bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase transformation under beam-target interactions during high-intensity pulsed ion beam irradiation at low pressure
Authors: Zhu X.P. , Zhang F.G. , Tang Y. , Lei M.K. 
Published: June 2011

AbstractNitrides and/or carbonitrides formation of high efficiency was found on titanium target under irradiation of high-intensity pulsed ion beam (HIPIB) with a few shots at a low pressure of 10−2 Pa order, which is extraordinary in comparison with conventional thermo-chemical diffusion process such as gas nitriding and/or carbonitriding of metals necessarily heated at high temperatures during a processing time of hours. The underlying mechanism of the nitrides and carbonitrides formation on titanium targets was explored by a comparative study on three typical HIPIB sources, i.e., TEMP-6, TEMP-4M, and ETIGO-II, varying the irradiation intensity within several J/cm2 per shot of a 60–70 ns pulse duration and the shot number of similar ion species. It is revealed that ambient gases and ion source material are the main sources providing the nitrogen and carbon species for the phase transformation on titanium target at the low pressures, whereas the ion species of HIPIB composition is negligible at a low implantation dose of 1013–1014 ions/cm2. The adsorbed gaseous species, the deposited layer of the ion source material, and in-situ formed compound top layer from reactions between ablation plasma and the ambient species during HIPIB irradiation, can be effectively incorporated into the irradiated target surfaces under a controlled HIPIB-target interaction.
Is prosodic development correlated with grammatical and lexical development? Evidence from emerging intonation in Catalan and Spanish
Authors: PRIETO PILAR , ESTRELLA ANA , THORSON JILL , VANRELL MARIA DEL MAR 
Published: June 2011

ABSTRACTThis investigation focuses on the development of intonation patterns in four Catalan-speaking children and two Spanish-speaking children between 0 ; 11 and 2 ; 4. Pitch contours were prosodically analyzed within the Autosegmental Metrical framework in all meaningful utterances, for a total of 6558 utterances. The pragmatic meaning and communicative function were also assessed. Three main conclusions arise from the results. First, the study shows that the Autosegmental Metrical model can be successfully used to transcribe early intonation contours. Second, results reveal that children's emerging intonation is largely independent of grammatical development, and generally it develops well before the appearance of two-word combinations. As for the relationship between lexical and intonational development, the data show that the emergence of intonational grammar is related to the onset of speech and the presence of a small lexicon. Finally, we discuss the implications of these results for the biological hypothesis of intonational production.
Risk factors for mortality in non-pregnancy-related listeriosis
Authors: MOOK P. , PATEL B. , GILLESPIE I. A. 
Published: June 2011

SUMMARYWe examined non-pregnancy-related listeriosis cases in England and Wales reported to the Health Protection Agency between 1990 and 2009 (n=1864) using unconditional multivariate logistic regression analysis to identify factors independently associated with mortality. A subset analysis of cases between 2005 and 2009 (n=694) investigated the additional effect of antibiotic therapy on survival. In these cases particular malignancies, alcoholism, cardiovascular disease, increasing age, and treatment to reduce gastric acid secretion were positively associated with mortality. The absence of a concurrent condition and presence of autoimmune disease had a protective effect. The subset analysis identified illness in winter or spring as a risk factor and antibiotic therapy as a protective factor for mortality. The impact of antibiotic therapy, seasonality and reduced gastric acid status on survival should be further investigated. Policy-makers and clinicians need to more broadly advise those at risk of contracting this disease and dying as a consequence.
Epidemiological and clinical aspects of human Brucella suis infection in Polynesia
Authors: GUERRIER G. , DARONAT J. M. , MORISSE L. , YVON J. F. , PAPPAS G. 
Published: June 2011

SUMMARYHigh brucellosis seroprevalence rates in domestic swine herds have been reported in Wallis and Futuna Islands and are associated with a significant burden of human infection by Brucella suis, a species that is rarely incriminated in human disease. Between 2003 and 2010, seven patients had a positive blood culture for B. suis biovar 1, 11 symptomatic patients had a positive Rose Bengal test (RBT) and a positive serum agglutination test (SAT) and three asymptomatic cases were found to be positive for RBT, SAT or ELISA IgM (after systematic screening of 52 family members of 15 index cases). Overall, Brucella infection was diagnosed in 21 people, corresponding to a mean annual incidence of 19 cases/100 000 inhabitants. Compared to series of patients infected with other more commonly encountered Brucella spp. such as B. melitensis and B. abortus, clinical presentation and percentage and distribution of complications were similar, apart from a marked observation of significantly increased median alanine aminotransferase levels, 20 times greater than upper normal rates, but not accompanied by any particular hepatic pathology. Wallis and Futuna, where people live in close proximity to animals and where the cultural significance of pig-raising precludes the implementation of adequate veterinary preventive measures, thus represents one of the few known B. suis foci worldwide and allows for evaluation of the peculiarities of this infection.
Linguistic validation of a disease-specific quality of life measure for children and teenagers with cardiac disease
Authors: Wray Jo , Franklin Rodney , Brown Kate , Blyth Jacqueline , Marino Bradley S. 
Published: June 2011

AbstractIntroductionTo anglicise an American – that is, English language – disease-specific health-related quality of life measure, using the Paediatric Cardiac Quality of Life Inventory, for children in the age group of 8–12 years and adolescents in the age group of 13–18 years with cardiac disease, and to assess conceptual equivalence of the American and British versions.MethodsA process of forward and backward translation of the measure was undertaken before focus groups and individual interviews with 40 participants – that is, 20 children/adolescents with cardiac disease and 20 parents of children/adolescents with cardiac disease – to determine their understanding of the meaning of the questions.ResultsInterviews established that participants understood the meaning of the questions, although some found it difficult to explain the meaning of questions in which the language was explicit and wanted instead to answer the individual questions as they applied to them/their child. There was agreement that all versions of the questionnaire were relevant and comprehensive, and that the length of the questionnaires was acceptable and practical.ConclusionsThe anglicised version of the Paediatric Cardiac Quality of Life Inventory appears to be a linguistically valid measure of health-related quality of life for children and adolescents with cardiac disease. The psychometric properties of the anglicised Paediatric Cardiac Quality of Life Inventory are now being tested in a multi-centre study in the United Kingdom.
Bergman metrics and geodesics in the space of Kähler metrics on principally polarized abelian varieties
Authors: Feng Renjie 
Published: June 2011

AbstractIt is well known in Kähler geometry that the infinite-dimensional symmetric space $\mathcal{H}$ of smooth Kähler metrics in a fixed Kähler class on a polarized Kähler manifold is well approximated by finite-dimensional submanifolds $\mathcal{B}_k\subset\mathcal{H}$ of Bergman metrics of height k. Then it is natural to ask whether geodesics in $\mathcal{H}$ can be approximated by Bergman geodesics in $\mathcal{B}_k$. For any polarized Kähler manifold, the approximation is in the C0 topology. For some special varieties, one expects better convergence: Song and Zelditch proved the C2 convergence for the torus-invariant metrics over toric varieties. In this article, we show that some C∞ approximation exists as well as a complete asymptotic expansion for principally polarized abelian varieties.
Hepatocytic differentiation of rhesus monkey embryonic stem cells promoted by collagen gels and growth factors
Authors: Wang Xihong , Jin Lifang , Ji Shaohui , Guo Xiangyu , Chen Hongwei , Ji Weizhi 
Published: June 2011

AbstractrES (rhesus monkey embryonic stem) cells have similar characteristics to human ES (embryonic stem) cells, and might be useful as a substitute model for preclinical research. Before their clinical application, it is critical to understand the roles of factors that control the differentiation of ES cells into hepatocytes. Here, we analysed the effect of collagen gels on rES cells differentiation into hepatocytes by stepwise protocols. About 80% of DE (definitive endoderm) cells were generated from rES cells after being treated with activin A. The DE cells were then plated on to collagen gels or type I collagen‐coated wells with growth factors to induce hepatocyte differentiation. In type I collagen systems, characteristics of immature hepatocytes were observed, including the expression of immature hepatic genes and the generation of 15±3% AFP (alpha fetoprotein)/CK (cytokeratin)18 double‐positive cells. In collagen gel culture, differentiated cells exhibited typical hepatocyte morphology and expressed adult liver‐specific genes. The mRNA expression of AFP (immature hepatic gene) was detected at day 11 but decreased at day 18. In contrast, mRNA expression of albumin (mature hepatic gene) was detected at day 11 and increased at day 18. Compared with type I collagen systems, significantly higher AFP/CK18 double‐positive cells (68±7%) were produced in collagen gel culture. Furthermore, some differentiated cells acquired the hepatocytic function of glycogen storage. However, only immature hepatic genes were observed in collagen gel systems if growth factors were absent. Thus, collagen gels combined with hepatocyte‐inducing growth factors efficiently promoted differentiation of hepatocytes from rES.
Structure of
Trypanosoma brucei
flagellum accounts for its bihelical motion
Authors: Koyfman Alexey Y. , Schmid Michael F. , Gheiratmand Ladan , Fu Caroline J. , Khant Htet A. , Huang Dandan , He Cynthia Y. , Chiu Wah 
Published: June 2011

Trypanosoma brucei
is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum contains a crystalline paraflagellar rod (PFR) and connecting proteins. We show here, by cryoelectron tomography, the structure of the flagellum in three bending states. The PFR lattice in straight flagella repeats every 56 nm along the length of the axoneme, matching the spacing of the connecting proteins. During flagellar bending, the PFR crystallographic unit cell lengths remain constant while the interaxial angles vary, similar to a jackscrew. The axoneme drives the expansion and compression of the PFR lattice. We propose that the PFR modifies the in-plane axoneme motion to produce the characteristic trypanosome bihelical motility as captured by high-speed light microscope videography.
Measuring single-cell density
Authors: Grover William H. , Bryan Andrea K. , Diez-Silva Monica , Suresh Subra , Higgins John M. , Manalis Scott R. 
Published: June 2011

We have used a microfluidic mass sensor to measure the density of single living cells. By weighing each cell in two fluids of different densities, our technique measures the single-cell mass, volume, and density of approximately 500 cells per hour with a density precision of 0.001 g mL
-1
. We observe that the intrinsic cell-to-cell variation in density is nearly 100-fold smaller than the mass or volume variation. As a result, we can measure changes in cell density indicative of cellular processes that would be otherwise undetectable by mass or volume measurements. Here, we demonstrate this with four examples: identifying
Plasmodium falciparum
malaria-infected erythrocytes in a culture, distinguishing transfused blood cells from a patient’s own blood, identifying irreversibly sickled cells in a sickle cell patient, and identifying leukemia cells in the early stages of responding to a drug treatment. These demonstrations suggest that the ability to measure single-cell density will provide valuable insights into cell state for a wide range of biological processes.
Varying coefficient model for gene–environment interaction: a non-linear look
Authors: Ma Shujie , Yang Lijian , Romero Roberto , Cui Yuehua 
Published: June 2011

Abstract
Motivation: The genetic basis of complex traits often involves the function of multiple genetic factors, their interactions and the interaction between the genetic and environmental factors. Gene–environment (G×E) interaction is considered pivotal in determining trait variations and susceptibility of many genetic disorders such as neurodegenerative diseases or mental disorders. Regression-based methods assuming a linear relationship between a disease response and the genetic and environmental factors as well as their interaction is the commonly used approach in detecting G×E interaction. The linearity assumption, however, could be easily violated due to non-linear genetic penetrance which induces non-linear G×E interaction.
Results: In this work, we propose to relax the linear G×E assumption and allow for non-linear G×E interaction under a varying coefficient model framework. We propose to estimate the varying coefficients with regression spline technique. The model allows one to assess the non-linear penetrance of a genetic variant under different environmental stimuli, therefore help us to gain novel insights into the etiology of a complex disease. Several statistical tests are proposed for a complete dissection of G×E interaction. A wild bootstrap method is adopted to assess the statistical significance. Both simulation and real data analysis demonstrate the power and utility of the proposed method. Our method provides a powerful and testable framework for assessing non-linear G×E interaction.
Contact: cui@stt.msu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
Authors: Pickrell Joseph K. , Gaffney Daniel J. , Gilad Yoav , Pritchard Jonathan K. 
Published: June 2011

Abstract
Motivation: Sequencing-based assays such as ChIP-seq, DNase-seq and MNase-seq have become important tools for genome annotation. In these assays, short sequence reads enriched for loci of interest are mapped to a reference genome to determine their origin. Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy.
Results: Using sequencing data from the 1000 Genomes Project, we systematically scanned the human genome for regions of high sequencing depth. These regions are highly enriched for erroneously inferred transcription factor binding sites, positions of nucleosomes and regions of open chromatin. We suggest a simple masking procedure to remove these regions and reduce false positive calls.
Availability: Files for masking out these regions are available at eqtl.uchicago.edu
Contact: pickrell@uchicago.edu; dgaffney@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Telomere Erosion and Senescence in Human Articular Cartilage Chondrocytes
Authors: Martin James A. , Buckwalter Joseph A. 
Published: June 2011

Abstract
Aging and the degeneration of articular cartilage in osteoarthritis are distinct processes, but a strong association exists between age and the incidence and prevalence of osteoarthritis. We hypothesized that this association is due to in vivo replicative senescence, which causes age-related declines in the ability of chondrocytes to maintain articular cartilage. For this hypothesis to be tested, senescence-associated markers were measured in human articular chondrocytes from donors ranging in age from 1 to 87 years. These measures included in situ staining for senescence-associated β-galactosidase activity, 3H-thymidine incorporation assays for mitotic activity, and Southern blots for telomere length determinations. We found that senescence-associated β-galactosidase activity increased with age, whereas both mitotic activity and mean telomere length declined. These findings indicate that chondrocyte replicative senescence occurs in vivo and support the hypothesis that the association between osteoarthritis and aging is due in part to replicative senescence. The data also imply that transplantation procedures performed to restore damaged articular surfaces could be limited by the inability of older chondrocytes to form new cartilage after transplantation.
Morphological and Functional Characteristics of Skeletal Muscle Fibers From Hormone-replaced and Nonreplaced Postmenopausal Women
Authors: Widrick Jeffrey J. , Maddalozzo Gianni F. , Lewis Danielle , Valentine Beth A. , Garner Dena P. , Stelzer Julian E. , Shoepe Todd C. , Snow Christine M. 
Published: June 2011

Abstract
We tested the hypothesis that cross-bridge mechanisms of contraction differed in early postmenopausal women who did or did not receive hormone replacement therapy (HRT). Vastus lateralis biopsies were obtained from 17 postmenopausal women (49–57 years old), 8 of whom were on HRT for the previous 24 ± 5 months and 9 of whom were never on HRT. Electrophoresis and enzyme histochemistry revealed that fiber myosin heavy chain (MHC) isoform distribution, the cross-sectional area (CSA) of slow and fast fibers, and the relative CSA occupied by each, were similar for HRT and non-HRT groups. Single permeabilized fibers containing type IIa MHC had greater Ca2+-activated peak specific force, unloaded shortening velocity, and peak power than fibers containing type I MHC, but in all cases the values for HRT and non-HRT groups were similar. In this cross-sectional study, we found no evidence that Ca2+-activated fiber function, MHC isoform distribution, or relative CSA occupied by slow and fast fibers differed between HRT and non-HRT groups.
Skeletal Muscle Aging in F344BN F1-Hybrid Rats: I. Mitochondrial Dysfunction Contributes to the Age-Associated Reduction in VO2max
Authors: Hagen Jason L. , Krause Daniel J. , Baker David J. , Fu Ming Hua , Tarnopolsky Mark A. , Hepple Russell T. 
Published: June 2011

Abstract
Although mitochondrial DNA damage accumulates in aging skeletal muscles, how this relates to the decline in muscle mass-specific skeletal muscle aerobic function is unknown. We used a pump-perfused rat hind-limb model to examine maximal aerobic performance (V̇O2max) in young adult (YA; 8–9-month-old), late middle aged (LMA; 28–30-month-old) and senescent (SEN; 36-month-old) Fischer 344 × Brown Norway F1-hybrid rats at matched rates of convective O2 delivery (QO2). Despite similar muscle QO2 during a 4-minute contraction bout, muscle mass-specific V̇O2max was reduced in LMA (15%) and SEN (52%) versus YA. In plantaris muscle homogenates, nested polymerase chain reaction revealed an increased frequency of mitochondrial DNA deletions in the older animals. A greater reduction in the flux through electron transport chain complexes I–III than citrate synthase activity in the older animals suggests mitochondrial dysfunction consequent to mitochondrial DNA damage with aging. These results support the hypothesis that a reduced oxidative capacity, due in part to age-related mitochondrial dysfunction, contributes to the decline in aerobic performance in aging skeletal muscles.
Skeletal Muscle Aging in F344BN F1-Hybrid Rats: II. Improved Contractile Economy in Senescence Helps Compensate for Reduced ATP-Generating Capacity
Authors: Hepple Russell T. , Hagen Jason L. , Krause Daniel J. , Baker David J. 
Published: June 2011

Abstract
We used a pump-perfused rat hind-limb preparation to compare young adult (YA: 8–9- month-old), late middle-aged (LMA: 28–29-month-old), and senescent (SEN: 36-month-old) rats at similar rates of convective O2 delivery during a 4-minute contraction bout. We hypothesized that not only would V̇O2 and lactate production be reduced, but also that contractile economy would be altered with aging. Peak tension was lower in LMA (42%) and SEN (71%) versus YA. V̇O2 and lactate efflux was progressively lower with increasing age. Estimated adenosine triphosphate per N of force was increased in LMA (35%) and reduced in SEN (31%) versus YA. Myosin heavy chain (MHC) analysis by sodium dodecyl sulphate–polyacrylamide gel electrophoresis showed a lower MHC type IIb and higher MHC type IIa/IIx in SEN versus YA. Therefore, whereas contractile economy is impaired in LMA, it is improved in SEN, and this latter effect may be due in part to reduced type IIb MHC.
Trends in Hearing Impairment in United States Adults: The National Health Interview Survey, 1986–1995
Authors: Lee David J. , Gómez-Marín Orlando , Lam Byron L. , Zheng D. Diane 
Published: June 2011

Abstract
Background. United States trends in the prevalence of hearing impairment have not been reported. These trends could be rising due to changes in environmental noise exposure; alternatively, rates could be declining via a compression of morbidity hypothesis that has been postulated to be occurring in older adults residing in developed nations.
Methods. The National Health Interview Survey is a continuous multistage area probability survey of the U.S. civilian noninstitutionalized population living at addressed dwellings. Adults within randomly selected households were administered a chronic conditions list that included questions about hearing impairment. Complete data were available on 107,100 white and 17,904 African-American adults aged 18 years and older in survey years 1986–1995. Race-specific rates of hearing impairment were adjusted for age and sample survey design.
Results. Annual age-adjusted rates of some hearing impairment ranged from 11.0% to 12.7% in whites and 5.9% to 8.5% in African Americans. Rates of severe bilateral hearing impairment in these race groups were 0.7% to 1.1% and 0.1% to 0.5%, respectively. There was no evidence of change in rates of hearing impairment among participants stratified by race and 10-year age groups.
Conclusions. Reported rates of hearing impairment remained relatively stable in the U.S. noninstitutionalized population from 1986 to 1995. There was no evidence of change in rates in adults grouped into 10-year age groups. Population-based studies designed to include clinical and self-reported measures of hearing impairment are needed to further examine trends in hearing impairment.