The SMFA program for quantum chemistry calculations on large molecules

SMFA is a general program package for performing quantum chemistry calculations on large molecules, using an energy-based fragmentation approach. The program can calculate electronic energies, energy gradients and second derivatives; perform geometry optimization; find first order saddle points (transition states); perform energy optimized scans along a user-defined path; and evaluate various molecular properties. The program can use any of the following quantum chemistry packages: GAMESS(US), GAUSSIAN, NWChem and Q-Chem. In addition, SMFA provides a number of utility programs that, inter alia, calculate vibrational frequencies and infrared spectra with isotopic substitutions, the electrostatic potential on the solvent-accessible-surface, and isodesmic and higher order near-iso-energetic reaction schemes. Calculations of the electronic energy and related properties can be carried out using a scheme that provides a computation time that is linearly dependent on the size of the molecule or, if the user has enough processing units available, in a walltime that is independent of the size of the molecule

Data Resource: The National Pupil Database (NPD)

Introduction: The National Pupil Database (NPD) is a record-level administrative data resource curated by the UK government's Department for Education that is used for funding purposes, school performance tables, policy making, and research. Processes Data are sourced from schools, exam awarding bodies, and local authorities who collect data on an on-going basis and submit to the Department for Education either termly or yearly. Data contents NPD contains child-level and school-level data on all pupils in state schools in England (6.6 million in the 2016/17 academic year). The primary module is the census, which has information on characteristics and school enrolment. Other modules include alternative provision, exam attainment, absence and exclusions. Data from children's social care are also available on children referred for support and those who become looked after. Children's records are linkable across different modules and across time using a nationally unique, anonymised child-level identifier. Linkage to external datasets has also been accomplished using child-level identifiers. Conclusions The NPD is an especially valuable data resource for researchers interested in the educational experience and outcomes of children and young people in England. Although limited by the fact that children in private schools or who are home schooled are not included, it provides a near-complete picture of school trajectories and outcomes for the majority of children. Linkage to other datasets can enhance analyses and provide answers to questions that would otherwise be costly, time consuming and difficult to find

Computational Analysis of Bubble-Structure Interactions in Near-Field Underwater Explosion

The response of underwater structures to a near-field explosion is coupled with the dynamics of the explosion bubble and the surrounding water. This multiphase fluid-structure interaction process is investigated using a model problem that features the yielding and collapse of a thin-walled aluminum cylinder. A recently developed computational framework that couples a compressible fluid dynamics solver with a structural dynamics solver is employed. The fluid-structure and liquid-gas interfaces are tracked using embedded boundary and level set methods. The conservation law across the interfaces is enforced by solving one-dimensional bimaterial Riemann problems. The initial pressure inside the explosion bubble is varied by two orders of magnitude in different test cases. Three different modes of collapse are discovered, including an horizontal collapse (i.e. with one lobe extending towards the explosive charge) that appears counterintuitive, yet has been observed in previous laboratory experiments. Because of the transition of modes, the time it takes for the structure to reach self-contact does not decrease monotonically as the explosion magnitude increases. The flow fields, the bubble dynamics, and the transient structural deformation are visualized to elucidate the cause of each collapse mode and the mode transitions. The result suggests that the pressure pulse resulting from the contraction of the explosion bubble has significant effect on the structure's collapse. The phase difference between the structural vibration and bubble oscillation influences the structure's mode of collapse. Furthermore, the transient structural deformation has clear effect on the bubble dynamics, leading to a two-way interaction. A liquid jet that points away from the structure is observed. Compared to the liquid jets produced by bubbles collapsing near a rigid wall, this jet is in the opposite direction

Cataract prevalence, cataract surgical coverage and barriers to uptake of cataract surgical services in Pakistan: the Pakistan National Blindness and Visual Impairment Survey.

AIM: To estimate the prevalence of visual impairment and blindness caused by cataract, the prevalence of aphakia/pseudophakia, cataract surgical coverage (CSC) and to identify barriers to the uptake of cataract services among adults aged >or=30 years in Pakistan. METHODS: Probability proportional-to-size procedures were used to select a nationally representative sample of adults. Each subject underwent interview, visual acuity measurement, autorefraction, biometry and ophthalmic examination. Those that saw <6/12 in either eye underwent a more intensive examination procedure including corrected visual acuity, slit lamp and dilated fundus examination. CSC was calculated for different levels of visual loss by person and by eye. Individuals with <6/60 in the better eye as a result of cataract were interviewed regarding barriers. RESULTS: 16 507 Adults were examined (95.5% response rate). The crude prevalence of blindness (presenting <3/60 in the better eye) caused by bilateral cataract was 1.75% (95% CI 1.55%, 1.96%). 1317 Participants (633 men; 684 women) had undergone cataract surgery in one or both eyes, giving a crude prevalence of 8.0% (95% CI 7.6%, 8.4%). The CSC (persons) at <3/60, <6/60 and <6/18 were 77.1%, 69.3% and 43.7%, respectively. The CSC (eyes) at <3/60, <6/60 and <6/18 were 61.4%, 52.2% and 40.7%, respectively. Cost of surgery (76.1%) was the main barrier to surgery. CONCLUSION: Approximately 570 000 adults are estimated to be blind (<3/60) as a result of cataract in Pakistan, and 3,560000 eyes have a visual acuity of <6/60 because of cataract. Overall, the national surgical coverage is good but underserved populations have been identified

Rabies Surveillance Identifies Potential Risk Corridors and Enables Management Evaluation

Intensive efforts are being made to eliminate the raccoon variant of rabies virus (RABV) from the eastern United States and Canada. The United States Department of Agriculture (USDA) Wildlife Services National Rabies Management Program has implemented enhanced rabies surveillance (ERS) to improve case detection across the extent of the raccoon oral rabies vaccination (ORV) management area. We evaluated ERS and public health surveillance data from 2006 to 2017 in three northeastern USA states using a dynamic occupancy modeling approach. Our objectives were to examine potential risk corridors for RABV incursion from the U.S. into Canada, evaluate the effectiveness of ORV management strategies, and identify surveillance gaps. ORV management has resulted in a decrease in RABV cases over time within vaccination zones (from occupancy (ψ) of 0.60 standard error (SE) = 0.03 in the spring of 2006 to ψ of 0.33 SE = 0.10 in the spring 2017). RABV cases also reduced in the enzootic area (from ψ of 0.60 SE = 0.03 in the spring of 2006 to ψ of 0.45 SE = 0.05 in the spring 2017). Although RABV occurrence was related to habitat type, greater impacts were associated with ORV and trap–vaccinate–release (TVR) campaigns, in addition to seasonal and yearly trends. Reductions in RABV occupancy were more pronounced in areas treated with Ontario Rabies Vaccine Bait (ONRAB) compared to RABORAL V-RG®. Our approach tracked changes in RABV occurrence across space and time, identified risk corridors for potential incursions into Canada, and highlighted surveillance gaps, while evaluating the impacts of management actions. Using this approach, we are able to provide guidance for future RABV management

Secondary Waves, and/or the "Reflection" From and "Transmission" Through a Coronal Hole of an EUV Wave Associated With the 2011 February 15 X2.2 Flare Observed With SDO/AIA and STEREO/EUVI

For the first time, the kinematic evolution of a coronal wave over the entire solar surface is studied. Full Sun maps can be made by combining images from the Solar Terrestrial Relations Observatory satellites, Ahead and Behind, and the Solar Dynamics Observatory, thanks to the wide angular separation between them. We study the propagation of a coronal wave, also known as "EIT" wave, and its interaction with a coronal hole resulting in secondary waves and/or reflection and transmission. We explore the possibility of the wave obeying the law of reflection of waves. In a detailed example we find that a loop arcade at the coronal hole boundary cascades and oscillates as a result of the EUV wave passage and triggers a wave directed eastwards that appears to have reflected. We find that the speed of this wave decelerates to an asymptotic value, which is less than half of the primary EUV wave speed. Thanks to the full Sun coverage we are able to determine that part of the primary wave is transmitted through the coronal hole. This is the first observation of its kind. The kinematic measurements of the reflected and transmitted wave tracks are consistent with a fast-mode MHD wave interpretation. Eventually, all wave tracks decelerate and disappear at a distance. A possible scenario of the whole process is that the wave is initially driven by the expanding coronal mass ejection and subsequently decouples from the driver and then propagates at the local fast-mode speed.Comment: 30 pages, 12 figures, accepted for publication in Ap

The Wave Properties of Coronal Bright Fronts Observed Using SDO/AIA

Coronal bright fronts (CBFs) are large scale wavefronts that propagate though the solar corona at hundreds of kilometers per second. While their kinematics have been studied in detail, many questions remain regarding the temporal evolution of their amplitude and pulse width. Here, contemporaneous high cadence, multi-thermal observations of the solar corona from the Solar Dynamic Observatory (SDO) and Solar TErrestrial RElations Observatory (STEREO) spacecraft are used to determine the kinematics and expansion rate of a CBF wavefront observed on 2010 August 14. The CBF was found to have a lower initial velocity with weaker deceleration in STEREO observations compared to SDO (~340 km/s and -72 m/s/s as opposed to ~410 km/s and -279 m/s/s). The CBF kinematics from SDO were found to be highly passband-dependent, with an initial velocity ranging from 379+/-12 km/s to 460+/-28 km/s and acceleration ranging from -128+/-28 m/s/s to -431+/-86 m/s/s in the 335A and 304A passbands respectively. These kinematics were used to estimate a quiet coronal magnetic field strength range of ~1-2 G. Significant pulse broadening was also observed, with expansion rates of ~130 km/s (STEREO) and ~220 km/s (SDO). By treating the CBF as a linear superposition of sinusoidal waves within a Gaussian envelope, the resulting dispersion rate of the pulse was found to be ~8-13 Mm^2 s^-1. These results are indicative of a fast-mode magnetoacoustic wave pulse propagating through an inhomogeneous medium.Comment: 14 pages, 2 figures. Accepted for publication in The Astrophysical Journal Letter

Associations of vitamin D pathway genes with circulating 25-hydroxyvitamin-D, 1,25-dihydroxyvitamin-D, and prostate cancer:a nested case-control study

Vitamin D pathway single nucleotide polymorphisms (SNPs) are potentially useful proxies for investigating whether circulating vitamin D metabolites [total 25-hydroxyvitamin-D, 25(OH)D; 1,25-dihydroxyvitamin, 1,25(OH)2D] are causally related to prostate cancer. We investigated associations of sixteen SNPs across seven genes with prostate-specific antigen-detected prostate cancer

From evidence based bioethics to evidence based social policies

In this issue, Norwegian authors demonstrate that causes of early expulsion out the workforce are rooted in childhood. They reconstruct individual biographies in administrative databases linked by an unique national identification number, looking forward 15 years in early adulthood and looking back 20 years till birth with close to negligible loss to follow up. Evidence based bioethics suggest that it is better to live in a country that allows reconstructing biographies in administrative databases then in countries that forbid access by restrictive legislation based on privacy considerations. The benefits of gained knowledge from existing and accessible information are tangible, particularly for the weak and the poor, while the harms of theoretical privacy invasion have not yet materialised. The study shows once again that disadvantage runs in families. Low parental education, parental disability and unstable marital unions predict early disability pensions and premature expulsion out gainful employment. The effect of low parental education is mediated by low education of the index person. However, in a feast of descriptive studies of socio-economic causes of ill health we still face a famine of evaluative intervention studies. An evidence based social policy should be based on effective interventions that are able to break the vicious circles of disability handed down from generation to generation