bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wavelet Support Vector Machines for Forecasting Precipitation in Tropical Cyclones: Comparisons with GSVM, Regression, and MM5
Authors: Wei Chih-Chiang 
Published: November 2011

Abstract
This study presents two support vector machine (SVM) based models for forecasting hourly precipitation during tropical cyclone (typhoon) events. The two SVM-based models are the traditional Gaussian kernel SVMs (GSVMs) and the advanced wavelet kernel SVMs (WSVMs). A comparison between the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) and statistical models, including SVM-based models and linear regressions (regression), was made in terms of performance of rainfall prediction at the Shihmen Reservoir watershed in Taiwan. Data from 73 typhoons affecting the Shihmen Reservoir watershed were included in the analysis. This study designed six attribute combinations with different lag times for the forecast target. The modified RMSE, bias, and estimated threat score (ETS) results were employed to assess the predicted outcomes. Results show that better attribute combinations for typhoon climatologic characteristics and typhoon precipitation predictions occurred at 0-h lag time with modified RMSE values of 0.288, 0.257, and 0.296 in GSVM, WSVM, and the regression, respectively. Moreover, WSVM having average bias and ETS values close to 1.0 gave better predictions than did the GSVM and regression models. In addition, Typhoons Zeb (1998) and Nari (2001) were selected for comparison between the MM5 model output and the developed statistical models. Results showed that the MM5 tended to overestimate the peak and cumulative rainfall amounts while the statistical models were inclined to yield underestimations.
Living with helicopter noise – evaluating sound insulation techniques for domestic dwellings using real helicopters
Authors: Kerry Geoff , Waddington David , Lomax Claire 
Published: November 2011

Specific remedial works designed to improve sound installation and reduce the noise level produced by helicopters inside dwellings are described. The theoretical problems and practical solutions to installing high-performance acoustic insulation to a traditional property in the United Kingdom are presented. A novel application of ISO 140-5 is presented using real helicopters to measure sound insulation in situ in the presence of multiple flanking transmission paths. Dedicated field trials to evaluate the performance of such acoustic double-glazing and associated modifications systems were performed and the precautions taken to minimise measurement uncertainties over the extended time period of the trials are detailed. The field trials involved the use of military training helicopters following selected flight paths around the property, while noise-level measurements were made internally and externally, before and after replacement of the existing single-glazed windows and attenuated ventilation units were installed. The results show that after replacing the main windows with acoustic insulated glazing units, sound insulation levels of 40 dB or above are achieved in most rooms. The results also illustrate the importance of effectively addressing ventilation when windows are replaced. It is concluded that despite complications due to sound flanking and regulatory ventilation, the use of acoustic double-glazing units and properly attenuated ventilation units can effectively reduce helicopter noise in suitable dwellings. Practical application: This article provides an evaluation of ways in which the sound insulation of dwellings can be practically improved to reduce the impact on everyday living of noise from helicopter operations. It addresses concerns about the practical use of high-performance acoustic insulated glazing units (IGUs) used in combination with acoustic through-the-wall ventilation. It also addresses the existence of multiple flanking sound paths. Sound insulation data from a field trial involving a conventional brick-built house obtained before modification is compared in a controlled manner with that obtained after fitting acoustic IGUs and after introducing ventilation to comply with current Building Regulations.
Force Measurements in the Medial Meniscus Posterior Horn Attachment
Authors: Markolf Keith L. , Jackson Steven R. , McAllister David R. 
Published: November 2011

Background: Tears of the medial meniscus posterior horn attachment (PHA) occur clinically, and an anterior cruciate ligament (ACL)–deficient knee may be more vulnerable to this injury. Hypothesis: The PHA forces from applied knee loadings will increase after removal of the ACL. Study Design: Controlled laboratory study. Methods: A cap of bone containing the medial meniscus PHA was attached to a load cell that measured PHA tensile force. Posterior horn attachment forces were recorded before and after ACL removal during anteroposterior (AP) laxity testing at ±200 N and during passive knee extension tests with 5 N·m tibial torque and varus-valgus moment. Selected tests were also performed with 500 N joint load. Results: For AP tests with no joint load, ACL removal increased laxity between 0° and 90° and increased PHA force generated by applied anterior tibial force between 30° and 90°. For AP tests with an intact ACL, application of joint load approximately doubled PHA forces. Anteroposterior testing of ACL-deficient knees was not possible with joint load because of bone cap failures from high PHA forces. Removal of the ACL during knee extension tests under joint load significantly increased PHA forces between 20° and 90° of flexion. For unloaded tests with applied tibial torque and varus-valgus moment, ACL removal had no significant effect on PHA forces. Conclusion: Applied anterior tibial force and external tibial torque were loading modes that produced relatively high PHA forces, presumably by impingement of the medial femoral condyle against the medial meniscus posterior horn rim. Under joint load, an ACL-deficient knee was particularly susceptible to PHA injury from applied anterior tibial force. Clinical Relevance: Because tensile forces developed in the PHA are also borne by meniscus tissue near the attachment site, loading mechanisms that produce high PHA forces could also produce complete or partial radial tears near the posterior horn, a relatively common clinical observation.
Assessment of oxidative stress and chromosomal aberration inducing potential of three medical grade silicone polymer materials
Authors: Vijayalakshmi P , Geetha CS , Mohanan PV 
Published: November 2011

Medical expenditures for devices are increasing along with the ageing of human population and the synthesis of materials such as silicone polymers is on upsurge for manufacturing these devices. The International Organization for Standardization (ISO) emphasizes a battery of tests for preclinical assessment of biocompatibility of medical devices. Genotoxicity assays have become an integral component of these test procedures and it employs a set of in vitro and in vivo experiments to detect mutagens. Hence, this study was performed with an intention to investigate the genotoxic potential of the physiological saline extracts of three medical grade silicone polymer materials by the in vitro chromosomal aberration assay using human peripheral blood lymphocytes. Further, the oxidative stress inducing potential of the material extracts was investigated in vivo in mice liver homogenates using cyclophosphamide as positive control. The investigation revealed that none of the three materials were able to produce marked human lymphocyte chromosomal aberration, suggesting the absence of mutagens. The materials also showed negative results in their oxidative stress inducing potential, which was revealed by the normal levels of lipid peroxidation and unaltered levels of glutathione and its metabolizing enzymes in the mice liver tissue homogenates. It was interesting to observe a significant correlation between the genotoxic and antioxidant parameters investigated. Hence, it is suggested that the estimation of antioxidant status would serve as a better preliminary testing procedure prior to evaluating the genetic and molecular toxicity mechanisms of medical devices and/or materials intended for manufacture of such devices.
Angiotensin converting enzyme insertion/deletion polymorphism and risk of pregnancy hypertensive disorders: a meta-analysis
Authors: Chen Zhen , Xu Fang , Wei Yonggang , Liu Fei , Qi Hongbo 
Published: November 2011

Background: The angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism has been reported inconsistently as being associated with risk of pregnancy hypertensive disorders (PHDs). We examined these associations by performing a meta-analysis. Methods: Two investigators independently consulted the Medline, Embase, CNKI, and Chinese Biomedicine databases. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated in ﬁxed- and random-effects models when appropriate. Subgroup analyses were performed by ethnicity, types of PHD (gestational hypertension, pre-eclampsia and eclampsia), country and Hardy–Weinberg equilibrium (HWE) in controls. Results: This meta-analysis included 30 case–control studies with 3523 cases and 4817 controls. Overall, we found that the DD variant of the ACE I/D polymorphism was associated with a significantly increased PHD risk. In the subgroup analysis by ethnicity, the results suggested that the DD genotype was significantly associated with risk of PHD development among Asians and Caucasians. Moreover, when stratifying by types of PHD, a significantly increased risk was observed for pre-eclampsia. Interestingly, when stratifying by country, a significantly elevated risk was found among ‘others’ countries (those that were not China or Korea). Limiting the analysis to the studies within HWE, the results were persistent and robust. Conclusion: This meta-analysis suggests that the I/D polymorphism of ACE may be associated with PHD risk, especially among Asians and Caucasians.
NOTCH1 mutations in CLL associated with trisomy 12
Authors: Balatti Veronica , Bottoni Arianna , Palamarchuk Alexey , Alder Hansjuerg , Rassenti Laura Z. , Kipps Thomas J. , Pekarsky Yuri , Croce Carlo M. 
Published: November 2011

Abstract
Two recent studies reported wholegenome sequencing of chronic lymphocytic leukemia (CLL) samples and found repeated mutations in the XPO1 and NOTCH1 genes. XPO1 was found mutated in 2.4% of cases, while NOTCH1 was found mutated in 12.2% or 15.1% of CLL samples. Here we report the results of sequencing of XPO1 and NOTCH1 in 186 CLL cases. Our results confirmed frequency of XPO1 mutations. However, we found only 5 NOTCH1 mutations in 127 IGVH unmutated/ZAP70+ CLL samples (4%), and one mutation was found in IGVH mutated/ZAP70− CLL for a total percentage of 1.5%. Because 4 of 6 mutated samples also showed trisomy 12, we sequenced NOTCH1 in an additional 77 cases with trisomy 12 CLLs, including 47 IGVH unmutated/ZAP70+ cases. Importantly, we found 41.9% NOTCH1 mutation frequency in aggressive trisomy 12 CLL cases. Our data suggest that activation of NOTCH1 plays a critical role in IGVH unmutated/ZAP70+ trisomy 12 CLL.
Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipesreveal birth-and-death evolution and strong purifying selection
Authors: Perina Alejandra , Seoane David , González-Tizón Ana M , Rodríguez-Fariña Fernanda , Martínez-Lage Andrés 
Published: November 2011

Abstract

Background
The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context.

Results
The nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types.

Conclusions
These results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection.
The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser
Authors: Simone Domenico , Calabrese Francesco Maria , Lang Martin , Gasparre Giuseppe , Attimonelli Marcella 
Published: November 2011

Abstract

Background
Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies.

Results
Here we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications.

Conclusions
We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.
Cytokine expression during early and late phase of acute Puumala hantavirus infection
Authors: Sadeghi Mahmoud , Eckerle Isabella , Daniel Volker , Burkhardt Ulrich , Opelz Gerhard , Schnitzler Paul 
Published: November 2011

AbstractBackgroundHantaviruses of the familyBunyaviridaeare emerging zoonotic pathogens which cause hemorrhagic fever with renal syndrome (HFRS) in the Old World and hantavirus pulmonary syndrome (HPS) in the New World. An immune-mediated pathogenesis is discussed for both syndromes. The aim of our study was to investigate cytokine expression during the course of acutePuumalahantavirus infection.ResultsWe retrospectively studied 64 patients hospitalised with acutePuumalahantavirus infection in 2010 during a hantavirus epidemic in Germany. Hantavirus infection was confirmed by positive anti-hantavirus IgG/IgM. Cytokine expression of IL-2, IL-5, IL-6, IL-8, IL-10, IFN-γ, TNF-α and TGF-β1 was analysed by ELISA during the early and late phase of acute hantavirus infection (average 6 and 12 days after onset of symptoms, respectively). A detailed description of the demographic and clinical presentation of severe hantavirus infection requiring hospitalization during the 2010 hantavirus epidemic in Germany is given. Acute hantavirus infection was characterized by significantly elevated levels of IL-2, IL-6, IL-8, TGF-β1 and TNF-α in both early and late phase compared to healthy controls. From early to late phase of disease, IL-6, IL-10 and TNF-α significantly decreased whereas TGF-β1 levels increased. Disease severity characterized by elevated creatinine and low platelet counts was correlated with high pro-inflammatory IL-6 and TNF-α but low immunosuppressive TGF-β1 levels andvice versa.ConclusionHigh expression of cytokines activating T-lymphocytes, monocytes and macrophages in the early phase of disease supports the hypothesis of an immune-mediated pathogenesis. In the late phase of disease, immunosuppressive TGF-β1 level increase significantly. We suggest that delayed induction of a protective immune mechanism to downregulate a massive early pro-inflammatory immune response might contribute to the pathologies characteristic of human hantavirus infection.
A historical and proteomic analysis of botulinum neurotoxin type/G
Authors: Terilli Rebecca R , Moura Hercules , Woolfitt Adrian R , Rees Jon , Schieltz David M , Barr John R 
Published: November 2011

Abstract

Background

Clostridium botulinum is the taxonomic designation for at least six diverse species that produce botulinum neurotoxins (BoNTs). There are seven known serotypes of BoNTs (/A through/G), all of which are potent toxins classified as category A bioterrorism agents. BoNT/G is the least studied of the seven serotypes. In an effort to further characterize the holotoxin and neurotoxin-associated proteins (NAPs), we conducted an in silico and proteomic analysis of commercial BoNT/G complex. We describe the relative quantification of the proteins present in the/G complex and confirm our ability to detect the toxin activity in vitro. In addition, we review previous literature to provide a complete description of the BoNT/G complex.

Results
An in-depth comparison of protein sequences indicated that BoNT/G shares the most sequence similarity with the/B serotype. A temperature-modified Endopep-MS activity assay was successful in the detection of BoNT/G activity. Gel electrophoresis and in gel digestions, followed by MS/MS analysis of/G complex, revealed the presence of four proteins in the complexes: neurotoxin (BoNT) and three NAPs--nontoxic-nonhemagglutinin (NTNH) and two hemagglutinins (HA70 and HA17). Rapid high-temperature in-solution tryptic digestions, coupled with MS/MS analysis, generated higher than previously reported sequence coverages for all proteins associated with the complex: BoNT 66%, NTNH 57%, HA70 91%, and HA17 99%. Label-free relative quantification determined that the complex contains 30% BoNT, 38% NTNH, 28% HA70, and 4% HA17 by weight comparison and 17% BoNT, 23% NTNH, 42% HA70, and 17% HA17 by molecular comparison.

Conclusions
The in silico protein sequence comparisons established that the/G complex is phenetically related to the other six serotypes of C. botulinum. Proteomic analyses and Endopep-MS confirmed the presence of BoNT and NAPs, along with the activity of the commercial/G complex. The use of data-independent MSE data analysis, coupled to label-free quantification software, suggested that the weight ratio BoNT:NAPs is 1:3, whereas the molar ratio of BoNT:NTNH:HA70:HA17 is 1:1:2:1, within the BoNT/G progenitor toxin.
Risk factors associated with symptomatic cholelithiasis in Taiwan: a population-based study
Authors: Hung Shih-Chang , Liao Kuan-Fu , Lai Shih-Wei , Li Chia-Ing , Chen Wen-Chi 
Published: November 2011

Abstract

Background
Cholelithiasis has become a major health problem in Taiwan. The predominant type of gallstone found in Asian populations differs from that in the West, indicating possible differences in the etiology and risk factors for cholelithiasis. The aim of this study is to investigate the risk factors for cholelithiasis using data representative of the general population.

Methods
We performed a population-based, case-control study in which we analyzed medical data for 3725 patients newly diagnosed with cholelithiasis and 11175 gender- and age-matched controls with no history of cholelithiasis, using information obtained from the 2005 Registry for Beneficiaries of the National Health Insurance Research Database. Coexisting medical conditions were included in the analysis. Relative risks were estimated by adjusted odds ratio (OR) and 95% confidence interval (CI) using a multivariate logistic regression analysis.

Results
After controlling for the other covariates, multivariate logistic regression analysis identified the following as risk factors for cholelithiasis (in descending order of contribution): Among all patients - hepatitis C (OR = 2.78), cirrhosis (OR = 2.47), hepatitis B (OR = 2.00), obesity (OR = 1.89), and hyperlipidemia (OR = 1.54); Among women - hepatitis C (OR = 3.05), cirrhosis (OR = 1.92), obesity (OR = 1.91), menopause (OR = 1.61), hepatitis B (OR = 1.54), and hyperlipidemia (OR = 1.49). Diabetes mellitus appeared to have a marked influence on the development of cholelithiasis but was not identified as a significant independent risk factor for cholelithiasis.

Conclusions
The risk factors for cholelithiasis were obesity, hyperlipidemia, hepatitis B infection, hepatitis C infection, and cirrhosis in both genders, and menopause in females. Despite differences in the predominate type of gallstone in Asian versus Western populations, we identified no unique risk factors among the population of Taiwan.
Improved sensitivity of an interferon-gamma release assay (T-SPOT.TB™) in combination with tuberculin skin test for the diagnosis of latent tuberculosis in the presence of HIV co-Infection
Authors: Elzi Luigia , Steffen Ingrid , Furrer Hansjakob , Fehr Jan , Cavassini Matthias , Hirschel Bernard , Hoffmann Matthias , Bernasconi Enos , Bassetti Stefano , Battegay Manuel 
Published: November 2011

Abstract

Background
Interferon-gamma release assays (IGRA) are more specific than the tuberculin skin test (TST) for the diagnosis of Mycobacterium tuberculosis infection. Data on sensitivity are controversial in HIV infection.

Methods
IGRA (T-SPOT.TB) was performed using lymphocytes stored within 6 months before culture-confirmed tuberculosis was diagnosed in HIV-infected individuals in the Swiss HIV Cohort Study.

Results
64 individuals (69% males, 45% of non-white ethnicity, median age 35 years (interquartile range [IQR] 31-42), 28% with prior AIDS) were analysed. Median CD4 cell count was 223 cells/μl (IQR 103-339), HIV-RNA was 4.7 log10 copies/mL (IQR 4.3-5.2). T-SPOT.TB resulted positive in 25 patients (39%), negative in 18 (28%) and indeterminate in 21 (33%), corresponding to a sensitivity of 39% (95% CI 27-51%) if all test results were considered, and 58% (95% CI 43-74%) if indeterminate results were excluded. Sensitivity of IGRA was independent of CD4 cell count (p = 0.698). Among 44 individuals with available TST, 22 (50%) had a positive TST. Agreement between TST and IGRA was 57% (kappa = 0.14, p = 0.177), and in 34% (10/29) both tests were positive. Combining TST and IGRA (at least one test positive) resulted in an improved sensitivity of 67% (95% CI 52-81%). In multivariate analysis, older age was associated with negative results of TST and T-SPOT.TB (OR 3.07, 95% CI 1,22-7.74, p = 0.017, per 10 years older).

Conclusions
T-SPOT.TB and TST have similar sensitivity to detect latent TB in HIV-infected individuals. Combining TST and IGRA may help clinicians to better select HIV-infected individuals with latent tuberculosis who qualify for preventive treatment.