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

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

Design and evaluation of an image-guidance system for robot-assisted radical prostatectomy

UNLABELLED: WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Systems for image guidance during laparoscopic surgery can be broadly defined as systems that enable the surgeon to refer to preoperatively gathered information during the procedure. For a laparoscopic system the preoperative information can be overlaid onto the laparoscopic video screen. Examples of surgical image-guidance systems and the results of early testing are not uncommon but the technical methodologies used vary widely as do the visualisation methods. This study reports our experience of using an image-guidance system on 13 patients. Furthermore, we use previously proposed methodology to form a development and evaluation framework specific to image-guided laparoscopic radical prostatectomy. Finally, we propose that if the system development process is properly designed, it should be possible to correlate system technical parameters with clinical outcomes. We present a possible plot for the key technical parameter of accuracy. Better understanding of this correlation should enable robust development and evaluation of surgical image-guidance systems to optimise patient outcomes. OBJECTIVE: To implement and test the feasibility of an image-guidance system for robot-assisted radical prostatectomy (RARP). Laparoscopic surgical outcomes may be improved through image guidance. However, to demonstrate improved outcomes rigorous evaluation techniques are required. Therefore we also present our work in establishing robust evaluation techniques. PATIENTS AND METHODS: Development work used three cadavers and an anatomy phantom. The system has been used on 13 patients. During surgery the surgeon can refer to the patient's magnetic resonance imaging (collected before the operation) overlaid on the endoscopic video image. The result of the overlay process was measured qualitatively by the surgeon with reference to the desired clinical outcomes. RESULTS: The use of the overlay system has not resulted in any measurable change in clinical outcomes. The surgeons found the system to be a useful tool for reference during surgery. A more rigorous evaluation method is proposed that will enable on-going development. CONCLUSION: Image guidance during RARP is feasible. We propose a series of measures that will improve further development and evaluation

The Impact of Venous Thromboembolism on Upper Tract Urothelial Carcinomas Undergoing Open or Minimally Invasive Radical Nephroureterectomy in the USA: Perioperative Outcomes and Health Care Costs from Insurance Claims Data

Background and objective: Venous thromboembolism (VTE) is a significant predictor of worse postoperative morbidity in cancer surgeries. No data have been available for patients with preoperative VTE and upper tract urothelial carcinoma (UTUC) undergoing radical nephroureterectomy (RNU). Our aim was to assess the impact of a preoperative VTE diagnosis on perioperative outcomes in the RNU context. Methods: Patients aged 18 yr or older with a UTUC diagnosis undergoing RNU were identified in the Merative Marketscan Research deidentified databases between 2007 and 2021. Multivariable logistic regression adjusted by relevant perioperative confounders was used to investigate the association between a diagnosis of VTE prior to RNU and 90-d complication rates, postoperative VTE, rehospitalization, and total costs. A sensitivity analysis on VTE severity (pulmonary embolism [PE] and/or deep venous thrombosis [DVT]) was examined. Key findings and limitations: Within the investigated cohort of 6922 patients, history of any VTE preceding RNU was reported in 568 (8.21%) cases, including DVT (n = 290, 51.06%), PE (n = 169, 29.75%), and superficial VTE (n = 109, 19.19%). The history of VTE before RNU was predictive of higher rates of complications, the most prevalent being respiratory complications (odds ratio [OR]: 1.78, 95% confidence interval [CI]: 1.43–2.22). Preoperative VTE was found to be associated with an increased risk of VTE following RNU (OR: 14.3, 95% CI: 11.48–17.82), higher rehospitalization rates (OR: 1.26, 95% CI 1.01–1.56) other than home discharge status (OR: 1.44, 95% CI: 1.18–1.77), and higher costs (OR 1.42, 95% CI: 1.20–1.68). Limitations include the retrospective nature and the use of an insurance database that relies on accurate coding and does not include information such as pathologic staging. Conclusions and clinical implications: The presented findings will contribute to the counseling process for patients. These patients may benefit from enhanced pre/postoperative anticoagulation. More research is needed before the following results can be used in the clinical setting. Patient summary: Patients aged 18 yr or older with an upper tract urothelial carcinoma (UTUC) diagnosis undergoing radical nephroureterectomy (RNU) were identified in the Merative Marketscan Research deidentified databases between 2007 and 2021. Multivariable logistic regression adjusted by relevant perioperative confounders was used to investigate the association between a diagnosis of venous thromboembolism (VTE) prior to RNU and 90-d complication rates, postoperative VTE, rehospitalization, and total costs. A sensitivity analysis on VTE severity (pulmonary embolism and/or deep venous thrombosis) was examined. The presented findings will contribute to the counseling of patients with UTUC and preoperative VTE

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

Genome-Wide Association Analysis Reveals Genetic Heterogeneity of Sjögren's Syndrome According to Ancestry

Objective: The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study of participants in whom genotyping was performed on the Omni2.5M platform and who had undergone deep phenotyping using common protocol-directed methods. The aim of this study was to examine the genetic etiology of Sjögren's syndrome (SS) across ancestry and disease subsets. Methods: We performed genome-wide association study analyses using SICCA subjects and external controls obtained from dbGaP data sets, one using all participants (1,405 cases, 1,622 SICCA controls, and 3,125 external controls), one using European participants (585, 966, and 580, respectively), and one using Asian participants (460, 224, and 901, respectively) with ancestry adjustments via principal components analyses. We also investigated whether subphenotype distributions differ by ethnicity, and whether this contributes to the heterogeneity of genetic associations. Results: We observed significant associations in established regions of the major histocompatibility complex (MHC), IRF5, and STAT4 (P=3 × 10-42, P=3 × 10-14, and P=9 × 10-10, respectively), and several novel suggestive regions (those with 2 or more associations at P&lt;1 × 10-5). Two regions have been previously implicated in autoimmune disease: KLRG1 (P=6 × 10-7 [Asian cluster]) and SH2D2A (P=2 × 10-6 [all participants]). We observed striking differences between the associations in Europeans and Asians, with high heterogeneity especially in the MHC; representative single-nucleotide polymorphisms from established and suggestive regions had highly significant differences in the allele frequencies in the study populations. We showed that SSA/SSB autoantibody production and the labial salivary gland focus score criteria were associated with the first worldwide principal component, indicative of higher non-European ancestry (P=4 × 10-15 and P=4 × 10-5, respectively), but that subphenotype differences did not explain most of the ancestry differences in genetic associations. Conclusion: Genetic associations with SS differ markedly according to ancestry; however, this is not explained by differences in subphenotypes.</p