bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spider Diagrams
Authors: Howse John , Stapleton Gem , Taylor John 
Published: August 2013

AbstractThe use of diagrams in mathematics has traditionally been restricted to guiding intuition and communication. With rare exceptions such as Peirce's alpha and beta systems, purely diagrammatic formal reasoning has not been in the mathematician's or logician's toolkit. This paper develops a purely diagrammatic reasoning system of “spider diagrams” that builds on Euler, Venn and Peirce diagrams. The system is known to be expressively equivalent to first-order monadic logic with equality. Two levels of diagrammatic syntax have been developed: an ‘abstract’ syntax that captures the structure of diagrams, and a ‘concrete’ syntax that captures topological properties of drawn diagrams. A number of simple diagrammatic transformation rules are given, and the resulting reasoning system is shown to be sound and complete.
Stable Model of X0(125)
Authors: McMurdy Ken 
Published: August 2013

AbstractIn this paper, the components in the stable model of X0(125) over C5 are determined by constructing (in the language of R. Coleman's ‘Stable maps of curves’, to appear in the Kato Volume of Doc. Math.) an explicit semi-stable covering. Empirical data is then offered regarding the placement of certain CM j-invariants in the supersingular disk of X(1) over C5, which suggests a moduli-theoretic interpretation for the components of the stable model. The paper then concludes with a conjecture regarding the stable model of X0(p3) for p > 3, which is as yet unknown.
Automating Symmetry-Breaking Calculations
Authors: Matthews P. C. 
Published: August 2013

AbstractThe process of classifying possible symmetry-breaking bifurcations requires a computation involving the subgroups and irreducible representations of the original symmetry group. It is shown how this calculation can be automated using a group theory package such as GAP. This enables a number of new results to be obtained for larger symmetry groups, where manual computation is impractical. Examples of symmetric and alternating groups are given, and the method is also applied to the spatial symmetry-breaking of periodic patterns observed in experiments.
Hurwitz Groups of Intermediate Rank
Authors: Vsemirnov M. 
Published: August 2013

AbstractThis paper is concerned with (2, 3, 7)-generated linear groups of ranks less than 287. In particular, sixty new values of n are found, such that the groups SLn(q) are Hurwitz for any prime powerq. This result provides the next step in deciding which classical groups are Hurwitz.
Improved Mixing Bounds for the Anti-Ferromagnetic Potts Model on Z2
Authors: Goldberg Leslie Ann , Jalsenius Markus , Martin Russell , Paterson Mike 
Published: August 2013

AbstractThe authors of this paper consider the anti-ferromagnetic Potts model on the the integer lattice Z2. The model has two parameters: q, the number of spins, and λ = exp(−β), where β 4 is ‘inverse temperature’. It is known that the model has strong spatial mixing if q > 7, or if q = 7 and λ = 0 or λ > 1/8, or if q = 6 and λ = 0 or λ > 1/4. The λ = 0 case corresponds to the model in which configurations are proper q-colourings of Z2. It is shown that the system has strong spatial mixing for q ≥ 6 and any λ. This implies that Glauber dynamics is rapidly mixing (so there is a fully-polynomial randomised approximation scheme for the partition function), and also that there is a unique infinite-volume Gibbs state. We also show that strong spatial mixing occurs for a larger range of λ than was previously known for q = 3, q = 4 and q = 5.
A Covariance Matrix Inversion Problem arising from the Construction of Phylogenetic Trees
Authors: Nye Tom M. W. , Baxter Brad J. C. , Gilks Walter R. 
Published: August 2013

AbstractWe describe an efficient algorithm for the inversion of covariance matrices that arise in the context of phylogenetic tree construction. Phylogenetic trees describe the evolutionary relationships between species, and their construction is computationally demanding. Many approaches involve the symmetric matrix of evolutionary distances between species. Regarding these distances as random variables, the corresponding set of variances and covariances form a rank-4 tensor, and the inner-product defined by its inverse can be used to assign statistical scores to candidate trees. We describe a natural set of assumptions for the phylogenetic tree under construction, and show how under these assumptions the covariance tensor for a tree with n leaves can be inverted inO(n2) operations. In addition to presenting the inversion algorithm, we hope this article will open algebraic and computational problems from the field of phylogeny to a wider audience.
An Indefinite Convection-Diffusion Operator
Authors: Davies E.B. 
Published: August 2013

AbstractWe give a mathematically rigorous analysis which confirms the surprising results in a recent paper of Benilov, O‘Brien and Sazonov [J. Fluid Mech. 497 (2003) 201-224] about the spectrum of a highly singular non-self-adjoint operator that arises in a problem in fluid mechanics. We also show that the set of eigenvectors does not form a basis for the operator.
Arithmetic E8 Lattices with Maximal Galois Action
Authors: Várilly-Alvarado Anthony , Zywina David 
Published: August 2013

AbstractWe construct explicit examples of E8 lattices occurring in arithmetic for which the natural Galois action is equal to the full group of automorphisms of the lattice, i.e., the Weyl group of E8. In particular, we give explicit elliptic curves over Q(t) whose Mordell-Weil lattices are isomorphic to E8 and have maximal Galois action.Our main objects of study are del Pezzo surfaces of degree 1 over number fields. The geometric Picard group, considered as a lattice via the negative of the intersection pairing, contains a sublattice isomorphic to E8. We construct examples of such surfaces for which the action of Galois on the geometric Picard group is maximal.
Computations in Relative Algebraic K-Groups
Authors: Bley Werner , Wilson Stephen M. J. 
Published: August 2013

Let G be finite group and K a number field or a p-adic field with ring of integers OK. In the first part of the manuscript we present an algorithm that computes the relative algebraic K-group K0(OK[G], K) as an abstract abelian group. We also give algorithms to solve the discrete logarithm problems in K0(OK[G], K) and in the locally free class group cl(OK[G]). All algorithms have been implemented in Magma for the case K = Q.In the second part of the manuscript we prove formulae for the torsion subgroup of K0(Z[G], Q) for large classes of dihedral and quaternion groups.
Interlimb communication to the knee flexors during walking in humans
Authors: Stevenson Andrew J. T. , Geertsen Svend S. , Andersen Jacob B. , Sinkjær Thomas , Nielsen Jens B. , Mrachacz‐Kersting Natalie 
Published: August 2013

Key points
Following unexpected ipsilateral knee extension joint rotations applied during the late stance phase of the gait cycle in humans, a crossed reflex response was observed in the contralateral biceps femoris (cBF) muscle with a mean onset latency of 76 ms.
Transcranial magnetic and electrical stimulation applied to the primary motor cortex revealed that a transcortical pathway probably contributes to the cBF response.
We hypothesize that the cBF response signifies a preparation of the contralateral leg for early load bearing, helping the body to maintain dynamic stability during walking.
This is the first study to show that a transcortical pathway contributes to an interlimb reflex in upper leg muscles. The transcortical nature of the response may allow for more adaptable responses than purely spinally mediated reflexes due to integration with other sensory information.
Abstract  A strong coordination between the two legs is important for maintaining a symmetric gait pattern and adapting to changes in the external environment. In humans as well as animals, receptors arising from the quadriceps muscle group influence the activation of ipsilateral muscles. Moreover, strong contralateral spinal connections arising from quadriceps and hamstring afferents have been shown in animal models. Therefore, the aims of the present study were to assess if such connections also exist in humans and to elucidate on the possible pathways. Contralateral reflex responses were investigated in the right leg following unexpected unilateral knee joint rotations during locomotion in either the flexion or extension direction. Strong reflex responses in the contralateral biceps femoris (cBF) muscle with a mean onset latency of 76 ± 6 ms were evoked only from ipsilateral knee extension joint rotations in the late stance phase. To investigate the contribution of a transcortical pathway to this response, transcranial magnetic and electrical stimulation were applied. Motor evoked potentials elicited by transcranial magnetic stimulation, but not transcranial electrical stimulation, were facilitated when elicited at the time of the cBF response to a greater extent than the algebraic sum of the cBF reflex and motor evoked potentials elicited separately, indicating that a transcortical pathway probably contributes to this interlimb reflex. The cBF reflex response may therefore be integrated with other sensory input, allowing for responses that are more flexible. We hypothesize that the cBF reflex response may be a preparation of the contralateral leg for early load bearing, slowing the forward progression of the body to maintain dynamic equilibrium during walking.
Exposure to cocaine regulates inhibitory synaptic transmission from the ventral tegmental area to the nucleus accumbens
Authors: Ishikawa Masago , Otaka Mami , Neumann Peter A. , Wang Zhijian , Cook James M. , Schlüter Oliver M. , Dong Yan , Huang Yanhua H. 
Published: August 2013

Key points
Synaptic projections from the ventral tegmental area (VTA) to the nucleus accumbens (NAc) make up the backbone of the brain reward pathway; in addition to the well‐known modulatory dopaminergic projection, the VTA also provides fast excitatory and inhibitory synaptic input to the NAc, but the cellular nature of VTA‐to‐NAc fast synaptic transmission and its roles in drug‐induced adaptations are not well understood.
Using optogenetic approaches, the present study profiled fast excitatory synaptic projection from dopaminergic neurons and inhibitory synaptic projection from GABAergic neurons in the VTA to NAc core (NAcCo) medium spiny neurons.
We further identified that, following repeated non‐contingent exposure to cocaine, VTA‐to‐NAcCo inhibitory synaptic transmission appears to be enhanced by an increase in the presynaptic release probability.
No postsynaptic alterations were detected at either excitatory or inhibitory synapses within the VTA‐to‐NAcCo projection.
Abstract  Synaptic projections from the ventral tegmental area (VTA) to the nucleus accumbens (NAc) make up the backbone of the brain reward pathway, a neural circuit that mediates behavioural responses elicited by natural rewards as well as by cocaine and other drugs of abuse. In addition to the well‐known modulatory dopaminergic projection, the VTA also provides fast excitatory and inhibitory synaptic input to the NAc, directly regulating NAc medium spiny neurons (MSNs). However, the cellular nature of VTA‐to‐NAc fast synaptic transmission and its roles in drug‐induced adaptations are not well understood. Using viral‐mediated in vivo expression of channelrhodopsin 2, the present study dissected fast excitatory and inhibitory synaptic transmission from the VTA to NAc MSNs in rats. Our results suggest that, following repeated exposure to cocaine (15 mg kg−1 day−1× 5 days, i.p., 1 or 21 day withdrawal), a presynaptic enhancement of excitatory transmission and suppression of inhibitory transmission occurred at different withdrawal time points at VTA‐to‐NAc core synapses. In contrast, no postsynaptic alterations were detected at either type of synapse. These results suggest that changes in VTA‐to‐NAc fast excitatory and inhibitory synaptic transmissions may contribute to cocaine‐induced alteration of the brain reward circuitry.
Simulations using patient data to evaluate systematic errors that may occur in 4D treatment planning: A proof of concept study
Authors: James Sara St. , Seco Joao , Mishra Pankaj , Lewis John H. 
Published: August 2013

Purpose:The purpose of this work is to present a framework to evaluate the accuracy of four‐dimensional treatment planning in external beam radiation therapy using measured patient data and digital phantoms.Methods:To accomplish this, 4D digital phantoms of two model patients were created using measured patient lung tumor positions. These phantoms were used to simulate a four‐dimensional computed tomography image set, which in turn was used to create a 4D Monte Carlo (4DMC) treatment plan. The 4DMC plan was evaluated by simulating the delivery of the treatment plan over approximately 5 min of tumor motion measured from the same patient on a different day. Unique phantoms accounting for the patient position (tumor position and thorax position) at 2 s intervals were used to represent the model patients on the day of treatment delivery and the delivered dose to the tumor was determined using Monte Carlo simulations.Results:For Patient 1, the tumor was adequately covered with 95.2% of the tumor receiving the prescribed dose. For Patient 2, the tumor was not adequately covered and only 74.3% of the tumor received the prescribed dose.Conclusions:This study presents a framework to evaluate 4D treatment planning methods and demonstrates a potential limitation of 4D treatment planning methods. When systematic errors are present, including when the imaging study used for treatment planning does not represent all potential tumor locations during therapy, the treatment planning methods may not adequately predict the dose to the tumor. This is the first example of a simulation study based on patient tumor trajectories where systematic errors that occur due to an inaccurate estimate of tumor motion are evaluated.
Vancomycin-Rifampin Combination Therapy Has Enhanced Efficacy against an Experimental Staphylococcus aureus Prosthetic Joint Infection
Authors: Niska Jared A. , Shahbazian Jonathan H. , Ramos Romela Irene , Francis Kevin P. , Bernthal Nicholas M. , Miller Lloyd S. 
Published: August 2013

ABSTRACT

Treatment of prosthetic joint infections often involves a two-stage exchange, with implant removal and antibiotic spacer placement followed by systemic antibiotic therapy and delayed reimplantation. However, if antibiotic therapy can be improved, one-stage exchange or implant retention may be more feasible, thereby decreasing morbidity and preserving function. In this study, a mouse model of prosthetic joint infection was used in which
Staphylococcus aureus
was inoculated into a knee joint containing a surgically placed metallic implant extending from the femur. This model was used to evaluate whether combination therapy of vancomycin plus rifampin has increased efficacy compared with vancomycin alone against these infections. On postoperative day 7, vancomycin with or without rifampin was administered for 6 weeks with implant retention.
In vivo
bioluminescence imaging,
ex vivo
CFU enumeration, X-ray imaging, and histologic analysis were carried out. We found that there was a marked therapeutic benefit when vancomycin was combined with rifampin compared with vancomycin alone. Taken together, our results suggest that the mouse model used could serve as a valuable
in vivo
preclinical model system to evaluate and compare efficacies of antibiotics and combinatory therapy for prosthetic joint infections before more extensive studies are carried out in human subjects.
Systematic Review and Meta-Analysis of
In Vitro
Synergy of Polymyxins and Carbapenems
Authors: Zusman Oren , Avni Tomer , Leibovici Leonard , Adler Amos , Friberg Lena , Stergiopoulou Theodouli , Carmeli Yehuda , Paul Mical 
Published: August 2013

ABSTRACT

Our objective was to examine the evidence of
in vitro
synergy of polymyxin-carbapenem combination therapy against Gram-negative bacteria (GNB). A systematic review and meta-analysis were performed. All studies examining
in vitro
interactions of antibiotic combinations consisting of any carbapenem with colistin or polymyxin B against any GNB were used. A broad search was conducted with no language, date, or publication status restrictions. Synergy rates, defined as a fractional inhibitory concentration index of ≤0.5 or a >2-log reduction in CFU, were pooled separately for time-kill, checkerboard, and Etest methods in a mixed-effect meta-analysis of rates. We examined whether the synergy rate depended on the testing method, type of antibiotic, bacteria, and resistance to carbapenems. Pooled rates with 95% confidence intervals (CI) are shown. Thirty-nine published studies and 15 conference proceeding were included, reporting on 246 different tests on 1,054 bacterial isolates. In time-kill studies, combination therapy showed synergy rates of 77% (95% CI, 64 to 87%) for
Acinetobacter baumannii
, 44% (95% CI, 30 to 59%) for
Klebsiella pneumoniae
, and 50% (95% CI, 30 to 69%) for
Pseudomonas aeruginosa
, with low antagonism rates for all. Doripenem showed high synergy rates for all three bacteria. For
A. baumannii
, meropenem was more synergistic than imipenem, whereas for
P. aeruginosa
the opposite was true. Checkerboard and Etest studies generally reported lower synergy rates than time-kill studies. The use of combination therapy led to less resistance development
in vitro
. The combination of a carbapenem with a polymyxin against GNB, especially
A. baumannii
, is supported
in vitro
by high synergy rates, with low antagonism and less resistance development. These findings should be examined in clinical studies.
Interaction of Ethambutol with Human Organic Cation Transporters of the SLC22 Family Indicates Potential for Drug-Drug Interactions during Antituberculosis Therapy
Authors: Pan Xiaolei , Wang Li , Gründemann Dirk , Sweet Douglas H. 
Published: August 2013

ABSTRACTAccording to the 2012 WHO global tuberculosis (TB) report (http://apps.who.int/iris/bitstream/10665/75938/1/9789241564502_eng.pdf), the death rate for tuberculosis was over 1.4 million patients in 2011, with ∼9 million new cases diagnosed. Moreover, the frequency of comorbidity with human immunodeficiency virus (HIV) and with diabetes is on the rise, increasing the risk of these patients for experiencing drug-drug interactions (DDIs) due to polypharmacy. Ethambutol is considered a first-line antituberculosis drug. Ethambutol is an organic cation at physiological pH, and its major metabolite, 2,2′-(ethylenediimino)dibutyric acid (EDA), is zwitterionic. Therefore, we assessed the effects of ethambutol and EDA on the function of human organic cation transporter 1 (hOCT1), hOCT2, and hOCT3 and that of EDA on organic anion transporter 1 (hOAT1) and hOAT3. Potent inhibition of hOCT1- and hOCT2-mediated transport by ethambutol (50% inhibitory concentration [IC50] = 92.6 ± 10.9 and 253.8 ± 90.8 μM, respectively) was observed. Ethambutol exhibited much weaker inhibition of hOCT3 (IC50= 4.1 ± 1.6 mM); however, significant inhibition (>80%) was observed at physiologically relevant concentrations in the gastrointestinal (GI) tract after oral dosing. EDA failed to exhibit any inhibitory effects that warranted further investigation. DDI analysis indicated a strong potential for ethambutol interaction on hOCT1 expressed in enterocytes and hepatocytes and on hOCT3 in enterocytes, which would alter absorption, distribution, and excretion of coadministered cationic drugs, suggesting thatin vivopharmacokinetic studies are necessary to confirm drug safety and efficacy. In particular, TB patients with coexisting HIV or diabetes might experience significant DDIs in situations of coadministration of ethambutol and clinical therapeutics known to be hOCT1/hOCT3 substrates (e.g., lamivudine or metformin).
New Role for DCR-1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27
Authors: Iatsenko Igor , Sinha Amit , Rödelsperger Christian , Sommer Ralf J. 
Published: August 2013

ABSTRACTBacillus thuringiensisproduces toxins that target invertebrates, includingCaenorhabditis elegans. Virulence ofBacillusstrains is often highly specific, such thatB. thuringiensisstrain DB27 is highly pathogenic toC. elegansbut shows no virulence for another model nematode,Pristionchus pacificus. To uncover the underlying mechanisms of the differential responses of the two nematodes toB. thuringiensisDB27 and to reveal theC. elegansdefense mechanisms against this pathogen, we conducted a genetic screen forC. elegansmutants resistant toB. thuringiensisDB27. Here, we describe aB. thuringiensisDB27-resistantC. elegansmutant that is identical tonasp-1, which encodes theC. eleganshomolog of the nuclear-autoantigenic-sperm protein. Gene expression analysis indicated a substantial overlap between the genes downregulated in thenasp-1mutant and targets ofC. elegansdcr-1/Dicer, suggesting thatdcr-1is repressed innasp-1mutants, which was confirmed by quantitative PCR. Consistent with this, thenasp-1mutant exhibits RNA interference (RNAi) deficiency and reduced longevity similar to those of adcr-1mutant. Building on these surprising findings, we further explored a potential role fordcr-1inC. elegansinnate immunity. We show thatdcr-1mutant alleles deficient in microRNA (miRNA) processing, but not those deficient only in RNAi, are resistant toB. thuringiensisDB27. Furthermore,dcr-1overexpression rescues thenasp-1mutant's resistance, suggesting that repression ofdcr-1determines thenasp-1mutant's resistance. Additionally, we identified the collagen-encoding genecol-92as one of the downstream effectors ofnasp-1that play an important role in resistance to DB27. Taken together, these results uncover a previously unknown role for DCR-1/Dicer inC. elegansantibacterial immunity that is largely associated with miRNA processing.
Reduced Virulence of the Vibrio cholerae
fadD
Mutant Is Due to Induction of the Extracytoplasmic Stress Response
Authors: Chatterjee Epshita , Chowdhury Rukhsana 
Published: August 2013

ABSTRACT

Vibrio cholerae
, an important human intestinal pathogen, is responsible for the diarrheal disease cholera. The pathogenesis of
V. cholerae
is a highly coordinated process that involves diverse regulatory factors. It has recently been demonstrated that disruption of the
V. cholerae
fadD
gene, encoding a long-chain fatty acyl coenzyme A (acyl-CoA) ligase, drastically reduces expression of the major virulence genes and
in vivo
lethality of this important human pathogen. This effect was due to reduced membrane localization of the central virulence regulator TcpP. In this study, the reason for the impaired membrane localization of TcpP in the
fadD
mutant was investigated. We demonstrate that extracytoplasmic stress is induced in the
V. cholerae
Δ
fadD
strain. In response to the extracytoplasmic stress, the integral membrane protease RseP is activated and degrades the membrane-localized TcpP in the
fadD
mutant strain. Indeed, disruption of the
rseP
gene in a
fadD
mutant background restored membrane localization of TcpP and expression of the downstream virulence genes
toxT
,
ctxA
, and
tcpA
. Increased expression of the σ
E
regulon genes in ethanol-treated wild-type
V. cholerae
indicated that ethanol exposure could induce an extracytoplasmic stress response in
V. cholerae
. Ethanol treatment also led to activation of the RseP protease activity and resulted in degradation of membrane-localized TcpP and subsequent reduction in expression of the virulence genes. Taken together, these results suggest that extracytoplasmic stress response
per se
reduces virulence of
V. cholerae
by impairing membrane localization of TcpP.