qualitative investigation into the maternal experience of having a young child with severe food allergy
Authors: Rouf Khadj , White Loretta , Evans Kathryn 
Published: August 2011

Background: Severe food allergy has potentially life threatening consequences. Despite the significant impact on quality of life for families affected by food allergy, there is still relatively little known about the psychosocial experience in this area, especially with regards to the parenting experience. Objectives: This study focused on the following areas of parental experience: (1) having a young child with severe food allergy; (2) perception of the effect of food allergy on family relationships; (3) managing the challenges associated with severe food allergy. Methods: Eight mothers of children with severe food allergy completed semi-structured interviews. Interview transcripts were analysed using Interpretative Phenomenological Analysis (IPA), a qualitative methodology. Results: Three superordinate themes emerged from the analysis: (1) Parental adjustment—re-establishing an “even keel”; (2) It’s a big responsibility: Living with risk; (3) Identity and the social aspects of allergy. This article focuses on the most psychologically salient findings within each of these superordinate themes. Conclusion: Mothers in this study shared similar concerns to mothers of children with other chronic illnesses. It is recommended that the experience of allergy should be viewed in the wider family context with specific consideration given to parental coping and anxiety. Services could better meet the psychological and social needs of those affected by allergy.
Cryobiopsy increases the diagnostic yield of endobronchial biopsy: a multicentre trial
Authors: Hetzel J. , Eberhardt R. , Herth F.J.F. , Petermann C. , Reichle G. , Freitag L. , Dobbertin I. , Franke K.J. , Stanzel F. , Beyer T. , Möller P. , Fritz P. , Ott G. , Schnabel P.A. , Kastendieck H. , Lang W. , Morresi-Hauf A.T. , Szyrach M.N. , Muche R. , Shah P.L. , Babiak A. , Hetzel M. 
Published: August 2011

Forceps, brushes or needles are currently the standard tools used during flexible bronchoscopy when diagnosing endobronchial malignancies. The new biopsy technique of cryobiopsy appears to provide better diagnostic samples. The aim of this study was to evaluate cryobiopsy over conventional endobronchial sampling.A total of 600 patients in eight centres with suspected endobronchial tumours were included in a prospective, randomised, single-blinded multicentre study. Patients were randomised to either sampling using forceps or the cryoprobe. After obtaining biopsy samples, a blinded histological evaluation was performed. According to the definitive clinical diagnosis, the diagnostic yield for malignancy was evaluated by a Chi-squared test.A total of 593 patients were randomised, of whom 563 had a final diagnosis of cancer. 281 patients were randomised to receive endobronchial biopsies using forceps and 282 had biopsies performed using a flexible cryoprobe. A definitive diagnosis was achieved in 85.1% of patients randomised to conventional forceps biopsy and 95.0% of patients who underwent cryobiopsy (p<0.001). Importantly, there was no difference in the incidence of significant bleeding.Endobronchial cryobiopsy is a safe technique with superior diagnostic yield in comparison with conventional forceps biopsy.
Day–night variations in endothelial dysfunction markers and haemostatic factors in sleep apnoea
Authors: Barceló A. , Piérola J. , de la Peña M. , Esquinas C. , Sanchez-de la Torre M. , Ayllón O. , Alonso A. , Agusti A.G.N. , Barbè F. 
Published: August 2011

Patients with sleep apnoea have a significant alteration in the day–night pattern of myocardial infarction and sudden cardiac death observed in the general population. The aim of this study was to investigate the influence of sleep apnoea on the diurnal variations in various haemostatic parameters (factor VII, von Willebrand factor and plasminogen activator inhibitor (PAI)-1) and markers of endothelial dysfunction (asymmetric dimethylarginine (ADMA) and soluble CD40 ligand (sCD40L)).We studied 26 male patients with obstructive sleep apnoea syndrome (OSAS; 13 patients with severe OSAS (apnoea/hypopnoea index (AHI) >30 events·h−1) and 13 patients with mild-to-moderate OSAS (AHI <30 events·h−1)) and 12 controls of similar body mass index (BMI) and waist circumference. In each subject, six different samples were obtained over 24 h.Although all the markers values tended to be higher in patients with severe OSAS, differences did not reach statistical significance at any time. PAI-1 levels were significantly related to BMI (p<0.001), mean (p<0.001) and minimal (p=0.047) nocturnal oxygenation saturation. ADMA levels were significantly related to arousal index (p=0.046).The results of this study suggest that day–night variations in factor VII:antigen (Ag), von Willebrand factor:Ag, PAI-1, sCD40L and ADMA levels may be dependent on either the obesity index or metabolic dysfunction rather than on sleep apnoea alone.
Canine scent detection in the diagnosis of lung cancer: revisiting a puzzling phenomenon
Authors: Ehmann R. , Boedeker E. , Friedrich U. , Sagert J. , Dippon J. , Friedel G. , Walles T. 
Published: August 2011

Patient prognosis in lung cancer largely depends on early diagnosis. The exhaled breath of patients may represent the ideal specimen for future lung cancer screening. However, the clinical applicability of current diagnostic sensor technologies based on signal pattern analysis remains incalculable due to their inability to identify a clear target. To test the robustness of the presence of a so far unknown volatile organic compound in the breath of patients with lung cancer, sniffer dogs were applied.Exhalation samples of 220 volunteers (healthy individuals, confirmed lung cancer or chronic obstructive pulmonary disease (COPD)) were presented to sniffer dogs following a rigid scientific protocol. Patient history, drug administration and clinicopathological data were analysed to identify potential bias or confounders.Lung cancer was identified with an overall sensitivity of 71% and a specificity of 93%. Lung cancer detection was independent from COPD and the presence of tobacco smoke and food odours. Logistic regression identified two drugs as potential confounders.It must be assumed that a robust and specific volatile organic compound (or pattern) is present in the breath of patients with lung cancer. Additional research efforts are required to overcome the current technical limitations of electronic sensor technologies to engineer a clinically applicable screening tool.
Dietary factors and lung function in the general population: wine and resveratrol intake
Authors: Siedlinski M. , Boer J.M.A. , Smit H.A. , Postma D.S. , Boezen H.M. 
Published: August 2011

Wine intake is associated with a better lung function in the general population, yet the source of this effect is unknown. Resveratrol, a polyphenol in wine, has anti-inflammatory properties in the lung, its effects being partially mediatedviainduction of Sirtuin (SIRT)1 activity. We assessed the impact of wine and resveratrol intake, andSIRT1single-nucleotide polymorphisms (SNPs) on lung function in the general population.Effects of red and white wine and resveratrol intake on forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC were analysed in the population-based Doetinchem cohort (n=3,224). Associations of four taggingSIRT1SNPs with lung function were analysed in the Doetinchem (n=1,152) and Vlagtwedde–Vlaardingen (n=1,390) cohorts.Resveratrol intake was associated with higher FVC levels, and white wine intake with higher FEV1levels and lower risk of airway obstruction.SIRT1SNPs were not significantly associated with level or course of lung function, either directly or indirectlyviawine or resveratrol intake.This study shows a positive association of resveratrol intake with lung function in the general population, confirms the previously reported positive association of white wine intake with higher levels of FEV1, and additionally shows an association with a higher FEV1/FVC ratio. These effects probably do not runviaSNPs inSIRT1.
Rhinovirus bronchiolitis and recurrent wheezing: 1-year follow-up
Authors: Midulla F. , Pierangeli A. , Cangiano G. , Bonci E. , Salvadei S. , Scagnolari C. , Moretti C. , Antonelli G. , Ferro V. , Papoff P. 
Published: August 2011

The association between bronchiolitis and recurrent wheezing remains controversial.In this prospective study, we assessed risk factors for recurrent wheezing during a 12-month follow-up in 313 infants aged <12 months hospitalised for their first episode of bronchiolitis. Demographic, clinical and laboratory data were obtained with a questionnaire and from medical files. A total of 14 respiratory viruses were concurrently assayed in nasal washings. Parents were interviewed 12 months after hospitalisation to check whether their infants experienced recurrent wheezing.The rate of recurrent wheezing was higher in infants with bronchiolitis than in controls (52.7versus10.3%; p<0.001). Multivariate analysis identified rhinovirus (RV) infection (OR 3.3, 95% CI 1.0–11.1) followed by a positive family history for asthma (OR 2.5, 95% CI 1.2–4.9) as major independent risk factors for recurrent wheezing.In conclusion, the virus most likely to be associated with recurrent wheezing at 12 months after initial bronchiolitis is RV, a viral agent that could predict infants prone to the development of recurrent wheezing.
Characterisation of marsupial PHLDA2 reveals eutherian specific acquisition of imprinting
Authors: Suzuki Shunsuke , Shaw Geoffrey , Kaneko-Ishino Tomoko , Ishino Fumitoshi , Renfree Marilyn B 
Published: August 2011

Abstract

Background
Genomic imprinting causes parent-of-origin specific gene expression by differential epigenetic modifications between two parental genomes. We previously reported that there is no evidence of genomic imprinting of CDKN1C in the KCNQ1 domain in the placenta of an Australian marsupial, the tammar wallaby (Macropus eugenii) whereas tammar IGF2 and H19, located adjacent to the KCNQ1 domain in eutherian mammals, are imprinted. We have now identified and characterised the marsupial orthologue of PHLDA2, another gene in the KCNQ1 domain (also known as IPL or TSSC3) that is imprinted in eutherians. In mice, Phlda2 is a dose-sensitive negative regulator of placental growth, as Cdkn1c is for embryonic growth.

Results
Tammar PHLDA2 is highly expressed in the yolk sac placenta compared to other fetal tissues, confirming a similar expression pattern to that of mouse Phlda2. However, tammar PHLDA2 is biallelically expressed in both the fetus and yolk sac placenta, so it is not imprinted. The lack of imprinting in tammar PHLDA2 suggests that the acquisition of genomic imprinting of the KCNQ1 domain in eutherian mammals, accompanied with gene dosage reduction, occurred after the split of the therian mammals into the marsupials and eutherians.

Conclusions
Our results confirm the idea that acquisition of genomic imprinting in the KCNQ1 domain occurred specifically in the eutherian lineage after the divergence of marsupials, even though imprinting of the adjacent IGF2-H19 domain arose before the marsupial-eutherian split. These data are consistent with the hypothesis that genomic imprinting of the KCNQ1 domain may have contributed to the evolution of more complex placentation in the eutherian lineage by reduction of the gene dosage of negative regulators for both embryonic and placental growth.
SAMQA: error classification and validation of high-throughput sequenced read data
Authors: Robinson Thomas , Killcoyne Sarah , Bressler Ryan , Boyle John 
Published: August 2011

Abstract

Background
The advances in high-throughput sequencing technologies and growth in data sizes has highlighted the need for scalable tools to perform quality assurance testing. These tests are necessary to ensure that data is of a minimum necessary standard for use in downstream analysis. In this paper we present the SAMQA tool to rapidly and robustly identify errors in population-scale sequence data.

Results
SAMQA has been used on samples from three separate sets of cancer genome data from The Cancer Genome Atlas (TCGA) project. Using technical standards provided by the SAM specification and biological standards defined by researchers, we have classified errors in these sequence data sets relative to individual reads within a sample. Due to an observed linearithmic speedup through the use of a high-performance computing (HPC) framework for the majority of tasks, poor quality data was identified prior to secondary analysis in significantly less time on the HPC framework than the same data run using alternative parallelization strategies on a single server.

Conclusions
The SAMQA toolset validates a minimum set of data quality standards across whole-genome and exome sequences. It is tuned to run on a high-performance computational framework, enabling QA across hundreds gigabytes of samples regardless of coverage or sample type.
Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby
Authors: Wong Emily SW , Papenfuss Anthony T , Heger Andreas , Hsu Arthur L , Ponting Chris P , Miller Robert D , Fenelon Jane C , Renfree Marilyn B , Gibbs Richard A , Belov Katherine 
Published: August 2011

Abstract

Background
The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby.

Results
We show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed.

Conclusion
This is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system.
The tammar wallaby major histocompatibility complex shows evidence of past genomic instability
Authors: Siddle Hannah V , Deakin Janine E , Coggill Penny , Wilming Laurens G , Harrow Jennifer , Kaufman Jim , Beck Stephan , Belov Katherine 
Published: August 2011

Abstract

Background
The major histocompatibility complex (MHC) is a group of genes with a variety of roles in the innate and adaptive immune responses. MHC genes form a genetically linked cluster in eutherian mammals, an organization that is thought to confer functional and evolutionary advantages to the immune system. The tammar wallaby (Macropus eugenii), an Australian marsupial, provides a unique model for understanding MHC gene evolution, as many of its antigen presenting genes are not linked to the MHC, but are scattered around the genome.

Results
Here we describe the 'core' tammar wallaby MHC region on chromosome 2q by ordering and sequencing 33 BAC clones, covering over 4.5 MB and containing 129 genes. When compared to the MHC region of the South American opossum, eutherian mammals and non-mammals, the wallaby MHC has a novel gene organization. The wallaby has undergone an expansion of MHC class II genes, which are separated into two clusters by the class III genes. The antigen processing genes have undergone duplication, resulting in two copies of TAP1 and three copies of TAP2. Notably, Kangaroo Endogenous Retroviral Elements are present within the region and may have contributed to the genomic instability.

Conclusions
The wallaby MHC has been extensively remodeled since the American and Australian marsupials last shared a common ancestor. The instability is characterized by the movement of antigen presenting genes away from the core MHC, most likely via the presence and activity of retroviral elements. We propose that the movement of class II genes away from the ancestral class II region has allowed this gene family to expand and diversify in the wallaby. The duplication of TAP genes in the wallaby MHC makes this species a unique model organism for studying the relationship between MHC gene organization and function.
The balance between intrahepatic IL-17+ T cells and Foxp3+ regulatory T cells plays an important role in HBV-related end-stage liver disease
Authors: Niu Yinghua , Liu Hongli , Yin Donglin , Yi Ruitian , Chen Tianyan , Xue Hong'an , Zhang Shulin , Lin Shumei , Zhao Yingren 
Published: August 2011

Abstract

Backgroud
IL-17+ T helper cells and Foxp3+ regulatory T cells are CD4+ T helper cells with reciprocally regulated differentiation and function. Their frequency and function vary in patients with chronic hepatitis B. In this study, we investigated the balance between IL-17+ T cells and Foxp3+ regulatory T cells and illustrated their function in the aggravation of chronic hepatitis B (CHB).

Results
Twenty-six patients with chronic HBV -related liver failure (CLF), thirty-one patients with acute on chronic HBV-related liver failure (ACLF) and twelve normal controls were enrolled in our study. The expressions of IL-17, Foxp3, CD4, CD8 and perforin in liver tissue were measured by immunochemistry for the evaluation of liver-infiltrating lymphocytes. The frequency of liver IL-17+ T cells on liver inflammatory cells and their proportion in the total CD4+ T cell population increased markedly in the ACLF group, while the frquency of Foxp3+ T cells and their proportion in the total CD4+ T cell population did not show a significant difference in the two HBV infection groups. In addition, the ACLF group showed a dramatically higher IL-17+ /Foxp3+ ratio than the CLF group. CD4+ T cells increased significantly in the liver of patients with ACLF, compared with those in the liver of patients with CLF.

Conclusions
Our findings suggest that intrahepatic IL-17+ T cells play an important role in the development of chronic HBV and that the imbalance between IL-17+ and Foxp3+ T cells in the liver may lead to progression of the disease but the mechanism should be further explored.
Immunome database for marsupials and monotremes
Authors: Wong Emily SW , Papenfuss Anthony T , Belov Katherine 
Published: August 2011

AbstractBackgroundTo understand the evolutionary origins of our own immune system, we need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organisms. This was required as many genes involved in immunity evolve rapidly and fail to be detected by automated gene annotation pipelines.DescriptionWe have developed a database of immune genes from the tammar wallaby, red-necked wallaby, northern brown bandicoot, brush-tail possum, opossum, echidna and platypus. The resource contains 2,235 newly identified sequences and 3,197 sequences which had been described previously. This comprehensive dataset was built from a variety of sources, including EST projects and expert-curated gene predictions generated through a variety of methods including chained-BLAST and sensitive HMMER searches. To facilitate systems-based research we have grouped sequences based on broad Gene Ontology categories as well as by specific functional immune groups. Sequences can be extracted by keyword, gene name, protein domain and organism name. Users can also search the database using BLAST.ConclusionThe Immunome Database for Marsupials and Monotremes (IDMM) is a comprehensive database of all known marsupial and monotreme immune genes. It provides a single point of reference for genomic and transcriptomic datasets. Data from other marsupial and monotreme species will be added to the database as it become available. This resource will be utilized by marsupial and monotreme immunologists as well as researchers interested in the evolution of mammalian immunity.