bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
Authors: Xi Ruibin , Hadjipanayis Angela G. , Luquette Lovelace J. , Kim Tae-Min , Lee Eunjung , Zhang Jianhua , Johnson Mark D. , Muzny Donna M. , Wheeler David A. , Gibbs Richard A. , Kucherlapati Raju , Park Peter J. 
Published: November 2011

DNA copy number variations (CNVs) play an important role in the pathogenesis and progression of cancer and confer susceptibility to a variety of human disorders. Array comparative genomic hybridization has been used widely to identify CNVs genome wide, but the next-generation sequencing technology provides an opportunity to characterize CNVs genome wide with unprecedented resolution. In this study, we developed an algorithm to detect CNVs from whole-genome sequencing data and applied it to a newly sequenced glioblastoma genome with a matched control. This read-depth algorithm, called BIC-seq, can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome. Eighty percent (14/16) of the small variants tested (110 bp to 14 kb) were experimentally validated by quantitative PCR, demonstrating high sensitivity and true positive rate of the algorithm. We also extended the algorithm to detect recurrent CNVs in multiple samples as well as deriving error bars for breakpoints using a Gibbs sampling approach. We propose this statistical approach as a principled yet practical and efficient method to estimate CNVs in whole-genome sequencing data.
Time-resolved structural dynamics of thin metal films heated with femtosecond optical pulses
Authors: Chen Jie , Chen Wei-Kan , Tang Jau , Rentzepis Peter M. 
Published: November 2011

We utilize 100 fs optical pulses to induce ultrafast disorder of 35- to 150-nm thick single Au(111) crystals and observe the subsequent structural evolution using 0.6-ps, 8.04-keV X-ray pulses. Monitoring the picosecond time-dependent modulation of the X-ray diffraction intensity, width, and shift, we have measured directly electron/phonon coupling, phonon/lattice interaction, and a histogram of the lattice disorder evolution, such as lattice breath due to a pressure wave propagating at sonic velocity, lattice melting, and recrystallization, including mosaic formation. Results of theoretical simulations agree and support the experimental data of the lattice/liquid phase transition process. These time-resolved X-ray diffraction data provide a detailed description of all the significant processes induced by ultrafast laser pulses impinging on thin metallic single crystals.
A novel structural position-specific scoring matrix for the prediction of protein secondary structures
Authors: Li Dapeng , Li Tonghua , Cong Peisheng , Xiong Wenwei , Sun Jiangming 
Published: November 2011

Abstract
Motivation: The precise prediction of protein secondary structure is of key importance for the prediction of 3D structure and biological function. Although the development of many excellent methods over the last few decades has allowed the achievement of prediction accuracies of up to 80%, progress seems to have reached a bottleneck, and further improvements in accuracy have proven difficult.
Results: We propose for the first time a structural position-specific scoring matrix (SPSSM), and establish an unprecedented database of 9 million sequences and their SPSSMs. This database, when combined with a purpose-designed BLAST tool, provides a novel prediction tool: SPSSMPred. When the SPSSMPred was validated on a large dataset (10 814 entries), the Q3 accuracy of the protein secondary structure prediction was 93.4%. Our approach was tested on the two latest EVA sets; accuracies of 82.7 and 82.0% were achieved, far higher than can be achieved using other predictors. For further evaluation, we tested our approach on newly determined sequences (141 entries), and obtained an accuracy of 89.6%. For a set of low-homology proteins (40 entries), the SPSSMPred still achieved a Q3 value of 84.6%.
Availability: The SPSSMPred server is available at http://cal.tongji.edu.cn/SPSSMPred/
Contact: lith@tongji.edu.cn
Physicochemical Properties of Oat Varieties and Their Potential for Breadmaking
Authors: Hüttner Edith K. , Bello Fabio Dal , Zannini Emanuele , Titze Jean , Beuch Steffen , Arendt Elke K. 
Published: November 2011

ABSTRACTThe breadmaking potential of six oat varieties was compared with and related to their physicochemical properties. The most significant differences in the bread characteristics were found in the crumb structure. The varieties Buggy, Energie, and Zorro resulted in good bread quality with an even gas‐cell distribution characterized by a high number of relatively small pores. In contrast, Typhon, Ivory, and Nord 08/311 each had a large hole in the center of the crumb and accordingly poor quality. Breads differed little in specific volume, bake loss, and density. Rheological analysis revealed positive effects of low batter resistance to deformation on oat bread quality. On the basis of the physicochemical characterization, protein and fat contents were identified as key factors responsible for differences observed in bread quality, provided that starch damage and water‐hydration capacity were low. Additionally, high setback and final viscosity, as determined by Rapid Visco Analyser (RVA) analysis, positively affected oat bread quality. High α‐amylase activity was found to influence negatively the breadmaking performance of oats. Overall, protein, fat, dietary fiber content, starch pasting properties, and α‐amylase activity were responsible for the breadmaking properties of oat varieties.
Implications of rapid virological response in hepatitis C therapy in the US veteran population
Authors: Hwang E. W. , Thomas I.‐C. , Cheung R. , Backus L. I. 
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 105–115SummaryBackground  Early predictors of response to hepatitis C virus (HCV) therapy, such as rapid virological response, are valuable for the identification of patients with a higher likelihood of treatment success.Aim  To identify predictors of rapid virological response in a real world setting.Methods  Using the VA Clinical Case Registry, we identified patients with HCV mono‐infection, without liver transplantation, who initiated peginterferon (PEG‐IFN) and ribavirin (RBV) in 2007 or 2008 and had HCV RNA testing for RVR. Significant baseline characteristics from genotype specific univariate analyses were used in backwards stepwise models to identify significant independent predictors of RVR.Results  The final cohort consisted of 2424 patients with genotype 1 (G1), 666 patients with genotype 2 (G2), and 419 patients with genotype 3 (G3). Rapid virological response rates were 15% for G1, 71% for G2 and 57% for G3. Sustained virological response rates were significantly higher in patients with rapid virological response than without, increasing from 18% to 52% in G1, 39% to 71% in G2, and 40% to 60% in G3 (P < 0.0001). A baseline HCV RNA<500 000 IU/mL positively predicted RVR across all genotypes studied. In addition, for G1, Black race, Hispanic ethnicity, aspartate aminotransferase/alanine aminotransferase (AST/ALT) ≥0.6, ferritin≥350 ng/mL, LDL<100 mg/dL and diabetes; for G2, BMI≥30 kg/m2, platelets<150 K/μL, LDL<100 mg/dL and the use of PEG‐IFN alfa‐2b; and for G3, AST/ALT≥1.0, all negatively predicted rapid virological response.Conclusion  We found several novel independent predictors of rapid virological response, including BMI, AST/ALT ratio, ferritin, platelets, LDL, diabetes and type of PEG‐IFN prescribed, which may be useful in guiding treatment decisions in routine medical practice.
The influence of clinical risk factors on pre‐operative B‐type natriuretic peptide risk stratification of vascular surgical patients
Authors: Biccard B. M. , Lurati Buse G. A. , Burkhart C. , Cuthbertson B. H. , Filipovic M. , Gibson S. C. , Mahla E. , Leibowitz D. W. , Rodseth R. N. 
Published: November 2011

SummaryThe role of the revised cardiac risk index in risk stratification has recently been challenged by studies reporting on the superior predictive ability of pre‐operative B‐type natriuretic peptides. We found that in 850 vascular surgical patients initially risk stratified using B‐type natriuretic peptides, reclassification with the number of revised cardiac risk index risk factors worsened risk stratification (p < 0.05 for > 0, > 2, > 3 and > 4 risk factors, and p = 0.23 for > 1 risk factor). When evaluated with pre‐operative B‐type natriuretic peptides, none of the revised cardiac risk index risk factors were independent predictors of major adverse cardiac events in vascular patients. The only independent predictor was B‐type natriuretic peptide stratification (OR 5.1, 95% CI 1.8–15 for the intermediate class, and OR 25, 95% CI 8.7–70 for the high‐risk class). The clinical risk factors in the revised cardiac risk index cannot improve a risk stratification model based on B‐type natriuretic peptides.
AToxoplasma gondiimutant highlights the importance of translational regulation in the apicoplast during animal infection
Authors: Payne T. Matthew , Payne Amanda J. , Knoll Laura J. 
Published: November 2011

SummaryToxoplasma gondiiis an obligate intracellular parasite of all warm‐blooded animals. We previously described a forward genetic screen to identifyT. gondiimutants defective in the establishment of a chronic infection. One of the mutants isolated was disrupted in the 3′ untranslated region (3′UTR) of an orthologue of bacterial translation elongation factor G (EFG). The mutant does not have a growth defect in tissue culture. Genetic complementation of this mutant with the genomic locus ofTgEFGrestores virulence in an acute infection mouse model. Epitope tagged TgEFG localized to the apicoplast, via a non‐canonical targeting signal, where it functions as an elongation factor for translation in the apicoplast. Comparisons of TgEFG expression constructs with wild‐type or mutant 3′UTRs showed that a wild‐type 3′UTR is necessary for translation of TgEFG. In tissue culture, theTgEFGtranscript is equally abundant in wild‐type and mutant parasites; however, during an animal infection, theTgEFGtranscript is increased more than threefold in the mutant. These results highlight that in tissue culture, translation in the apicoplast can be diminished, but during an animal infection, translation in the apicoplast must be fully functional.
Probing the mechanistic role of the long α‐helix in subunit L of respiratory Complex I from Escherichia coli by site‐directed mutagenesis
Authors: Belevich Galina , Knuuti Juho , Verkhovsky Michael I. , Wikström Mårten , Verkhovskaya Marina 
Published: November 2011

SummaryThe C‐terminus of the NuoL subunit of Complex I includes a long amphipathic α‐helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston‐like function. First, NuoL was truncated at its C‐ and N‐termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α‐helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild‐type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α‐helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α‐helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed.
Renal function after tandem high‐dose chemotherapy and autologous stem cell transplantation in children with Wilms tumor
Authors: Lee Soo Hyun , Paik Kyung Hoon , Sung Ki Woong , Son Meong Hi , Yoo Keon Hee , Koo Hong Hoe , Kim Ju Youn , Cho Eun Joo 
Published: November 2011

Lee SH, Paik KH, Sung KW, Son MH, Yoo KH, Koo HH, Kim JY, Cho EJ. Renal function after tandem high‐dose chemotherapy and autologous stem cell transplantation in children with Wilms tumor. Pediatr Transplantation 2011: 15: 855–860. © 2011 John Wiley & Sons A/S.Abstract:  Despite increasing evidence that tandem HDCT and autoSCT might improve the survival of patients with high‐risk solid tumors, patients with Wilms tumor may be at high risk of acute and chronic renal impairment during and after tandem HDCT/autoSCT because they usually have a single kidney. We investigated the feasibility of tandem HDCT/autoSCT in patients with Wilms tumor, focusing on renal function. Six patients with relapsed/progressed Wilms tumor were assigned to undergo tandem HDCT/autoSCT. One patient developed transient ARF during the first HDCT/autoSCT. All other patients underwent the second HDCT/autoSCT as scheduled. Acute renal dysfunction during the second HDCT/autoSCT was transient and manageable. Indicators of glomerular function such as creatinine clearance, serum creatinine, and albumin excretion were in the normal range at three yr after tandem HDCT/autoSCT. Subclinical tubular dysfunctions, such as increased excretion of β‐N‐acetylglucosaminidase and β2‐microglobulin, were identified at one and three yr after tandem HDCT/autoSCT; however, no patient required treatment for these conditions. These results are helpful to consider tandem HDCT/autoSCT as a treatment option in patients with Wilms tumor. Longer duration of follow‐up and close monitoring of tubular function are required if tandem HDCT/autoSCT is indicated in patients with Wilms tumor.
Effect of Dilution Temperature on Boar Semen Quality
Authors: López Rodríguez A , Rijsselaere T , Vyt P , Van Soom A , Maes D 
Published: November 2011

ContentsAs boar semen is very sensitive to cold shock and changes in temperature during semen processing can have a profound impact on semen quality, the effect of the extender temperature at the time of dilution was investigated in a two‐step dilution protocol for boar semen being processed for liquid storage. Fifteen boars of different breeds and ages from a commercial artificial insemination centre were included. One ejaculate per boar was collected and processed with Beltsville Thawing Solution semen extender. Each ejaculate was diluted (1  :  1) at 30°C, and subsequently, the samples were diluted (30  × 106 sperm / ml) with either preheated extender [29.3°C  ± 0.2°C, group A (GA)] or extender at room temperature [22.7°C  ± 0.6°C, group B (GB)]. Samples were transported to the Faculty of Veterinary Medicine (University of Ghent, Belgium) in two isotherm boxes (one per group), stored at 17°C and investigated for three consecutive days (D0 to D2). At D0, D1 and D2, motility parameters [computer‐assisted semen analysis (CASA)] and the per cent of sperm with intact membrane (% IM) by eosin nigrosin staining were evaluated. At D0 and D2, the % of sperm with intact acrosome (% IA) was studied by Pisum sativum agglutinin staining. The average temperature of the 1 : 1 dilution was 29.4°C ± 1.1°C immediately after extender addition. No significant differences were found between groups for per cent motility [79.3 ± 9.0 for GA and 81.1 ± 9.2 for GB (p = 0.372)], % progressive motility [56.5 ± 13.3 for GA and 58.4 ± 13.8 for GB (p = 0.737)] or any CASA parameter. No differences were found for % IM [85.1 ± 10.7 and 84.5 ± 3.8 for GA and GB, respectively (p = 0.761)] and % IA [72.2 ± 9.4 for GA and 68.3 ± 16.6 for GB (p = 0.792)]. In conclusion, when a two‐step dilution is performed, preheating the extender for the second dilution to match the semen temperature did not result in better semen quality compared to a dilution at a moderate room temperature.
Usefulness of a semi‐quantitative procalcitonin test and the A‐DROP Japanese prognostic scale for predicting mortality among adults hospitalized with community‐acquired pneumonia
Authors: KASAMATSU YU , YAMAGUCHI TOSHIMASA , KAWAGUCHI TAKASHI , TANAKA NAGAAKI , OKA HIROKO , NAKAMURA TOMOYUKI , YAMAGAMI KEIKO , YOSHIOKA KATSUNOBU , IMANISHI MASAHITO 
Published: November 2011

ABSTRACTBackground and objective:  The solid‐phase immunoassay, semi‐quantitative procalcitonin (PCT) test (B R A H M S PCT‐Q) can be used to rapidly categorize PCT levels into four grades. However, the usefulness of this kit for determining the prognosis of adult patients with community‐acquired pneumonia (CAP) is unclear.Methods:  A prospective study was conducted in two Japanese hospitals to evaluate the usefulness of this PCT test in determining the prognosis of adult patients with CAP. The accuracy of the age, dehydration, respiratory failure, orientation disturbance, pressure (A‐DROP) scale proposed by the Japanese Respiratory Society for prediction of mortality due to CAP was also investigated. Hospitalized CAP patients (n = 226) were enrolled in the study. Comprehensive examinations were performed to determine PCT and CRP concentrations, disease severity based on the A‐DROP, pneumonia severity index (PSI) and confusion, urea, respiratory rate, blood pressure, age ≥65 (CURB‐65) scales and the causative pathogens. The usefulness of the biomarkers and prognostic scales for predicting each outcome were then examined.Results:  Twenty of the 170 eligible patients died. PCT levels were strongly positively correlated with PSI (ρ = 0.56, P < 0.0001), A‐DROP (ρ = 0.61, P < 0.0001) and CURB‐65 scores (ρ = 0.58, P < 0.0001). The areas under the receiver operating characteristic curves (95% CI) for prediction of survival, for CRP, PCT, A‐DROP, CURB‐65, and PSI were 0.54 (0.42–0.67), 0.80 (0.70–0.90), 0.88 (0.82–0.94), 0.88 (0.82–0.94), and 0.89 (0.85–0.94), respectively. The 30‐day mortality among patients who were PCT‐positive (≥0.5 ng/mL) was significantly higher than that among PCT‐negative patients (log–rank test, P < 0.001).Conclusions:  The semi‐quantitative PCT test and the A‐DROP scale were found to be useful for predicting mortality in adult patients with CAP.
Breeding biology and incremental benefits of outcrossing for the restoration wildflower, Hedysarum boreale Nutt. (Fabaceae)
Authors: SWOBODA KATHARINE A. , CANE JAMES H. 
Published: November 2011

AbstractNorthern sweetvetch (Hedysarum boreale Nutt.) is an herbaceous perennial legume of the Rocky Mountains, USA, whose seed is desired for rehabilitating degraded plant communities. Through experimental pollinations, the necessity of pollinators was shown by the failure of autogamy, despite stigmas first becoming receptive in the bud in close proximity to the dehiscing anthers. Nonetheless, the species proved to be self‐fertile, initiating as many fruits through selfing as outcrossing. Incremental benefits of outcrossing only later manifested in superior fruit development, seed maturation and seed germination. Farming of H. boreale can yield abundant viable seed if adequately visited by pollinating bees.
Accumulation and attrition of peat soils in the Australian Alps: Isotopic dating evidence
Authors: GROVER SAMANTHA P. P. , BALDOCK JEFFERY A. , JACOBSEN GERALDINE E. 
Published: November 2011

AbstractBog peat soils have been accumulating at Wellington Plain peatland, Victoria, Australia for the last 3300 years. Now, dried peat soils are common adjacent to bog peats. The 14C basal age of dried peat is not different from the 14C basal age of bog peat, which supports the theory that dried peat formed from bog peat. A novel application of 210Pb dating links the timing of this change with the introduction of livestock to Wellington Plain in the mid‐1800s. Physical loss of material appears to have been the dominant process removing material as bog peats drained to form dried peats, as indicated by the mass balances of carbon and lead. This research has implications for the post‐fire and post‐grazing restoration of bogs in Victoria's Alpine National Park, and the contribution of peat soils to Australia's carbon emissions.
Unmarked individuals in mark–recapture studies: Comparisons of marked and unmarked southern elephant seals at Marion Island
Authors: OOSTHUIZEN W. CHRIS , DE BRUYN P. J. NICO , BESTER MARTHÁN N. 
Published: November 2011

AbstractThe presence of unmarked individuals is common in mark–recapture study populations; however, their origin and significance in terms of population dynamics remain poorly understood. At Marion Island, southern Indian Ocean, where virtually all southern elephant seal Mirounga leonina pups born annually (1983–2008) were marked in a long‐term mark–resight study, large numbers of unmarked seals occur. Unmarked seals originate either from marker (tag) loss or from immigration. We aimed to identify patterns in the occurrence of marked and unmarked individuals that will allude to the possible origin and significance of the untagged component of the population, predicting that tag loss will add untagged seals to mainly adult age categories whereas migrating untagged individuals will be mostly juveniles. We fitted a generalized linear model using the factors month, year and age‐class to explain the relative abundance of untagged seals (tag ratio) from 1997 to 2009. Site usage of untagged seals relative to tagged seals was assessed using a binomial test. Untagged seals, predominantly juveniles, were present in the highest proportions relative to tagged seals during the winter haulout (tagged seals/total seals less than 0.3) and the lowest proportion (approximately 0.5) during the female breeding haulout, increasing in relative abundance from 1997 to 2009. Untagged seals were distributed evenly across suitable haulout sites while tagged seals displayed high local site fidelity and occurred in greater numbers at or near large breeding beaches. Untagged seals are considered to be mostly migrant seals that disperse from other islands within the southern Indian Ocean and haul out at Marion Island during non‐breeding haulouts in particular. Some of these seals immigrate to the breeding population, which can be a key component of the local population dynamics. We emphasize the need for mark–recapture studies to evaluate the role of the unmarked component of a population, thereby inducing a more confident estimation of demographic parameters from the marked sample.