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https://www.readbyqxmd.com/read/28960343/prediction-of-seebeck-coefficient-for-compounds-without-restriction-to-fixed-stoichiometry-a-machine-learning-approach
#1
Al'ona Furmanchuk, James E Saal, Jeff W Doak, Gregory B Olson, Alok Choudhary, Ankit Agrawal
The regression model-based tool is developed for predicting the Seebeck coefficient of crystalline materials in the temperature range from 300 K to 1000 K. The tool accounts for the single crystal versus polycrystalline nature of the compound, the production method, and properties of the constituent elements in the chemical formula. We introduce new descriptive features of crystalline materials relevant for the prediction the Seebeck coefficient. To address off-stoichiometry in materials, the predictive tool is trained on a mix of stoichiometric and nonstoichiometric materials...
September 27, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28875027/viscous-hydrophilic-injection-matrices-for-serial-crystallography
#2
Gabriela Kovácsová, Marie Luise Grünbein, Marco Kloos, Thomas R M Barends, Ramona Schlesinger, Joachim Heberle, Wolfgang Kabsch, Robert L Shoeman, R Bruce Doak, Ilme Schlichting
Serial (femtosecond) crystallography at synchrotron and X-ray free-electron laser (XFEL) sources distributes the absorbed radiation dose over all crystals used for data collection and therefore allows measurement of radiation damage prone systems, including the use of microcrystals for room-temperature measurements. Serial crystallography relies on fast and efficient exchange of crystals upon X-ray exposure, which can be achieved using a variety of methods, including various injection techniques. The latter vary significantly in their flow rates - gas dynamic virtual nozzle based injectors provide very thin fast-flowing jets, whereas high-viscosity extrusion injectors produce much thicker streams with flow rates two to three orders of magnitude lower...
July 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28853740/erratum-structural-and-conformational-determinants-of-macrocycle-cell-permeability
#3
Björn Over, Pär Matsson, Christian Tyrchan, Per Artursson, Bradley C Doak, Michael A Foley, Constanze Hilgendorf, Stephen E Johnston, Maurice D Lee, Richard J Lewis, Patrick McCarren, Giovanni Muncipinto, Ulf Norinder, Matthew W D Perry, Jeremy R Duvall, Jan Kihlberg
No abstract text is available yet for this article.
July 18, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28743469/energy-and-food-intake-are-associated-with-specific-intestinal-parasitic-infections-in-children-of-rural-mexico
#4
Gerardo A Zavala, Jorge L Rosado, Colleen M Doak, Maria Del Carmen Caamaño, Maiza Campos-Ponce, Dolores Ronquillo, Katja Polman, Olga P García
No abstract text is available yet for this article.
December 2017: Parasitology International
https://www.readbyqxmd.com/read/28703770/exposure-to-engineered-nanomaterials-impact-on-dna-repair-pathways
#5
REVIEW
Neenu Singh, Bryant C Nelson, Leona D Scanlan, Erdem Coskun, Pawel Jaruga, Shareen H Doak
Some engineered nanomaterials (ENMs) may have the potential to cause damage to the genetic material in living systems. The mechanistic machinery functioning at the cellular/molecular level, in the form of DNA repair processes, has evolved to help circumvent DNA damage caused by exposure to a variety of foreign substances. Recent studies have contributed to our understanding of the various DNA damage repair pathways involved in the processing of DNA damage. However, the vast array of ENMs may present a relatively new challenge to the integrity of the human genome; therefore, the potential hazard posed by some ENMs necessitates the evaluation and understanding of ENM-induced DNA damage repair pathways...
July 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28659454/correction-to-wind-and-rain-are-the-primary-climate-factors-driving-changing-phenology-of-an-aerial-insectivore
#6
Rachel D Irons, April Harding Scurr, Alexandra P Rose, Julie C Hagelin, Tricia Blake, Daniel F Doak
No abstract text is available yet for this article.
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28622829/investigation-of-j-shaped-dose-responses-induced-by-exposure-to-the-alkylating-agent-n-methyl-n-nitrosourea
#7
Katherine E Chapman, George R Hoffmann, Shareen H Doak, Gareth J S Jenkins
Hormesis is defined as a biphasic dose-response where biological effects of low doses of a stressor demonstrate the opposite effect to high-dose effects of the same stressor. Hormetic, or J-shaped, dose-response relationships are relatively rarely observed in toxicology, resulting in a limited understanding and even some skepticism of the concept. Low dose-response studies for genotoxicity endpoints have been performed at Swansea University for over a decade. However, no statistically significant decreases below control genotoxicity levels have been detected until recently...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28619032/the-role-of-intracellular-trafficking-of-cdse-zns-qds-on-their-consequent-toxicity-profile
#8
Bella B Manshian, Thomas F Martens, Karsten Kantner, Kevin Braeckmans, Stefaan C De Smedt, Jo Demeester, Gareth J S Jenkins, Wolfgang J Parak, Beatriz Pelaz, Shareen H Doak, Uwe Himmelreich, Stefaan J Soenen
BACKGROUND: Nanoparticle interactions with cellular membranes and the kinetics of their transport and localization are important determinants of their functionality and their biological consequences. Understanding these phenomena is fundamental for the translation of such NPs from in vitro to in vivo systems for bioimaging and medical applications. Two CdSe/ZnS quantum dots (QD) with differing surface functionality (NH2 or COOH moieties) were used here for investigating the intracellular uptake and transport kinetics of these QDs...
June 15, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28500237/resistance-to-ret-inhibition-in-ret-rearranged-nsclc-is-mediated-by-reactivation-of-ras-mapk-signaling
#9
Sarah K Nelson-Taylor, Anh T Le, Minjae Yoo, Laura Schubert, Katie M Mishall, Andrea Doak, Marileila Varella-Garcia, Aik-Choon Tan, Robert C Doebele
Oncogenic rearrangements in RET are present in 1%-2% of lung adenocarcinoma patients. Ponatinib is a multi-kinase inhibitor with low-nanomolar potency against the RET kinase domain. Here, we demonstrate that ponatinib exhibits potent antiproliferative activity in RET fusion-positive LC-2/ad lung adenocarcinoma cells and inhibits phosphorylation of the RET fusion protein and signaling through ERK1/2 and AKT. Using distinct dose escalation strategies, two ponatinib-resistant LC-2/ad cell lines, PR1 and PR2, were derived...
August 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28446701/wind-and-rain-are-the-primary-climate-factors-driving-changing-phenology-of-an-aerial-insectivore
#10
Rachel D Irons, April Harding Scurr, Alexandra P Rose, Julie C Hagelin, Tricia Blake, Daniel F Doak
While the ecological effects of climate change have been widely observed, most efforts to document these impacts in terrestrial systems have concentrated on the impacts of temperature. We used tree swallow (Tachycineta bicolor) nest observations from two widely separated sites in central Alaska to examine the aspects of climate affecting breeding phenology at the northern extent of this species' range. We found that two measures of breeding phenology, annual lay and hatch dates, are more strongly predicted by windiness and precipitation than by temperature...
April 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28398334/diffraction-data-of-core-shell-nanoparticles-from-an-x-ray-free-electron-laser
#11
Xuanxuan Li, Chun-Ya Chiu, Hsiang-Ju Wang, Stephan Kassemeyer, Sabine Botha, Robert L Shoeman, Robert M Lawrence, Christopher Kupitz, Richard Kirian, Daniel James, Dingjie Wang, Garrett Nelson, Marc Messerschmidt, Sébastien Boutet, Garth J Williams, Elisabeth Hartmann, Aliakbar Jafarpour, Lutz M Foucar, Anton Barty, Henry Chapman, Mengning Liang, Andreas Menzel, Fenglin Wang, Shibom Basu, Raimund Fromme, R Bruce Doak, Petra Fromme, Uwe Weierstall, Michael H Huang, John C H Spence, Ilme Schlichting, Brenda G Hogue, Haiguang Liu
X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28373085/choose-your-cell-model-wisely-the-in-vitro-nanoneurotoxicity-of-differentially-coated-iron-oxide-nanoparticles-for-neural-cell-labeling
#12
Freya Joris, Daniel Valdepérez, Beatriz Pelaz, Tianqiang Wang, Shareen H Doak, Bella B Manshian, Stefaan J Soenen, Wolfgang J Parak, Stefaan C De Smedt, Koen Raemdonck
Currently, there is a large interest in the labeling of neural stem cells (NSCs) with iron oxide nanoparticles (IONPs) to allow MRI-guided detection after transplantation in regenerative medicine. For such biomedical applications, excluding nanotoxicity is key. Nanosafety is primarily evaluated in vitro where an immortalized or cancer cell line of murine origin is often applied, which is not necessarily an ideal cell model. Previous work revealed clear neurotoxic effects of PMA-coated IONPs in distinct cell types that could potentially be applied for nanosafety studies regarding neural cell labeling...
April 1, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28341647/estimating-seven-coefficients-of-pairwise-relatedness-using-population-genomic-data
#13
Matthew S Ackerman, Parul Johri, Ken Spitze, Sen Xu, Thomas G Doak, Kimberly Young, Michael Lynch
Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic of which are the pairwise relatedness coefficients between any two individuals. There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data...
May 2017: Genetics
https://www.readbyqxmd.com/read/28280722/tissue-engineered-solutions-in-plastic-and-reconstructive-surgery-principles-and-practice
#14
REVIEW
Sarah Al-Himdani, Zita M Jessop, Ayesha Al-Sabah, Emman Combellack, Amel Ibrahim, Shareen H Doak, Andrew M Hart, Charles W Archer, Catherine A Thornton, Iain S Whitaker
Recent advances in microsurgery, imaging, and transplantation have led to significant refinements in autologous reconstructive options; however, the morbidity of donor sites remains. This would be eliminated by successful clinical translation of tissue-engineered solutions into surgical practice. Plastic surgeons are uniquely placed to be intrinsically involved in the research and development of laboratory engineered tissues and their subsequent use. In this article, we present an overview of the field of tissue engineering, with the practicing plastic surgeon in mind...
2017: Frontiers in Surgery
https://www.readbyqxmd.com/read/28231421/varying-demographic-impacts-of-different-fisheries-on-three-mediterranean-seabird-species
#15
Meritxell Genovart, Daniel F Doak, José-Manuel Igual, Stefano Sponza, Jelena Kralj, Daniel Oro
Fisheries have an enormous economic importance, but reconciling their socio-economic features with the conservation and sustainability of marine ecosystems presents major challenges. Bycatch mortality from fisheries is clearly among the most serious global threats for marine ecosystems, affecting a wide range of top predators. Recent estimates report ca. 200,000 seabirds killed annually by bycatch in European waters. However, there is an urgent need to rigorously estimate actual mortality rates and quantify effects of bycatch on populations...
February 23, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28204679/population-genomics-of-paramecium-species
#16
Parul Johri, Sascha Krenek, Georgi K Marinov, Thomas G Doak, Thomas U Berendonk, Michael Lynch
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes...
May 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28202732/atomic-structure-of-granulin-determined-from-native-nanocrystalline-granulovirus-using-an-x-ray-free-electron-laser
#17
Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D Bunker, Francesco Stellato, Elaine Chiu, Shin-Mei Yeh, Andrew Aquila, Shibom Basu, Richard Bean, Kenneth R Beyerlein, Sabine Botha, Sébastien Boutet, Daniel P DePonte, R Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R James, Christopher Kupitz, Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberly Rendek, Robert L Shoeman, Dingjie Wang, Uwe Weierstall, Thomas A White, Garth J Williams, Nadia A Zatsepin, Petra Fromme, John C H Spence, Kenneth N Goldie, Johannes A Jehle, Peter Metcalf, Anton Barty, Henry N Chapman
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28112402/portfolio-effects-climate-change-and-the-persistence-of-small-populations-analyses-on-the-rare-plant-saussurea-weberi
#18
Ronald E Abbott, Daniel F Doak, Megan L Peterson
The mechanisms that stabilize small populations in the face of environmental variation are crucial to their long-term persistence. Building from diversity-stability concepts in community ecology, within-population diversity is gaining attention as an important component of population stability. Genetic and microhabitat variation within populations can generate diverse responses to common environmental fluctuations, dampening temporal variability across the population as a whole through portfolio effects. Yet, the potential for portfolio effects to operate at small scales within populations or to change with systematic environmental shifts, such as climate change, remain largely unexplored...
April 2017: Ecology
https://www.readbyqxmd.com/read/28011747/nanogenotoxicology-present-and-the-future
#19
EDITORIAL
Shareen H Doak, Maria Dusinska
This Mutagenesis special issue is on the topic of nanogenotoxicology. It unites a collection of reports that provide insight into: (i) the properties of engineered nanomaterials (ENMs) that contribute to genotoxicity, (ii) the genotoxic mechanisms associated with DNA damage observed in both in vitro and in vivo tests and (iii) the future test systems that will provide more accurate prediction of ENM genotoxicity to support regulatory hazard assessment frameworks. The contributions within therefore provide collective oversight of our current understanding, coupled to future perspectives aimed at overcoming technical hurdles and describing novel analytical methods to further advance the field...
January 2017: Mutagenesis
https://www.readbyqxmd.com/read/27942789/evaluation-of-the-automated-microflow-%C3%A2-and-metafer%C3%A2-platforms-for-high-throughput-micronucleus-scoring-and-dose-response-analysis-in-human-lymphoblastoid-tk6-cells
#20
Jatin R Verma, Benjamin J Rees, Eleanor C Wilde, Catherine A Thornton, Gareth J S Jenkins, Shareen H Doak, George E Johnson
The use of manual microscopy for the scoring of chromosome damage in the in vitro micronucleus assay is often associated with user subjectivity. This level of subjectivity can be reduced by using automated platforms, which have added value of faster with high-throughput and multi-endpoint capabilities. However, there is a need to assess the reproducibility and sensitivity of these automated platforms compared with the gold standard of the manual scoring. The automated flow cytometry-based MicroFlow(®) and image analysis-based Metafer™ were used for dose response analyses in human lymphoblastoid TK6 cells exposed to the model clastogen, methyl methanesulfonate (MMS), aneugen, carbendazim, and the weak genotoxic carcinogen, ochratoxin A (OTA)...
July 2017: Archives of Toxicology
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