Histogram Reweighting Method for Dynamic Properties

The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation functions in systems in thermodynamic equilibrium are averages over initial conditions of functions of the trajectory of the system in phase-space, the latter depending on the volume, the total number of particles and the classical Hamiltonian. Thus, the well-known histogram reweighting method can almost straightforwardly be applied to reconstruct the probability distribution of initial states at different thermodynamic conditions, without extra computational effort. Correlation functions and transport coefficients are obtained with this method from few simulation data sets.Comment: 4 pages, 3 figure

Prevalence and antimicrobial susceptibilities of bacteria isolated from blood cultures of hospitalized patients in the United States in 2002

BACKGROUND: Bloodstream infections are associated with significant patient morbidity and mortality. Antimicrobial susceptibility patterns should guide the choice of empiric antimicrobial regimens for patients with bacteremia. METHODS: From January to December of 2002, 82,569 bacterial blood culture isolates were reported to The Surveillance Network (TSN) Database-USA by 268 laboratories. Susceptibility to relevant antibiotic compounds was analyzed using National Committee for Clinical Laboratory Standards guidelines. RESULTS: Coagulase-negative staphylococci (42.0%), Staphylococcus aureus (16.5%), Enterococcus faecalis (8.3%), Escherichia coli (7.2%), Klebsiella pneumoniae (3.6%), and Enterococcus faecium (3.5%) were the most frequently isolated bacteria from blood cultures, collectively accounting for >80% of isolates. In vitro susceptibility to expanded-spectrum β-lactams such as ceftriaxone were high for oxacillin-susceptible coagulase-negative staphylococci (98.7%), oxacillin-susceptible S. aureus (99.8%), E. coli (97.3%), K. pneumoniae (93.3%), and Streptococcus pneumoniae (97.2%). Susceptibilities to fluoroquinolones were variable for K. pneumoniae (90.3–91.4%), E. coli (86.0–86.7%), oxacillin-susceptible S. aureus (84.0–89.4%), oxacillin-susceptible coagulase-negative staphylococci (72.7–82.7%), E. faecalis (52.1%), and E. faecium (11.3%). Combinations of antimicrobials are often prescribed as empiric therapy for bacteremia. Susceptibilities of all blood culture isolates to one or both agents in combinations of ceftriaxone, ceftazdime, cefepime, piperacillin-tazobactam or ciprofloxacin plus gentamicin were consistent (range, 74.8–76.3%) but lower than similar β-lactam or ciprofloxacin combinations with vancomycin (range, 93.5–96.6%). CONCLUSION: Ongoing surveillance for antimicrobial susceptibility remains essential, and will enhance efforts to identify resistance and attempt to limit its spread

Prevalence of antimicrobial resistance in bacteria isolated from central nervous system specimens as reported by U.S. hospital laboratories from 2000 to 2002

BACKGROUND: Bacterial infections of the central nervous system, especially acute infections such as bacterial meningitis require immediate, invariably empiric antibiotic therapy. The widespread emergence of resistance among bacterial species is a cause for concern. Current antibacterial susceptibility data among central nervous system (CNS) pathogens is important to define current prevalence of resistance. METHODS: Antimicrobial susceptibility of pathogens isolated from CNS specimens was analyzed using The Surveillance Database (TSN(®)) USA Database which gathers routine antibiotic susceptibility data from >300 US hospital laboratories. A total of 6029 organisms derived from CNS specimen sources during 2000–2002, were isolated and susceptibility tested. RESULTS: Staphylococcus aureus (23.7%) and Streptococcus pneumoniae (11.0%) were the most common gram-positive pathogens. Gram-negative species comprised approximately 25% of isolates. The modal patient age was 1 or <1 year for most organisms. Prevalence of MRSA among S. aureus from cerebrospinal fluid (CSF) and brain abscesses were 29.9–32.9%. Penicillin resistance rates were 16.6% for S. pneumoniae, 5.3% for viridans group streptococci, and 0% for S. agalactiae. For CSF isolates, ceftriaxone resistance was S. pneumoniae (3.5%), E. coli (0.6%), Klebsiella pneumoniae (2.8%), Serratia marcescens (5.6%), Enterobacter cloacae (25.0%), Haemophilus influenzae (0%). Listeria monocytogenes and N. meningitidis are not routinely susceptibility tested. CONCLUSIONS: Resistance is commonly detected, albeit still at relatively low levels for key drugs classes such as third-generation cephalosporins. This data demonstrates the need to consider predominant resistance phenotypes when choosing empiric therapies to treat CNS infections

Aspects of asphaltene aggregation obtained from coarse-grained molecular modeling

We have performed a molecular-simulation-based study to explore some of the underlying mechanisms of asphaltene aggregation. The daunting complexity of the crude oil + asphaltene system precludes any type of meaningful molecular simulation unless some assumptions are made with respect to the key physical and chemical properties that must be explicitly described. In the present work, we focus on molecular simulations of a coarse-grained model of asphaltene molecules in pure solvents, which are based on the assumption that the general size asymmetry and asphaltene morphology play a key role in the aggregation process. We use simple single isotropic Lennard-Jones sites to represent paraffinic and aromatic C₆ segments, which are used as building blocks for the description of continental asphaltene models and solvent moieties. The energy and size parameters for the intermolecular models (ε and σ) for solute and solvent molecules are chosen to reproduce the experimental density of the liquid phase for different mixtures. An explicit pure solvent is considered, and the relationship between the aggregation mechanism and the solvent nature is investigated through direct simulation of the aggregation process. The results reproduce accurately expected trends observed for more-complex models as well as experiments, for example, strong aggregation of asphaltene molecules in <i>n-</i>heptane and high solubility in toluene. Different asphaltene models based on different geometries reveal that even at this level of simplification the topology of the molecules (number and position of aliphatic branches) does affect the way molecules aggregate

Emerging resistance among bacterial pathogens in the intensive care unit – a European and North American Surveillance study (2000–2002)

Background Globally ICUs are encountering emergence and spread of antibiotic-resistant pathogens and for some pathogens there are few therapeutic options available. Methods Antibiotic in vitro susceptibility data of predominant ICU pathogens during 2000–2 were analyzed using data from The Surveillance Network (TSN) Databases in Europe (France, Germany and Italy), Canada, and the United States (US). Results Oxacillin resistance rates among Staphylococcus aureus isolates ranged from 19.7% to 59.4%. Penicillin resistance rates among Streptococcus pneumoniae varied from 2.0% in Germany to as high as 20.2% in the US; however, ceftriaxone resistance rates were comparably lower, ranging from 0% in Germany to 3.4% in Italy. Vancomycin resistance rates among Enterococcus faecalis were ≤ 4.5%; however, among Enterococcus faecium vancomycin resistance rates were more frequent ranging from 0.8% in France to 76.3% in the United States. Putative rates of extended-spectrum β-lactamase (ESBL) production among Enterobacteriaceae were low, \u3c6% among Escherichia coli in the five countries studied. Ceftriaxone resistance rates were generally lower than or similar to piperacillin-tazobactam for most of the Enterobacteriaceae species examined. Fluoroquinolone resistance rates were generally higher for E. coli (6.5% – 13.9%), Proteus mirabilis (0–34.7%), and Morganella morganii (1.6–20.7%) than other Enterobacteriaceae spp (1.5–21.3%). P. aeruginosa demonstrated marked variation in β-lactam resistance rates among countries. Imipenem was the most active compound tested against Acinetobacter spp., based on resistance rates. Conclusion There was a wide distribution in resistance patterns among the five countries. Compared with other countries, Italy showed the highest resistance rates to all the organisms with the exception of Enterococcus spp., which were highest in the US. This data highlights the differences in resistance encountered in intensive care units in Europe and North America and the need to determine current local resistance patterns by which to guide empiric antimicrobial therapy for intensive care infections

Tracking the implementation of NCCLS M100-S12 expanded-spectrum cephalosporin MIC breakpoints for nonmeningeal isolates of Streptococcus pneumoniae by clinical laboratories in the United States during 2002 and 2003

BACKGROUND: The Performance Standards for Antimicrobial Susceptibility Testing, Twelfth Informational Supplement, M100-S12, published by the National Committee for Clinical Laboratory Standards (NCCLS) in January 2002 introduced distinct minimum inhibitory concentration (MIC) interpretative breakpoints for ceftriaxone, cefotaxime, and cefepime for nonmeningeal isolates of Streptococcus pneumoniae. Previously, a single set of interpretative breakpoints was used for both meningeal and nonmeningeal isolates. METHODS: To estimate the rate of adoption of the M100-S12 interpretive breakpoints by clinical laboratories, antimicrobial susceptibility test results for ceftriaxone and cefotaxime from nonmeningeal S. pneumoniae isolates were studied using data collected from January 2002 to June 2003 by The Surveillance Network(® )Database – USA (TSN(®)), an electronic surveillance database. RESULTS: Of the 262 laboratories that provided data that could be evaluated, 67.6% had adopted the M100-S12 breakpoints one and one-half years after they were published. CONCLUSIONS: The NCCLS M100-S12 recommendation to interpret MICs to expanded-spectrum cephalosporins using two distinct sets of breakpoints for meningeal and nonmeningeal isolates of S. pneumoniae was steadily implemented by clinical microbiology laboratories in the United States following their initial publication in January 2002. The use of these new breakpoints more accurately reflects the clinical activities of expanded-spectrum cephalosporins than did the single set of interpretative breakpoints previously used for both meningeal and nonmeningeal isolates

Programmed cell death-1, PD-1, is dysregulated in T cells from children with new onset type 1 diabetes

Programmed death cell 1 (PD-1) is an inhibitor of T cell activation and is also functionally linked to glycolysis. We hypothesized that PD-1 expression is defective in activated T cells from children with type 1 diabetes (T1D), resulting in abnormal T cell glucose metabolism

Bayesboost: Identifying and Handling Bias Using Synthetic Data Generators

Paper presented at the Third International Workshop on Learning with Imbalanced Domains: Theory and Applications (LIDTA 2021), online, 17 September 2021.Advanced synthetic data generators can model sensitive personal datasets by creating simulated samples of data with realistic correlation structures and distributions, but with a greatly reduced risk of identifying individuals. This has huge potential in medicine where sensitive patient data can be simulated and shared, enabling the development and robust validation of new AI technologies for diagnosis and disease management. However, even when massive ground truth datasets are available (such as UK-NHS databases which contain patient records in the order of millions) there is a high risk that biases still exist which are carried over to the data generators. For example, certain cohorts of patients may be under-represented due to cultural sensitivities amongst some communities, or due to institutionalised procedures in data collection. The under-representation of groups is one of the forms in which bias can manifest itself in machine learning, and it is the one we investigate in this work.These factors may also lead to structurally missing data or incorrect correlations and distributions which will be mirrored in the synthetic data generated from biased ground truth datasets. In this paper, we explore methods to improve synthetic data generators by using probabilistic methods to firstly identify the difficult to predict data samples in ground truth data, and then to boost these types of data when generating synthetic samples. The paper explores attempts to create synthetic data that contain more realistic distributions and that lead to predictive models with better performance.NHSX

The transmission of unconventional monetary policy to bank credit supply : evidence from the TLTRO

We assess the transmission of the Targeted Longer-Term Refinancing Operations (TLTRO) to the bank credit supply for the Euro area (2014:05-2018:01) and for Portugal (2011:01-2018:01), using a panel data setup. For the Euro area, we find a positive relationship between the TLTRO and the amount of credit granted to the real economy. For the vulnerable countries, the effects of the TLTRO on the stock of credit increased from 2016 to 2017. Among the group of small banks, the effects are stronger in less vulnerable countries. We also find that competition has no statistically significant impact on the transmission of the TLTRO to the bank credit supply for the Euro area. For Portugal, using a difference-in-differences model, we find no statistically significant impact of the TLTRO on credit granted by banks. Finally, bidding banks set lower interest rates than non-bidding banks and the difference seems to be larger in 2017. In Portugal, the effects of the TLTRO on loan interest rates also increased from 2016 to 2017 and are stronger for small banks.info:eu-repo/semantics/publishedVersio