Delayed Slater determinant update algorithms for high efficiency quantum Monte Carlo

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is therefore formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core CPUs and GPUs

An Integrated Programming and Development Environment for Adiabatic Quantum Optimization

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware has raised challenging questions about how to evaluate adiabatic quantum optimization programs. Processor behavior depends on multiple steps to synthesize an adiabatic quantum program, which are each highly tunable. We present an integrated programming and development environment for adiabatic quantum optimization called JADE that provides control over all the steps taken during program synthesis. JADE captures the workflow needed to rigorously specify the adiabatic quantum optimization algorithm while allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation engine that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its potential use for benchmarking adiabatic quantum optimization programs by the quantum computer science community.Comment: 28 pages, 17 figures, feedback welcomed, even if it's criticism; v2 manuscript updated based on reviewer feedback; v3 manuscript updated based on reviewer feedback, title modifie

Necrotizing pneumonia due to methicillin-resistant Staphylococcus aureus

The aim of this study was to describe a case of necrotizing pneumonia caused by methicillin-resistant Staphylococcus aureus. The sample was isolated from a blood culture collected less than 48 hours after hospital admission. The patient had been healthy until the infectious process started. The isolate had the mecA gene with staphylococcal cassette chromosome mec (SCCmec) type IVa. The possibility that Staphylococcus aureus harboring this genetic determinant might be present in our setting should be considered in situations of severe pneumonia within the community.O objetivo desse estudo foi descrever um caso de pneumonia necrotizante por Staphylococcus aureus resistente a meticilina. A amostra foi isolada em hemocultura coletada menos de 48 horas da admissão hospitalar. A paciente era previamente hígida quando do início do processo infeccioso. O isolado possuía o gene mecA, com staphylococcal cassette chromosome mec tipo IVa. A presença de Staphylococcus aureus carreando esse determinante genético em nosso meio deve ser considerada em pneumonias comunitárias graves.Universidade Federal de São Paulo (UNIFESP) Laboratório Especial de Microbiologia ClínicaUniversidade Federal de Ciências da Saúde de Porto Alegre Departamento de Ciências Básicas da SaúdeHospital Nove de JulhoUNIFESP, Laboratório Especial de Microbiologia ClínicaSciEL

In vitro antimicrobial susceptibility of coagulase negative staphylococcal ocular isolates

PURPOSE: To assess the in vitro susceptibility of conjunctival and corneal coagulase negative Staphylococcus (CoNS) to methicillin, fluoroquinolones and aminoglycosides. METHODS: A total of 707 conjunctival and corneal CoNS disk diffusion test results were retrospectively analyzed, from January 2000 through December 2003. RESULTS: From 2000 to 2003, there was an increase in number of CoNS isolated from conjunctiva (n=57 to n=153) and cornea (n=28 to n=78). The frequency of conjunctival and corneal methicillin-resistant CoNS also increased (1.8 to 19.6% and 14.3 to 29.3%, respectively). There was no statistically significant difference between fluoroquinolones-resistant CoNS percentages in conjunctiva (ofloxacin: 1.8 to 7.8% and ciprofloxacin: 3.5 to 9.2%) and cornea (ofloxacin: 14.3 to 9.0% and ciprofloxacin: 14.3 to 10.3%). Evaluating the results of the conjunctival samples, there was increased resistance to tobramycin (15.8 to 34.0%) and to gentamycin (10.5 to 25.5%). There was no change in resistance of corneal isolates to tobramycin (28.6 to 26.9%) and to gentamycin (21.4 to 23.1%). CONCLUSIONS: there was a decrease in in vitro CoNS susceptibility to methicillin, tobramycin and gentamycin. Fuoroquinolones represented by ofloxacin and ciprofloxacin demonstrated stable in vitro susceptibility.OBJETIVO: Avaliar a suscetibilidade, in vitro, de Staphylococcus coagulase negativa (SCoN), isolados da conjuntiva e córnea, à meticilina, às fluoroquinolonas e aos aminoglicosídeos. MÉTODOS: Foram analisadas retrospectivamente 707 amostras oculares de SCoN quanto à suscetibilidade aos antimicrobianos pelo teste de disco difusão, durante o período de janeiro de 2000 a dezembro de 2003. RESULTADOS: Houve um aumento do número de SCoN em isolados da conjuntiva (n=57, ano de 2000 e n=153, ano de 2003) e da córnea (n=28, ano de 2000 e n=78, ano de 2003). A freqüência de SCoN resistentes à meticilina isolados da conjuntiva e da córnea, aumentou (1,8 a 19,6% e 14,3 a 29,3% respectivamente) durante o período avaliado. Não houve diferença estatisticamente significante nos anos estudados, nos percentuais de SCoN resistentes às fluoroquinolonas, nas conjuntivas (ofloxacina: 1,8 a 7,8% e ciprofloxacina: 3,5 a 9,2%) e nas córneas (ofloxacina: 14,3 a 9,0% e ciprofloxacina:14,3 a 10,3%). Avaliando-se os resultados das amostras isoladas da conjuntiva, observou-se um aumento na resistência à tobramicina: 15,8 a 34,6%; e à gentamicina: 10,5 a 25,5%; mas não houve mudança no perfil de resistência das amostras da córnea à tobramicina: 28,6 a 26,9% e à gentamicina: 21,4 a 23,1%). CONCLUSÃO: Houve diminuição na suscetibilidade in vitro dos SCoN para meticilina, tobramicina e gentamicina. As fluoroquinolonas, representadas pela ofloxacina e ciprofloxacina, demonstraram ter um padrão estável de suscetibilidade in vitro.Universidade Federal de São Paulo (UNIFESP)UNIFESPUNIFESP Departamento de Oftalmologia Laboratório de MicrobiologiaUNIFESP Departamento de OftalmologiaUniversidade de São Paulo Instituto de Ciências Biológicas Departamento de MicrobiologiaUNIFESP, Depto. de Oftalmologia Laboratório de MicrobiologiaUNIFESP, Depto. de OftalmologiaSciEL

Optimal Point Placement for Mesh Smoothing

We study the problem of moving a vertex in an unstructured mesh of triangular, quadrilateral, or tetrahedral elements to optimize the shapes of adjacent elements. We show that many such problems can be solved in linear time using generalized linear programming. We also give efficient algorithms for some mesh smoothing problems that do not fit into the generalized linear programming paradigm.Comment: 12 pages, 3 figures. A preliminary version of this paper was presented at the 8th ACM/SIAM Symp. on Discrete Algorithms (SODA '97). This is the final version, and will appear in a special issue of J. Algorithms for papers from SODA '9

Métodos laboratoriais para a detecção da resistência à meticilina nos Staphylococcus coagulase negativos de infecções oculares

PURPOSE: To evaluate different methods of oxacillin susceptibility testing of ocular isolates, considering polymerase chain reaction (PCR) as the 'gold standard', and to compare the in vitro susceptibility to oxacillin with that of other antimicrobials used in ophthalmologic practice. METHODS: The Vitek gram-positive identification card was used to identify ocular coagulase negative Staphylococcus species. The presence of the mecA gene was determined by the polymerase chain reaction assay with a combination of two primer sets (mecA and 16S rRNA) in a single region. Results were analyzed and compared with other oxacillin susceptibility methods: PBP2a detection by rapid slide latex agglutination test (SLA); oxacillin E-test; the Vitek automated gram-positive susceptibility card (GPS-105); the oxacillin salt agar screening test (OSAS) at a concentration of 6.0, 1.0 and 0.75 µg oxacillin per ml and the cefoxitin disk diffusion test (CDD). Automated susceptibility was also determined to other antimicrobial agents (fluoroquinolones, penicillin G, amoxicillin-ampicillin, cefazolin, ampicillin-sulbactam, erythromycin, clindamycin, gentamicin, tetracycline, trimethoprim-sulfamethoxazole, vancomycin and rifampin. RESULTS: Of the 69 CoNS isolates tested, 71% were mecA-positive and 29% mecA-negative. All methods tested had a statistically significant agreement with polymerase chain reaction. There was a tendency of positive polymerase chain reaction predomination among the S. epidermidis isolates in comparison to non-epidermidis isolates, although this was not statistically significant (78.3% vs. 56.5%; chi2= 2.54; P= 0.11). The oxacillin salt agar screening test (0.75 µg oxacillin/ml) showed the best performance, with 100% sensitivity and negative predictive value; 95% specificity and 98% positive predictive value. Using the E-test, the mecA-positive isolates were statistically significantly more resistant to ciprofloxacin, ofloxacin, gatifloxacin and moxifloxacin (P= 0.002; P= 0.008; P= 0.002 and P= 0.003, respectively). There was a statistically significant higher proportion of resistance of the coagulase negative Staphylococcus mecA-positives for: penicillin G, amoxicillin-ampicillin, cefazolin, ampicillin-sulbactam, erythromycin, clindamycin, gentamicin and tetracycline (P<0.05). All coagulase negative Staphylococcus species were susceptible to vancomycin and there was no statistically significant correlation between the mecA-positive isolates and resistance to trimethoprim-sulfamethoxazole or to rifampin. CONCLUSIONS: In the present study, we found that the E-test and the oxacillin salt agar screening test S (0.75 µg oxacillin per ml), when compared with polymerase chain reaction, were the most accurate currently available methods to phenotypically detect oxacillin resistance of coagulase negative Staphylococcus species. This study demonstrated that a good option for screening of ocular isolates for oxacillin resistance in the microbiology laboratory is the cefoxitin disk diffusion test and the automated Vitek system. We believe it is important to have available methods that accurately detect methicillin resistance of the less commonly encountered species, chiefly because of their increasing importance as opportunistic pathogens.OBJETIVOS: Avaliar os diferentes métodos de suscetibilidade à oxacillina, em isolados oculares, considerando a reação em cadeia da polimerase (PCR) como padrão-ouro e comparar a suscetibilidade in vitro para outros antimicrobianos de uso oftalmológico. MÉTODOS: O sistema automatizado Vitek foi utilizado para identificar as diferentes espécies de Staphylococcus coagulase negativo (SCoN). A presença do gene mecA foi determinado pela reação em cadeia da polimerase com a combinação de 2 primer sets (mecA e 16S rRNA) em uma única região. Estes resultados foram analisados e comparados com outros métodos de suscetibilidade à oxacilina: detecção da proteína PBP2a pelo teste de aglutinação em látex (SLA); E-test oxacilina; o sistema automatizado Vitek (GPS-105); o teste de triagem em ágar (OSAS) com oxacilina nas concentrações de 6,0, 1,0 e 0,75 µg oxacilina por ml e o teste de disco difusão com cefoxitina (CDD). A suscetibilidade automatizada foi obtida para os seguintes agentes antimicrobianos: fluorquinolonas, penicilina G, amoxicilina-ampicilina, cefazolina, ampicilina-sulbactam, eritromicina, clindamicina, gentamicina, tetraciclina, sulfametoxazol-trimetoprima, vancomicina e rifampicina. RESULTADOS: Dos 69 Staphylococcus coagulase negativo testados, 71% foram mecA-positivos e 29%, mecA-negativos. Todos os métodos testados apresentaram concordância estatisticamente significante com a reação em cadeia da polimerase. Houve tendência à predominância da positividade da reação em cadeia da polimerase entre os S. epidermidis comparado aos não-epidermidis, embora sem significância estatistica (78,3% vs. 56,5%; chi2= 2,54; p=0,11). O teste de triagem em ágar (0,75 µg oxacilina/ml) apresentou a melhor performance com resultados de: 100% de sensibilidade e valor preditivo negativo, 95% de especificidade e 98% de valor preditivo positivo. Os isolados mecA-positivos foram estatisticamente significativavos mais resistentes para ciprofloxacina, ofloxacina, gatifloxacina e moxifloxacina, no E-test (p=0,002; p=0,008; p=0,002 e p=0,003). Houve maior proporção estatisticamente significativa de resistência entre os Staphylococcus coagulase negativo mecA-positivos para: penicilina G, amoxicilina-ampicilina, cefazolina, ampicilina-sulbactam, eritromicina, clindamicina, gentamicina e tetraciclina. (p<=0,05) Todos os Staphylococcus coagulase negativos foram suscetíveis à vancomicina e não houve correlação estatisticamente significativa entre as amostras mecA-positivas e a resistência para sulfametoxazol-trimetoprima e rifampicina. CONCLUSÕES: No presente estudo, foi observado que o E-test e o OSAS (0,75 µg oxacilina por ml), comparado à reação em cadeia da polimerase, foram os métodos fenotípicos mais acurados em detectar a resistência à oxacilina nos Staphylococcus coagulase negativos. Foi demonstrado que os testes de disco difusão com cefoxitina e o método automatizado (Vitek) são boas opções para a triagem da resistência à oxacilina em laboratórios de microbiologia ocular. Destacou-se a importância de métodos acurados para detectar a resistência à meticilina dentre as espécies menos freqüentemente encontradas, considerando a crescente importância destes patógenos oportunistas.Universidade Federal de São Paulo (UNIFESP) Departamento de OftalmologiaFundação Faculdade Federal de Ciências Médicas de Porto Alegre Departamento de Microbiologia e ParasitologiaUNIFESP Divisão de Doenças Infecciosas Laboratório Especial de Microbiologia ClínicaUNIFESP Departamento de OftalmologiaUNIFESP Departamento de MicrobiologiaSanta Casa de Misericórdia de São Paulo Faculdade de Ciências Médicas Departamento de PatologiaHospital Israelita Albert EinsteinUNIFESP, Depto. de OftalmologiaUNIFESP, Divisão de Doenças Infecciosas Laboratório Especial de Microbiologia ClínicaUNIFESP, Depto. de OftalmologiaUNIFESP, Depto. de MicrobiologiaSciEL

Clemmer et al., eds.: Julian Steward and the Great Basin: The Making of an Anthropologist

Julian Steward and the Great Basin: The Making of an Anthropologist. Richard O. Clemmer, L. Daniel Myers, and Mary Elizabeth Rudden, eds. University of Utah Press, 1999, 288 pp. bibliography, index, $45.00 (hard cover),$19.95 (paper)