Donor-Acceptor Co-Adsorption Ratio Controls the Structure and Electronic Properties of Two-Dimensional Alkali-Organic Networks on Ag(100).

The results are presented of a detailed combined experimental and theoretical investigation of the influence of coadsorbed electron-donating alkali atoms and the prototypical electron acceptor molecule 7,7,8,8-tetracyanoquinodimethane (TCNQ) on the Ag(100) surface. Several coadsorption phases were characterized by scanning tunneling microscopy, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy. Quantitative structural data were obtained using normal-incidence X-ray standing wave (NIXSW) measurements and compared with the results of density functional theory (DFT) calculations using several different methods of dispersion correction. Generally, good agreement between theory and experiment was achieved for the quantitative structures, albeit with the prediction of the alkali atom heights being challenging for some methods. The adsorption structures depend sensitively on the interplay of molecule-metal charge transfer and long-range dispersion forces, which are controlled by the composition ratio between alkali atoms and TCNQ. The large difference in atomic size between K and Cs has negligible effects on stability, whereas increasing the ratio of K/TCNQ from 1:4 to 1:1 leads to a weakening of molecule-metal interaction strength in favor of stronger ionic bonds within the two-dimensional alkali-organic network. A strong dependence of the work function on the alkali donor-TCNQ acceptor coadsorption ratio is predicted.

Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. I. Theory.

Reactions involving adsorbates on metallic surfaces and impurities in bulk metals are ubiquitous in a wide range of technological applications. The theoretical modeling of such reactions presents a formidable challenge for theory because nuclear quantum effects (NQEs) can play a prominent role and the coupling of the atomic motion with the electrons in the metal gives rise to important non-adiabatic effects (NAEs) that alter atomic dynamics. In this work, we derive a theoretical framework that captures both NQEs and NAEs and, due to its high efficiency, can be applied to first-principles calculations of reaction rates in high-dimensional realistic systems. More specifically, we develop a method that we coin ring polymer instanton with explicit friction (RPI-EF), starting from the ring polymer instanton formalism applied to a system-bath model. We derive general equations that incorporate the spatial and frequency dependence of the friction tensor and then combine this method with the ab initio electronic friction formalism for the calculation of thermal reaction rates. We show that the connection between RPI-EF and the form of the electronic friction tensor presented in this work does not require any further approximations, and it is expected to be valid as long as the approximations of both underlying theories remain valid.

Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. II. Benchmarks and applications.

In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles.

A deep neural network for molecular wave functions in quasi-atomic minimal basis representation.

The emergence of machine learning methods in quantum chemistry provides new methods to revisit an old problem: Can the predictive accuracy of electronic structure calculations be decoupled from their numerical bottlenecks? Previous attempts to answer this question have, among other methods, given rise to semi-empirical quantum chemistry in minimal basis representation. We present an adaptation of the recently proposed SchNet for Orbitals (SchNOrb) deep convolutional neural network model [K. T. Schütt et al., Nat. Commun. 10, 5024 (2019)] for electronic wave functions in an optimized quasi-atomic minimal basis representation. For five organic molecules ranging from 5 to 13 heavy atoms, the model accurately predicts molecular orbital energies and wave functions and provides access to derived properties for chemical bonding analysis. Particularly for larger molecules, the model outperforms the original atomic-orbital-based SchNOrb method in terms of accuracy and scaling. We conclude by discussing the future potential of this approach in quantum chemical workflows.

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions.

Machine learning advances chemistry and materials science by enabling large-scale exploration of chemical space based on quantum chemical calculations. While these models supply fast and accurate predictions of atomistic chemical properties, they do not explicitly capture the electronic degrees of freedom of a molecule, which limits their applicability for reactive chemistry and chemical analysis. Here we present a deep learning framework for the prediction of the quantum mechanical wavefunction in a local basis of atomic orbitals from which all other ground-state properties can be derived. This approach retains full access to the electronic structure via the wavefunction at force-field-like efficiency and captures quantum mechanics in an analytically differentiable representation. On several examples, we demonstrate that this opens promising avenues to perform inverse design of molecular structures for targeting electronic property optimisation and a clear path towards increased synergy of machine learning and quantum chemistry.

The Structure of VOPc on Cu(111): Does V=O Point Up, or Down, or Both?

The local structure of the nonplanar phthalocyanine, vanadyl phthalocyanine (VOPc), adsorbed on Cu(111) at a coverage of approximately one-half of a saturated molecular layer, has been investigated by a combination of normal-incidence X-ray standing waves (NIXSW), scanned-energy mode photoelectron diffraction (PhD), and density-functional theory (DFT), complemented by scanning tunnelling microscopy (STM). Qualitative assessment of the NIXSW data clearly shows that both "up" and "down" orientations of the molecule (with V=O pointing out of, and into, the surface) must coexist on the surface. O 1s PhD proves to be inconclusive regarding the molecular orientation. DFT calculations, using two different dispersion correction schemes, show good quantitative agreement with the NIXSW structural results for equal co-occupation of the two different molecular orientations and clearly favor the many body dispersion (MBD) method to deal with long-range dispersion forces. The calculated relative adsorption energies of the differently oriented molecules at the lowest coverage show a strong preference for the "up" orientation, but at higher local coverages, this energetic difference decreases, and mixed orientation phases are almost energetically equivalent to pure "up"-oriented phases. DFT-based Tersoff-Hamann simulations of STM topographs for the two orientations cast some light on the extent to which such images provide a reliable guide to molecular orientation.

Stimulated Raman gas sensing by backward UV lasing from a femtosecond filament.

We perform a proof-of-principle demonstration of chemically specific standoff gas sensing, in which a coherent stimulated Raman signal is detected in the direction anticollinear to a two-color laser excitation beam traversing the target volume. The proposed geometry is intrinsically free space as it does not involve back-scattering (reflection) of the signal or excitation beams at or behind the target. A beam carrying an intense mid-IR femtosecond (fs) pulse and a parametrically generated picosecond (ps) UV Stokes pulse is fired in the forward direction. A fs filament, produced by the intense mid-IR pulse, emits a backward-propagating narrowband ps laser pulse at the 337 and 357 nm transitions of excited molecular nitrogen, thus supplying a counter-propagating Raman pump pulse. The scheme is linearly sensitive to species concentration and provides both transverse and longitudinal spatial resolution.

[Alveolar adenoma--a rare pulmonary mass: case report and review of the literature]. / Das alveoläre Adenom als Differenzialdiagnose zum Bronchialkarzinom: Fallvorstellung und Literaturreview.

This report describes the case of a 58-year-old man presenting with haemoptysis. Chest X-ray and CT scans showed a solitary pulmonary mass in the right lower lobe without radiographic signs of malignancy. Definitive histology following thoracoscopic wedge resection showed the distinctive findings of an alveolar adenoma, a very rare benign tumour of the lung of unknown histogenesis. Its existence was first described in 1986 with less than 30 cases published to this day. Alveolar adenoma usually presents as a peripheral solitary lesion in asymptomatic, older patients. Its histological features, the benign proliferation of alveolar epithelium and septal mesenchyme, allow for its distinction from other benign lesions of the lung. Complete excision is considered curative on the basis of current knowledge.

MAGE-C1/CT-7 expression in plasma cell myeloma: sub-cellular localization impacts on clinical outcome.

Plasma cell myelomas (PMs) have a poor prognosis. Cancer-testis (CT) antigens are immunogenic proteins, representing potential targets for tumor vaccination strategies. The expression of the CT antigens GAGE, MAGE-A4, MAGE-C1/CT-7, and NY-ESO-1 was investigated on paraffin-embedded bone marrow biopsies from 219 PM and 8 monoclonal gammopathy of undetermined significance (MGUS) patients. The frequency and prognostic impact of these CT antigens were compared with known morphological prognostic markers (i.e. Mib1 labeling index) and the presence of the translocations t(4;14)(p16.3; q32) and t(11;14)(q13;q32). We show that MAGE-C1/CT-7 is the most prevalent CT antigen, expressed in 57% of PMs in a high percentage of tumor cells. While MAGE-C1/CT-7 was absent in non-malignant plasma cells, plasma cells of patients with MGUS did express MAGE-C1/CT-7, but no other CT antigens. MAGE-C1/CT-7 was more frequently expressed in PMs with an elevated proliferation rate (Mib1 >10%) compared to PMs with a low proliferation rate (Mib1

Endoscopic pH monitoring for patients with suspected or refractory gastroesophageal reflux disease.

BACKGROUND: Wireless pH studies can offer prolonged pH monitoring, which may potentially facilitate the diagnosis and management of patients with gastroesophageal reflux disease (GERD). The aim of the present study was to evaluate the detection rate of abnormal esophageal acid exposure using prolonged pH monitoring in patients with suspected or refractory GERD symptoms. METHODS: Patients undergoing prolonged ambulatory pH studies for the evaluation of GERD-related symptoms were assessed. Patients with a known diagnosis of GERD were tested on medical therapy, while patients with suspected GERD were tested off therapy. The wireless pH capsules were placed during upper endoscopy 6 cm above the squamocolumnar junction. RESULTS: One hundred ninety-one patients underwent a total of 198 pH studies. Fifty ambulatory pH studies (25%) were excluded from the analysis: 27 patients (14%) had insufficient data capture (less than 18 h on at least one day of monitoring), 15 patients had premature capsule release (7%), seven were repeat studies (3.5%) and one had intolerable pain requiring capsule removal (0.5%). There were 115 patients undergoing pH studies who were off medication, and 33 patients were on therapy. For the two groups of patients, results were as follows: 32 (28%) and 22 (67%) patients with normal studies on both days; 58 (50%) and five (15%) patients with abnormal studies on both days; 18 (16%) and three (9%) patients with abnormal studies on day 1 only; and seven (6%) and three (9%) patients with abnormal studies on day 2 only, respectively. CONCLUSIONS: Prolonged 48 h pH monitoring can detect more abnormal esophageal acid exposure but is associated with a significant rate of incomplete studies.

Abdominal angiostrongyliasis in rodent experimental infection: evidence for systemic circulation of first stage larvae.

Eggs of Angiostrongylus costaricensis embrionate and hatch in the course of their migration in the intestinal wall, and first stage larvae (L1) are released in feces. Aiming to investigate the possible systemic circulation of L1, we inoculated mice and, four weeks later, examined their peritoneal cavities and several organs for the presence of L1. A total of 65 larvae were found in extra-intestinal organs (kidney, heart, spleen, liver, lungs). No larvae were found in blood or in the peritoneal cavity. 320 and 578 L1 were found in intestinal wall and intestinal contents, respectively. The experiment was repeated and it confirmed that the metastrongylid larvae found in several organs were larval stages of A. costaricensis. Ten Oligoryzomis sp. rodents, a natural host for A. costaricensis, were also infected and in three animals L1 could be recovered from several organs as well as from bronchoalveolar lavage (BAL) in one of them. These data indicate that systemic circulation and bronchial elimination of L1 may represent an alternative route for release of L1 of A. costaricensis into the environment for transmission to the intermediate host.

Determination of acidic and basic species by headspace gas chromatography.

This paper reported a novel headspace gas chromatographic (GC) technique on quantification of acidic and basic species. It is based on an acid-base reaction between the measured species and bicarbonate in an aqueous solution, which generates carbon dioxide in a closed headspace sample vial. By operating at 60 degrees C, carbon dioxide is completely released to the headspace and thus can be measured by GC with a thermal conductivity detector. Bicarbonate concentrations of 0.030 and 0.0025 mol/L are recommended for general applications and very small species content, respectively. This method is able to accurately measure small sample sizes (down to few milligrams or microliters). The present method is simple, accurate, and automatic.

[17 year old patient with acute abdominal pain, hematochezia and exanthema]. / 17-jähriger Mann mit akuten Bauchschmerzen, Hämatochezie und Exanthem.

A 17-year old adolescent presented with abdominal pain, petechial lesions, arthralgia, and hematochezia. Abdominal ultrasound showed a suspicious ileocecal region and a lower endoscopy revealed the picture of an ileitis terminalis. The diagnosis of Purpura Henoch Schoenlein was made and confirmed by skin-biopsy showing a leucocytoclastic vasculitis. This case report demonstrates the various clinical symptoms of Purpura Henoch Schoenlein and its clinical course.

Identification of organic acids in secondary organic aerosol and the corresponding gas phase from chamber experiments.

Organic acids in the gas and aerosol phase from photooxidation of 1,3,5-trimethylbenzene in the presence of 300 ppb propene and 300 ppb NOx in smog chamber experiments were determined using a wet effluent diffusion denuder/aerosol collector coupled to ion chromatography (IC) with conductivity detection. Behind the IC, the samples were collected using a fraction collector, for identification of unresolved/unidentified organic acids with IC-mass spectrometry (MS). In total, 20 organic acids were found with MS of which 10 were identified. The organic acids identified offline by IC-MS were then further quantified based on the online IC data. The identification was additionally confirmed with gas chromatography-mass spectrometry. At the maximum aerosol concentration, organic acids comprised 20-45% of the total aerosol mass. The method has a detection limit of 10-100 ng/m3 for the identified carboxylic acids.

Rare expression of KIT (CD117) in lymphomas: a tissue microarray study of 1166 cases.

AIMS: Imatinib mesylate specifically inhibits KIT tyrosine kinase activity, and has been proven to be effective in the treatment of gastrointestinal stromal tumours. Because other KIT-expressing malignancies might benefit from Imatinib therapy, we evaluated the distribution and expression of KIT in 1166 cases of malignant lymphoma. MATERIALS AND RESULTS: Tissue microarrays (TMAs) containing 824 non-Hodgkin's lymphoma (NHL) and 342 Hodgkin's lymphoma (HL) cases were immunohistochemically analysed for the expression of the KIT protein. Two KIT-positive NHLs were sequenced using polymerase chain reaction analysis. One T-cell lymphoma and one follicular lymphoma of the 747 NHL cases (0.3%) were positive for KIT. All HLs were Kit-negative. None of the KIT-positive cases showed a kit gene mutation. CONCLUSIONS: KIT expression is a very rare event in NHL and virtually absent in HL. In the few positive cases, the aberrant expression is not caused by a mutation in the 'hot-spots' of the kit gene, indicating that treatment of these tumours with Imatinib may be ineffective.

[Expression profile and prognostic significance of CD24, p53 and p21 in lymphomas. A tissue microarray study of over 600 non-Hodgkin lymphomas]. / Expressionsmuster und prognostische Bedeutung von CD24, p53 und p21 in Lymphomen. Eine Gewebe-Mikroarray-Studie an über 600 Non-Hodgkin-Lymphomen.

BACKGROUND AND OBJECTIVE: Tissue microarrays allow the simultanous, rapid and standardized in-situ analysis of up to 1000 different tissue samples on a single glass slide. We investigated the expression profil and the prognostic significance of CD24, p53 and p21 using a Non-Hodgkin-Lymphoma tissue microarray. METHODS: Over 600 well documented Non-Hodgkin-Lymphomas, consisting of 341 diffuse large B-cell lymphomas, 86 follicular lymphomas, 81 chronic lymphatic leukemias/small lymphocytic lymphomas, 51 primary mediastinal diffuse large B-cell lymphomas, 26 mantle cell lymphomas, 8 lymphoplasmocytic lymphomas, 8 T-cell-lymphomas NOS und 2 Burkitt lymphomas were brought into array format. The expression of CD24, p53 and p21 was analysed semiquantitatively by immunohistochemistry. The immunophenotype p53+/p21- (Deltap53) was used as a surrogat for p53 gene mutations. The expression profile was compared to clinical data and the overall survival in the subgroup of diffuse large B-cell lymphomas. RESULTS: 91% of the analyzed Non-Hodgkin-lymphomas (473 of 522 cases) showed CD24 positivity. CD24 Expression was not associated with survival. Deltap53 was found in thirteen percent of all lymphomas (70 of 539 cases), the subgroup of the diffuse large B-cell lymphomas demonstrated the highest Deltap53 (21%). In a multivariate cox regression analysis, a high international prognostic index and Deltap53 were independent markers of bad survival. CONCLUSION: The TMA-technology allows also in lymphoma research the simultanous, cost-effective and standardized analysis of large patient cohorts. Deltap53 revealed as an independent negative prognostic factor in diffuse large B-cell lymphomas. It can easily be determined in daily routine practice.

Clinical and pathological characterisation of primary pulmonary hypertension in a dog.

Primary pulmonary hypertension was diagnosed in an eight-year-old labrador retriever on the basis of echocardiographic findings of severe right ventricular eccentric hypertrophy, abnormally high systolic and diastolic pulmonary arterial pressures calculated by applying the modified Bernoulli equation to the tricuspid and pulmonary insufficiency peak velocities, and the absence of any underlying disease known to cause secondary pulmonary hypertension. The clinical abnormalities developed gradually, from exercise intolerance starting early in life to terminal right-sided congestive heart failure. Consistent histopathological findings were severe intimal and medial thickening of small arteries and arterioles that led to vascular obliteration.