Evaluation of PD-1 T lymphocytes in bronchoalveolar lavage in lung cancer compared to benign lung diseases.

The expression of the programmed cell death protein 1 (PD-1) has been shown to be markedly increased in tumor-infiltrating lymphocytes. However, the proportion of PD-1 + T cells in the bronchoalveolar lavage (BAL) of lung cancer patients has not been sufficiently evaluated so far. In this prospective study, the proportion of PD-1 + CD4 + as well as PD-1 + CD8 + T cells in BAL samples, isolated from patients with lung cancer, asthma or interstitial lung disease (ILD), were determined via flow cytometry and compared for differences. Bronchoalveolar lavage was performed in 34 patients (14 patients with lung cancer, 10 patients with asthma, 10 patients with ILD). The highest median proportion of PD-1 + CD4 + or PD-1 + CD8 + T cells were found in patients with ILD (83.1% [IQR 72.1; 87.5] and 73.8% [IQR 60.3; 86.3]) followed by patients with lung cancer (66.4% [IQR 59; 69] and 77.1% [IQR 35.8; 82.3]) and patients with asthma (61.3% [IQR 57.4; 70.5] and 57.3% [IQR 46; 65]). Thereby, the difference in the proportion of PD-1 + CD3 + CD4 + BAL cells between ILD patients and asthmatics was significantly different (p = 0.04). The proportion of PD-1 + CD4 + and PD-1 + CD8 + T cells in the BAL of patients with lung cancer did not differ significantly to patients with benign lung diseases. The highest proportion was observed in ILD patients suggesting further research to evaluate the role of the PD-1/PD-L1 pathway in ILD patients.

Accelerating atomic structure search with cluster regularization.

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Rotation and diffusion of naphthalene on Pt(111).

The behavior of naphthalene on Pt(111) surfaces is studied by combining insight from scanning tunneling microscopy (STM) and van der Waals enabled density functional theory. Adsorption, diffusion, and rotation are investigated by a series of variable temperature STM experiments revealing naphthalene ability to rotate on-site with ease with a rotational barrier of 0.69 eV. Diffusion to neighbouring sites is found to be more difficult. The experimental results are in good agreement with the theoretical investigations which confirm that the barrier for diffusion is slightly higher than the one for rotation. The theoretical barriers for rotation and translation are found to be 0.75 and 0.78 eV, respectively. An automatic mapping of the possible diffusion pathways reveals very detailed diffusion paths with many small local minima that would have been practically impossible to find manually. This automated procedure provides detailed insight into the preferred diffusion pathways that are important for our understanding of molecule-substrate interactions.

On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization.

Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO_{2}(110)-(4×1) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.

Porous monolith microfluidics for bacterial cell-to-cell communication assays.

Genetically engineered bacteria can be used for a wide range of applications, from monitoring environmental toxins to studying complex communication networks in the human digestive system. Although great strides have been made in studying single strains of bacteria in well-controlled microfluidic environments, there remains a need for tools to reliably control and measure communication between multiple discrete bacterial populations. Stable long-term experiments (e.g., days) with controlled population sizes and regulated input (e.g., concentration) and output measurements can reveal fundamental limits of cell-to-cell communication. In this work, we developed a microfluidic platform that utilizes a porous monolith to reliably and stably partition adjacent strains of bacteria while allowing molecular communication between them for several days. We measured small molecule production by the bacterial populations in response to stimuli using analytical chemistry methods and measured fluorescent output. The results are compared with communication and diffusion delay models. This porous monolith microfluidic system enables bacterial cell-to-cell communication assays with dynamic control of inputs, relatively long-term experimentation with no cross contamination, and stable bacterial population size. This system can serve as a valuable tool in understanding bacterial communication and improving biosensor design capabilities.

Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers.

Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamellae structures. From statistical analysis of Scanning Tunnelling Microscopy (STM) data we observe a clear selection of specific conformational states after self-assembly. Using Density Functional Theory (DFT) calculations we rationalise how this selection is correlated to the orientation of the alkyl moieties in mirror-image domains of the lamellae structures, leading to selection of three out of the eight possible enantiomeric pairs.

Structure and role of metal clusters in a metal-organic coordination network determined by density functional theory.

We present a comprehensive theoretical investigation of the structures formed by self-assembly of tetrahydroxybenzene (THB)-derivatives on Cu(111). The THB molecule is known to dehydrogenate completely during annealing, forming a reactive radical which assembles into a close-packed structure or a porous metal-coordinated network depending on the coverage of the system. Here, we present details on how the structures are determined by density functional theory calculations, using scanning tunneling microscopy-derived information on the periodicity. The porous network is based on adatom trimers. By analysing the charge distribution of the structure, it is found that this unusual coordination motif is preferred because it simultaneously provides a good coordination of all oxygen atoms and allows for the formation of a two-dimensional network on the surface.

Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch.

Supra-molecular self-assembly on surfaces often involves molecular conformational flexibility which may act to enrich the variation and complexity of the structures formed. However, systematic and explicit investigations of how molecular conformational states are selected in surface self-assembly processes are relatively scarce. Here, we use a combination of high-resolution scanning tunneling microscopy and Density Functional Theory (DFT) calculations to investigate self-assembly for a custom-designed molecule capable of assuming eight distinct surface conformations (four enantiomeric pairs). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure, respectively. These structures each involve molecules in two conformational states, and there is a clear separation between the conformers involved in the two types of structures. On Cu(111), individual molecules isolated by carboxylate-substrate binding show a distribution involving all possible conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules.

Nucleation and growth of Pt nanoparticles on reduced and oxidized rutile TiO2 (110).

The nucleation and growth of Pt nanoparticles (NP's) on rutile TiO2 (110) surfaces with O on-top atoms (oxidized TiO2), surface O vacancies, and H adatoms, respectively (reduced TiO2), was studied by means of scanning tunneling microscopy (STM) experiments and density functional theory calculations. At room temperature, Pt was found to be trapped at O on-top atoms and surface O vacancies, leading to rather small Pt NP's. In contrast, on surfaces with H adatoms the mobility of Pt was much larger. As a result, large Pt NP's were found at room temperature on TiO2 (110) surfaces with H adatoms. However, at ∼150 K the diffusion of Pt was kinetically hindered on all TiO2 (110) surfaces considered. STM data acquired after vacuum-annealing at 800 K showed comparable results on all TiO2 (110) surfaces because the diffusion of Pt is not influenced by surface defects at such high temperatures.

Thermodynamic aspects of dehydrogenation reactions on noble metal surfaces.

The reaction free energy for dehydrogenation of phenol, aniline, thiophenol, benzoic acid, and 1,4-benzenediol on the close packed copper, silver, and gold surfaces has been studied by density functional theory calculations. Dehydrogenation of thiophenol is found to be favourable on all three surfaces while aniline does not dehydrogenate on any of them. For phenol, benzenediol and benzoic acid dehydrogenation is favourable on copper and silver only, following the general trend of an increasing reaction free energy when going form gold to silver to copper. This trend can be correlated with the changes in bond lengths within the molecule upon dehydrogenation. While copper is able to replace hydrogen, leaving small changes in the bond lengths of the aromatic ring, the metal-molecule bond is weaker for silver and gold, resulting in a partial loss of aromaticity. This difference in bond strength leads to pronounced differences in adsorption geometries upon multiple dehydrogenations.

Optimization of the interface between radiology, surgery, radiotherapy, and pathology in head and neck tumor surgery: a navigation-assisted multidisciplinary network.

A navigation-assisted multidisciplinary network to improve the interface between radiology, surgery, radiotherapy, and pathology in the field of head and neck cancer is described. All implicated fields are integrated by a common server platform and have remote data access in a ready-to-use format. The margins of resection and exact locations of biopsies are mapped intraoperatively. The pathologist uses the numerical coordinates of these samples to precisely trace each specimen in the anatomical field. Subsequently, map-guided radiotherapy is planned. In addition to the benefits of image-guided resection, this model enables radiotherapy planning according to the specific coordinates of the resection defect plus any residually affected sites identified by the pathologist. Irradiation of adjacent healthy structures is thereby minimized. In summary, the navigation-assisted network described grants timely multidisciplinary feedback between all fields involved, attains meticulous pathological definition, and permits optimized coordinate-directed radiotherapy.

The accuracy of three-dimensional model generation. What makes it accurate to be used for surgical planning?

Computerized treatment planning is routinely used in cranio-maxillofacial applications. For these therapeutic applications, it is of critical importance to have a precise model of the structures in question. Improved imaging techniques and advances in software engineering have moved three-dimensional (3D) computer models from the research and development area into routine clinical application. The importance of high-resolution source imaging is well understood by surgeons. The influence of image processing is poorly understood in the surgical community and we hypothesize that this may be a source of significant error. We evaluated the workflow for creating a virtual model using computed tomography data, and the impact that image processing decisions have on final virtual model accuracy. We chose to create a model of the dental surface since it is one of the most complex structures in the area. Individual image processing steps are explained and the magnitudes of their influence on model quality are demonstrated and compared. This study demonstrates that inappropriate image processing can introduce errors of similar magnitude as the use of inadequate source data. Finally, the study shows that errors caused by inappropriate image processing amplify the inaccuracies of low-resolution source imagery and eliminate the benefits of high-resolution source imaging.

Le Fort I osteotomies using Bio-Oss® collagen to promote bony union: a prospective clinical split-mouth study.

The purpose of this study was to evaluate whether a bone substitute can be used to promote bony union in patients undergoing maxillary advancement after Le Fort l osteotomy. Nine patients were treated bilaterally with Le Fort I osteotomies and maxillary advancements of 5mm or less. In each patient, one gap was grafted with the bone substitute Bio-Oss(®) Collagen (BOC). The contralateral site was left empty and served as control. After 6 months there were still empty gaps in the control sites of three patients, while in the grafted sites all gaps were completely filled with bone. The histomorphometric analysis performed with biopsies from the region of the original gap showed a similar amount of new bone in both groups, however, in the test group the mean overall amount of the mineralized fraction was higher compared to the control group (test site 65.0±6.2%, control site 38.9±32.6%). The bone substitute seemed to be a suitable material to promote bony union in Le Fort I osteotomies. Further studies are needed to analyse whether this technique is efficient in preventing relapse and promoting bony union in larger advancements.

Role of steps in the dissociative adsorption of water on rutile TiO2(110).

The water-TiO(2) interaction is of paramount importance for many processes occurring on TiO(2), and the rutile TiO(2)(110)-(1×1) surface has often been considered as a test case. Yet, no consensus has been reached whether the well-studied surface O vacancies on the terraces are the only active sites for water dissociation on rutile TiO(2)(110)-(1 × 1), or whether another channel for the creation of H adatoms exists. Here we use high-resolution scanning tunneling microscopy and density functional theory calculations to tackle this long-standing question. Evidence is presented that a second water dissociation channel exists on the surfaces of vacuum-annealed TiO(2)(110) crystals that is associated with the ⟨111⟩ step edges. This second water dissociation channel can be suppressed by blocking of the ⟨111⟩ step edges using ethanol.

Reduced step edges on rutile TiO2(110) as competing defects to oxygen vacancies on the terraces and reactive sites for ethanol dissociation.

The rutile TiO2(110) surface is the most studied surface of titania and considered as a prototype of transition metal oxide surfaces. Reactions on flat TiO2(110)-(1×1) surfaces are well studied, but the processes occurring on the step edges have barely been considered. Based on scanning tunneling microscopy studies, we here present experimental evidence for the existence of O vacancies along the [11¯1](R) step edges (O(S) vac.'s) on rutile TiO(2)(110). Both the distribution of bridging O vacancies on the terraces and temperature-programed reaction experiments of ethanol-covered TiO(2)(110) point to the existence of the O(S) vac.'s. Based on experiments and density functional theory calculations, we show that O(S) vac.'s are reactive sites for ethanol dissociation via O-H bond scission. Implications of these findings are discussed.

Packing defects into ordered structures: strands on TiO2.

We have studied vicinal TiO2(110) surfaces by high-resolution scanning tunneling microscopy and density functional theory calculations. On TiO2 surfaces characterized by a high density of <111> steps, scanning tunneling microscopy reveals a high density of oxygen-deficient strandlike adstructures. With the help of density functional theory calculations we develop a complete structural model for the entire strand and demonstrate these adstructures to be more stable than an equivalent amount of bulk defects such as Ti interstitials. We argue that strands can form particularly easy on stepped surfaces because building material is available at step sites. The strands on TiO2(110) represent point defects that are densely packed into ordered adstructures.

Assessment of tissue-engineered islet graft viability by fluorine magnetic resonance spectroscopy.

INTRODUCTION: Despite significant progress in the last decade, islet transplantation remains an experimental therapy for a limited number of patients with type 1 diabetes. Tissue-engineered approaches may provide promising alternatives to the current clinical protocol and would benefit greatly from concurrent development of graft quality assessment techniques. This study was designed to evaluate whether viability of tissue-engineered islet grafts can be assessed using fluorine magnetic resonance spectroscopy ((19)F-MRS), by the noninvasive measurement of oxygen partial pressure (pO(2)) and the subsequent calculation of islet oxygen consumption rate (OCR). METHODS: Scaffolds composed of porcine plasma were seeded with human islets and perfluorodecalin. Each graft was covered with the same volume of culture media in a Petri dish. Four scaffolds were seeded with various numbers (0-8000) of islet equivalents (IE) aliquoted from the same preparation. After randomizing run order, grafts were examined by (19)F-MRS at 37°C using a 5T spectrometer and a single-loop surface coil placed underneath. A standard inversion recovery sequence was used to obtain characteristic (19)F spin-lattice relaxation times (T1), which were converted to steady-state average pO(2) estimates using a previously determined linear calibration (R(2) = 1.000). Each condition was assessed using replicate (19)F-MRS measurements (n = 6-8). RESULTS: Grafts exhibited IE dose-dependent increases in T1 and decreases in pO(2) estimates. From the difference between scaffold pO(2) estimates and ambient pO(2), the islet preparation OCR was calculated to be 95 ± 12 (mean ± standard error of the mean) nmol/(min·mg DNA) using theoretical modeling. This value compared well with OCR values measured using established methods for human islet preparations. CONCLUSIONS: (19)F-MRS can be used for noninvasive pre- and possibly posttransplant assessment of tissue-engineered islet graft viability by estimating the amount of viable, oxygen-consuming tissue in a scaffold.

Direct evidence for ethanol dissociation on rutile TiO2(110).

We have studied the interaction of ethanol with reduced TiO(2)(110)-(1 × 1) by high-resolution scanning tunneling microscopy (STM) measurements and density functional theory calculations. The STM data revealed direct evidence for the coexistence of molecularly and dissociatively adsorbed ethanol species on surface Ti sites. In addition, we found evidence for dissociation of ethanol at bridge-bonded O vacancies. The density functional theory calculations support these findings and rationalize the distinct diffusion behaviors of molecularly and dissociatively adsorbed ethanol species, as revealed in time-lapsed STM images.

Surgical protocol involving the infusion of paramagnetic microparticles for preferential incorporation within porcine islets.

INTRODUCTION: Despite significant advances, widespread applicability of islet cell transplantation remains elusive. Refinement of current islet isolation protocols may improve transplant outcomes. Islet purification by magnetic separation has shown early promise. However, surgical protocols must be optimized to maximize the incorporation of paramagnetic microparticles (MP) within a greater number of islets. This study explores the impact of MP concentration and infusion method on optimizing MP incorporation within islets. METHODS: Five porcine pancreata were procured from donors after cardiac death. Splenic lobes were isolated and infused with varying concentrations of MP (8, 16, and 32 × 10(8) MP/L of cold preservation solution) and using one of two delivery techniques (hanging bag versus hand-syringe). After procurement and infusion, pancreata were stored at 0°C to 4°C during transportation (less than 1 hour), fixed in 10% buffered formalin, and examined by standard magnetic resonance imaging (MRI) and histopathology. RESULTS: T2*-weighted MRI showed homogeneous distribution of MP in all experimental splenic lobes. In addition, histologic analysis confirmed that MP were primarily located within the microvasculature of islets (82% to 85%), with few MP present in acinar tissue (15% to 18%), with an average of five to seven MP per islet (within a 5-µm thick section). The highest MP incorporation was achieved at a concentration of 16 × 10(8) MP/L using the hand-syringe technique. CONCLUSION: This preliminary study suggests that optimization of a surgical protocol, MP concentrations, and applied infusion pressures may enable more uniform distribution of MP in the porcine pancreas and better control of MP incorporation within islets. These results may have implications in maximizing the efficacy of islet purification by magnetic separation.

Window-based example selection in learning vector quantization.

A variety of modifications have been employed to learning vector quantization (LVQ) algorithms using either crisp or soft windows for selection of data. Although these schemes have been shown in practice to improve performance, a theoretical study on the influence of windows has so far been limited. Here we rigorously analyze the influence of windows in a controlled environment of gaussian mixtures in high dimensions. Concepts from statistical physics and the theory of online learning allow an exact description of the training dynamics, yielding typical learning curves, convergence properties, and achievable generalization abilities. We compare the performance and demonstrate the advantages of various algorithms, including LVQ 2.1, generalized LVQ (GLVQ), Learning from Mistakes (LFM) and Robust Soft LVQ (RSLVQ). We find that the selection of the window parameter highly influences the learning curves but not, surprisingly, the asymptotic performances of LVQ 2.1 and RSLVQ. Although the prototypes of LVQ 2.1 exhibit divergent behavior, the resulting decision boundary coincides with the optimal decision boundary, thus yielding optimal generalization ability.