bluuebunny/crossref_metadata_2025 huggingface dataset:
Invasive hybrid tiger salamander genotypes impact native amphibians
Authors: Ryan Maureen E. , Johnson Jarrett R. , Fitzpatrick Benjamin M.
Published: June 2009

Although the ecological consequences of species invasions are well studied, the ecological impacts of genetic introgression through hybridization are less understood. This is particularly true of the impacts of hybridization on “third party” community members not genetically involved in hybridization. We also know little about how direct interactions between hybrid and parental individuals influence fitness. Here, we examined the ecological effects of hybridization between the native, threatened California Tiger Salamander (Ambystoma californiense) and the introduced Barred Tiger Salamander (Ambystoma tigrinum mavortium). Native x introduced hybrids are widespread in California, where they are top predators in seasonal ponds. We examined the impacts of early generation hybrids (first 2 generations of parental crosses) and contemporary hybrids derived from ponds where hybrids have been under selection in the wild for 20 generations. We found that most classes of hybrid tiger salamander larvae dramatically reduced survival of 2 native community members, the Pacific Chorus Frog (Pseudacris regilla) and the California Newt (Taricha torosa). We also found that nativeA. californienselarvae were negatively impacted by the presence of hybrid larvae: Native survival and size at metamorphosis were reduced and time to metamorphosis was extended. We also observed a large influence of Mendelian dominance on size, metamorphic timing and predation rate of hybrid tiger salamanders. These results suggest that both genetic and ecological factors are likely to influence the dynamics of admixture, and that tiger salamander hybridization might constitute a threat to additional pond-breeding species of concern in the region.
Large and unexpected enrichment in stratospheric
16
O
13
C
18
O and its meridional variation
Authors: Yeung Laurence Y. , Affek Hagit P. , Hoag Katherine J. , Guo Weifu , Wiegel Aaron A. , Atlas Elliot L. , Schauffler Sue M. , Okumura Mitchio , Boering Kristie A. , Eiler John M.
Published: June 2009

The stratospheric CO
2
oxygen isotope budget is thought to be governed primarily by the O(
1
D)+CO
2
isotope exchange reaction. However, there is increasing evidence that other important physical processes may be occurring that standard isotopic tools have been unable to identify. Measuring the distribution of the exceedingly rare CO
2
isotopologue
16
O
13
C
18
O, in concert with
18
O and
17
O abundances, provides sensitivities to these additional processes and, thus, is a valuable test of current models. We identify a large and unexpected meridional variation in stratospheric
16
O
13
C
18
O, observed as proportions in the polar vortex that are higher than in any naturally derived CO
2
sample to date. We show, through photochemical experiments, that lower
16
O
13
C
18
O proportions observed in the midlatitudes are determined primarily by the O(
1
D)+CO
2
isotope exchange reaction, which promotes a stochastic isotopologue distribution. In contrast, higher
16
O
13
C
18
O proportions in the polar vortex show correlations with long-lived stratospheric tracer and bulk isotope abundances opposite to those observed at midlatitudes and, thus, opposite to those easily explained by O(
1
D)+CO
2
. We believe the most plausible explanation for this meridional variation is either an unrecognized isotopic fractionation associated with the mesospheric photochemistry of CO
2
or temperature-dependent isotopic exchange on polar stratospheric clouds. Unraveling the ultimate source of stratospheric
16
O
13
C
18
O enrichments may impose additional isotopic constraints on biosphere–atmosphere carbon exchange, biosphere productivity, and their respective responses to climate change.
Site-specific regulation of cell cycle and DNA repair in post-mitotic GABA cells in schizophrenic versus bipolars
Authors: Benes Francine M. , Lim Benjamin , Subburaju Sivan
Published: June 2009

GABA cell dysfunction in both schizophrenia (SZ) and bipolar disorder (BD) involves decreased GAD
67
expression, although this change involves fundamentally different networks of genes in the 2 disorders. One gene that is common to these 2 networks is cyclin D2, a key component of cell cycle regulation that shows increased expression in SZ, but decreased expression in BD. Because of the importance of cell cycle regulation in maintaining functional differentiation and DNA repair, the current study has examined the genes involved in the G
1
and G
2
checkpoints to generate new hypotheses regarding the regulation of the GABA cell phenotype in the hippocampus of SZ and BD. The results have demonstrated significant changes in cell cycle regulation in both SZ and BD and these changes include the transcriptional complex (TC) that controls the expression of E2F/DP-1 target genes critical for progression to G
2
/M. The methyl-CpG binding domain protein (MBD4) that is pivotal for DNA repair, is significantly up-regulated in the stratum oriens (SO) of CA3/2 and CA1 in SZs and BDs. However, other genes associated with the TC, and the G
1
and G
2
checkpoints, show complex changes in expression in the SO of CA3/2 and CA1 of both SZs and BDS. Overall, the patterns of expression observed have suggested that the regulation of functional differentiation and/or genomic integrity of hippocampal GABA cells varies according to diagnosis and their location within the trisynaptic pathway.
Cognitive fitness of cost-efficient brain functional networks
Authors: Bassett Danielle S. , Bullmore Edward T. , Meyer-Lindenberg Andreas , Apud José A. , Weinberger Daniel R. , Coppola Richard
Published: June 2009

The human brain's capacity for cognitive function is thought to depend on coordinated activity in sparsely connected, complex networks organized over many scales of space and time. Recent work has demonstrated that human brain networks constructed from neuroimaging data have economical small-world properties that confer high efficiency of information processing at relatively low connection cost. However, it has been unclear how the architecture of complex brain networks functioning at different frequencies can be related to behavioral performance on cognitive tasks. Here, we show that impaired accuracy of working memory could be related to suboptimal cost efficiency of brain functional networks operating in the classical β frequency band, 15–30 Hz. We analyzed brain functional networks derived from magnetoencephalography data recorded during working-memory task performance in 29 healthy volunteers and 28 people with schizophrenia. Networks functioning at higher frequencies had greater global cost efficiency than low-frequency networks in both groups. Superior task performance was positively correlated with global cost efficiency of the β-band network and specifically with cost efficiency of nodes in left lateral parietal and frontal areas. These results are consistent with biophysical models highlighting the importance of β-band oscillations for long-distance functional connections in brain networks and with pathophysiological models of schizophrenia as a dysconnection syndrome. More generally, they echo the saying that “less is more”: The information processing performance of a network can be enhanced by a sparse or low-cost configuration with disproportionately high efficiency.
Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact
Authors: Létoffé Sylvie , Heuck Gesine , Delepelaire Philippe , Lange Norbert , Wandersman Cécile
Published: June 2009

Because heme is a major iron-containing molecule in vertebrates, the ability to use heme-bound iron is a determining factor in successful infection by bacterial pathogens. Until today, all known enzymes performing iron extraction from heme did so through the rupture of the tetrapyrrol skeleton. Here, we identified 2
Escherichia coli
paralogs, YfeX and EfeB, without any previously known physiological functions. YfeX and EfeB promote iron extraction from heme preserving the tetrapyrrol ring intact. This novel enzymatic reaction corresponds to the deferrochelation of the heme. YfeX and EfeB are the sole proteins able to provide iron from exogenous heme sources to
E. coli
. YfeX is located in the cytoplasm. EfeB is periplasmic and enables iron extraction from heme in the periplasm and iron uptake in the absence of any heme permease. YfeX and EfeB are widespread and highly conserved in bacteria. We propose that their physiological function is to retrieve iron from heme.
High-precision optical measurements of
13
C/
12
C isotope ratios in organic compounds at natural abundance
Authors: Zare Richard N. , Kuramoto Douglas S. , Haase Christa , Tan Sze M. , Crosson Eric R. , Saad Nabil M. R.
Published: June 2009

A continuous-flow cavity ring-down spectroscopy (CRDS) system integrating a chromatographic separation technique, a catalytic combustor, and an isotopic
13
C/
12
C optical analyzer is described for the isotopic analysis of a mixture of organic compounds. A demonstration of its potential is made for the geochemically important class of short-chain hydrocarbons. The system proved to be linear over a 3-fold injection volume dynamic range with an average precision of 0.95‰ and 0.67‰ for ethane and propane, respectively. The calibrated accuracy for methane, ethane, and propane is within 3‰ of the values determined using isotope ratio mass spectrometry (IRMS), which is the current method of choice for compound-specific isotope analysis. With anticipated improvements, the low-cost, portable, and easy-to-use CRDS-based instrumental setup is poised to evolve into a credible challenge to the high-cost and complex IRMS-based technique.
A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry
Authors: Yu Yonghao , Anjum Rana , Kubota Kazuishi , Rush John , Villen Judit , Gygi Steven P.
Published: June 2009

Most kinases are capable of recognizing and phosphorylating peptides containing short, linear sequence motifs. To measure the activation state of many kinases from the same cell lysate, we created a multiplexed, mass-spectrometry-based in vitro kinase assay. Ninety chemically synthesized peptides derived from well-characterized peptide substrates and in vivo phosphorylation sites with either known or previously unidentified upstream kinases were reacted individually in a plate format with crude cell lysates and ATP. Phosphorylation rates were directly measured based on the addition of 90 same-sequence, site-specific phosphopeptides enriched in stable isotopes to act as ideal quantitative internal standards for analysis by liquid chromatography coupled to tandem mass spectrometry. This approach concurrently measured up to 90 site-specific peptide phosphorylation rates, reporting a diagnostic fingerprint for activated kinase pathways. We applied this unique kinome-activity profiling strategy in a variety of cellular settings, including mitogen stimulation, cell cycle, pharmacological inhibition of pathways, and to a panel of breast cancer cell lines. Finally, we identified the source of activity for a peptide (derived from a PI3K regulatory subunit) from our library. This peptide substrate demonstrated mitotic and tyrosine-specific phosphorylation, which was confirmed to be a novel Src family kinase site in vivo.
High-resolution profiling and discovery of planarian small RNAs
Authors: Friedländer Marc R. , Adamidi Catherine , Han Ting , Lebedeva Svetlana , Isenbarger Thomas A. , Hirst Martin , Marra Marco , Nusbaum Chad , Lee William L. , Jenkin James C. , Alvarado Alejandro Sánchez , Kim John K. , Rajewsky Nikolaus
Published: June 2009

Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for Piwi-interacting RNA (piRNA) expression in planarians. Nevertheless, the full complement of piRNAs and microRNAs (miRNAs) in this organism has yet to be defined. Here we report on the large-scale cloning and sequencing of small RNAs from the planarian
Schmidtea mediterranea
, yielding altogether millions of sequenced, unique small RNAs. We show that piRNAs are in part organized in genomic clusters and that they share characteristic features with mammalian and fly piRNAs. We further identify 61 novel miRNA genes and thus double the number of known planarian miRNAs. Sequencing, as well as quantitative PCR of small RNAs, uncovered 10 miRNAs enriched in planarian stem cells. These miRNAs are down-regulated in animals in which stem cells have been abrogated by irradiation, and thus constitute miRNAs likely associated with specific stem-cell functions. Altogether, we present the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, and single out a number of miRNAs that may function in regeneration. Several of these miRNAs are deeply conserved in animals.
Toll-like receptor signaling controls reactivation of KSHV from latency
Authors: Gregory Sean M. , West John A. , Dillon Patrick J. , Hilscher Chelsey , Dittmer Dirk P. , Damania Blossom
Published: June 2009

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease. Like other herpesviruses, KSHV establishes life-long latency in the human host with intermittent periods of reactivation. Physiological triggers of herpesviral reactivation are poorly defined. Toll-like receptors (TLRs) recognize pathogens and are vital for the host innate immune response. We screened multiple TLR agonists for their ability to initiate KSHV replication in latently infected PEL. Agonists specific for TLR7/8 reactivated latent KSHV and induced viral lytic gene transcription and replication. Furthermore, vesicular stomatitis virus (VSV), a bonafide physiological activator of TLR7/8, also reactivated KSHV from latency. This demonstrates that secondary pathogen infection of latently infected cells can reactivate KSHV. Human herpesviruses establish life-long latency in the host, and it is plausible that a latently infected cell will encounter multiple pathogens during its lifetime and that these encounters lead to episodic reactivation. Our findings have broad implications for physiological triggers of latent viral infections, such as herpesviral reactivation and persistence in the host.
Evidence for a memory threshold in second-choice recognition memory responses
Authors: Parks Colleen M. , Yonelinas Andrew P.
Published: June 2009

A fundamental question in the study of cognition is whether memory strength varies continuously or whether memories sometimes fall below a threshold and fail completely. Previous studies examining this question have relied exclusively on 1 method—receiver operating characteristics—so in the current study, we addressed this issue by using a completely different approach. We tested memory for single items and for arbitrary associations (e.g., memory for random word pairs) by using a 4-alternative forced-choice test in which subjects either made a single choice or a first and a second choice. In item recognition, single- and second-choice scores were directly related, as expected if a continuous strength signal supported performance. In contrast, in associative recognition, single- and second-choice scores were found to be unrelated, as predicted by high-threshold theories. However, when the word pairs were encoded as single compound words rather than arbitrary associations, associative recognition appeared to rely more on a continuous strength process. The results support memory models that include both a continuous familiarity process and a threshold recollection process.
TRPV1-expressing primary afferents generate behavioral responses to pruritogens via multiple mechanisms
Authors: Imamachi Noritaka , Park Goon Ho , Lee Hyosang , Anderson David J. , Simon Melvin I. , Basbaum Allan I. , Han Sang-Kyou
Published: June 2009

The mechanisms that generate itch are poorly understood at both the molecular and cellular levels despite its clinical importance. To explore the peripheral neuronal mechanisms underlying itch, we assessed the behavioral responses (scratching) produced by s.c. injection of various pruritogens in PLCβ3- or TRPV1-deficient mice. We provide evidence that at least 3 different molecular pathways contribute to the transduction of itch responses to different pruritogens: 1) histamine requires the function of both PLCβ3 and the TRPV1 channel; 2) serotonin, or a selective agonist, α-methyl-serotonin (α-Me-5-HT), requires the presence of PLCβ3 but not TRPV1, and 3) endothelin-1 (ET-1) does not require either PLCβ3 or TRPV1. To determine whether the activity of these molecules is represented in a particular subpopulation of sensory neurons, we examined the behavioral consequences of selectively eliminating 2 nonoverlapping subsets of nociceptors. The genetic ablation of MrgprD
+
neurons that represent ≈90% of cutaneous nonpeptidergic neurons did not affect the scratching responses to a number of pruritogens. In contrast, chemical ablation of the central branch of TRPV1
+
nociceptors led to a significant behavioral deficit for pruritogens, including α-Me-5-HT and ET-1, that is, the TRPV1-expressing nociceptor was required, whether or not TRPV1 itself was essential. Thus, TRPV1 neurons are equipped with multiple signaling mechanisms that respond to different pruritogens. Some of these require TRPV1 function; others use alternate signal transduction pathways.
Inhibition of serine/threonine phosphatase PP2A enhances cancer chemotherapy by blocking DNA damage induced defense mechanisms
Authors: Lu Jie , Kovach John S. , Johnson Francis , Chiang Jeffrey , Hodes Richard , Lonser Russell , Zhuang Zhengping
Published: June 2009

A variety of mechanisms maintain the integrity of the genome in the face of cell stress. Cancer cell response to chemotherapeutic and radiation-induced DNA damage is mediated by multiple defense mechanisms including polo-like kinase 1 (Plk-1), protein kinase B (Akt-1), and/or p53 pathways leading to either apoptosis or cell cycle arrest. Subsequently, a subpopulation of arrested viable cancer cells may remain and recur despite aggressive and repetitive therapy. Here, we show that modulation (activation of Akt-1 and Plk-1 and repression of p53) of these pathways simultaneously results in paradoxical enhancement of the effectiveness of cytotoxic chemotherapy. We demonstrate that a small molecule inhibitor, LB-1.2, of protein phosphatase 2A (PP2A) activates Plk-1 and Akt-1 and decreases p53 abundance in tumor cells. Combined with temozolomide (TMZ; a DNA-methylating chemotherapeutic drug), LB-1.2 causes complete regression of glioblastoma multiforme (GBM) xenografts without recurrence in 50% of animals (up to 28 weeks) and complete inhibition of growth of neuroblastoma (NB) xenografts. Treatment with either drug alone results in only short-term inhibition/regression with all xenografts resuming rapid growth. Combined with another widely used anticancer drug, Doxorubicin (DOX, a DNA intercalating agent), LB-1.2 also causes marked GBM xenograft regression, whereas DOX alone only slows growth. Inhibition of PP2A by LB-1.2 blocks cell-cycle arrest and increases progression of cell cycle in the presence of TMZ or DOX. Pharmacologic inhibition of PP2A may be a general method for enhancing the effectiveness of cancer treatments that damage DNA or disrupt components of cell replication.
Surgical versus medical treatment for secondary post‐partum hemorrhage
Authors: FEIGENBERG TOMER , EITAN YAEL , SELA HEN Y. , ELCHALAL URIEL , BEN‐MEIR ASSAF , ROJANSKY NATHAN
Published: June 2009

Background. Secondary post‐partum hemorrhage (PPH) is defined as any abnormal bleeding from the birth canal occurring between 24 hours and 12 weeks postnatally. Treatment usually falls into one of the two categories: surgical evacuation of the uterus or medical treatment. Objective. To compare the two different clinical approaches and the implications on future fertility. Study design. A retrospective study. Setting. From 1990 to 2002, 168 women diagnosed with late PPH were admitted to the Hadassah Medical Centers in Jerusalem. The cases were divided into two groups according to the planned initial treatment: primary surgical treatment vs. primary medical treatment. Results. Primary surgical treatment was associated with significantly more primary negative events (p = 0.01). After the primary event, primary surgical treatment was associated with fewer future deliveries (p = 0.04) and resulted in increased rate of secondary infertility of borderline significance (p = 0.06). Conclusions. Our results show that secondary PPH is related to high rates of immediate and long‐term complications. It is possible that a conservative medical approach for secondary PPH may be superior to surgical treatment.
Teachers’ conceptions of teacher professionalism in England in 2003 and 2006
Authors: Swann Mandy , McIntyre Donald , Pell Tony , Hargreaves Linda , Cunningham Mark
Published: June 2009

Theoretical and political perspectives on the nature of professionalism in teaching are abundant, but little is known about the views of teachers themselves. We asked primary and secondary school teachers in England what teacher professionalism means to them. We explored what teachers think about professionalism, on what dimensions their thinking varies, and how much it varies. We researched how successful the government had already been, and how successful it would be in the future, in changing teachers’ conceptions of professionalism. Two large‐scale national surveys were conducted, with a longitudinal element. We found that teachers’ thinking about their professionalism may be construed as consisting of an inner core of strong, shared beliefs and commitments; an intermediate set of coherent but contested components of professionalism; and an outer layer of disparate elements which are generally highly disputed and which remain unintegrated into broader ways of thinking.
Dendritic cells require a systemic type I interferon response to mature and induce CD4+ Th1 immunity with poly IC as adjuvant
Authors: Longhi M. Paula , Trumpfheller Christine , Idoyaga Juliana , Caskey Marina , Matos Ines , Kluger Courtney , Salazar Andres M. , Colonna Marco , Steinman Ralph M.
Published: June 2009

Relative to several other toll-like receptor (TLR) agonists, we found polyinosinic:polycytidylic acid (poly IC) to be the most effective adjuvant for Th1 CD4+ T cell responses to a dendritic cell (DC)–targeted HIV gag protein vaccine in mice. To identify mechanisms for adjuvant action in the intact animal and the polyclonal T cell repertoire, we found poly IC to be the most effective inducer of type I interferon (IFN), which was produced by DEC-205+ DCs, monocytes, and stromal cells. Antibody blocking or deletion of type I IFN receptor showed that IFN was essential for DC maturation and development of CD4+ immunity. The IFN-AR receptor was directly required for DCs to respond to poly IC. STAT 1 was also essential, in keeping with the type I IFN requirement, but not type II IFN or IL-12 p40. Induction of type I IFN was mda5 dependent, but DCs additionally used TLR3. In bone marrow chimeras, radioresistant and, likely, nonhematopoietic cells were the main source of IFN, but mda5 was required in both marrow–derived and radioresistant host cells for adaptive responses. Therefore, the adjuvant action of poly IC requires a widespread innate type I IFN response that directly links antigen presentation by DCs to adaptive immunity.
Regulation of TLR7/9 responses in plasmacytoid dendritic cells by BST2 and ILT7 receptor interaction
Authors: Cao Wei , Bover Laura , Cho Minkwon , Wen Xiaoxia , Hanabuchi Shino , Bao Musheng , Rosen David B. , Wang Yi-Hong , Shaw Joanne L. , Du Qiumei , Li Chun , Arai Naoko , Yao Zhengbin , Lanier Lewis L. , Liu Yong-Jun
Published: June 2009

Plasmacytoid dendritic cells (pDCs) produce copious type I interferon (IFN) upon sensing nucleic acids through Toll-like receptor (TLR) 7 and TLR9. Uncontrolled pDC activation and IFN production are implicated in lymphopenia and autoimmune diseases; therefore, a mechanism controlling pDC IFN production is essential. Human pDCs specifically express an orphan receptor, immunoglobulin-like transcript 7 (ILT7). Here, we discovered an ILT7 ligand expressed by human cell lines and identified it as bone marrow stromal cell antigen 2 (BST2; CD317). BST2 directly binds to purified ILT7 protein, initiates signaling via the ILT7–FcεRIγ complex, and strongly inhibits production of IFN and proinflammatory cytokines by pDCs. Readily induced by IFN and other proinflammatory cytokines, BST2 may modulate the human pDC’s IFN responses through ILT7 in a negative feedback fashion.
French National Program for Prevention of Healthcare-Associated Infections and Antimicrobial Resistance, 1992–2008: Positive Trends, But Perseverance Needed
Authors: Carlet Jean , Astagneau Pascal , Brun-Buisson Christian , Coignard Bruno , Salomon Valérie , Tran Béatrice , Desenclos Jean-Claude , Jarlier Vincent , Schlemmer Benoît , Parneix Pierre , Regnier Bernard , Fabry Jacques ,   French National Program for Prevention of Healthcare-Associated Infections and Antimicrobial Resistance
Published: June 2009

Objective.

To describe the French program for the prevention of healthcare-associated infections and antibiotic resistance and provide results for some of the indicators available to evaluate the program. In addition to structures and process indicators, the 2 outcome indicators selected were the rate of surgical site infection and the proportion of methicillin-resistant Staphylococcus aureus (MRSA) isolates among the S. aureus isolates recovered.

Design.

Descriptive study of the evolution of the national structures for control of healthcare-associated infections since 1992. Through national surveillance networks, process indicators were available from 1993 to 2006, surgical site infection rates were available from 1999 to 2005, and prevalence rates for MRSA infection were available from 2001 to 2007.

Results.

A comprehensive national program has gradually been set up in France during the period from 1993 to 2004, which included strengthening of organized infection control activities at the local, regional, and national levels and developing large networks for surveillance of specific infections and antibiotic resistance. These achievements were complemented by instituting mandatory notification for unusual nosocomial events, especially outbreaks. The second phase of the program involved the implementation of 5 national quality indicators with public reporting. Surgical site infection rates decreased by 25% over a 6-year period. In France, the median proportion of MRSA among S. aureus isolates recovered from patients with bacteremia decreased from 33.4% to 25.7% during the period from 2001 to 2007, whereas this proportion increased in many other European countries.

Conclusions.

Very few national programs have been evaluated since the Study on the Efficacy of Nosocomial Infection Control. Although continuing efforts are required, the French program appears to have been effective at reducing infection rates.
Epidemiology of Antimicrobial Resistance among Gram-Negative Organisms Recovered from Patients in a Multistate Network of Long-Term Care Facilities
Authors: Lautenbach Ebbing , Marsicano Roseann , Tolomeo Pam , Heard Michael , Serrano Steve , Stieritz Donald D.
Published: June 2009

We identified 1,805 gram-negative organisms in cultures of urine samples obtained over a 10-month period from residents of 63 long-term care facilities. The prevalence of fluoroquinolone resistance in Escherichia coli was 51% (446 of 874 isolates), whereas the preva¬lences of ceftazidime and imipenem resistance in Klebsiella species were 26% and 6% (84 and 19 of 323 isolates), respectively. The prevalence of resistance varied significantly by facility type, size, and geographic location.
Error and stability estimates for surface-divergence free RBF interpolants on the sphere
Authors: Fuselier Edward , Narcowich Francis , Ward Joseph , Wright Grady
Published: June 2009

Recently, a new class of surface-divergence free radial basis function interpolants has been developed for surfaces inR3\mathbb {R}^3. In this paper, several approximation results for this class of interpolants will be derived in the case of the sphere,S2\mathbb {S}^2. In particular, Sobolev-type error estimates are obtained, as well as optimal stability estimates for the associated interpolation matrices. In addition, a Bernstein estimate and an inverse theorem are also derived. Numerical validation of the theoretical results is also given.
Computation of 𝑝-units in ray class fields of real quadratic number fields
Authors: Chapdelaine Hugo
Published: June 2009

Let

K
K

be a real quadratic field, let

p
p

be a prime number which is inert in

K
K

and let

K
p

K_p

be the completion of

K
K

at

p
p

. As part of a Ph.D. thesis, we constructed a certain

p
p

-adic invariant

u
∈

K
p

×

u\in K_p^{\times }

, and conjectured that

u
u

is, in fact, a

p
p

-unit in a suitable narrow ray class field of

K
K

. In this paper we give numerical evidence in support of that conjecture. Our method of computation is similar to the one developed by Dasgupta and relies on partial modular symbols attached to Eisenstein series.
Local oscillations in finite difference solutions of hyperbolic conservation laws
Authors: Li Jiequan , Tang Huazhong , Warnecke Gerald , Zhang Lumei
Published: June 2009

It was generally expected that monotone schemes are oscillation-free for hyperbolic conservation laws. However, recently local oscillations were observed and usually understood to be caused by relative phase errors. In order to further explain this, we first investigate the discretization of initial data that trigger the chequerboard mode, the highest frequency mode. Then we proceed to use the discrete Fourier analysis and the modified equation analysis to distinguish the dissipative and dispersive effects of numerical schemes for low frequency and high frequency modes, respectively. It is shown that the relative phase error is of order

O

(
1
)

{\mathcal O}(1)

for the high frequency modes

u
j
n

=

λ
k
n

e

i
ξ
j

u_j^n=\lambda ^n_k e^{i\xi j}

,

ξ
≈
π

\xi \approx \pi

, but of order

O

(

ξ
2

)

{\mathcal O}(\xi ^2)

for low frequency modes (

ξ
≈
0

\xi \approx 0

). In order to avoid numerical oscillations, the relative phase errors should be offset by numerical dissipation of at least the same order. Numerical damping, i.e. the zero order term in the corresponding modified equation, is important to dissipate the oscillations caused by the relative phase errors of high frequency modes. This is in contrast to the role of numerical viscosity, the second order term, which is the lowest order term usually present to suppress the relative phase errors of low frequency modes.
Conservative stochastic differential equations: Mathematical and numerical analysis
Authors: Faou Erwan , Lelièvre Tony
Published: June 2009

We consider stochastic differential equations on the whole Euclidean space possessing a scalar invariant along their solutions. The stochastic dynamics therefore evolves on a hypersurface of the ambient space. Using orthogonal coordinate systems, we show the existence and uniqueness of smooth solutions of the Kolmogorov equation under some ellipticity conditions over the invariant hypersurfaces. If we assume, moreover, the existence of an invariant measure, we show the exponential convergence of the solution towards its average. In the second part, we consider numerical approximation of the stochastic differential equation, and show the convergence and numerical ergodicity of a class of projected schemes. In the context of molecular dynamics, this yields numerical schemes that are ergodic with respect to the microcanonical measure over isoenergy surfaces.
High precision computation of a constant in the theory of trigonometric series
Authors: de Reyna J. , van de Lune J.
Published: June 2009

Using the bisection as well as the Newton-Raphson method, we compute to high precision the Littlewood-Salem-Izumi constant frequently occurring in the theory of trigonometric sums.
The ratio monotonicity of the Boros-Moll polynomials
Authors: Chen William , Xia Ernest
Published: June 2009

In their study of a quartic integral, Boros and Moll discovered a special class of Jacobi polynomials, which we call the Boros-Moll polynomials. Kauers and Paule proved the conjecture of Moll that these polynomials are log-concave. In this paper, we show that the Boros-Moll polynomials possess the ratio monotone property which implies the log-concavity and the spiral property. We conclude with a conjecture which is stronger than Moll’s conjecture on the

∞
\infty

-log-concavity.
A piecewise linear finite element method for the buckling and the vibration problems of thin plates
Authors: Mora David , Rodríguez Rodolfo
Published: June 2009

The aim of this paper is to analyze a piecewise linear finite element method to approximate the buckling and the vibration problems of a thin plate. The method is based on a conforming discretization of a bending moment formulation for the Kirchhoff-Love model. The analysis restricts to simply connected polygonal clamped plates, not necessarily convex. The method is proved to converge with optimal order for both spectral problems, including an improved order for the eigenvalues. Numerical experiments are reported to assess its performance and to compare it with other low-order finite element methods.
First derivatives estimates for finite-difference schemes
Authors: Gyöngy István , Krylov Nicolai
Published: June 2009

We give sufficient conditions under which solutions of discretized in space second-order parabolic and elliptic equations, perhaps degenerate, admit estimates of the first derivatives in the space variables independent of the mesh size.
Algebraic solutions of Jacobi equations
Authors: Coutinho S. , Ferreira Marcos
Published: June 2009

We propose an algorithm to compute exactly the algebraic solutions of Jacobi equations over the projective plane.
A new approach to Richardson extrapolation in the finite element method for second order elliptic problems
Authors: Asadzadeh M. , Schatz A. , Wendland W.
Published: June 2009

This paper presents a nonstandard local approach to Richardson extrapolation, when it is used to increase the accuracy of the standard finite element approximation of solutions of second order elliptic boundary value problems in

R

N

\mathbb R^N

,

N
≥
2

N \ge 2

. The main feature of the approach is that it does not rely on a traditional asymptotic error expansion, but rather depends on a more easily proved weaker a priori estimate, derived in [19], called an asymptotic error expansion inequality. In order to use this inequality to verify that the Richardson procedure works at a point, we require a local condition which links the different subspaces used for extrapolation. Roughly speaking, this condition says that the subspaces are similar about a point, i.e., any one of them can be made to locally coincide with another by a simple scaling of the independent variable about that point. Examples of finite element subspaces that occur in practice and satisfy this condition are given.
Convergence of the linearized Bregman iteration for ℓ₁-norm minimization
Authors: Cai Jian-Feng , Osher Stanley , Shen Zuowei
Published: June 2009

One of the key steps in compressed sensing is to solve the basis pursuit problem

min

u
∈

R

n

{
‖
u

‖
1

:
A
u
=
f
}

\min _{u\in \mathbb {R}^n}\{\|u\|_1:Au=f\}

. Bregman iteration was very successfully used to solve this problem in [40]. Also, a simple and fast iterative algorithm based on linearized Bregman iteration was proposed in [40], which is described in detail with numerical simulations in [35]. A convergence analysis of the smoothed version of this algorithm was given in [11]. The purpose of this paper is to prove that the linearized Bregman iteration proposed in [40] for the basis pursuit problem indeed converges.
Multilevel finite element preconditioning for √3 refinement
Authors: Maes Jan , Oswald Peter
Published: June 2009

We develop a BPX-type multilevel method for the numerical solution of second order elliptic equations in

R

2

\mathbb {R}^2

using piecewise linear polynomials on a sequence of triangulations given by regular

3

\sqrt {3}

refinement. A multilevel splitting of the finest grid space is obtained from the nonnested sequence of spaces on the coarser triangulations using prolongation operators based on simple averaging procedures. The main result is that the condition number of the corresponding BPX preconditioned linear system is uniformly bounded independent of the size of the problem. The motivation to consider

3

\sqrt {3}

refinement stems from the fact that it is a slower topological refinement than the usual dyadic refinement, and that it alternates the orientation of the refined triangles. Therefore we expect a reduction of the amount of work when compared to the classical BPX preconditioner, although both methods have the same asymptotical complexity. Numerical experiments confirm this statement.
Optimized general sparse grid approximation spaces for operator equations
Authors: Griebel M. , Knapek S.
Published: June 2009

This paper is concerned with the construction of optimized sparse grid approximation spaces for elliptic pseudodifferential operators of arbitrary order. Based on the framework of tensor-product biorthogonal wavelet bases and stable subspace splittings, we construct operator-adapted subspaces with a dimension smaller than that of the standard full grid spaces but which have the same approximation order as the standard full grid spaces, provided that certain additional regularity assumptions on the solution are fulfilled. Specifically for operators of positive order, their dimension isO(2J)O(2^{J})independent of the dimensionnnof the problem, compared toO(2Jn)O(2^{Jn})for the full grid space. Also, for operators of negative order the overall cost is significantly in favor of the new approximation spaces. We give cost estimates for the case of continuous linear information. We show these results in a constructive manner by proposing a Galerkin method together with optimal preconditioning. The theory covers elliptic boundary value problems as well as boundary integral equations.
Computing prime harmonic sums
Authors: Bach Eric , Klyve Dominic , Sorenson Jonathan
Published: June 2009

We discuss a method for computing

∑

p
≤
x

1

/

p

\sum _{p \le x} 1/p

, using time about

x

2

/

3

x^{2/3}

and space about

x

1

/

3

x^{1/3}

. It is based on the Meissel-Lehmer algorithm for computing the prime-counting function

π
(
x
)

\pi (x)

, which was adapted and improved by Lagarias, Miller, and Odlyzko. We used this algorithm to determine the first point at which the prime harmonic sum first crosses 4.
An 𝐸-based mixed formulation for a time-dependent eddy current problem
Authors: Acevedo Ramiro , Meddahi Salim , Rodríguez Rodolfo
Published: June 2009

In this paper, we analyze a mixed form of a time-dependent eddy current problem formulated in terms of the electric fieldE\boldsymbol {E}. We show that this formulation admits a well-posed saddle point structure when the constraints satisfied by the primary unknown in the dielectric material are handled by means of a Lagrange multiplier. We use Nédélec edge elements and standard nodal finite elements to define a semi-discrete Galerkin scheme. Furthermore, we introduce the corresponding backward-Euler fully-discrete formulation and prove error estimates.
Two-cover descent on hyperelliptic curves
Authors: Bruin Nils , Stoll Michael
Published: June 2009

We describe an algorithm that determines a set of unramified covers of a given hyperelliptic curve, with the property that any rational point will lift to one of the covers. In particular, if the algorithm returns an empty set, then the hyperelliptic curve has no rational points. This provides a relatively efficiently tested criterion for solvability of hyperelliptic curves. We also discuss applications of this algorithm to curves of genus

1
1

and to curves with rational points.
Biophysical annotation and representation of CellML models
Authors: Wimalaratne S. M. , Halstead M. D. B. , Lloyd C. M. , Crampin E. J. , Nielsen P. F.
Published: June 2009

Motivation: CellML is an implementation-independent model description language for specifying and exchanging biological processes. The focus of CellML is the representation of mathematical formulations of biological processes. The language captures the mathematical and model building constructs well, but does not lend itself to capturing the biology these models represent.

Results: This article describes the development of an ontological framework for annotating CellML models with biophysical concepts. We demonstrate that, by using these ontological mappings, in combination with a set of graph reduction rules, it is possible to represent the underlying biological process described in a CellML model.

Contact:  sarala.dissanayake@auckland.ac.nz

Supplementary information:  Supplementary data are available at Bioinformatics online.
Antiviral treatments reduce severity of diabetes in Ljungan virus‐infected CD‐1 mice and delay onset in diabetes‐prone BB rats
Authors: Holmberg Rebecka , Klitz William , Blixt Martin , Berggren Per‐Olof , Juntti‐Berggren Lisa , Niklasson Bo
Published: June 2009

The effects of LV in two different species, CD‐1 mice, without a genetic disposition for diabetes, and BB rats prone to T1D were examined. Male CD‐1 mice that had been exposed to LV in utero developed a type 2‐like diabetes with increased blood glucose, insulin levels and epididymal fat at the age of 10–15 weeks. Combination therapy including LV‐antiserum and an antiviral drug, Pleconaril, significantly reduced the levels of blood glucose and insulin and the amount of abdominal fat. In BB rats, LV has been found in both prediabetic‐ and diabetic diabetes‐prone rats, as well as in diabetes‐resistant rats. To evaluate whether the presence of LV has any influence on the onset of T1D, prediabetic BB rats were treated with an antiserum against LV or a combination of the antiviral drugs Pleconaril and Ribavirin. In the group treated with antiviral drugs, the onset was significantly delayed. These results indicate that the presence of LV can be involved in the pathogenesis of diabetes in these animal models.
Systematic review: the prevalence of idiopathic bile acid malabsorption as diagnosed by SeHCAT scanning in patients with diarrhoea‐predominant irritable bowel syndrome
Authors: WEDLAKE L. , A’HERN R. , RUSSELL D. , THOMAS K. , WALTERS J. R. F. , ANDREYEV H. J. N.
Published: June 2009

Background  Recurrent, watery diarrhoea affects one‐third of patients diagnosed with irritable bowel syndrome (‘IBS‐D’). Idiopathic bile acid malabsorption (‘I‐BAM’) may be the cause.

Aim  To determine the prevalence of I‐BAM in patients suffering from IBS‐D.

Methods  A systematic search was performed of publications reporting patients presenting with IBS‐D type symptoms, who were subsequently confirmed as having I‐BAM by SeHCAT scanning.

Results  Eighteen relevant studies, 15 prospective, comprising 1223 patients were identified. Five studies (429 patients) indicated that 10% (CI: 7–13) patients had severe bile acid malabsorption (SeHCAT 7 day retention <5% of baseline value). 17 studies (1073 patients) indicated that 32% (CI: 29–35) patients had moderate bile acid malabsorption (SeHCAT <10%). 7 studies (618 patients) indicated that 26% (CI: 23–30) patients had mild (SeHCAT <15%) bile acid malabsorption. Pooled data from 15 studies showed a dose‐response relationship according to severity of malabsorption to treatment with a bile acid binder: response to colestyramine occurred in 96% of patients with <5% retention, 80% at <10% retention and 70% at <15% retention.

Conclusions  Idiopathic adult‐onset bile acid malabsorption is not rare. International guidelines for the management of irritable bowel syndrome need to be revised so that clinicians become more aware of this possibility.
In vitroandin vivoevaluation of the inhibition potential of risperidone toward clozapine biotransformation
Authors: Chetty Manoranjenni , D'Esposito Fabrizio , Zhang Wei V. , Glen John , Dore Glenys , Stankovic Zvijezdana , Edwards Robert J. , Ramzan Iqbal , Murray Michael
Published: June 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The clozapine (CLZ)–risperidone (RISP) combination is effective in schizophrenic patients but may lead to elevated plasma CLZ concentrations and adverse effects.

• Reports of potential inhibitory effects of RISP on cytochrome P450 (CYP)‐dependent CLZ oxidation have been inconsistent.

• It has been suggested that variations in expression of CLZ/RISP oxidases, such as CYPs 1A2, 2D6 and 3A4, may influence inhibitory interactions.

WHAT THIS STUDY ADDS

• Inhibition of CLZ biotransformation by RISP was assessed in microsomal fractions that expressed varying amounts of CYPs 1A2, 2D6 and 3A4.

• RISP did not inhibit the formation of major oxidized CLZ metabolites, regardless of the CYP expression profile; findings from anin vivostudy in patients were consistent with this finding.

• Pharmacokinetic interactions due to the RISP–CLZ combination are unlikely to involve CYPs.

AIMS

To study the impact of risperidone (RISP) on clozapine (CLZ) biotransformationin vitroin microsomal fractions containing varying expression of CYP oxidases andin vivoin patients.

METHODS

Human liver microsomes (n= 11) were assessed for expression of CYPs 1A2, 2D6 and 3A4, because these enzymes mediate RISP and CLZ oxidation. Inhibition of CLZ oxidation by RISP was assessed. Plasma CLZ elimination was estimated in patients with schizophrenia who received either CLZ alone or the CLZ–RISP combination (n= 10 per group).

RESULTS

(i) The CYP3A4 and CYP1A2 inhibitors ketoconazole and fluvoxamine inhibited CLZ oxidation to varying extents in individual microsomal fractions. (ii) RISP did not inhibit CLZ oxidation, regardless of variations in CYP expression. (iii) RISP co‐administration did not impair CLZ clearance.

CONCLUSIONS

No evidence was found for CYP‐mediated inhibitory or pharmacokinetic interactions between RISP and CLZ. Occasional literature reports of such interactions may involve other pathways that participate in CLZ disposition.
Progenitors in motion: mechanisms of mobilization of endothelial progenitor cells
Authors: Tilling Lindsey , Chowienczyk Philip , Clapp Brian
Published: June 2009

Endothelial progenitor cells are a population of bone marrow‐derived mononuclear cells thought to engage in endothelial repair and hence are considered potential therapeutic agents in many pathological conditions. The mechanism of their exit from the bone marrow to the circulation and damaged tissues, termed mobilization, has not been fully elucidated. Despite this, several pharmacological interventions have been shown to influence mobilization of these specialized cells. Here we review the current understanding of their mobilization.