Geometry Optimization of Crystals by the Quasi-Independent Curvilinear Coordinate Approximation

The quasi-independent curvilinear coordinate approximation (QUICCA) method [K. N\'emeth and M. Challacombe, J. Chem. Phys. {\bf 121}, 2877, (2004)] is extended to the optimization of crystal structures. We demonstrate that QUICCA is valid under periodic boundary conditions, enabling simultaneous relaxation of the lattice and atomic coordinates, as illustrated by tight optimization of polyethylene, hexagonal boron-nitride, a (10,0) carbon-nanotube, hexagonal ice, quartz and sulfur at the $\Gamma$-point RPBE/STO-3G level of theory.Comment: Submitted to Journal of Chemical Physics on 7/7/0

Design and Evaluation of Image Guidance Systems for RARP

INTRODUCTION: There is a strong appetite amongst laparoscopic surgeons for image guidance during the procedure. It seems intuitively obvious that providing the surgeon with additional information on the location of unseen anatomy can only improve patient outcomes. This is not necessarily the case however. If the system gives information that is not relevant to the procedure it becomes a distraction. Similarly, if the system has large alignment errors the information may be dangerously wrong. One danger is that image guidance systems can be developed on an ad-hoc basis based not on targeted clinical goals but on the technical expertise and research goals of the scientists and engineers involved. Such a system may or may not benefit the patient. However, there is a real danger, as discussed by [1], that such systems will be introduced into surgical practice without proper assessment. We present our minimalist image guidance system for robot assisted radical prostatectomy together with a design and evaluation framework built upwards from the desired clinical outcomes

Molecular-orbital-free algorithm for excited states in time-dependent perturbation theory

A non-linear conjugate gradient optimization scheme is used to obtain excitation energies within the Random Phase Approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a modified Thouless functional, which is based upon an asymmetric Rayleigh quotient, in an orthogonalized atomic orbital representation. In this way, the computational bottleneck of calculating molecular orbitals is avoided. The variational space is reduced to the physically-relevant transitions by projections. The feasibility of an RPA implementation scaling linearly with system size, N, is investigated by monitoring convergence behavior with respect to the quality of initial guess and sensitivity to noise under thresholding, both for well- and ill-conditioned problems. The molecular- orbital-free algorithm is found to be robust and computationally efficient providing a first step toward a large-scale, reduced complexity calculation of time-dependent optical properties and linear response. The algorithm is extensible to other forms of time-dependent perturbation theory including, but not limited to, time-dependent Density Functional theory.Comment: 9 pages, 7 figure

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Surgical innovation revisited: A historical narrative of the minimally invasive "Agarwal sliding-clip renorrhaphy" technique for partial nephrectomy and its application to an Australian cohort.

Objective To evaluate local clinical outcomes of sliding clip renorrhaphy, from inception to current utilization for open, laparoscopic, and robotically assisted partial nephrectomy. Methods We reviewed prospectively maintained databases of three surgeons performing partial nephrectomies with the sliding-clip technique at teaching hospitals between 2005 and 2019. Baseline characteristics, operative parameters, including surgical approach, RENAL Nephrometry Score, and post-operative outcomes, including Clavien-Dindo classification of complications, were recorded for 76 consecutive cases. We compared perioperative and 90-day events with patient and tumor characteristics, stratified by operative approach and case complexity, using Wilcoxon rank-sum test for continuous variables and the Chi-squared or Fisher's exact test, for binary and categorical variables, respectively. Results Open surgery (n = 15) reduced ischemia time and operative time, but increased hospital admission time. Pre- and post-operative estimated glomerular filtration rates did not change significantly by operative approach. Older patients (P = .007) and open surgery (P = .003) were associated with a higher rate of complications (any-grade). Six grade ≥3 complications occurred: these were associated with higher RENAL Nephrometry Score (P = .016) and higher pathological tumor stage (P = .045). Limits include smaller case volumes which incorporate the learning curve cases; therefore, these data are most applicable to lower volume teaching hospitals. Conclusion The sliding-clip technique for partial nephrectomy was first described by Agarwal et al and has low complication rates, acceptable operative time, and preserves renal function across open and minimally invasive surgeries. This series encompasses the initial learning curve with developing the technique through to present-day emergence as a routine standard of practice

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production

<p>Abstract</p> <p>Background</p> <p>Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi-billion dollar petrochemical market into one based on renewable resources. <it>Actinobacillus succinogenes </it>naturally converts sugars and CO₂into high concentrations of succinic acid as part of a mixed-acid fermentation. Efforts are ongoing to maximize carbon flux to succinate to achieve an industrial process.</p> <p>Results</p> <p>Described here is the 2.3 Mb <it>A. succinogenes </it>genome sequence with emphasis on <it>A. succinogenes</it>'s potential for genetic engineering, its metabolic attributes and capabilities, and its lack of pathogenicity. The genome sequence contains 1,690 DNA uptake signal sequence repeats and a nearly complete set of natural competence proteins, suggesting that <it>A. succinogenes </it>is capable of natural transformation. <it>A. succinogenes </it>lacks a complete tricarboxylic acid cycle as well as a glyoxylate pathway, and it appears to be able to transport and degrade about twenty different carbohydrates. The genomes of <it>A. succinogenes </it>and its closest known relative, <it>Mannheimia succiniciproducens</it>, were compared for the presence of known Pasteurellaceae virulence factors. Both species appear to lack the virulence traits of toxin production, sialic acid and choline incorporation into lipopolysaccharide, and utilization of hemoglobin and transferrin as iron sources. Perspectives are also given on the conservation of <it>A. succinogenes </it>genomic features in other sequenced Pasteurellaceae.</p> <p>Conclusions</p> <p>Both <it>A. succinogenes </it>and <it>M. succiniciproducens </it>genome sequences lack many of the virulence genes used by their pathogenic Pasteurellaceae relatives. The lack of pathogenicity of these two succinogens is an exciting prospect, because comparisons with pathogenic Pasteurellaceae could lead to a better understanding of Pasteurellaceae virulence. The fact that the <it>A. succinogenes </it>genome encodes uptake and degradation pathways for a variety of carbohydrates reflects the variety of carbohydrate substrates available in the rumen, <it>A. succinogenes</it>'s natural habitat. It also suggests that many different carbon sources can be used as feedstock for succinate production by <it>A. succinogenes</it>.</p

Suitability of PSA-detected localised prostate cancers for focal therapy: Experience from the ProtecT study

This article is available through a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License. Copyright @ 2011 Cancer Research UK.Background: Contemporary screening for prostate cancer frequently identifies small volume, low-grade lesions. Some clinicians have advocated focal prostatic ablation as an alternative to more aggressive interventions to manage these lesions. To identify which patients might benefit from focal ablative techniques, we analysed the surgical specimens of a large sample of population-detected men undergoing radical prostatectomy as part of a randomised clinical trial. Methods: Surgical specimens from 525 men who underwent prostatectomy within the ProtecT study were analysed to determine tumour volume, location and grade. These findings were compared with information available in the biopsy specimen to examine whether focal therapy could be provided appropriately. Results: Solitary cancers were found in prostatectomy specimens from 19% (100 out of 525) of men. In addition, 73 out of 425 (17%) men had multiple cancers with a solitary significant tumour focus. Thus, 173 out of 525 (33%) men had tumours potentially suitable for focal therapy. The majority of these were small, well-differentiated lesions that appeared to be pathologically insignificant (38–66%). Criteria used to select patients for focal prostatic ablation underestimated the cancer's significance in 26% (34 out of 130) of men and resulted in overtreatment in more than half. Only 18% (24 out of 130) of men presumed eligible for focal therapy, actually had significant solitary lesions. Conclusion: Focal therapy appears inappropriate for the majority of men presenting with prostate-specific antigen-detected localised prostate cancer. Unifocal prostate cancers suitable for focal ablation are difficult to identify pre-operatively using biopsy alone. Most lesions meeting criteria for focal ablation were either more aggressive than expected or posed little threat of progression.National Institute for Health Researc

Outcomes and predictors of benign histology in patients undergoing robotic partial or radical nephrectomy for renal masses: A multicenter study

Introduction Theaim of this study was to assess preoperative factors associated with benign histology in patients undergoing surgical removal of a renal mass and to analyze outcomes of robotic partial nephrectomy (PN) and radical nephrectomy (RN) for these masses. Material and methods Overall, 2,944 cases (543 benign and 2,401 malignant) who underwent robotic PN and RN between 2003–2018 at 10 institutions worldwide were included. The assessment of the predictors of benign histology was made at the final surgical pathology report. Descriptive statistics, Mann-Whitney U, Pearson’s χ2, and logistic regression analysis were used. Results Patients in the benign group were mostly female (61 vs. 33%; p <0.001), with lower body mass index (BMI) (26.0 vs. 27.1 kg/m2; p <0.001). The benign group presented smaller tumor size (2.8 vs. 3.5 cm; p <0.001), R.E.N.A.L. score (6.0 vs. 7.0; p <0.001). There was a lower rate of hilar (11 vs.18%; p = 0.001), cT≥3 (1 vs. 4.5%; p <0.001) tumors in the benign group. There was a statistically significant higher rate of PN in the benign group (97 vs. 86%; p <0.001) as well as a statistically significant lower 30-day re-admission rate (2 vs. 5%; p = 0.081). Multivariable analysis showed male gender (OR: 0.52; p <0.001), BMI (OR: 0.95; p <0.001), and cT3a (OR: 0.22; p = 0.005) to be inversely associated to benign histology. Conclusions In 18% of cases, a benign histologic type was found. Only 3% of these tumors were treated with RN. Female gender, lower BMI, and higher T staging showed to be independent predictors of benign histology

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Management of patients who opt for radical prostatectomy during the COVID‐19 pandemic: An International Accelerated Consensus Statement

BACKGROUND: Coronavirus disease-19 (COVID-19) pandemic caused delays in definitive treatment of patients with prostate cancer. Beyond the immediate delay a backlog for future patients is expected. Such delays can lead to disease progression. OBJECTIVE: We aimed to develop guidance on criteria for prioritization for surgery and reconfiguring management pathways for non-metastatic stage of prostate cancer who opt for surgical treatment. A second aim was to identify the infection prevention and control (IPC) measures to achieve low likelihood of COVID-19 hazard if radical prostatectomy was to be carried out during the outbreak and whilst the disease is endemic. DESIGN, SETTING AND PARTICIPANTS: An accelerated consensus process and systematic review. We conducted a systematic review of the evidence on COVID-19 and reviewed international guidance on prostate cancer. These were presented to an international prostate cancer expert panel (n=34) through an online meeting. The consensus process underwent three rounds of survey in total. Additions to the second- and third-round surveys were formulated based on the answers and comments from the previous rounds. OUTCOME MEASURES: Consensus opinion was defined as ≥80% agreement, which were used to reconfigure the prostate cancer pathways. RESULTS: Evidence on the delayed management of patients with prostate cancer is scarce. There was 100% agreement that prostate cancer pathways should be reconfigured and develop measures to prevent nosocomial COVID-19 for patients treated surgically. Consensus was reached on prioritization criteria of patients for surgery and management pathways for those who have delayed treatment. IPC measures to achieve a low likelihood of nosocomial COVID-19 were coined as "COVID-19 cold sites". CONCLUSION: Re-configuring management pathways for prostate cancer patients is recommended if significant delay (>3-6 months) in surgical management is unavoidable. The mapped pathways provide guidance for such patients. The IPC processes proposed provide a framework for providing radical prostatectomy within an environment with low COVID-19 risk during the outbreak or when the disease remains endemic. The broader concepts could be adapted to other indications beyond prostate cancer surgery