A hierarchical Bayesian model for predicting ecological interactions using scaled evolutionary relationships

Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and covariates are limited to only a fraction of species. On the other hand, evolutionary relationships, encoded as phylogenetic trees, can act as proxies for underlying traits and historical patterns of parasite sharing among hosts. We show that using a network-based conditional model, phylogenetic information provides strong predictive power in a recently published global database of host-parasite interactions. By scaling the phylogeny using an evolutionary model, our method allows for biological interpretation often missing from latent variable models. To further improve on the phylogeny-only model, we combine a hierarchical Bayesian latent score framework for bipartite graphs that accounts for the number of interactions per species with the host dependence informed by phylogeny. Combining the two information sources yields significant improvement in predictive accuracy over each of the submodels alone. As many interaction networks are constructed from presence-only data, we extend the model by integrating a correction mechanism for missing interactions, which proves valuable in reducing uncertainty in unobserved interactions.Comment: To appear in the Annals of Applied Statistic

Mechanisms, molecular and sero-epidemiology of antimicrobial resistance in bacterial respiratory pathogens isolated from Japanese children

Abstract Background The clinical management of community-acquired respiratory tract infections (RTIs) is complicated by the increasing worldwide prevalence of antibacterial resistance, in particular, β-lactam and macrolide resistance, among the most common causative bacterial pathogens. This study aimed to determine the mechanisms and molecular- and sero-epidemiology of antibacterial resistance among the key paediatric respiratory pathogens in Japan. Methods Isolates were collected at 18 centres in Japan during 2002 and 2003 from children with RTIs as part of the PROTEKT surveillance programme. A proportion of Haemophilus influenzae isolates was subjected to sequencing analysis of the ftsI gene; phylogenetic relatedness was assessed using multilocus sequence typing. Streptococcus pneumoniae isolates were screened for macrolide-resistance genotype by polymerase chain reaction and serotyped using the capsular swelling method. Susceptibility of isolates to selected antibacterials was performed using CLSI methodology. Results and Discussion Of the 557 H. influenzae isolates collected, 30 (5.4%) were β-lactamase-positive [BL+], 115 (20.6%) were BL-nonproducing ampicillin-resistant (BLNAR; MIC ≥ 4 mg/L) and 79 (14.2%) were BL-nonproducing ampicillin-intermediate (BLNAI; MIC 2 mg/L). Dabernat Group III penicillin binding protein 3 (PBP3) amino acid substitutions in the ftsI gene were closely correlated with BLNAR status but phylogenetic analysis indicated marked clonal diversity. PBP mutations were also found among BL+ and BL-nonproducing ampicillin-sensitive isolates. Of the antibacterials tested, azithromycin and telithromycin were the most active against H. influenzae (100% and 99.3% susceptibility, respectively). A large proportion (75.2%) of the 468 S. pneumoniae isolates exhibited macrolide resistance (erythromycin MIC ≥ 1 mg/L); erm(B) was the most common macrolide resistance genotype (58.8%), followed by mef(A) (37.2%). The most common pneumococcal serotypes were 6B (19.7%), 19F (13.7%), 23F (13.5%) and 6A (12.8%). Telithromycin and amoxicillin-clavulanate were the most active antibacterials against S. pneumoniae (99.8% and 99.6% susceptibility, respectively). Conclusion Approximately one-third of H. influenzae isolates from paediatric patients in Japan are BLNAI/BLNAR, mainly as a result of clonally diverse PBP3 mutations. Together with the continued high prevalence of pneumococcal macrolide resistance, these results may have implications for the clinical management of paediatric RTIs in Japan.</p

Computing equilibrium states of cholesteric liquid crystals in elliptical channels with deflation algorithms

We study the problem of a cholesteric liquid crystal confined to an elliptical channel. The system is geometrically frustrated because the cholesteric prefers to adopt a uniform rate of twist deformation, but the elliptical domain precludes this. The frustration is resolved by deformation of the layers or introduction of defects, leading to a particularly rich family of equilibrium configurations. To identify the solution set, we adapt and apply a new family of algorithms, known as deflation methods, that iteratively modify the free energy extremisation problem by removing previously known solutions. A second algorithm, deflated continuation, is used to track solution branches as a function of the aspect ratio of the ellipse and preferred pitch of the cholesteric.Comment: 9 pages, 6 figure

Trends in antibacterial resistance among Streptococcus pneumoniae isolated in the USA: update from PROTEKT US Years 1–4

© 2008 Jenkins et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Antibiotic activity of telithromycin and comparators against bacterial pathogens isolated from 3,043 patients with acute exacerbation of chronic bronchitis

BACKGROUND: Antimicrobial therapy is considered an important component in the medical management of most patients with acute exacerbation of chronic bronchitis (AECB). The three predominant bacterial species isolated are nontypeable Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. Staphylococcus aureus is also frequently isolated while atypical bacteria are thought to cause up to 10% of exacerbations. Antibacterial resistance is increasing worldwide and little surveillance data exist concerning pathogens isolated from patients with AECB. METHODS: This study examines the prevalence of antibacterial resistance in isolates obtained from patients with clinically diagnosed AECB. A total of 3043 isolates were obtained from 85 centres in 29 countries, between 1999–2003, and were tested against the new ketolide telithromycin and a panel of commonly used antibiotics. RESULTS AND DISCUSSION: Of the S. pneumoniae isolates, 99.9% were susceptible to telithromycin, but only 71% were susceptible to erythromycin and 75.3% to penicillin. Of the H. influenzae isolates, 99.6% were susceptible to telithromycin. 11.7% of these isolates produced β-lactamase. Almost 10% of S. pneumoniae were multidrug-resistant; 99.0% of these isolates were susceptible to telithromycin. Telithromycin also demonstrated good in vitro activity against M. catarrhalis (MIC(90 )= 0.12 mg/L) and was the most active compound against methicillin-susceptible S. aureus (98.9% susceptible). CONCLUSION: Telithromycin demonstrated similar or better activity against the bacterial species investigated than the other agents, with the most complete coverage overall. These species are the predominant causative bacterial pathogens in AECB and thus the spectrum of activity of telithromycin makes it a potential alternative for the empirical treatment of AECB

The series Bi2Sr2Ca(n-1) Cu(n)O(2n+4) (1 less than or equal to n less than or equal to 5): Phase stability and superconducting properties

Phase relations at 850 and 870 C, melting transitions in air, oxygen, and helium were studied for Bi(2.1)Sr(1.9) CuO6 and for the Bi2Sr2Ca(n-1) Cu(n)O(2n+4) for n = 1, 2, 3, 4, 5, and infinity (CaCuO2). Up to 870 C, the n = 2 composition resides in the compatibility tetrahedron bounded by Bi(2+x)(Sr,Ca)(3-y) Cu2O8, (Sr,Ca)14 Cu24O41, Ca2CuO3, and a Bi-Sr-Ca-O phase. The n is greater than or equal to 3 compositions reside in the compatibility tetrahedron Bi(2+x)(Sr,Ca)(3-y) Cu2O8 - (Sr,Ca)14 Cu24O41 - Ca2CuO3 - CuO up to 850 C. However, Bi(2+x)Sr(4-y) Cu3O10 forms for n is greater than or equal to 3 after extended heating at 870 C. Bi(2+x)Sr(2-y) CuO6 and Bi(2+x)(Sr,Ca)(3-y) Cu2O8 melt in air at 914 C and 895 C respectively. During melting, all of the compositions studied lose 1 to 2 percent by weight of oxygen from the reduction of copper. Bi(2+x)Sr(2-y) CuO6, Bi(2+n)(Sr,Ca)(3-y) Cu2O8, and Bi(2+x)(Sr,Ca)(4-y) Cu3O10 exhibit crystallographic alignment in a magnetic field, with the c-axes orienting parallel to the field

Riding the Right Wavelet:Quantifying Scale Transitions in Fractured Rocks

Peer reviewedPublisher PD

Ceftobiprole Activity against over 60,000 Clinical Bacterial Pathogens Isolated in Europe, Turkey, and Israel from 2005 to 2010

Ceftobiprole medocaril is a newly approved drug in Europe for the treatment of hospital-acquired pneumonia (HAP) (excluding patients with ventilator-associated pneumonia but including ventilated HAP patients) and community-acquired pneumonia in adults. the aim of this study was to evaluate the in vitro antimicrobial activity of ceftobiprole against prevalent Gram-positive and -negative pathogens isolated in Europe, Turkey, and Israel during 2005 through 2010. A total of 60,084 consecutive, nonduplicate isolates from a wide variety of infections were collected from 33 medical centers. Species identification was confirmed, and all isolates were susceptibility tested using reference broth microdilution methods. Ceftobiprole had high activity against methicillin-susceptible Staphylococcus aureus (MSSA) (100.0% susceptible), methicillin-susceptible coagulase-negative staphylococci (CoNS), beta-hemolytic streptococci, and Streptococcus pneumoniae (99.3% susceptible), with MIC90 values of 0.25, 0.12, 80% inhibited at 8 mu g/ml; 64.6% at MIC values of 16 mu g/ml; 75.4% susceptible), but limited activity was observed against Acinetobacter spp. and Stenotrophomonas maltophilia. High activity was also observed against all Haemophilus influenzae (MIC90, <= 0.06 mu g/ml) and Moraxella catarrhalis (MIC50/90, <= 0.06/0.25 mu g/ml) isolates. Ceftobiprole demonstrated a wide spectrum of antimicrobial activity against this very large longitudinal sample of contemporary pathogens.Basilea Pharmaceutica International AG (Basel, Switzerland)AchaogenAiresAmerican Proficiency Institute (API)AnacorAstellasAstraZenecaBayerbioMerieuxCempraCerexaContrafectCubist PharmaceuticalsDaiichiDipexiumEnantaFuriexGlaxoSmithKlineJohnson JohnsonLegoChem Biosciences Inc.Meiji Seika KaishaMerckNabrivaNovartisParatekPfizerPPD TherapeuticsPremier Research GroupRempexRib-X PharmaceuticalsSeachaidShionogiThe Medicines Co.TheravanceThermo FisherJMI Labs, North Liberty, IA 52317 USAUniv Toronto, Dept Lab Med & Pathobiol, Toronto, ON, CanadaUniversidade Federal de São Paulo, Div Infect Dis, São Paulo, BrazilTufts Univ, Sch Med, Boston, MA 02111 USAUniversidade Federal de São Paulo, Div Infect Dis, São Paulo, BrazilWeb of Scienc