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https://www.readbyqxmd.com/read/29458163/dna-adduct-profiling-of-in-vitro-colonic-meat-digests-to-map-red-vs-white-meat-genotoxicity
#1
Lieselot Y Hemeryck, Caroline Rombouts, Ellen De Paepe, Lynn Vanhaecke
The consumption of red meat has been linked to an increased colorectal cancer (CRC) risk. One of the major hypotheses states that heme iron (present in red meat) stimulates the formation of genotoxic N-nitroso compounds (NOCs) and lipid peroxidation products (LPOs). By means of DNA adductomics, chemically induced DNA adduct formation can be mapped in relation to e.g. dietary exposures. In this study, this state-of-the-art methodology was used to investigate alkylation and (lipid per)oxidation induced DNA adduct formation in in vitro red vs...
February 16, 2018: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29457713/probing-structural-changes-among-analogous-inhibitor-bound-forms-of-hiv-1-protease-and-a-drug-resistant-mutant-in-solution-by-nuclear-magnetic-resonance
#2
Shahid N Khan, John D Persons, Janet L Paulsen, Michel Guerrero, Celia A Schiffer, Nese Kurt-Yilmaz, Rieko Ishima
In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR...
February 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/29457148/platelets-at-the-vascular-interface
#3
Wolfgang Bergmeier, Lucia Stefanini
In this brief review paper, we will summarize the State-of-the-Art on how platelet reactivity is regulated in circulation and at sites of vascular injury. Our review discusses recent and ongoing work, presented at this year's International Society on Thrombosis and Haemostasis (ISTH) meeting, on the role of platelets in (1) classical hemostasis at sites of mechanical injury, and (2) the maintenance of vascular integrity at sites of inflammation.
January 2018: Research and Practice in Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/29455369/intradural-spinal-tumors-in-adults-update-on-management-and-outcome
#4
REVIEW
Malte Ottenhausen, Georgios Ntoulias, Imithri Bodhinayake, Finn-Hannes Ruppert, Stefan Schreiber, Annette Förschler, John A Boockvar, Andreas Jödicke
Among spinal tumors that occur intradurally, meningiomas, nerve sheath tumors, ependymomas, and astrocytomas are the most common. While a spinal MRI is the state of the art to diagnose intradural spinal tumors, in some cases CT scans, angiography, CSF analyses, and neurophysiological examination can be valuable. The management of these lesions depends not only on the histopathological diagnosis but also on the clinical presentation and the anatomical location, allowing either radical resection as with most extramedullary lesions or less invasive strategies as with intramedullary lesions...
February 17, 2018: Neurosurgical Review
https://www.readbyqxmd.com/read/29455260/performance-evaluation-of-state-of-the-art-local-feature-detectors-and-descriptors-in-the-context-of-longitudinal-registration-of-retinal-images
#5
Sajib K Saha, Di Xiao, Shaun Frost, Yogesan Kanagasingam
In this paper we systematically evaluate the performance of several state-of-the-art local feature detectors and descriptors in the context of longitudinal registration of retinal images. Longitudinal (temporal) registration facilitates to track the changes in the retina that has happened over time. A wide number of local feature detectors and descriptors exist and many of them have already applied for retinal image registration, however, no comparative evaluation has been made so far to analyse their respective performance...
February 17, 2018: Journal of Medical Systems
https://www.readbyqxmd.com/read/29455111/deepmitosis-mitosis-detection-via-deep-detection-verification-and-segmentation-networks
#6
Chao Li, Xinggang Wang, Wenyu Liu, Longin Jan Latecki
Mitotic count is a critical predictor of tumor aggressiveness in the breast cancer diagnosis. Nowadays mitosis counting is mainly performed by pathologists manually, which is extremely arduous and time-consuming. In this paper, we propose an accurate method for detecting the mitotic cells from histopathological slides using a novel multi-stage deep learning framework. Our method consists of a deep segmentation network for generating mitosis region when only a weak label is given (i.e., only the centroid pixel of mitosis is annotated), an elaborately designed deep detection network for localizing mitosis by using contextual region information, and a deep verification network for improving detection accuracy by removing false positives...
January 31, 2018: Medical Image Analysis
https://www.readbyqxmd.com/read/29454545/characterization-of-urinary-stone-composition-by-use-of-whole-body-photon-counting-detector-ct
#7
Andrea Ferrero, Ralf Gutjahr, Ahmed F Halaweish, Shuai Leng, Cynthia H McCollough
RATIONAL AND OBJECTIVES: This study aims to investigate the performance of a whole-body, photon-counting detector (PCD) computed tomography (CT) system in differentiating urinary stone composition. MATERIALS AND METHODS: Eighty-seven human urinary stones with pure mineral composition were placed in four anthropomorphic water phantoms (35-50 cm lateral dimension) and scanned on a PCD-CT system at 100, 120, and 140 kV. For each phantom size, tube current was selected to match CTDIvol (volume CT dose index) to our clinical practice...
February 14, 2018: Academic Radiology
https://www.readbyqxmd.com/read/29454184/exploration-and-exploitation-of-the-environment-for-novel-specialized-metabolites
#8
REVIEW
Catarina Loureiro, Marnix H Medema, John van der Oost, Detmer Sipkema
Microorganisms are Nature's little engineers of a remarkable array of bioactive small molecules that represent most of our new drugs. The wealth of genomic and metagenomic sequence data generated in the last decade has shown that the majority of novel biosynthetic gene clusters (BGCs) is identified from cultivation-independent studies, which has led to a strong expansion of the number of microbial taxa known to harbour BGCs. The large size and repeat sequences of BGCs remain a bioinformatic challenge, but newly developed software tools have been created to overcome these issues and are paramount to identify and select the most promising BGCs for further research and exploitation...
February 14, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29453541/detection-of-dna-damage-induced-by-cerium-dioxide-nanoparticles-from-models-to-molecular-mechanism-activated
#9
Tiago Alves Jorge de Souza, Thiago Lopes Rocha, Leonardo Pereira Franchi
This chapter will present an original effort to summarize the relevant data about the cyto-genotoxicity induced by cerium dioxide nanoparticles (nanoceria) in physiologically (in vivo and in vitro) relevant models. In this way, this chapter should be extremely useful to everyone who wants to plan their research and publishing their results. Massive application of nanoceria at different fields is increasing year after year, and it is urgent to address and discuss their use and its safety-related issues. Specifically, the nanoceria are being designed for nanomedicine, cosmetics, polishing materials and additives for automotive fuels...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29453452/systematic-and-stochastic-influences-on-the-performance-of-the-minion-nanopore-sequencer-across-a-range-of-nucleotide-bias
#10
Raga Krishnakumar, Anupama Sinha, Sara W Bird, Harikrishnan Jayamohan, Harrison S Edwards, Joseph S Schoeniger, Kamlesh D Patel, Steven S Branda, Michael S Bartsch
Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453388/identifying-noncoding-risk-variants-using-disease-relevant-gene-regulatory-networks
#11
Long Gao, Yasin Uzun, Peng Gao, Bing He, Xiaoke Ma, Jiahui Wang, Shizhong Han, Kai Tan
Identifying noncoding risk variants remains a challenging task. Because noncoding variants exert their effects in the context of a gene regulatory network (GRN), we hypothesize that explicit use of disease-relevant GRNs can significantly improve the inference accuracy of noncoding risk variants. We describe Annotation of Regulatory Variants using Integrated Networks (ARVIN), a general computational framework for predicting causal noncoding variants. It employs a set of novel regulatory network-based features, combined with sequence-based features to infer noncoding risk variants...
February 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29452978/the-management-of-antibodies-in-heart-transplantation-an-ishlt-consensus-document
#12
Jon Kobashigawa, Monica Colvin, Luciano Potena, Duska Dragun, Maria G Crespo-Leiro, Juan F Delgado, Michael Olymbios, Jayan Parameshwar, Jignesh Patel, Elaine Reed, Nancy Reinsmoen, E Rene Rodriguez, Heather Ross, Randall C Starling, Dolly Tyan, Simon Urschel, Andreas Zuckermann
Despite the successes from refined peri-operative management techniques and immunosuppressive therapies, antibodies remain a serious cause of morbidity and mortality for patients both before and after heart transplantation. Patients awaiting transplant who possess antibodies against human leukocyte antigen are disadvantaged by having to wait longer to receive an organ from a suitably matched donor. The number of pre-sensitized patients has been increasing, a trend that is likely due to the increased use of mechanical circulatory support devices...
January 31, 2018: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/29452923/statistical-and-machine-learning-approaches-to-predicting-protein-ligand-interactions
#13
REVIEW
Lucy J Colwell
Data driven computational approaches to predicting protein-ligand binding are currently achieving unprecedented levels of accuracy on held-out test datasets. Up until now, however, this has not led to corresponding breakthroughs in our ability to design novel ligands for protein targets of interest. This review summarizes the current state of the art in this field, emphasizing the recent development of deep neural networks for predicting protein-ligand binding. We explain the major technical challenges that have caused difficulty with predicting novel ligands, including the problems of sampling noise and the challenge of using benchmark datasets that are sufficiently unbiased that they allow the model to extrapolate to new regimes...
February 13, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29452791/untapped-reserves-controlling-primordial-follicle-growth-activation
#14
REVIEW
Amanda Kallen, Alex J Polotsky, Joshua Johnson
Even with the benefit of assisted reproductive technologies (ART), many women are unable to conceive and deliver healthy offspring. One common cause of infertility is the inability to produce eggs capable of contributing to live birth. This can occur despite standard-of-care treatment to maximize the recovery of eggs from growing ovarian follicles. Dormant primordial follicles in the human ovary are a 'reserve ' that can be exploited clinically to overcome this problem. We discuss how controlling primordial follicle growth activation (PFGA) can produce increased numbers of high-quality eggs available for fertility treatment(s)...
February 13, 2018: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/29451898/integrating-linear-optimization-with-structural-modeling-to-increase-hiv-neutralization-breadth
#15
Alexander M Sevy, Swetasudha Panda, James E Crowe, Jens Meiler, Yevgeniy Vorobeychik
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods...
February 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29451398/examining-heat-treatment-for-stabilization-of-the-lipidome
#16
Jeremy P Koelmel, Christina M Jones, Candice Z Ulmer, Timothy J Garrett, Richard A Yost, Tracey B Schock, John A Bowden
AIM: To confidently determine lipid-based biomarkers, it is important to minimize variation introduced during preanalytical steps. We evaluated reducing variation associated with lipid measurements in invertebrate sentinel species using a state-of-the-art heat treatment technique. MATERIALS AND METHODS: Earthworms (Eisenia fetida), house crickets (Acheta domestica) and ghost shrimp (Palaemonetes paludosus) were euthanized either by flash freezing or heat treatment...
February 16, 2018: Bioanalysis
https://www.readbyqxmd.com/read/29451272/the-ndpk-nme-superfamily-state-of-the-art
#17
EDITORIAL
Mathieu Boissan, Uwe Schlattner, Marie-Lise Lacombe
Nucleoside diphosphate kinases (NDPK) are nucleotide metabolism enzymes encoded by NME genes (also called NM23). Given the fact that not all NME-encoded proteins are catalytically active NDPKs and that NM23 generally refers to clinical studies on metastasis, we use here NME/NDPK to denote the proteins. Since their discovery in the 1950's, NMEs/NDPKs have been shown to be involved in multiple physiological and pathological cellular processes, but the molecular mechanisms have not been fully determined. Recent progress in elucidating these underlying mechanisms has been presented by experts in the field at the 10th International Congress on the NDPK/NME/AWD protein family in October 2016 in Dubrovnik, Croatia, and is summarized in review articles or original research in this and an upcoming issue of Laboratory Investigation...
February 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29450693/the-effect-of-assisted-reproductive-technology-on-the-incidence-of-birth-defects-among-livebirths
#18
Gil Shechter-Maor, Nicholas Czuzoj-Shulman, Andrea R Spence, Haim Arie Abenhaim
PURPOSE: Our study objective is to examine the association between births conceived with assisted reproductive technology (ART) and birth defects using a large database from the United States. METHODS: Using the Centers for Disease Control and Prevention's Period-linked birth-infant death data files and fetal death database for 2011-2013, we conducted a retrospective cohort study comprised of live births that occurred in the USA during that time. Multivariate logistic regression was used to estimate the association between ART and birth defects, both overall and by specific defects...
February 15, 2018: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/29450674/risk-assessment-of-pesticides-in-estuaries-a-review-addressing-the-persistence-of-an-old-problem-in-complex-environments
#19
Nagore Cuevas, Marta Martins, Pedro M Costa
Estuaries, coastal lagoons and other transition ecosystems tend to become the ultimate reservoirs of pollutants transported by continental runoff, among which pesticides constitute the class of most concern. High amounts of dissolved and particulated organic matter greatly contribute to the accumulation of pesticides that eventually become trapped in sediments or find their way along food chains. Perhaps not so surprisingly, it is common to find elevated levels of pesticides in estuarine sediments decades after their embargo...
February 15, 2018: Ecotoxicology
https://www.readbyqxmd.com/read/29450473/elevated-blood-viscosity-and-micro-recirculation-linked-to-coronary-stent-malapposition
#20
Eric Poon, Vikas Thondapu, Umair Hayat, Peter Barlis, Chooi Yap, Po Kuo, Qisen Wang, Jiawei Ma, Shuang Zhu, Stephen Moore, Andrew Ooi
One particular complexity of coronary artery is the natural tapering of the vessel with proximal segments having larger caliber and distal tapering as the vessel get smaller. The natural tapering of a coronary artery often leads to proximal incomplete stent apposition (ISA). ISA alters coronary hemodynamics and creates pathological path to develop complications such as in-stent restenosis, and more worryingly, stent thrombosis. By employing state-of-the-art computer-aided design software, generic stent hoops were virtually deployed in an idealized tapered coronary artery with decreasing malapposition distance...
February 14, 2018: Journal of Biomechanical Engineering
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