Multi-Lattice Kinetic Monte Carlo Simulations from First-Principles: Reduction of the Pd(100) Surface Oxide by CO

We present a multi-lattice kinetic Monte Carlo (kMC) approach that efficiently describes the atomistic dynamics of morphological transitions between commensurate structures at crystal surfaces. As an example we study the reduction of a $(\sqrt{5}\times \sqrt{5})R27^{\circ}$ PdO(101) overlayer on Pd(100) in a CO atmosphere. Extensive density-functional theory calculations are used to establish an atomistic pathway for the oxide reduction process. First-principles multi-lattice kMC simulations on the basis of this pathway fully reproduce the experimental temperature dependence of the reduction rate [Fernandes et al., Surf. Sci. 2014, 621, 31-39] and highlight the crucial role of elementary processes special to the boundary between oxide and metal domains.Comment: 19 pages, 10 figure

Preface

Since the late eighties, a sequel of annual workshops on logic and analytic philosophy has been held on the Island of Poel near Wismar, close to both Gottlob Frege’s grave and to his house in Bad Kleinen. The meeting last year, however, was held in Graal-Müritz and was devoted to Ontologic. It was organised by Jerzy Perzanowski, Uwe Scheffler and Max Urchs.The present number of Logic and Logical Philosophy is not exactly the proceedings of the 94’ conference. On one hand, not all the papers presented at the workshop (see next page for the programme) are included in this volume, while others were changed considerably. On the other hand, colleagues who were to come but had to cancel for some reason were invited to submit their material, too

Length Dependence of Ionization Potentials of Trans-Acetylenes: Internally-Consistent DFT/GW Approach

We follow the evolution of the Ionization Potential (IP) for the paradigmatic quasi-one-dimensional trans-acetylene family of conjugated molecules, from short to long oligomers and to the infinite polymer trans-poly-acetylene (TPA). Our results for short oligomers are very close to experimental available data. We find that the IP varies with oligomer length and converges to the given value for TPA with a smooth, coupled inverse-length-exponential behavior. Our prediction is based on an "internally-consistent" scheme to adjust the exchange mixing parameter $\alpha$ of the PBEh hybrid density functional, so as to obtain a description of the electronic structure consistent with the quasiparticle approximation for the IP. This is achieved by demanding that the corresponding quasiparticle correction, in the GW@PBEh approximation, vanishes for the IP when evaluated at PBEh($\alpha^{ic}$). We find that $\alpha^{ic}$ is also system-dependent and converges with increasing oligomer length, allowing to capture the dependence of IP and other electronic properties.Comment: 22 pages with 9 figures, submitted to Physical Review

Improving the Efficiency of FP-LAPW Calculations

The full-potential linearized augmented-plane wave (FP-LAPW) method is well known to enable most accurate calculations of the electronic structure and magnetic properties of crystals and surfaces. The implementation of atomic forces has greatly increased it's applicability, but it is still generally believed that FP-LAPW calculations require substantial higher computational effort compared to the pseudopotential plane wave (PPW) based methods. In the present paper we analyse the FP-LAPW method from a computational point of view. Starting from an existing implementation (WIEN95 code), we identified the time consuming parts and show how some of them can be formulated more efficiently. In this context also the hardware architecture plays a crucial role. The remaining computational effort is mainly determined by the setup and diagonalization of the Hamiltonian matrix. For the latter, two different iterative schemes are compared. The speed-up gained by these optimizations is compared to the runtime of the ``original'' version of the code, and the PPW approach. We expect that the strategies described here, can also be used to speed up other computer codes, where similar tasks must be performed.Comment: 20 pages, 3 figures. Appears in Comp. Phys. Com. Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Ampullectomy for an unexpected ampullary hamartoma in a heterotaxic patient

AbstractINTRODUCTIONHeterotaxy designates rare congenital disorders of organ positioning in the thoracic and abdominal cavities, which can be associated with numerous anomalies, complicating the surgical management because of the loss of conventional anatomic landmarks.PRESENTATION OF CASEA 72-year-old man was found to have asymptomatic cholestasis. Further workup included computed tomography and magnetic resonance cholangiopancreatography that revealed anomalies of lateralization of digestive organs associated with intestinal malrotation and polysplenia, and a stone-like element in the main bile duct. Endoscopic retrograde cholangiopancreatography failed to extract the lesion. Laparotomy found no stone, but a polypoid tumor with ampullary implantation. Pancreaticoduodenectomy was judged unreasonable due to the presence of macroscopic cirrhosis and a complete ampullectomy was performed. Histopathological examination revealed a hamartomatous polyp.DISCUSSIONThe unusual angle of the duodenoscope in a left-sided duodenum may have contributed to the improper pre-operative diagnosis. Endosonography could have recognized the tissular origin of the lesion and prompted a more detailed preoperative planning. It was fortunate that the patient ended up receiving the appropriate treatment despite the absence of an adequate pre-operative diagnosis, as the option of performing an extended resection was ruled out due to the presence of cirrhosis.CONCLUSIONAlthough heterotaxy leads to increased technical difficulties in performing usual endoscopic and surgical procedures, it can be safely managed by experienced surgeons as illustrated by the present case. Imaging modalities have limited sensitivity in the diagnosis of small ampullary tumors. As false-negatives are likely to occur, this possibility should guide the choice of the best operation

ATN profile classification across two independent prospective cohorts

BACKGROUND The ATN model represents a research framework used to describe in subjects the presence or absence of Alzheimer's disease (AD) pathology through biomarkers. The aim of this study was to describe the prevalence of different ATN profiles using quantitative imaging biomarkers in two independent cohorts, and to evaluate the pertinence of ATN biomarkers to identify comparable populations across independent cohorts. METHODS A total of 172 subjects from the Geneva Memory Clinic and 113 volunteers from a study on healthy aging at the University Hospital of Zurich underwent amyloid (A) and tau (T) PET, as well as T1-weigthed MRI scans using site-specific protocols. Subjects were classified by cognition (cognitively unimpaired, CU, or impaired, CI) based on clinical assessment by experts. Amyloid data converted into the standardized centiloid scale, tau PET data normalized to cerebellar uptake, and hippocampal volume expressed as a ratio over total intracranial volume ratio were considered as biomarkers for A, T, and neurodegeneration (N), respectively. Positivity for each biomarker was defined based on previously published thresholds. Subjects were then classified according to the ATN model. Differences among profiles were tested using Kruskal-Wallis ANOVA, and between cohorts using Wilcoxon tests. RESULTS Twenty-nine percent of subjects from the Geneva cohorts were classified with a normal (A-T-N-) profile, while the Zurich cohort included 64% of subjects in the same category. Meanwhile, 63% of the Geneva and 16% of the Zurich cohort were classified within the AD continuum (being A+ regardless of other biomarkers' statuses). Within cohorts, ATN profiles were significantly different for age and mini-mental state examination scores, but not for years of education. Age was not significantly different between cohorts. In general, imaging A and T biomarkers were significantly different between cohorts, but they were no longer significantly different when stratifying the cohorts by ATN profile. N was not significantly different between cohorts. CONCLUSION Stratifying subjects into ATN profiles provides comparable groups of subjects even when individual recruitment followed different criteria

Patterns of amyloid accumulation in amyloid-negative cases

Amyloid staging models showed that regional abnormality occurs before global positivity. Several studies assumed that the trajectory of amyloid spread is homogeneous, but clinical evidence suggests that it is highly heterogeneous. We tested whether different amyloid-β (Aβ) patterns exist by applying clustering on negative scans and investigating their demographics, clinical, cognitive, and biomarkers correlates, and cognitive trajectories. 151 individuals from Geneva and Zurich cohorts with T1-MRI, negative Aβ positron emission tomography (PET,centiloid<12) and clinical assessment were included. N=123 underwent tau PET, and N=65 follow-up neuropsychological assessment. We performed k-means clustering using 33 Aβ regional Standardized Uptake Vales ratio. Demographics, clinical, cognitive, and biomarkers differences were investigated. Longitudinal cognitive changes by baseline cluster status were estimated using a linear mixed model. The cluster analysis identified two clusters: temporal predominant (TP) and cingulate predominant (CP). TP tau deposition was higher than CP. A trend for a higher cognitive decline in TP compared to CP was observed. This study suggests the existence of two Aβ deposition patterns in the earliest phases of Aβ accumulation, differently prone to tau pathology and cognitive decline

Potential of hybrid 18F-fluorocholine PET/MRI for prostate cancer imaging

Purpose: To report the first results of hybrid 18F-fluorocholine PET/MRI imaging for the detection of prostate cancer. Methods: This analysis included 26 consecutive patients scheduled for prostate PET/MRI before radical prostatectomy. The examinations were performed on a hybrid whole-body PET/MRI scanner. The MR acquisitions which included T2-weighted, diffusion-weighted and dynamic contrast-enhanced sequences were followed during the same session by whole-body PET scans. Parametric maps were constructed to measure normalized T2-weighted intensity (nT2), apparent diffusion coefficient (ADC), volume transfer constant (K trans), extravascular extracellular volume fraction (v e) and standardized uptake values (SUV). With pathology as the gold standard, ROC curves were calculated using logistic regression for each parameter and for the best combination with and without PET to obtain a MR model versus a PETMR model. Results: Of the 26 patients initially selected, 3 were excluded due to absence of an endorectal coil (2 patients) or prosthesis artefacts (1 patient). In the whole prostate, the area under the curve (AUC) for SUVmax, ADC, nT2, K trans and v e were 0.762, 0.756, 0.685, 0.611 and 0.529 with a best threshold at 3.044 for SUVmax and 1.075×10−3mm2/s for ADC. The anatomical distinction between the transition zone and the peripheral zone showed the potential of the adjunctive use of PET. In the peripheral zone, the AUC of 0.893 for the PETMR model was significantly greater (p = 0.0402) than the AUC of 0.84 for the MR model only. In the whole prostate, no relevant correlation was observed between ADC and SUVmax. The SUVmax was not affected by the Gleason score. Conclusion: The performance of a hybrid whole-body 18F-fluorocholine PET/MRI scan in the same session combined with a prostatic MR examination did not interfere with the diagnostic accuracy of the MR sequences. The registration of the PET data and the T2 anatomical MR sequence data allowed precise localization of hypermetabolic foci in the prostate. While in the transition zone the adenomatous hyperplasia interfered with cancer detection by PET, the quantitative analysis tool performed well for cancer detection in the peripheral zone

Plasma biomarkers for Alzheimer’s disease: a field-test in a memory clinic

BACKGROUND: The key Alzheimer's disease (AD) biomarkers are traditionally measured with techniques/exams that are either expensive (amyloid-positron emission tomography (PET) and tau-PET), invasive (cerebrospinal fluid Aβ42 and p-tau181), or poorly specific (atrophy on MRI and hypometabolism on fluorodeoxyglucose-PET). Recently developed plasma biomarkers could significantly enhance the efficiency of the diagnostic pathway in memory clinics and improve patient care. This study aimed to: (1) confirm the correlations between plasma and traditional AD biomarkers, (2) assess the diagnostic accuracy of plasma biomarkers as compared with traditional biomarkers, and (3) estimate the proportion of traditional exams potentially saved thanks to the use of plasma biomarkers. METHODS: Participants were 200 patients with plasma biomarkers and at least one traditional biomarker collected within 12 months. RESULTS: Overall, plasma biomarkers significantly correlated with biomarkers assessed through traditional techniques: up to r=0.50 (p<0.001) among amyloid, r=0.43 (p=0.002) among tau, and r=-0.23 (p=0.001) among neurodegeneration biomarkers. Moreover, plasma biomarkers showed high accuracy in discriminating the biomarker status (normal or abnormal) determined by using traditional biomarkers: up to area under the curve (AUC)=0.87 for amyloid, AUC=0.82 for tau, and AUC=0.63 for neurodegeneration status. The use of plasma as a gateway to traditional biomarkers using cohort-specific thresholds (with 95% sensitivity and 95% specificity) could save up to 49% of amyloid, 38% of tau, and 16% of neurodegeneration biomarkers. CONCLUSION: The implementation of plasma biomarkers could save a remarkable proportion of more expensive traditional exams, making the diagnostic workup more cost-effective and improving patient care