Metrics for measuring distances in configuration spaces

In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional configuration space. We show that these metrics correlate well with the RMSD between two configurations if this RMSD is obtained from a global minimization over all translations, rotations and permutations of atomic indices. We introduce a Monte Carlo approach to obtain this global minimum of the RMSD between configurations

Identification and characterization of FAM124B as a novel component of a CHD7 and CHD8 containing complex

BACKGROUND: Mutations in the chromodomain helicase DNA binding protein 7 gene (CHD7) lead to CHARGE syndrome, an autosomal dominant multiple malformation disorder. Proteins involved in chromatin remodeling typically act in multiprotein complexes. We previously demonstrated that a part of human CHD7 interacts with a part of human CHD8, another chromodomain helicase DNA binding protein presumably being involved in the pathogenesis of neurodevelopmental (NDD) and autism spectrum disorders (ASD). Because identification of novel CHD7 and CHD8 interacting partners will provide further insights into the pathogenesis of CHARGE syndrome and ASD/NDD, we searched for additional associated polypeptides using the method of stable isotope labeling by amino acids in cell culture (SILAC) in combination with mass spectrometry. PRINCIPLE FINDINGS: The hitherto uncharacterized FAM124B (Family with sequence similarity 124B) was identified as a potential interaction partner of both CHD7 and CHD8. We confirmed the result by co-immunoprecipitation studies and showed a direct binding to the CHD8 part by direct yeast two hybrid experiments. Furthermore, we characterized FAM124B as a mainly nuclear localized protein with a widespread expression in embryonic and adult mouse tissues. CONCLUSION: Our results demonstrate that FAM124B is a potential interacting partner of a CHD7 and CHD8 containing complex. From the overlapping expression pattern between Chd7 and Fam124B at murine embryonic day E12.5 and the high expression of Fam124B in the developing mouse brain, we conclude that Fam124B is a novel protein possibly involved in the pathogenesis of CHARGE syndrome and neurodevelopmental disorders

Mass Transfer through Vapor-Liquid Interfaces Studied by Non-Stationary Molecular Dynamics Simulations

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Effect of RasGAP N2 Fragment-Derived Peptide on Tumor Growth in Mice

Peptides that interfere with the natural resistance of cancer cells to genotoxin-induced apoptosis may improve the efficacy of anticancer regimens. We have previously reported that a cell-permeable RasGAP-derived peptide (TAT-RasGAP317-326) specifically sensitizes tumor cells to genotoxin-induced apoptosis in vitro. Here, we examined the in vivo stability of a protease-resistant D-form of the peptide, RI·TAT-RasGAP317-326, and its effect on tumor growth in nude mice bearing subcutaneous human colon cancer HCT116 xenograft tumors. After intraperitoneal injection, RI·TAT-RasGAP317-326 persisted in the blood of nude mice for more than 1 hour and was detectable in various tissues and subcutaneous tumors. Tumor-bearing mice treated daily for 7 days with RI·TAT-RasGAP317-326 (1.65 mg/kg body weight) and cisplatin (0.5 mg/kg body weight) or doxorubicin (0.25 mg/kg body weight) displayed reduced tumor growth compared with those treated with either genotoxin alone (n = 5-7 mice per group; P = .004 and P = .005, respectively; repeated measures analysis of variance [ANOVA, two-sided]). This ability of the RI·TAT-RasGAP317-326 peptide to enhance the tumor growth inhibitory effect of cisplatin was still observed at peptide doses that were at least 150-fold lower than the dose lethal to 50% of mice. These findings provide the proof of principle that RI·TAT-RasGAP317-326 may be useful for improving the efficacy of chemotherapy in patient

Absence of ectopic epithelial inclusions in 3,904 axillary lymph nodes examined in sentinel technique

Intraoperative examination of sentinel axillary lymph nodes can be done by imprint cytology, frozen section, or, most recently, by PCR-based amplification of a cytokeratin signal. Using this technique, benign epithelial inclusions, representing mammary tissue displaced along the milk line, will likely generate a positive PCR signal and lead to a false-positive diagnosis of metastatic disease. To better appreciate the incidence of ectopic epithelial inclusions in axillary lymph nodes, we have performed an autopsy study, examining on 100μm step sections3,904 lymph nodes obtained from 160 axillary dissections in 80 patients. The median number of lymph nodes per axilla was 23 (15, 6, and 1 in levels 1, 2, and 3, respectively). A total of 30,450 hematoxylin-eosin stained slides were examined, as well as 8,825 slides immunostained with pan-cytokeratin antibodies. Despite this meticulous work-up, not a single epithelial inclusion was found in this study, suggesting that the incidence of such inclusions is much lower than the assumed 5% reported in the literatur

Hepatitis E Virus ORF2 Protein Activates the Pro-Apoptotic Gene CHOP and Anti-Apoptotic Heat Shock Proteins

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Molecular imaging by micro-CT: specific E-selectin imaging

The primary goal of this study was to design a fluorescent E-selectin-targeted iodine-containing liposome for specific E-selectin imaging with the use of micro-CT. The secondary goal was to correlate the results of micro-CT imaging with other imaging techniques with cellular resolution, i.e., confocal and intravital microscopy. E-selectin-targeted liposomes were tested on endothelial cells in culture and in vivo in HT-29 tumor-bearing mice (n = 12). The liposomes contained iodine (as micro-CT contrast medium) and fluorophore (as optical contrast medium) for confocal and intravital microscopy. Optical imaging methods were used to confirm at the cellular level, the observations made with micro-CT. An ischemia-reperfusion model was used to trigger neovessel formation for intravital imaging. The E-selectin-targeted liposomes were avidly taken up by activated endothelial cells, whereas nontargeted liposomes were not. Direct binding of the E-selectin-targeted liposomes was proved by intravital microscopy, where bright spots clearly appeared on the activated vessels. Micro-CT imaging also demonstrated accumulation of the targeted lipsomes into subcutaneous tumor by an increase of 32 ± 8HU. Hence, internalization by activated endothelial cells was rapid and mediated by E-selectin. We conclude that micro-CT associated with specific molecular contrast agent is able to detect specific molecular markers on activated vessel walls in viv

Tumor architecture exerts no bias on nuclear grading in breast cancer diagnosis

We recently reported that nuclear grading in prostate cancer is subject to a strong confirmation bias induced by the tumor architecture. We now wondered whether a similar bias governs nuclear grading in breast carcinoma. An unannounced test was performed at a pathology conference. Pathologists were asked to grade nuclei in a PowerPoint presentation. Circular high power fields of 27 invasive ductal carcinomas were shown, superimposed over low power background images of either tubule-rich or tubule-poor carcinomas. We found (a) that diagnostic reproducibility of nuclear grades was poor to moderate (weighed kappa values between 0.07 and 0.54, 27 cases, 44 graders), but (b) that nuclear grades were not affected by the tumor architecture. We speculate that the categorized grading in breast cancer, separating tubule formation, nuclear pleomorphism, and mitotic figure counts in a combined three tier score, prevents the bias that architecture exerts on nuclear grades in less well-controlled situation

Glacial lakes of the Central and Patagonian Andes

The prevalence and increased frequency of high-magnitude Glacial Lake Outburst Floods (GLOFs) in the Chilean and Argentinean Andes suggests this region will be prone to similar events in the future as glaciers continue to retreat and thin under a warming climate. Despite this situation, monitoring of glacial lake development in this region has been limited, with past investigations only covering relatively small regions of Patagonia. This study presents new glacial lake inventories for 1986, 2000 and 2016, covering the Central Andes, Northern Patagonia and Southern Patagonia. Our aim was to characterise the physical attributes, spatial distribution and temporal development of glacial lakes in these three sub-regions using Landsat satellite imagery and image datasets available in Google Earth and Bing Maps. Glacial lake water volume was also estimated using an empirical area-volume scaling approach. Results reveal that glacial lakes across the study area have increased in number (43%) and areal extent (7%) between 1986 and 2016. Such changes equate to a glacial lake water volume increase of 65?km3 during the 30-year observation period. However, glacial lake growth and emergence was shown to vary sub-regionally according to localised topography, meteorology, climate change, rate of glacier change and the availability of low gradient ice areas. These and other factors are likely to influence the occurrence of GLOFs in the future. This analysis represents the first large-scale census of glacial lakes in Chile and Argentina and will allow for a better understanding of lake development in this region, as well as, providing a basis for future GLOF risk assessments.authorsversionPeer reviewe

Comparison of different methods for post-therapeutic dosimetry in [177Lu]Lu-PSMA-617 radioligand therapy

Background Dosimetry is of high importance for optimization of patient-individual PSMA-targeted radioligand therapy (PSMA-RLT). The aim of our study was to evaluate and compare the feasibility of different approaches of image-based absorbed dose estimation in terms of accuracy and effort in clinical routine. Methods Whole-body planar images and SPECT/CT images were acquired from 24 patients and 65 cycles at 24h, 48h, and ≥96h after administration of a mean activity of 6.4 GBq [177Lu]Lu-PSMA-617 (range 3–10.9 GBq). Dosimetry was performed by use of the following approaches: 2D planar-based dosimetry, 3D SPECT/CT-based dosimetry, and hybrid dosimetry combining 2D and 3D data. Absorbed doses were calculated according to IDAC 2.1 for the kidneys, the liver, the salivary glands, and bone metastases. Results Mean absorbed doses estimated by 3D dosimetry (the reference method) were 0.54 ± 0.28 Gy/GBq for the kidneys, 0.10 ± 0.05 Gy/GBq for the liver, 0.81 ± 0.34 Gy/GBq for the parotid gland, 0.72 ± 0.39 Gy/GBq for the submandibular gland, and 1.68 ± 1.32 Gy/GBq for bone metastases. Absorbed doses of normal organs estimated by hybrid dosimetry showed small, non-significant differences (median up to 4.0%) to the results of 3D dosimetry. Using 2D dosimetry, in contrast, significant differences (median up to 10.9%) were observed. Regarding bone metastases, small, but significant differences (median up to 7.0%) of absorbed dose were found for both, 2D dosimetry and hybrid dosimetry. Bland-Altman analysis revealed high agreement between hybrid dosimetry and 3D dosimetry for normal organs and bone metastases, but substantial differences between 2D dosimetry and 3D dosimetry. Conclusion Hybrid dosimetry provides high accuracy in estimation of absorbed dose in comparison to 3D dosimetry for all important organs and is therefore feasible for use in individualized PSMA-RLT