bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-similar flow and contact line geometry at the rear of cornered drops
Authors: Snoeijer Jacco H. , Rio Emmanuelle , Le Grand Nolwenn , Limat Laurent
Published: June 2005

Partially wetting drops sliding down an inclined plane develop a “corner singularity” at the rear, consisting of two dynamic contact lines that intersect. We analyze the three-dimensional flow in the vicinity of this singularity by exploring similarity solutions of the lubrication equations. These predict a self-similar structure of the velocity field, in which the fluid velocity does not depend on the distance to the corner tip; this is verified experimentally by particle image velocimetry. The paper then addresses the small-scale structure of the corner, at which the singularity is regularized by a nonzero radius of curvature R of the contact line. Deriving the lubrication equation up to the lowest order in 1∕R, we show that contact line curvature postpones the destabilization of receding contact lines to liquid deposition, and that 1∕R increases dramatically close to the “pearling” instability. The general scenario is thus that sliding drops avoid a forced wetting transition by forming a corner of two inclined contact lines, which is regularized by a rounded section of rapidly decreasing size.
Influence of grain sizes on the mobility of organic thin-film transistors
Authors: Di Carlo A. , Piacenza F. , Bolognesi A. , Stadlober B. , Maresch H.
Published: June 2005

A mobility model for organic thin-film transistors (OTFTs) has been considered that fully accounts for the effect of grains and grain boundaries of the organic layer. The model has been applied to a top contact pentacene OTFT. Comparison between simulation results and experimental data shows a strong dependence of mobility as a function of grain size. The field-effect-extracted mobility is not linearly related to the grain size, but presents a rather abrupt reduction for a grain size smaller than 2μm.
Atmospheric-pressure plasma treatment to modify hydrogen storage properties of multiwalled carbon nanotubes
Authors: Han Kyu Sung , Kim Hyun Seok , Song Min Sang , Park Min Sik , Han Sang Soo , Lee Jai Young , Kang Jeung Ku , Kim Yoon Kee
Published: June 2005

We prepared multiwalled carbon nanotubes by a floating catalyst method using thermal chemical vapor deposition, but then the structures of the nanotubes were modified by the atmospheric-pressure plasma treatment to enable practical applications to hydrogen storage media. As is usually observed in multiwalled carbon nanotubes grown by thermal chemical vapor deposition, the as-grown multiwalled carbon nanotubes showed closed-cap structures and continuous walls that could not provide enough sites for hydrogen storage at ambient conditions. A thermal desorption spectra analysis showed that hydrogen was released at a temperature range of 100–150K, where the total amount of evolved hydrogen was 4.9wt%. However, after the atmospheric-pressure plasma treatment performed to open closed caps and create nanopores in multiwalled carbon nanotubes, it was found that the modified structures of the nanotubes released hydrogen not only at a subambient temperature range of 100–150K, but also at an ambient temperature range of 300–330K. The amount of released hydrogen was 5.1wt% and 0.6wt%, respectively.
Monolithic Fabry-Perot resonator for the measurement of optical constants in the terahertz range
Authors: Dobroiu Adrian , Beigang René , Otani Chiko , Kawase Kodo
Published: June 2005

A prism-shaped monolithic Fabry-Perot resonator is shown to allow absorption measurements of liquid samples in the terahertz wave range. As the radiation source a backward-wave oscillator was chosen for its tunable, highly monochromatic, continuous wave. The resonator is made of high-resistivity silicon, with two surfaces acting as partial mirrors and forming the cavity, while a third one contributes with a total internal reflection. When a liquid sample is placed on this latter surface the total reflection is attenuated and the finesse of the resonator decreases, providing absorption information about the sample. The measurement method relying on Fourier processing of the signal, as well as experimental data are presented.
Direct observation of the magnetic-field-induced entropy change in Gd5(SixGe1−x)4 giant magnetocaloric alloys
Authors: Casanova Fèlix , Labarta Amílcar , Batlle Xavier , Pérez-Reche Francisco J. , Vives Eduard , Mañosa Lluís , Planes Antoni
Published: June 2005

Direct observation of the entropy change in a first-order phase transition is obtained by using a differential scanning calorimeter in which the transition is field-induced under the application of an external magnetic field. This procedure enables direct evaluation of the magnetocaloric effect in materials showing first-order magnetostructural phase transitions. Results for Gd5(SixGe1−x)4 giant magnetocaloric alloys are reported. Calorimetric curves sweeping the field through the transition reveal a unusual increase of the entropy change with cycling. This increase is accounted for by considering both the structural and magnetic contributions to the total entropy change.
Altering cannabinoid signaling during development disrupts neuronal activity
Authors: Bernard C. , Milh M. , Morozov Y. M. , Ben-Ari Y. , Freund T. F. , Gozlan H.
Published: June 2005

In adult cortical tissue, recruitment of GABAergic inhibition prevents the progression of synchronous population discharges to epileptic activity. However, at early developmental stages, GABA is excitatory and thus unable to fulfill this role. Here, we report that retrograde signaling involving endocannabinoids is responsible for the homeostatic control of synaptic transmission and the resulting network patterns in the immature hippocampus. Blockade of cannabinoid type 1 (CB1) receptor led to epileptic discharges, whereas overactivation of CB1 reduced network activity
in vivo
. Endocannabinoid signaling thus is able to keep population discharge patterns within a narrow physiological time window, balancing between epilepsy on one side and sparse activity on the other, which may result in impaired developmental plasticity. Disturbing this delicate balance during pregnancy in either direction, e.g., with marijuana as a CB1 agonist or with an antagonist marketed as an antiobesity drug, can have profound consequences for brain maturation even in human embryos.
Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP
Authors: Nienhaus Karin , Nienhaus G. Ulrich , Wiedenmann Jörg , Nar Herbert
Published: June 2005

Genetically encoded fusion constructs derived from fluorescent proteins (FPs) can be designed to report on a multitude of events and signals in cells, tissues, and entire organs without interfering with the complex machinery of life. EosFP is a novel FP from the scleractinian coral
Lobophyllia hemprichii
that switches its fluorescence emission from green (516 nm) to red (581 nm) upon irradiation with ≈400-nm light. This property enables localized tagging of proteins and thus provides a valuable tool for tracking protein movements within live cells. Here, we present the x-ray structures of the green and red forms of WT EosFP. They reveal that formation of the red chromophore is associated with cleavage of the peptide backbone, with surprisingly little change elsewhere in the structure, and provide insights into the mechanism that generates this interesting posttranslational polypeptide modification.
Structure of a peptide:
N
-glycanase-Rad23 complex: Insight into the deglycosylation for denatured glycoproteins
Authors: Lee Jung-Hoon , Choi Jung Min , Lee Changwook , Yi Ki Joung , Cho Yunje
Published: June 2005

In eukaryotes, misfolded proteins must be distinguished from correctly folded proteins during folding and transport processes by quality control systems. Yeast peptide:
N
-glycanase (yPNGase) specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists proteasome-mediated glycoprotein degradation by forming a complex with 26S proteasome through DNA repair protein, yRad23. Here, we describe the crystal structures of a yPNGase and XPC-binding domain of yRad23 (yRad23XBD, residues 238-309) complex and of a yPNGase-yRad23XBD complex bound to a caspase inhibitor, Z-VAD-fmk. yPNGase is formed with three domains, a core domain containing a Cys-His-Asp triad, a Zn-binding domain, and a Rad23-binding domain. Both N- and C-terminal helices of yPNGase interact with yRad23 through extensive hydrophobic interactions. The active site of yPNGase is located in a deep cleft that is formed with residues conserved in all PNGase members, and three sugar molecules are bound to this cleft. Complex structures in conjunction with mutational analyses revealed that the walls of the cleft block access to the active site of yPNGase by native glycoprotein, whereas the cleft is sufficiently wide to accommodate denatured glycoprotein, thus explaining the specificity of PNGase for denatured substrates.
Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein
Authors: Yin Hsien-Sheng , Paterson Reay G. , Wen Xiaolin , Lamb Robert A. , Jardetzky Theodore S.
Published: June 2005

Class I viral fusion proteins share common mechanistic and structural features but little sequence similarity. Structural insights into the protein conformational changes associated with membrane fusion are based largely on studies of the influenza virus hemagglutinin in pre- and postfusion conformations. Here, we present the crystal structure of the secreted, uncleaved ectodomain of the paramyxovirus, human parainfluenza virus 3 fusion (F) protein, a member of the class I viral fusion protein group. The secreted human parainfluenza virus 3 F forms a trimer with distinct head, neck, and stalk regions. Unexpectedly, the structure reveals a six-helix bundle associated with the postfusion form of F, suggesting that the anchor-minus ectodomain adopts a conformation largely similar to the postfusion state. The transmembrane anchor domains of F may therefore profoundly influence the folding energetics that establish and maintain a metastable, prefusion state.
Determinants of plasma dihydrophylloquinone in men and women
Authors: Erkkilä Arja T. , Lichtenstein Alice H. , Jacques Paul F. , Hu Frank B. , Wilson Peter W. F. , Booth Sarah L.
Published: June 2005

Commercial hydrogenation results in the formation of trans fatty acids. An unintended consequence of the hydrogenation process is conversion of phylloquinone (vitamin K1) to dihydrophylloquinone. Plasma dihydrophylloquinone concentrations have yet to be characterized in population-based studies. Dietary determinants of plasma dihydrophylloquinone were estimated using a semi-quantitative food frequency questionnaire in 803 men and 913 women in the Framingham Offspring Study. Geometric mean dihydrophylloquinone intake was 21·3 (95 % CI 20·4, 22·3) μg/d in men and 19·4 (95 % CI 18·5, 20·2) μg/d in women. Detectable (>0·05 nmol/l) plasma dihydrophylloquinone concentrations were measured in 41 % and 30 % of men and women, respectively. The multivariate odds ratio (OR) of detectable plasma dihydrophylloquinone from the lowest to the highest quartile category of dihydrophylloquinone intake were 1 (referent), 1·13 (95 % CI 0·83, 1·53), 1·66 (95 % CI 1·21, 2·26) and 1·84 (95 % CI 1·31, 2·58), P for trend <0·001, adjusted for sex, age, body mass index, triacylglycerols, season and energy intake. Higher trans fatty acid intake was associated with higher multivariate OR for detectable plasma dihydrophylloquinone (OR comparing extreme quartiles 2·41 (95 % CI 1·59, 3·64), P for trend <0·001). There were limitations in the use of plasma dihydrophylloquinone, evident in the high proportion of the population that had non-detectable dihydrophylloquinone concentrations. Despite this caveat, higher plasma dihydrophylloquinone was associated with higher dihydrophylloquinone intake and higher trans fatty acid intake.
Effect of consumption of soy isoflavones on behavioural, somatic and affective symptoms in women with premenstrual syndrome
Authors: Bryant M. , Cassidy A. , Hill C. , Powell Jonathan , Talbot Duncan , Dye L.
Published: June 2005

Up to 80 % of the Western female population experience premenstrual syndrome (PMS). Long-term pharmacological therapy is unacceptable to most women, and is not warranted for moderate symptoms. Nutritional therapies are popular, but lack a clear evidence base. Anecdotal evidence suggests beneficial effects of soy isoflavones because of their influence on endogenous oestrogen and actions on specific tissues. The effect of isolated soya protein (ISP) containing 68 mg/d (aglycone equivalents) soy isoflavones (IF) on premenstrual symptom severity was studied in a seven-menstrual cycle, double-blind, placebo-controlled, crossover intervention study in twenty-three women with prospectively confirmed PMS aged 18–35 years and BMI 19–30 kg/m2. ISP containing IF or milk protein placebo was consumed for two complete menstrual cycles. ISP containing IF (genistein, daidzein, equol) were measured in 24 h urine samples. After two cycles of ISP containing IF intervention, total symptoms (F(2,36)8·20,P=0·000) and physical symptoms (F(2,36)8·18,P=0·000) were significantly reduced compared with baseline after both active and placebo treatments, although differences between active and placebo treatment were non-significant. Specific premenstrual symptoms, headache (F(2,32)4·10,P=0·026) and breast tenderness (F(2,32)4·59,P=0·018), were reduced from baseline after soy IF, but not milk protein placebo. Cramps (F(2,32)4·15,P=0·025) and swelling (F(2,32)4·64,P=0·017) were significantly lower after active treatment compared with placebo. Concentrations of genistein and daidzein were increased following soy IF consumption, but equol production did not enhance symptom reduction. The present study showed that ISP containing IF may have potential to reduce specific premenstrual symptoms via non-classical actions.
The ‘anomalous’ absorption of labelled and unlabelled vitamin C in man
Authors: Bluck Leslie J. C. , Jones Kerry S. , Coward W. Andy , Bates Christopher J.
Published: June 2005

Previous studies of vitamin C absorption in man using stable isotope probes have given results which cannot easily be reconciled with those obtained using non-isotope measurement. In order to investigate some of the apparent paradoxes we have conducted a study using two consecutive doses of vitamin C, one labelled and one unlabelled, given 90 min apart. Compatibility of the experimental results with two feasible models was investigated. In Model 1, ingested vitamin C enters a pre-existing pool before absorption, which occurs only when a threshold is exceeded; in Model 2, ingested vitamin C is exchanged with a pre-existing flux before absorption. The key difference between these two models lies in the predicted profile of labelled material in plasma. Model 1 predicts that the second unlabelled dose will produce a secondary release of labelled vitamin C which will not be observed on the basis of Model 2. In all subjects Model 1 failed to predict the observed plasma concentration profiles for labelled and unlabelled vitamin C, but Model 2 fitted the experimental observations. We speculate on possible physiological explanations for this behaviour, but from the limited information available cannot unequivocally confirm the model structure by identifying the source of the supposed flux.
Validation of energy intake by 24-hour multiple pass recall: comparison with total energy expenditure in children aged 5–7 years
Authors: Montgomery Colette , Reilly John J. , Jackson Diane M. , Kelly Louise A. , Slater Christine , Paton James Y. , Grant Stan
Published: June 2005

Accurate measurement of energy intake (EI) is essential in studies of energy balance in all age groups. Reported values for EI can be validated against total energy expenditure (TEE) measured using doubly labelled water (DLW). Our previous work has indicated that the use of the standardized 24 h multiple pass recall (24 h MPR) method produces slight overestimates of EI in pre-school children which are inaccurate at individual level but acceptable at group level. To extend this work, the current study validated EI by 24 h MPR against TEE by DLW in sixty-three (thirty-two boys) school-aged children (median age 6 years). In both boys and girls, reported EI was higher than TEE, although this difference was only significant in the girls (median difference 420 kJ/d, P=0·05). On analysis of agreement between TEE and EI, the group bias was an overestimation of EI by 250 kJ/d with wide limits of agreement (−2880, 2380 kJ/d). EI was over-reported relative to TEE by 7 % and 0·9 % in girls and boys, respectively. The bias in the current study was lower than in our previous study of pre-school children, suggesting that estimates of EI become less inaccurate as children age. However, the current study suggests that the 24 h MPR is inaccurate at the individual level.
Some aspects of the pyridoxine (vitamin B6) requirement in weanling piglets
Authors: Matte J. J. , Giguère A. , Girard C. L.
Published: June 2005

Four trials were carried out to determine the optimal level of dietary pyridoxine (vitamin B6) and its interaction with riboflavin (vitamin B2) in early-weaned piglets. In Trial 1, twelve piglets were tube-fed graded supplements of B6, 0, 10, 50 or 100 mg/kg. The level of 50 mg/kg maximized B6in red blood cells (P<0·05). In Trial 2, thirty-six piglets were tube-fed with four combinations of B6(0v. 50 mg/kg) and B2(0v. 25 mg/kg). The B6supplement increased (P<0·01) B6in red blood cells. C-peptide and insulin responses to intravenous glucose tended (P<0·08) to or decreased (P<0·03) with B2while no effect was observed on glucose. After gastro-enteral glucose, dietary B2depressed C-peptide and insulin responses in B6-unsupplemented piglets and increased them in B6-supplemented piglets (P<0·03). The glucose response tended to be higher in B6-supplemented piglets (P<0·06). Trials 3 and 4 were carried out in commercial conditions using either B6and/or B2supplements given during 2 weeks after weaning (Trial 3) or a B6supplement alone (50 mg/kg) given between 2 (weaning) and 10 weeks of age. Despite a marked and persistent increase (P<0·01) of B6in red blood cells in B6-supplemented piglets, the effect on growth performance was either none (P>0·39; Trial 3) or marginally lower (<−2 %;P<0·03; Trial 4). In conclusion, it appears that a dietary supplement of 50 mg/kg B6saturated the red blood cell pool in B6and influenced, along with B2, the glucose homeostasis through the entero-insular axis. Nevertheless, such metabolic effects are not reflected on growth performance.
Long-term sucrose-drinking causes increased body weight and glucose intolerance in normal male rats
Authors: Kawasaki Takahiro , Kashiwabara Akiko , Sakai Tadashi , Igarashi Kanji , Ogata Nobuyuki , Watanabe Hiroyuki , Ichiyanagi Kaoru , Yamanouchi Toshikazu
Published: June 2005

The current epidemic of diabetes likely reflects marked changes in environmental factors, although genetic susceptibility plays a powerful role in the occurrence of diabetes in certain populations. We investigated whether long-term sucrose-drinking causes hyperglycaemia in male Wistar-Imamichi littermates (n 32), which are not genetically susceptible to diabetes or obesity. Each litter was divided equivalently into two groups, the sucrose group and the control group. The sucrose group received 300 g/l sucrose water and the control group received regular water until 42 weeks of age. Rats were weighed every 1 or 2 weeks. Oral glucose tolerance tests were performed at 28 and 36 weeks of age. Plasma glucose and insulin concentrations were measured. Body weights were significantly greater in the sucrose group than in the control group in 18-week-old rats (P<0·05), and the difference between the two groups reached 163 g by the end of the study (P<0·01). The 120 min post-load plasma glucose concentration in the sucrose group was 11·4 (sd 2·8) mmol/l in 28-week-old rats and 12·7 (sd 2·2) mmol/l in 36-week-old rats, while that of the control group remained approximately 7·3–7·7 mmol/l. In the sucrose group, the plasma insulin peak occurred 30 min post-load at 28 weeks of age; but the peak disappeared and hyperinsulinaemia was prolonged at 36 weeks of age. In conclusion, long-term sucrose-drinking causes increased body weight and glucose intolerance in normal male rats.
Concentrations of cholesterol oxidation products in raw, heat-processed and frozen-stored meat of broiler chickens fed diets differing in the type of fat and vitamin E concentrations
Authors: Eder Klaus , Grünthal Gerit , Kluge Holger , Hirche Frank , Spilke Joachim , Brandsch Corinna
Published: June 2005

The present study was performed to investigate the effect of dietary fat and vitamin E on concentrations of cholesterol oxidation products (COP) in broiler muscle. A total of 144 1-d-old broiler chicks were fed diets with either palm oil, soyabean oil or linseed oil and vitamin E concentrations of 20, 40 or 200 mg/kg for 35 d. COP concentrations were analysed in raw, heat-processed (180°C, 20 min) and frozen-stored (−20°C, 6 months) breast and thigh muscles. COP concentrations were influenced by dietary vitamin E concentration, dietary fat, treatment and type of muscle (P<0·001). Increasing the dietary vitamin E concentration generally reduced the concentration of COP. This effect was strongest in broilers fed linseed oil and weakest in broilers fed palm oil; the effect of vitamin E was also stronger in heated muscles than in raw or frozen-stored muscles. Moreover, the concentration of COP in thigh muscle was more strongly influenced by dietary vitamin E than that in breast muscle. COP concentrations in muscles were on average highest in broilers fed linseed oil and lowest in broilers fed palm oil, but the effect of the dietary fat also depended on the vitamin E concentration, the treatment and the type of muscle. In conclusion, our study shows that dietary fat and vitamin E influence the concentrations of total COP in broiler muscle. However, the effects of these factors were not only influenced by interactions between each other, but also depended on the treatment of the muscle and the type of muscle.
Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth
Authors: Luedeke Cosima , Frei Stéphanie Buvelot , Sbalzarini Ivo , Schwarz Heinz , Spang Anne , Barral Yves
Published: June 2005

Polarized cells frequently use diffusion barriers to separate plasma membrane domains. It is unknown whether diffusion barriers also compartmentalize intracellular organelles. We used photobleaching techniques to characterize protein diffusion in the yeast endoplasmic reticulum (ER). Although a soluble protein diffused rapidly throughout the ER lumen, diffusion of ER membrane proteins was restricted at the bud neck. Ultrastructural studies and fluorescence microscopy revealed the presence of a ring of smooth ER at the bud neck. This ER domain and the restriction of diffusion for ER membrane proteins through the bud neck depended on septin function. The membrane-associated protein Bud6 localized to the bud neck in a septin-dependent manner and was required to restrict the diffusion of ER membrane proteins. Our results indicate that Bud6 acts downstream of septins to assemble a fence in the ER membrane at the bud neck. Thus, in polarized yeast cells, diffusion barriers compartmentalize the ER and the plasma membrane along parallel lines.
Epigenetic manipulation of gene expression
Authors: Juliano Rudy L. , Dixit Vidula R. , Kang Hyunmin , Kim Tai Young , Miyamoto Yuko , Xu Dong
Published: June 2005

Cell biologists have been afforded extraordinary new opportunities for experimentation by the emergence of powerful technologies that allow the selective manipulation of gene expression. Currently, RNA interference is very much in the limelight; however, significant progress has also been made with two other approaches. Thus, antisense oligonucleotide technology is undergoing a resurgence as a result of improvements in the chemistry of these molecules, whereas designed transcription factors offer a powerful and increasingly convenient strategy for either up- or down-regulation of targeted genes. This mini-review will highlight some of the key features of these three approaches to gene regulation, as well as provide pragmatic guidance concerning their use in cell biological experimentation based on our direct experience with each of these technologies. The approaches discussed here are being intensely pursued in terms of possible therapeutic applications. However, we will restrict our comments primarily to the cell culture situation, only briefly alluding to fundamental differences between utilization in animals versus cells.
Combined loss of proapoptotic genes Bak or Bax with Bim synergizes to cause defects in hematopoiesis and in thymocyte apoptosis
Authors: Hutcheson Jack , Scatizzi John C. , Bickel Emily , Brown Nathaniel J. , Bouillet Philippe , Strasser Andreas , Perlman Harris
Published: June 2005

The proapoptotic members of the Bcl-2 family can be subdivided into members that contain several Bcl-2 homology (BH) domains and those that contain only the BH3 domain. Although it is known that BH3-only proteins and the multi-BH domain proteins, Bak and Bax, are essential for programmed cell death, the overlapping role of these two subgroups has not been examined in vivo. To investigate this, we generated Bak/Bim and Bax/Bim double deficient mice. We found that although Bax−/−Bim−/−, but not Bak−/−Bim−/−, mice display webbed hind and front paws and malocclusion of the incisors, both groups of mice present with dysregulated hematopoiesis. Combined loss of Bak and Bim or Bax and Bim causes defects in myeloid and B-lymphoid development that are more severe than those found in the single knock-out mice. Bak−/−Bim−/− mice have a complement of thymocytes that resembles those in control mice, whereas Bax−/−Bim−/− mice are more similar to Bim−/− mice. However, thymocytes isolated from Bak−/−Bim−/− or Bax−/−Bim−/− mice are markedly more resistant to apoptotic stimuli mediated by the intrinsic pathway as compared with thymocytes from single-knockout mice. These data suggest an essential overlapping role for Bak or Bax and Bim in the intrinsic apoptotic pathway.
Repertoire, diversity, and differentiation of specific CD8 T cells are associated with immune protection against human cytomegalovirus disease
Authors: Sacre Karim , Carcelain Guislaine , Cassoux Nathalie , Fillet Anne-Marie , Costagliola Dominique , Vittecoq Daniel , Salmon Dominique , Amoura Zahir , Katlama Christine , Autran Brigitte
Published: June 2005

To determine the correlates of immune recovery from active human CMV (HCMV) disease, we compared the antigenic repertoire, diversity, magnitude, and differentiation of HCMV-specific CD8+ T cells in HIV-HCMV coinfected subjects with no, cured, or active HCMV disease and in healthy HIV-negative HCMV-positive controls. ELISPOT–IFN-γ assays using peptide pools spanning the pp65 and immediate early 1 (IE1) HCMV proteins showed that HCMV-specific CD8+ T cells had a significantly broader antigenic repertoire and greater diversity in HIV-positive patients controlling HCMV replication than in those with active HCMV disease, but the magnitude of the CD8 T cell response did not differ between the different groups. HCMV-specific T cells mainly were focused against IE1 during the short-term recovery from retinitis, and switched toward pp65 during long-term recovery. HCMV-specific T cells displaying an “early” (CD8+CD27+CD28+) and “intermediate” (CD8+CD27−CD28+) differentiation phenotype were increased significantly during long-term recovery compared with other HIV-positive patients and were nearly undetectable during active HCMV disease. HCMV-specific T cells with a “late” (CD8+CD27−28−) differentiation phenotype predominated in all cases. Therefore, restoration of immune protection against HCMV after active HCMV disease in immunodeficient individuals is associated with enlarged repertoire and diversity, and with early differentiation of virus-specific CD8+ T cells, thus defining immune correlates of protection against diseases caused by persistent viruses.
B cells from hyper-IgM patients carrying UNG mutations lack ability to remove uracil from ssDNA and have elevated genomic uracil
Authors: Kavli Bodil , Andersen Sonja , Otterlei Marit , Liabakk Nina B. , Imai Kohsuke , Fischer Alain , Durandy Anne , Krokan Hans E. , Slupphaug Geir
Published: June 2005

The generation of high-affinity antibodies requires somatic hypermutation (SHM) and class switch recombination (CSR) at the immunoglobulin (Ig) locus. Both processes are triggered by activation-induced cytidine deaminase (AID) and require UNG-encoded uracil-DNA glycosylase. AID has been suggested to function as an mRNA editing deaminase or as a single-strand DNA deaminase. In the latter model, SHM may result from replicative incorporation of dAMP opposite U or from error-prone repair of U, whereas CSR may be triggered by strand breaks at abasic sites. Here, we demonstrate that extracts of UNG-proficient human B cell lines efficiently remove U from single-stranded DNA. In B cell lines from hyper-IgM patients carrying UNG mutations, the single-strand–specific uracil-DNA glycosylase, SMUG1, cannot complement this function. Moreover, the UNG mutations lead to increased accumulation of genomic uracil. One mutation results in an F251S substitution in the UNG catalytic domain. Although this UNG form was fully active and stable when expressed in Escherichia coli, it was mistargeted to mitochondria and degraded in mammalian cells. Our results may explain why SMUG1 cannot compensate the UNG2 deficiency in human B cells, and are fully consistent with the DNA deamination model that requires active nuclear UNG2. Based on our findings and recent information in the literature, we present an integrated model for the initiating steps in CSR.
Nonhuman primate models of asthma
Authors: Coffman Robert L. , Hessel Edith M.
Published: June 2005

Asthma is a complex human disease that does not have an accurate counterpart in any common model organism. Most of our understanding of the immune mechanisms underlying asthma comes from studies in man and mouse. However, there are fundamental differences between the spontaneous disease in man and the experimentally induced counterparts in mice. We advocate more extensive use of nonhuman primate asthma models to reconcile these differences between man and mouse.
A note on Weyl’s theorem
Authors: Cao Xiaohong , Guo Maozheng , Meng Bin
Published: June 2005

The Kato spectrum of an operator is deployed to give necessary and sufficient conditions for Browder’s theorem to hold.
The Rokhlin lemma for homeomorphisms of a Cantor set
Authors: Bezuglyi S. , Dooley A. , Medynets K.
Published: June 2005

For a Cantor set

X
X

, let

H
o
m
e
o
(
X
)

Homeo(X)

denote the group of all homeomorphisms of

X
X

. The main result of this note is the following theorem. Let

T
∈
H
o
m
e
o
(
X
)

T\in Homeo(X)

be an aperiodic homeomorphism, let

μ
1

,

μ
2

,
…
,

μ
k

\mu _1,\mu _2,\ldots ,\mu _k

be Borel probability measures on

X
X

, and let

ε
>
0

\varepsilon > 0

and

n
≥
2

n\ge 2

. Then there exists a clopen set

E
⊂
X

E\subset X

such that the sets

E
,
T
E
,
…
,

T

n
−
1

E

E,TE,\ldots , T^{n-1}E

are disjoint and

μ
i

(
E
∪
T
E
∪
…
∪

T

n
−
1

E
)
>
1
−
ε
,
 
i
=
1
,
…
,
k

\mu _i(E\cup TE\cup \ldots \cup T^{n-1}E) > 1 - \varepsilon ,\ i= 1,\ldots ,k

. Several corollaries of this result are given. In particular, it is proved that for any aperiodic

T
∈
H
o
m
e
o
(
X
)

T\in Homeo(X)

the set of all homeomorphisms conjugate to

T
T

is dense in the set of aperiodic homeomorphisms.
Spectra of upper triangular operator matrices
Authors: Benhida C. , Zerouali E. , Zguitti H.
Published: June 2005

LetX,YX, Ybe given Banach spaces. ForA∈L(X),B∈L(Y)A\in {\mathcal L}(X),\,B\in {\mathcal L}(Y)andC∈L(Y,X)C\in {\mathcal L}(Y,X), letMCM_Cbe the operator defined onX⊕YX\oplus YbyMC=[Aamp;C0amp;B]M_C = [\begin {smallmatrix} A & C 0 & B \end {smallmatrix}]. We give sufficient conditions onCCto getΣ(MC)=Σ(M0),\Sigma (M_C) = \Sigma (M_0),whereΣ\Sigmaruns over a large class of spectra. We also discuss the case of some spectra for which the latter equality fails.
Regularization for a class of ill-posed Cauchy problems
Authors: Huang Yongzhong , Zheng Quan
Published: June 2005

This paper is concerned with the ill-posed Cauchy problem associated with a densely defined linear operator

A
A

in a Banach space. Our main result is that if

−
A

-A

is the generator of an analytic semigroup of angle

≥
π

/

4

\ge \pi /4

, then there exists a family of regularizing operators for such an ill-posed Cauchy problem by using the Gajewski and Zacharias quasi-reversibility method, and semigroups of linear operators.
A characterization of positive self-adjoint extensions and its application to ordinary differential operators
Authors: Wei Guangsheng , Jiang Yaolin
Published: June 2005

A new characterization of the positive self-adjoint extensions of symmetric operators,

T
0

T_0

, is presented, which is based on the Friedrichs extension of

T
0

,

T_0,

a direct sum decomposition of domain of the adjoint

T
0

∗

T_0^{*}

and the boundary mapping of

T
0

∗

T_0^{*}

. In applying this result to ordinary differential equations, we characterize all positive self-adjoint extensions of symmetric regular differential operators of order

2
n

2n

in terms of boundary conditions.
Orderings and maximal ideals of rings of analytic functions
Authors: Díaz-Cano A.
Published: June 2005

We prove that there is a natural injective correspondence between the maximal ideals of the ring of analytic functions on a real analytic set

X
X

and those of its subring of bounded analytic functions. By describing the maximal ideals in terms of ultrafilters we see that this correspondence is surjective if and only if

X
X

is compact. This approach is also useful for studying the orderings of the field of meromorphic functions on

X
X

.
A new characterization of gaps between two subspaces
Authors: Du Hong-Ke , Deng Chun-Yuan
Published: June 2005

In this note, a new characterization of gaps between two subspaces of a Hilbert space is established.
The backward shift on Dirichlet-type spaces
Authors: Garcia Stephan
Published: June 2005

We study the backward shift operator on Hilbert spaces

H

α

{\mathcal {H}}_{\alpha }

(for

α
≥
0

{\alpha \geq 0}

) which are norm equivalent to the Dirichlet-type spaces

D

α

D_{\alpha }

. Although these operators are unitarily equivalent to the adjoints of the forward shift operator on certain weighted Bergman spaces, our approach is direct and completely independent of the standard Cauchy duality. We employ only the classical Hardy space theory and an elementary formula expressing the inner product on

H

α

{\mathcal {H}}_{\alpha }

in terms of a weighted superposition of backward shifts.
Isochronicity of a class of piecewise continuous oscillators
Authors: Mañosas Francesc , Torres Pedro
Published: June 2005

Motivated by a classical pendulum clock model suggested by Andrade in 1920, we study the equation

x
¨

+
g
(
x
)
sgn
⁡

x
˙

+
x
=
0

\ddot x+g(x)\operatorname {sgn}{\dot x}+x=0

and prove that for a nonlinear analytic

g
g

the origin is never an isochronous focus or an isochronous center.
Real 𝑘-flats tangent to quadrics in ℝⁿ
Authors: Sottile Frank , Theobald Thorsten
Published: June 2005

Let

d

k
,
n

d_{k,n}

and

#

k
,
n

\#_{k,n}

denote the dimension and the degree of the Grassmannian

G

k
,
n

\mathbb {G}_{k,n}

, respectively. For each

1
≤
k
≤
n
−
2

1 \le k \le n-2

there are

2

d

k
,
n

⋅

#

k
,
n

2^{d_{k,n}} \cdot \#_{k,n}

(a priori complex)

k
k

-planes in

P

n

\mathbb {P}^n

tangent to

d

k
,
n

d_{k,n}

general quadratic hypersurfaces in

P

n

\mathbb {P}^n

. We show that this class of enumerative problems is fully real, i.e., for

1
≤
k
≤
n
−
2

1 \le k \le n-2

there exists a configuration of

d

k
,
n

d_{k,n}

real quadrics in (affine) real space

R

n

\mathbb {R}^n

so that all the mutually tangent

k
k

-flats are real.
Integrability of subdifferentials of directionally Lipschitz functions
Authors: Thibault Lionel , Zlateva Nadia
Published: June 2005

Using a quantitative version of the subdifferential characterization of directionally Lipschitz functions, we study the integrability of subdifferentials of such functions over arbitrary Banach space.
On the Waring–Goldbach problem for seventh powers
Authors: Kumchev Angel
Published: June 2005

We use sieve theory and recent estimates for Weyl sums over almost primes to prove that every sufficiently large even integer is the sum of

46
46

seventh powers of prime numbers.
Blocks with 𝑝-power character degrees
Authors: Navarro Gabriel , Robinson Geoffrey
Published: June 2005

Let

B
B

be a

p
p

-block of a finite group

G
G

. If

χ
(
1
)

\chi (1)

is a

p
p

-power for all

χ
∈
Irr
⁡
(
B
)

\chi \in \operatorname {Irr}(B)

, then

B
B

is nilpotent.
Densities of quartic fields with even Galois groups
Authors: Wong Siman
Published: June 2005

Let

N
(
d
,
G
,
X
)

N(d, G, X)

be the number of degree

d
d

number fields

K
K

with Galois group

G
G

and whose discriminant

D
K

D_K

satisfies

|

D
K

|

≤
X

|D_K| \le X

. Under standard conjectures in diophantine geometry, we show that

N
(
4
,

A
4

,
X
)

≪
ϵ

X

2

/

3
+
ϵ

N(4, A_4, X) \ll _\epsilon X^{2/3+\epsilon }

, and that there are

≪
ϵ

N

3
+
ϵ

\ll _\epsilon N^{3+\epsilon }

monic, quartic polynomials with integral coefficients of height

≤
N

\le N

whose Galois groups are smaller than

S
4

S_4

, confirming a question of Gallagher. Unconditionally we have

N
(
4
,

A
4

,
X
)

≪
ϵ

X

5

/

6
+
ϵ

N(4, A_4, X) \ll _\epsilon X^{5/6 + \epsilon }

, and that the

2
2

-class groups of almost all Abelian cubic fields

k
k

have size

≪
ϵ

D
k

1

/

3
+
ϵ

\ll _\epsilon D_k^{1/3+\epsilon }

. The proofs depend on counting integral points on elliptic fibrations.
On congruence properties of 𝑝(𝑛,𝑚)
Authors: Kronholm Brandt
Published: June 2005

In the late 19th century, Sylvester and Cayley investigated the properties of the partition function

p
(
n
,
m
)

p(n,m)

. This function enumerates the partitions of a non-negative integer

n
n

into exactly

m
m

parts. Here we investigate the congruence properties of such functions and we obtain several infinite classes of Ramanujan-type congruences.
A remark on a conjecture of Borwein and Choi
Authors: Osburn Robert
Published: June 2005

We prove the remaining case of a conjecture of Borwein and Choi concerning an estimate on the square of the number of solutions to

n
=

x
2

+
N

y
2

n=x^2+Ny^2

for a squarefree integer

N
N

.
Finite speed of propagation and local boundary conditions for wave equations with point interactions
Authors: Kurasov Pavel , Posilicano Andrea
Published: June 2005

We show that the boundary conditions entering in the definition of the self-adjoint operator

Δ

A
,
B

\Delta ^{A,B}

describing the Laplacian plus a finite number of point interactions are local if and only if the corresponding wave equation

ϕ
¨

=

Δ

A
,
B

ϕ

\ddot \phi =\Delta ^{A,B}\phi

has finite speed of propagation.
The polynomial analogue of a theorem of Rényi
Authors: Morrison Kent
Published: June 2005

Rényi’s result on the density of integers whose prime factorizations have excess multiplicity has an analogue for polynomials over a finite field.
A note on the zero Mach number limit of compressible Euler equations
Authors: Yong Wen-An
Published: June 2005

This note presents a short and elementary justification of the classical zero Mach number limit for isentropic compressible Euler equations with prepared initial data. We also show the existence of smooth compressible flows, with the Mach number sufficiently small, on the (finite) time interval where the incompressible Euler equations have smooth solutions.
Operator-valued free Fisher information and modular frames
Authors: Meng Bin , Guo Maozheng , Cao Xiaohong
Published: June 2005

We introduce the operator-valued free Fisher information for a random variable in an operator-valued noncommutative probability space and point out its relations to the amalgamated freeness. Using M. Frank and D. Larson’s modular frame notion we can construct the conjugate variable for an operator-valued semicircle variable with conditional expectation covariance. Then we obtain its free Fisher information and show it is equal to the index of the conditional expectation. At last the conjugate variable with respect to a modular frame operator for a semicircle variable is also constructed.
Generalized subdifferential of the distance function
Authors: Dutta S.
Published: June 2005

We derive the proximal normal formula for almost proximinal sets in a smooth and locally uniformly convex Banach space. Our technique leads us to show the generic Fréchet smoothness of the distance function in the case the norm is Fréchet smooth, and we derive a necessary and sufficient condition for the convexity of a Chebyshev set in a Banach space

X
X

with norms on

X
X

and

X
∗

X^*

locally uniformly convex.
The net of life: Reconstructing the microbial phylogenetic network
Authors: Kunin Victor , Goldovsky Leon , Darzentas Nikos , Ouzounis Christos A.
Published: June 2005

It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the “net of life.” We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as “vines,” and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Authors: Horvath Julie E. , Gulden Cassandra L. , Vallente Rhea U. , Eichler Marla Y. , Ventura Mario , McPherson John D. , Graves Tina A. , Wilson Richard K. , Schwartz Stuart , Rocchi Mariano , Eichler Evan E.
Published: June 2005

Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within human pericentromeric regions—areas of particularly rapid change in genomic structure. Here, we present a systematic analysis of the evolutionary history of one ∼700-kb region of 2p11, including the first autosomal transition from pericentromeric sequence to higher-order α-satellite DNA. We show that this region is composed of segmental duplications corresponding to 14 ancestral segments ranging in size from 4 kb to ∼115 kb. These duplicons show 94%–98.5% sequence identity to their ancestral loci. Comparative FISH and phylogenetic analysis indicate that these duplicons are differentially distributed in human, chimpanzee, and gorilla genomes, whereas baboon has a single putative ancestral locus for all but one of the duplications. Our analysis supports a model where duplicative transposition events occurred during a narrow window of evolution after the separation of the human/ape lineage from the Old World monkeys (10–20 million years ago). Although dramatic secondary dispersal events occurred during the radiation of the human, chimpanzee, and gorilla lineages, duplicative transposition seeding events of new material to this particular pericentromeric region abruptly ceased after this time period. The multiplicity of initial duplicative transpositions prior to the separation of humans and great-apes suggests a punctuated model for the formation of highly duplicated pericentromeric regions within the human genome. The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions.
Isolation, Characterization, and Cloning of α-l-Arabinofuranosidase Expressed during Fruit Ripening of Japanese Pear
Authors: Tateishi Akira , Mori Hitoshi , Watari Junya , Nagashima Kenji , Yamaki Shohei , Inoue Hiroaki
Published: June 2005

α-l-Arabinofuranosidase (α-l-arafase) was purified from fruit of Japanese pear (Pyrus pyrifolia). The enzyme solubilized from the cell wall by NaCl and Triton X-100 had the homogeneity of a single 62-kD polypeptide on SDS-PAGE after purification through the steps of hydroxyapatite, anion-exchange chromatography, and size-exclusion chromatography. A related cDNA clone was isolated (PpARF2). The transcript and related protein were detected solely in the ripening fruit corresponding to the increase of α-l-arafase activity. Transcripts of PpARF2 were not detected in buds, leaves, roots, or shoots of the Japanese pear. The deduced amino acid sequences of PpARF2 had low identity with those of other plants or bacteria. This α-l-arafase belonged to glycoside hydrolase family 3, which includes some β-xylosidases. The purified enzyme hydrolyzed mainly p-nitrophenyl α-l-arabinofuranoside and also reacted bifunctionally with p-nitrophenyl β-d-xylopyranoside. However, it released only arabinose from native cell wall polysaccharides prepared from Japanese pear and from sugar beet arabinan. The enzyme did not release xylose from arabinoxylan and xylan. The only activity of the α-l-arafase presented here was hydrolyzing the arabinosyl residue from native polysaccharides, whereas it showed bifunctional activity against artificial substrates. According to the expression pattern and properties of the enzyme, it is a new member of the glycoside hydrolase family 3 isolated from fruit, and it may be responsible for modification of the cell wall architecture during fruit softening.
A RING Domain Gene Is Expressed in Different Cell Types of Leaf Trace, Stem, and Juvenile Bundles in the Stem Vascular System of Zinnia
Authors: Dahiya Preeti , Milioni Dimitra , Wells Brian , Stacey Nicola , Roberts Keith , McCann Maureen C.
Published: June 2005

The in vitro zinnia (Zinnia elegans) mesophyll cell system, in which leaf mesophyll cells are induced to transdifferentiate into tracheary elements with high synchrony, has become an established model for studying xylogenesis. The architecture of the stem vascular system of zinnia cv Envy contains three anatomically distinct vascular bundles at different stages of development. Juvenile vascular strands of the subapical region develop into mature vascular strands with leaf trace segments and stem segments. Characteristic patterns of gene expression in juvenile, leaf trace, and stem bundles are revealed by a molecular marker, a RING domain-encoding gene, ZeRH2.1, originally isolated from a zinnia cDNA library derived from differentiating in vitro cultures. Using RNA in situ hybridization, we show that ZeRH2.1 is expressed preferentially in two specific cell types in mature zinnia stems. In leaf trace bundles, ZeRH2.1 transcript is abundant in xylem parenchyma cells, while in stem bundles it is abundant in phloem companion cells. Both of these cell types show wall ingrowths characteristic of transfer cells. In addition, ZeRH2.1 transcript is abundant in some phloem cells of juvenile bundles and in leaf palisade parenchyma. The complex and developmentally regulated expression pattern of ZeRH2.1 reveals heterogeneity in the vascular anatomy of the zinnia stem. We discuss a potential function for this gene in intercellular transport processes.