Reliable Transition State Searches Integrated with the Growing String Method.

The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess.

Growing string method with interpolation and optimization in internal coordinates: method and examples.

The growing string method (GSM) has proven especially useful for locating chemical reaction paths at low computational cost. While many string methods use Cartesian coordinates, these methods can be substantially improved by changes in the coordinate system used for interpolation and optimization steps. The quality of the interpolation scheme is especially important because it determines how close the initial path is to the optimized reaction path, and this strongly affects the rate of convergence.

Automated discovery of chemically reasonable elementary reaction steps.

Due to the significant human effort and chemical intuition required to locate chemical reaction pathways with quantum chemical modeling, only a small subspace of possible reactions is usually investigated for any given system. Herein, a systematic approach is proposed for locating reaction paths that bypasses the required human effort and expands the reactive search space, all while maintaining low computational cost. To achieve this, a range of intermediates are generated that represent potential single elementary steps away from a starting structure.

A correlated electron view of singlet fission.

Singlet fission occurs when a single exciton splits into multiple electron-hole pairs, and could dramatically increase the efficiency of organic solar cells by converting high energy photons into multiple charge carriers. Scientists might exploit singlet fission to its full potential by first understanding the underlying mechanism of this quantum mechanical process. The pursuit of this fundamental mechanism has recently benefited from the development and application of new correlated wave function methods.

Red blood cell polymorphism and susceptibility to Plasmodium vivax.

Resistance to Plasmodium vivax blood-stage infection has been widely recognised to result from absence of the Duffy (Fy) blood group from the surface of red blood cells (RBCs) in individuals of African descent. Interestingly, recent studies from different malaria-endemic regions have begun to reveal new perspectives on the association between Duffy gene polymorphism and P. vivax malaria.

Automated Transition State Searches without Evaluating the Hessian.

Accurate and speedy determination of transition structures (TSs) is essential for computational studies on reaction pathways, particularly when the process involves expensive electronic structure calculations. Many search algorithms require a good initial guess of the TS geometry, as well as a Hessian input that possesses a structure consistent with the desired saddle point. Among the double-ended interpolation methods for generation of the guess for the TS, the freezing string method (FSM) is proven to be far less expensive compared to its predecessor, the growing string method (GSM).

Variation in human β-defensin genes: new insights from a multi-population study.

Human β-defensin 2 (hBD-2) and hBD-3, encoded by DEFB4 and DEFB103A, respectively, have shown anti-HIV activity, and both genes exhibit copy number variation (CNV). Although the role of hBD-1, encoded by DEFB1, in HIV-1 infection is less clear, single nucleotide polymorphisms (SNPs) in DEFB1 may influence viral loads and disease progression. We examined the distribution of DEFB1 SNPs and DEFB4/103A CNV, and the relationship between DEFB1 SNPs and DEFB4/103A CNV using samples from two HIV/AIDS cohorts from the United States (n = 150) and five diverse populations from the Coriell Cell Repositories (n = 46).

Restricted active space spin-flip (RAS-SF) with arbitrary number of spin-flips.

The restricted active space spin-flip (RAS-SF) approach is a multistate, spin-complete, variational and size consistent method applicable to systems featuring electronic (near-)degeneracies. In contrast to CASSCF it does not involve orbital optimizations and so avoids issues such as root-flipping and state averaging. This also makes RAS-SF calculations roughly 100-1000 times faster.

Restricted active space spin-flip configuration interaction: theory and examples for multiple spin flips with odd numbers of electrons.

The restricted active space spin flip (RAS-SF) method is extended to allow ground and excited states of molecular radicals to be described at low cost (for small numbers of spin flips). RAS-SF allows for any number of spin flips and a flexible active space while maintaining pure spin eigenfunctions for all states by maintaining a spin complete set of determinants and using spin-restricted orbitals. The implementation supports both even and odd numbers of electrons, while use of resolution of the identity integrals and a shared memory parallel implementation allow for fast computation.

Evaluating infection control: a review of implementation of an infection prevention and control program in a low-income country setting.

Background: This study was conducted to review the status of the comprehensive infection prevention and control program (IPCP) established in the Republic of Kiribati in 2005, and to identify opportunities to continue and expand the integration of the IPCP into health service delivery.

Methods: The review was conducted in 2010 using 2 empirical tools: a pilot IPCP evaluation (IPCPE) tool that evaluated the activities of the program and its implementation, and a previously validated self-administered survey that assessed health care worker (HCW) knowledge, application, and confidence in infection control principles and practice. The survey was given to all 186 clinicians at Tungaru Central Hospital; the response rate was 59.

Ab initio simulations reveal that reaction dynamics strongly affect product selectivity for the cracking of alkanes over H-MFI.

Product selectivity of alkane cracking catalysis in the H-MFI zeolite is investigated using both static and dynamic first-principles quantum mechanics/molecular mechanics simulations. These simulations account for the electrostatic- and shape-selective interactions in the zeolite and provide enthalpic barriers that are closely comparable to experiment. Cracking transition states for n-pentane lead to a metastable intermediate (a local minimum with relatively small barriers to escape to deeper minima) where the proton is shared between two hydrocarbon fragments.

Reduced risk of Plasmodium vivax malaria in Papua New Guinean children with Southeast Asian ovalocytosis in two cohorts and a case-control study.

Background: The erythrocyte polymorphism, Southeast Asian ovalocytosis (SAO) (which results from a 27-base pair deletion in the erythrocyte band 3 gene, SLC4A1Δ27) protects against cerebral malaria caused by Plasmodium falciparum; however, it is unknown whether this polymorphism also protects against P. vivax infection and disease.

Methods And Findings: The association between SAO and P.

Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax.

Background: An estimated 2.85 billion people live at risk of Plasmodium vivax transmission. In endemic countries vivax malaria causes significant morbidity and its mortality is becoming more widely appreciated, drug-resistant strains are increasing in prevalence, and an increasing number of reports indicate that P.

Partnering parasites: evidence of synergism between heavy Schistosoma haematobium and Plasmodium species infections in Kenyan children.

Background: Residents of resource-poor tropical countries carry heavy burdens of concurrent parasitic infections, leading to high rates of morbidity and mortality. This study was undertaken to help identify the social and environmental determinants of multiple parasite infection in one such community.

Methodology/principal Findings: Residents of Kingwede, Kenya aged 8 years and older were tested for presence and intensity of S.

Increased reticulocyte count from cord blood samples using hypotonic lysis.

Human reticulocytes are one of the fundamental components needed to study the in vitro invasion processes of the human malaria parasite Plasmodium vivax. Additionally examinations of reticulocytes and their binding proteins are difficult in areas of the world that do not have access to advanced equipment or stem cell lines. These issues are particularly relevant to malaria vaccine candidate studies that are directed against surface proteins that the parasites use to gain entry into erythrocytes.

Estimating workload using EEG spectral power and ERPs in the n-back task.

Previous studies indicate that both electroencephalogram (EEG) spectral power (in particular the alpha and theta band) and event-related potentials (ERPs) (in particular the P300) can be used as a measure of mental work or memory load. We compare their ability to estimate workload level in a well-controlled task. In addition, we combine both types of measures in a single classification model to examine whether this results in higher classification accuracy than either one alone.

Transient CD8-memory contraction: a potential contributor to latent cytomegalovirus reactivation.

It is clear that latent CMV can reactivate in immunocompetent individuals, but the mechanism triggering such reactivations remains unclear. Recent clinical data suggest that reactivation can be subverted by CMV-specific T-memory. We therefore monitored CMV-specific T cells in immunocompetent mice with latent mCMV after a known reactivation trigger (LPS).

Genetic influences on right ventricular systolic pressure (RVSP) in chronic obstructive pulmonary disease (COPD).

Background: Pulmonary hypertension (PH) is a complication of chronic obstructive pulmonary disease (COPD). This study examined genetic variations in mediators of vascular remodelling and their association with PH in patients with COPD. In patients with COPD, we genotyped 7 SNPs in 6 candidate PH genes (NOS3, ACE, EDN1, PTGIS, SLC6A4, VEGFA).

Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children.

Genotyping Plasmodium falciparum parasites in longitudinal studies provides a robust approach to estimating force of infection (FOI) in the presence of superinfections. The molecular parameter (mol)FOI, defined as the number of new P. falciparum clones acquired over time, describes basic malaria epidemiology and is suitable for measuring outcomes of interventions.

Intermittent preventive treatment for malaria in Papua New Guinean infants exposed to Plasmodium falciparum and P. vivax: a randomized controlled trial.

Background: Intermittent preventive treatment in infants (IPTi) has been shown in randomized trials to reduce malaria-related morbidity in African infants living in areas of high Plasmodium falciparum (Pf) transmission. It remains unclear whether IPTi is an appropriate prevention strategy in non-African settings or those co-endemic for P. vivax (Pv).

Queensland Lung Cancer Screening Study: rationale, design and methods.

Background: Lung cancer is the leading cause of cancer-related mortality in Australia. Screening using low-dose computed tomography (LDCT) can reduce lung cancer mortality. The feasibility of screening in Australia is unknown.