ALBERT

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Mónica Andrea Vargas, Jesús E. Diosa, Edgar Mosquera〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This article presents the data on α-Fe〈sub〉2〈/sub〉O〈sub〉3〈/sub〉 nanoparticles synthesized via Pechini method using iron(III) oxide precursor from steel industry. It is important to highlight the added value that is given to an industrial waste. The samples were characterized by thermal analysis (DTA, TG), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The TG showed three mass changes, whereas DTA resulted in three anomalies. X-ray diffraction pattern of the samples disclosed rhombohedral structure characteristic of the nanocrystalline α-Fe〈sub〉2〈/sub〉O〈sub〉3〈/sub〉 phase. The crystallite size was estimated for each thermal treatment. Fourier transform infrared spectroscopy confirms the phase purity of prepared nanoparticles. A detailed study on the local structure of the samples was carry out in the region of 800 and 400 cm〈sup〉−1〈/sup〉, where the associated bands of Fe–O bonds are presents. The data have not been reported nor discussed for now.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Samyr M. Querobino, Naially C. de Faria, Aryane A. Vigato, Bruna G.M. da Silva, Ian P. Machado, Maricilia S. Costa, Fanny N. Costa, Daniele R. de Araujo, Carlos Alberto-Silva〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Functional polymeric nanoparticles have attracted attention for different biomedical applications, including drug delivery. Poloxamers (PL), a synthetic copolymers of poly(ethyleneoxide)-b-poly(propylene oxide)-b-poly(ethylene oxide), that exhibit thermoreversible behavior in aqueous solutions. Physicochemical properties of Oleic Acid-Poloxamer (OA-PL) organogel for intravaginal controlled Voriconazole (VRC) delivery were assessed using three different oils (isopropyl myristate - IPM, isopropyl palmitate - IPP, and oleic acid – OA, in order to select the most suitable oil phase for increasing the solubility of the drug and its dispersion in the final aqueous phase. Organogel structural organization was assessed by VRC partition coefficient, differential scanning calorimetry (DSC), rheological analysis, and drug release assay. These data are complementary to the research article entitled “Sodium alginate in oil-poloxamer organogels for intravaginal drug delivery: influence on structural parameters, drug release mechanisms, cytotoxicity and 〈em〉in vitro〈/em〉 antifungal activity” - Materials Science and Engineering: C, 2019. 99: p. 1350–1361.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Muhamad Aidil Zahidin, Norehan Abd Jalil, Nur Mukminah Naharuddin, Mohd Ridwan Abd Rahman, Millawati Gani, Mohd Tajuddin Abdullah〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (〈em〉Carlito syrichta〈/em〉), Sulawesi (〈em〉Tarsius〈/em〉 tarsier-complex) and Borneo (〈em〉Cephalopachus bancanus〈/em〉). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of 〈em〉C. bancanus〈/em〉 in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome 〈em〉b〈/em〉) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Willams Oliveira, Jéssica Luiza Souza e Silva, Marcela Tomaz Pontes de Oliveira, Oswaldo Cruz-Neto, Luanda Augusta Pinheiro da Silva, Laís Angélica Borges, Mellissa Sousa Sobrinho, Ariadna Valentina Lopes〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this article, we supply raw data on the reproductive biology and frequency of pollinators of 〈em〉Paubrasilia echinata〈/em〉, a threatened tree, endemic to the Brazilian Atlantic forest, which is largely used in Brazilian urban areas (e.g. avenues, parks and squares) due to its ornamental potential. Specifically, we share data on the reproductive phenology, pollen/flower, floral visitors and seed set of 〈em〉P. echinata〈/em〉 in urban and natural ecosystems. This dataset article is related to the original research article "〈strong〉Reduced reproductive success of the endangered tree brazilwood (〈em〉Paubrasilia echinata〈/em〉, Leguminosae) in urban ecosystem compared to Atlantic forest remnant: lessons for tropical urban ecology〈/strong〉" (Oliveira et al., 2019). As urbanization is thought to negatively impact the maintenance of plant communities by affecting ecological key interactions, such as pollination, we believe that data as the supplied here are relevant and could support the planning of urban green spaces to maintain viable communities of plants and animals. This is especially valid for tropical urban ecosystems since most of the studies on plant ecology have been developed in temperate regions and there are still several gaps on the knowledge of ecological functions and ecosystems services (e.g. pollination) in urban green areas in the tropics.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): R. Sathish Kumar, K. Sureshkumar〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This data article presents the experimental data set on the optimization of four important parameters which are type of blending fuel, blending ratio, compression ratio and injection timing for four objective functions namely higher brake thermal efficiency, lower brake specific fuel consumption, lower oxides of nitrogen emission and lower unburnt hydrocarbon emission using grey relational analysis and orthogonal array based experimental design. Each parameter was fixed with three levels and L9 orthogonal array has been chosen for experimental analysis. The data obtained from the experimental work reported that butanol as blending fuel, 40% of maximum blending ratio, compression ratio of 16:1 and injection timing of 26 °CA before top dead centre were identified as optimized set of parameters.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Vladimir Kolmakov, Alexandra Polyakova〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This data article provides estimates on the Russian regions' aggregate free cash flow, which is not covered by national statistics of major countries. A proper microeconomic model was adapted to regional level data to derive a synthetic indicator of a regional economy's performance. The data contributes to the set of regional performance measures thus enabling a new look at studies of economic growth and development. Conventional economic growth indicators, such as GDP, fixed capital investment or industrial output, are widely criticized since they can have negative values only in terms of growth rates thus showing no evidence of value creation or deterioration. Our data on regional free cash flow eliminates this drawback.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Sacha Varone, Corentin Beffa〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉“Passeport Vacances”, abbreviated PV, is a set of leisure activities proposed to children to discover and enjoy during school holidays. During PV, activities are proposed several times, each one being an occurrence. This data set contains real data, collected by online registration during the summer of 2017. Children express their preferences for each available time slot. Organizers should assign activities to children by maximizing their expressed preferences, subject to several types of constraints: age limit, group size limit for each occurrence of an activity, diversification of the type of activities for each child, restrictions on costly activities, restrictions on the number of activities per period, and cost balancing. The CSV files in this data set represent the preferences of 634 children for 1121 activities over a two-week period. These data were used to develop the Morges 2017 Vacation Passport model, which is associated with the research article entitled ““Passeport Vacances”: an assignment problem with cost balancing” Beffa and Varone, 2018.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Prashant Kaushik, Shashi Kumar〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉〈em〉Aegle marmelos〈/em〉 L. (Bael), of family Rutaceae, produces nutritious and medicinally important fruits. Here, we provide the first information regarding the de novo transcriptome assembly of 〈em〉Aegle marmelos〈/em〉 L. fruit. The information on the fruit transcriptome sequencing data will be useful to gain a better insight into the important pathways in the 〈em〉Aegle marmelos〈/em〉 L. fruits. The data can be accessed via NCBI BioProject (id PRJNA433585).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Solomon Kassa, Haylay Tsegab, Chow Weng Sum, Choong CheeMeng〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Fission tracks are linear trails of intense radiation damage in the crystal structure of a mineral, produced by spontaneous fissioning of uranium-238 (〈sup〉238〈/sup〉U) atoms. Detail information on the low-temperature thermal histories of rocks, below∼120 °C for tracks in apatite and below∼350 °C for zircon, can be provided by Fission-track (FT) analysis. The purpose of this article is to present apatite and zircon fission-track data, and U–Pb granite ages that provide information about the cooling histories of a rock which can be crucial in comprehending the exhumation episodes of the study area, in particular, and the region, in general. Granite samples were collected along the same vertical profile at different elevation, 178–944 m.a.s.l. These samples were used to determine Fission-Track and crystallization ages. HeFTy software was employed to interpret the cooling histories of the samples using forward and inverse models. The inverse model was an approach of reproducing the observed data, and it was carried out only for fission-track data from the apatite grains. And it was constructed after generating a number of forward models, where in each of these models the predicted apatite fission-track parameters were compared to the measured values. The apatite fission track (AFT) and zircon fission track (ZFT) data indicated expected age trends, 〈em〉i.e.〈/em〉 the older ages at higher elevations and the younger ages at lower elevations. Similarly, the data shows that the apatite and zircon FT ages appear younger than the age of the rock crystallization. The U–Pb age in zircon consistently suggest the age of the granite is Late Triassic.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 2 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 1〈/p〉 〈p〉Author(s): Jade D. Bailey, Marina Diotallevi, Thomas Nicol, Eileen McNeill, Andrew Shaw, Surawee Chuaiphichai, Ashley Hale, Anna Starr, Manasi Nandi, Elena Stylianou, Helen McShane, Simon Davis, Roman Fischer, Benedikt M. Kessler, James McCullagh, Keith M. Channon, Mark J. Crabtree〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Classical activation of macrophages (M(LPS+IFNγ)) elicits the expression of inducible nitric oxide synthase (iNOS), generating large amounts of NO and inhibiting mitochondrial respiration. Upregulation of glycolysis and a disrupted tricarboxylic acid (TCA) cycle underpin this switch to a pro-inflammatory phenotype. We show that the NOS cofactor tetrahydrobiopterin (BH〈sub〉4〈/sub〉) modulates IL-1β production and key aspects of metabolic remodeling in activated murine macrophages via NO production. Using two complementary genetic models, we reveal that NO modulates levels of the essential TCA cycle metabolites citrate and succinate, as well as the inflammatory mediator itaconate. Furthermore, NO regulates macrophage respiratory function via changes in the abundance of critical N-module subunits in Complex I. However, NO-deficient cells can still upregulate glycolysis despite changes in the abundance of glycolytic intermediates and proteins involved in glucose metabolism. Our findings reveal a fundamental role for iNOS-derived NO in regulating metabolic remodeling and cytokine production in the pro-inflammatory macrophage.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719307843-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 2 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 1〈/p〉 〈p〉Author(s): Marie-Kristin Raulf, Timo Johannssen, Svea Matthiesen, Konstantin Neumann, Severin Hachenberg, Sabine Mayer-Lambertz, Fridolin Steinbeis, Jan Hegermann, Peter H. Seeberger, Wolfgang Baumgärtner, Christina Strube, Jürgen Ruland, Bernd Lepenies〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Malaria represents a major cause of death from infectious disease. Hemozoin is a 〈em〉Plasmodium〈/em〉-derived product that contributes to progression of cerebral malaria. However, there is a gap of knowledge regarding how hemozoin is recognized by innate immunity. Myeloid C-type lectin receptors (CLRs) encompass a family of carbohydrate-binding receptors that act as pattern recognition receptors in innate immunity. In the present study, we identify the CLR CLEC12A as a receptor for hemozoin. Dendritic cell-T cell co-culture assays indicate that the CLEC12A/hemozoin interaction enhances CD8〈sup〉+〈/sup〉 T cell cross-priming. Using the 〈em〉Plasmodium berghei〈/em〉 Antwerpen-Kasapa (ANKA) mouse model of experimental cerebral malaria (ECM), we find that CLEC12A deficiency protects mice from ECM, illustrated by reduced ECM incidence and ameliorated clinical symptoms. In conclusion, we identify CLEC12A as an innate sensor of plasmodial hemozoin.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719307818-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 2 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 1〈/p〉 〈p〉Author(s): Xuezhou Hou, Guobao Chen, William Bracamonte-Baran, Hee Sun Choi, Nicola L. Diny, Jungeun Sung, David Hughes, Taejoon Won, Megan Kay Wood, Monica V. Talor, David Joel Hackam, Karin Klingel, Giovanni Davogustto, Heinrich Taegtmeyer, Isabelle Coppens, Jobert G. Barin, Daniela Čiháková〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Two types of monocytes, Ly6C〈sup〉hi〈/sup〉 and Ly6C〈sup〉lo〈/sup〉, infiltrate the heart in murine experimental autoimmune myocarditis (EAM). We discovered a role for cardiac fibroblasts in facilitating monocyte-to-macrophage differentiation of both Ly6C〈sup〉hi〈/sup〉 and Ly6C〈sup〉lo〈/sup〉 cells, allowing these macrophages to perform divergent functions in myocarditis progression. During the acute phase of EAM, IL-17A is highly abundant. It signals through cardiac fibroblasts to attenuate efferocytosis of Ly6C〈sup〉hi〈/sup〉 monocyte-derived macrophages (MDMs) and simultaneously prevents Ly6C〈sup〉lo〈/sup〉 monocyte-to-macrophage differentiation. We demonstrated an inverse clinical correlation between heart IL-17A levels and efferocytic receptor expressions in humans with heart failure (HF). In the absence of IL-17A signaling, Ly6C〈sup〉hi〈/sup〉 MDMs act as robust phagocytes and are less pro-inflammatory, whereas Ly6C〈sup〉lo〈/sup〉 monocytes resume their differentiation into MHCII〈sup〉+〈/sup〉 macrophages. We propose that MHCII〈sup〉+〈/sup〉Ly6C〈sup〉lo〈/sup〉 MDMs are associated with the reduction of cardiac fibrosis and prevention of the myocarditis sequalae.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S221112471930765X-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Farah Alkhatib, John-John Cabibihan, Elsadig Mahdi〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this article, three different data sets are presented to evaluate a representative of openly accessible 3D printed prosthetic hand. The first data set includes grasping force measurements of human hand and low-cost 3D printed hand. Three grasping functions were evaluated, spherical, cylindrical, and precision grasps. The experimental test was performed using a wearable tactile sensor. The second data set includes the numerical analysis of prosthetic fingers made from Acrylonitrile Butadiene Styrene (ABS) and Polylactic Acid (PLA) materials under different carrying loads. The numerical analyses were carried out by LS-DYNA software. The files can be used for the prosthetic fingers’ evaluation and for the selection of suitable material. The third data set includes the experimental tensile test of ABS and PLA materials. The mechanical properties were calculated from the results, which can be used in the design and fabrication of products from these materials. All the datasets are available from Harvard Dataverse: https://doi.org/10.7910/DVN/GCPAIL.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Manuela Stan, Ildiko Lung, Maria-Loredana Soran, Ocsana Opris, Cristian Leostean, Adriana Popa, Florina Copaciu, Mihaela Diana Lazar, Irina Kacso, Teofil-Danut Silipas, Alin Sebastian Porav〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this data article, we present supplementary data related to the research article entitled “Starch-coated green synthesized magnetite nanoparticles for removal of textile dye Optilan Blue from aqueous media” Stan et al., 2019. Data interpretations are included in the related research article Stan et al., 2019. The synthesized starch-coated Fe〈sub〉3〈/sub〉O〈sub〉4〈/sub〉 nanoparticles (ST-coated Fe〈sub〉3〈/sub〉O〈sub〉4〈/sub〉 NPs) were analyzed by scanning electron microscopy (SEM) and high resolution transmission electron microscopy (HRTEM) to illustrate the shape and surface coating of nanoparticles. Moreover, the Brunauer-Emmett-Teller (BET) technique was used to evidence starch deposition on magnetite nanoparticles. The obtained nanocomposites were used for adsorption of Optilan Blue (OB) in batch conditions and the optimum agitation speed and point of zero charge (pH〈sub〉pzc〈/sub〉) were established. After OB adsorption on ST-coated Fe〈sub〉3〈/sub〉O〈sub〉4〈/sub〉 NPs, the nanocomposites were analyzed by transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR). The stability of starch coated Fe〈sub〉3〈/sub〉O〈sub〉4〈/sub〉 NPs in the acidic as well as alkaline pH was also evidenced by FTIR spectroscopy. In addition, to test the stability of ST-coated Fe〈sub〉3〈/sub〉O〈sub〉4〈/sub〉 NPs, leaching experiments were carried out. The experimental data were compared with isotherm and kinetic models in order to determine the most suitable for fitting.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Svetlana Vladislavl'evna Lobova, Julia Vyacheslavovna Ragulina, Aleksei Valentinovich Bogoviz, Alexander Nikolaevich Alekseev〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This paper presents a rich collection of data used to construct an energy security performance index of the eight countries of the Commonwealth of Independent States (CIS). Namely, the index covers Azerbaijan, Armenia, Belarus, Kazakhstan, Kyrgyz Republic, Russia, Tajikistan, Ukraine, Uzbekistan. The data include results of Z-score normalization of 12 distinct indicators, constituting a total of 4 dimensions of energy security performance. These dimensions are the following: energy availability (oil import dependence, coal import dependence, natural gas import dependence), energy affordability (access to electricity, pump price for gasoline, pump price for diesel fuel), energy and economic efficiency (renewable energy consumption, GDP per unit of energy use, electric power consumption), and environmental stewardship (CO〈sub〉2〈/sub〉, N〈sub〉2〈/sub〉O, and SO〈sub〉2〈/sub〉 emissions). Z-scores are calculated for 2000 and 2014, which allows to evaluate energy security performance of the CIS countries in each dimension and in total over the period of 14 years.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Liliana Anjos, Patricia I.S. Pinto, Theofania Tsironi, George Dimopoulos, Soraia Santos, Cátia Santa, Bruno Manadas, Adelino Canario, Petros Taoukis, Deborah M. Power〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation and leads to waste, which has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as high pressure (HP) processing, prolong shelf-life while assuring high food quality. The effect of HP processing (600MPa, 25ºC, 5min) on European sea bass (〈em〉Dicentrarchus labrax〈/em〉) fillet quality and shelf life was investigated. The data presented comprises microbiome and proteome profiles of control and HP-processed sea bass fillets from 1 to 67 days of isothermal storage at 2°C. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 〈em〉16S rRNA〈/em〉 gene in pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. Yeast and fungi diversity were analysed by high-throughput sequencing of the internal transcribed spacer (ITS) region for control and HP-processed fillets at the end of storage (11 or 67 days, respectively) and have the SRA accession number PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed filets after 1, 11 and 67 days of storage. Proteome data was deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD012737. These data support the findings reported in the associated manuscript “High pressure processing of European sea bass (〈em〉Dicentrarchus labrax〈/em〉) fillets and tools for flesh quality and shelf life monitoring”, Tsironi et al. 2019, JFE 262:83-91, doi.org/10.1016/j.jfoodeng.2019.05.010.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Carsten Posovszky, Mehtap Sirin, Eva Jacobsen, Myriam Lorenz, Klaus Schwarz, Anjona Schmidt-Choudhury, Catharina Schütz, Manfred Hönig, Klaus-Michael Debatin, Ansgar Schulz, Peter Möller, Thomas F. Barth〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Major histocompatibility complex class II (MHC II) is essential for adaptive immune response. We recently reported on disturbed adaptive mucosal immunity due to MHC II deficiency and prolonged enteropathy. Here, we share medical history, flow cytometric analysis of blood lymphocytes, immunohistopathology, and fecal analysis of seven genetically confirmed patients with MHC II deficiency suffering from enteropathy. Data on flow cytometric analysis of HLA-DR expression on monocytes and B cells before hematopoietic stem cell transplantation (HSCT) and after 〈em〉in-vitro〈/em〉 stimulation is shown. The course of immune reconstitution after HSCT of MHC II deficient patients in comparison to severe combined immunodeficiency (SCID) patients is described. In addition, immunohistopathology illustrating CD4 and CD8 T cell infiltration, absence of B lymphocytes and plasma cells, and disturbed immunoglobulin expression in the gut as well as absent HLA-DR expression in the liver is shown. Furthermore, data from fecal analysis such as stool fat, nitrogen, and water fraction as well as faecal markers such as alpha-1-antitrypsin, pancreas specific elastase 1, eosinophilic protein X (EPX), and beta defensin 2 are presented. Altogether this data demonstrates the complex phenotype of MHC II deficiency. The data can be valuable for researchers interested in mucosal immunity. For further interpretation of the data presented in this article, please see the research article “Persisting enteropathy and disturbed adaptive mucosal immunity due to MHC class II deficiency”[1].〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Estefanía Alfaro Mejía, Humberto Loaiza Correa, Édinson Franco Mejía, Andrés David Restrepo Girón, Sandra Esperanza Nope Rodríguez〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉〈em〉This article presents a dataset for thermal characterization of photovoltaic systems to identify snail trails and hot spot failures. This dataset has 277 thermographic aerial images that were acquired by a Zenmuse XT IR camera (7-13〈/em〉 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"〉〈mrow〉〈mi〉μ〈/mi〉〈mi〉m〈/mi〉〈/mrow〉〈/math〉 〈em〉wavelength) from a DJI Matrice 100〈/em〉 〈sup〉〈em〉1〈/em〉〈/sup〉〈em〉drone (quadcopter). Additionally, our dataset includes the next environmental measurements: temperature, wind speed, and irradiance. The experimental set up consisted in a photovoltaic array of 4 serial monocrystalline Si panels (string) and an electronic equipment emulating a real load. The conditions for images acquisition were stablished in a flight protocol in which we defined altitude, attitude, and weather conditions.〈/em〉〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Dongjing Li, Jianghua Liu, Yang Wang, Aixia Wu, Ruolin Ruan, Zeping Li, Zhimou Xu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉GaN is one of the most promising materials for high PEC efficiency to produce clean, renewable hydrogen in an ecofriendly manner [1], [2], [3], [4]. Trough assays of nanoporous gallium nitride (GaN) photoelectrode, we recently demonstrated an improved PEC efficiency and photocurrent density of nanoporous GaN photoelectrode by 470 % times with respect to planar counterpart [5]. Here, we report original data acquired under UV-visible spectrometer, X-ray diffraction (XRD), room temperature PL measurements and PEC measurements, based on the characterization of different sapphire substrate, different GaN samples and different GaN photoelectrodes. The optical properties and photoelectrochemical properties of the corresponding samples and possible mechanisms are presented, which is freely available [5]. The data can be valuable for researchers interested in photoelectrochemical water splitting, as well as to researchers developing fabrication of nanoporous photoelectrode. For more insight please see the research article “A nanoporous GaN photoelectrode on patterned sapphire substrates for high-efficiency photoelectrochemical water splitting”, 〈a href="https://doi.org/10.1016/j.jallcom.2019.06.234" target="_blank"〉https://doi.org/10.1016/j.jallcom.2019.06.234〈/a〉.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Zhanni Luo, Yu Wang〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Data in this article revealed the eye movement differences of visualizers and verbalizers in viewing four pictures-in-text by analyzing gaze path and fixation data (fixation duration, fixation counts and the average time on each fixation). After imported the documents into Tobii eye-tracker, authors triggered participants’ natural reading habits, recorded their eye movement data, and predicted participants as visualizers or verbalizers based on the Felder and Silverman Learning Style Model (FSLSM). Comparing the predictions with self-report results tested by the Index of Learning Styles (ILS) questionnaire, authors got the accuracy results of using eye-tracking technology in identifying visualizers and verbalizers. The data revealed natural preferences of people with different styles, and it can be used in future studies in the field of adaptive learning systems, individual differences, neuroscience in reading habits, and individualized instruction.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Nicholas A. Howell, Jack V. Tu, Rahim Moineddin, Hong Chen, Anna Chu, Perry Hystad, Gillian L. Booth〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Individuals’ risk for cardiovascular disease is shaped by lifestyle factors such as participation in physical activity. Some studies have suggested that rates of physical activity may be higher in walkable neighborhoods that are more supportive of engaging in physical activity in daily life. However, walkable neighborhoods may also contain increased levels of traffic-related air pollution (TRAP). Traffic-related air pollution, often measured through a surrogate marker (e.g. NO〈sub〉2〈/sub〉) has been associated cardiovascular disease risk and risk factors [1], [2], [3], [4]. The higher levels of TRAP in walkable neighborhoods may in turn increase the likelihood of developing conditions like hypertension and diabetes. Our recent work assessed how walkability and TRAP jointly affect the odds of diabetes and hypertension in a sample of community-dwelling adults from Southern Ontario, Canada [5]. This article contains additional data on the probability and odds of hypertension and diabetes among different populations according to their walkability and TRAP exposures. Data on cardiovascular risk factors were collected using health administrative databases and environmental exposures were assessed using national land use regression models predicting ground level concentrations of NO〈sub〉2〈/sub〉 and validated walkability indices. The included data were generated using logistic regression accounting for exposures, covariates, and neighborhood clustering. These data may be used as primary data in future health risk assessments and systematic reviews, or to aid in the design of studies examining interactions between built environment and TRAP exposures (e.g. sample size calculations).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Diletta Di Mitri, Michela Mirenda, Jelena Vasilevska, Arianna Calcinotto, Nicolas Delaleu, Ajinkya Revandkar, Veronica Gil, Gunther Boysen, Marco Losa, Simone Mosole, Emiliano Pasquini, Rocco D’Antuono, Michela Masetti, Elena Zagato, Giovanna Chiorino, Paola Ostano, Andrea Rinaldi, Letizia Gnetti, Mariona Graupera, Ana Raquel Martins Figueiredo Fonseca〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Tumor-associated macrophages (TAMs) represent a major component of the tumor microenvironment supporting tumorigenesis. TAMs re-education has been proposed as a strategy to promote tumor inhibition. However, whether this approach may work in prostate cancer is unknown. Here we find that 〈em〉Pten〈/em〉-null prostate tumors are strongly infiltrated by TAMs expressing C-X-C chemokine receptor type 2 (CXCR2), and activation of this receptor through CXCL2 polarizes macrophages toward an anti-inflammatory phenotype. Notably, pharmacological blockade of CXCR2 receptor by a selective antagonist promoted the re-education of TAMs toward a pro-inflammatory phenotype. Strikingly, CXCR2 knockout monocytes infused in 〈em〉Pten〈/em〉〈sup〉pc−/−〈/sup〉; 〈em〉Trp53〈/em〉〈sup〉pc−/−〈/sup〉 mice differentiated in tumor necrosis factor alpha (TNF-α)-releasing pro-inflammatory macrophages, leading to senescence and tumor inhibition. Mechanistically, 〈em〉PTEN〈/em〉-deficient tumor cells are vulnerable to TNF-α-induced senescence, because of an increase of 〈em〉TNFR1〈/em〉. Our results identify TAMs as targets in prostate cancer and describe a therapeutic strategy based on CXCR2 blockade to harness anti-tumorigenic potential of macrophages against this disease.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309726-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): John D. Gagnon, Robin Kageyama, Hesham M. Shehata, Marlys S. Fassett, Darryl J. Mar, Eric J. Wigton, Kristina Johansson, Adam J. Litterman, Pamela Odorizzi, Dimitre Simeonov, Brian J. Laidlaw, Marisella Panduro, Sana Patel, Lukas T. Jeker, Margaret E. Feeney, Michael T. McManus, Alexander Marson, Mehrdad Matloubian, Shomyseh Sanjabi, K. Mark Ansel〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Coordinate control of T cell proliferation, survival, and differentiation are essential for host protection from pathogens and cancer. Long-lived memory cells, whose precursors are formed during the initial immunological insult, provide protection from future encounters, and their generation is the goal of many vaccination strategies. microRNAs (miRNAs) are key nodes in regulatory networks that shape effective T cell responses through the fine-tuning of thousands of genes. Here, using compound conditional mutant mice to eliminate miR-15/16 family miRNAs in T cells, we show that miR-15/16 restrict T cell cycle, survival, and memory T cell differentiation. High throughput sequencing of RNA isolated by cross-linking immunoprecipitation of AGO2 combined with gene expression analysis in miR-15/16-deficient T cells indicates that these effects are mediated through the direct inhibition of an extensive network of target genes within pathways critical to cell cycle, survival, and memory.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309684-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Mingyi Chen, Ouyang Dongxu, Jiahao Liu, Jian Wang〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The data presented in this article are related to research article “Investigation on thermal and fire propagation behaviors of multiple lithium-ion batteries within the package” [1]. This data article provides the data information including the experiment pictures, flame temperatures, pressure and heat flux sensors temperatures, and gas concentrations of 6×6 batteries and 10×10 batteries. The video of the whole thermal and fire propagation behaviors of 6×6 batteries is also provided.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Yahaya Gavamukulya, Esther N. Maina, Amos M. Meroka, Hany A. El-Shemy, Gabriel Magoma, Fred Wamunyokoli〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this article, we present data on the anticancer activities of green synthesized silver nanoparticles (AgNPs) from ethanolic extracts of fruits (AgNPs-F) and leaves (AgNPs-L) of 〈em〉Annona muricata〈/em〉 and standard anticancer drug 5-Fluorouracil (5-FU) on two cancer cell lines, i.e. cervical adenocarcinoma (HeLa cells) and prostate adenocarcinoma (PC3 cells) as well as on an immortalized normal prostate cell line, PNT1A. The cytotoxicity on the cells was determined by measuring the absorbance signal of resazurin dye. It has long been known that metabolically active cells change the resazurin from blue (oxidized) to red (reduced) forms, corresponding to the absorbance signals at a wavelength of 570nm (A570) and 600nm (A600) respectively, from which therefore the effects of any treatments on percentage cell viability/death can be elucidated. The raw data values of the treatments against the HeLa, PC3 and PNT1A cells are shown in the different Tables. Examples of how the data can be analyzed have been illustrated using different growth inhibition curves. The data can be used by academics, students, and researchers working on development of anticancer drugs.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Jaeyres Jani, Zainal Arifin Mustapha, Norfazirah Binti Jamal, Cheronie Shely Stanis, Chin Kai Ling, Richard Avoi, Naing Oo Tha, Valentine Gantul, Daisuke Mori, Kamruddin Ahmed〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉A 〈em〉Mycobacterium tuberculosis〈/em〉 strain SBH162 was isolated from a 49-year-old male with pulmonary tuberculosis. GeneXpert MDR/RIF identified the strain as rifampicin-resistant 〈em〉M. tuberculosis〈/em〉. The whole genome sequencing was performed using Illumina HiSeq 4000 system to further investigate and verify the mutation sites of the strain through genetic analyses namely variant calling using bioinformatics tools. The 〈em〉de novo〈/em〉 assembly of genome generated 100 contigs with N50 of 156,381bp. The whole genome size was 4,343,911 bp with G+C content of 65.58% and consisted of 4,306 predicted genes. The mutation site, S450L, for rifampicin resistance was detected in the 〈em〉rpoB〈/em〉 gene. Based on the phylogenetic analysis using the Maximum Likelihood method, the strain was identified as belonging to the Europe America Africa lineage (Lineage 4). The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number SMOE00000000.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Alexander Matul, Andrea Abelmann, Rainer Gersonde〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present an extensive dataset on the modern radiolarian distribution in new samples of the surface sediments from the North Pacific and Bering Sea north of 38°N. Samples came from the RV Sonne cruises SO201-2 and SO202-1 in 2009 within the KALMAR II and INOPEX projects [1], [2]. We have analyzed 46 surface sediment samples from the multicorers following the standard laboratory treatment, preparation of the micropaleontological slides, and counting of the radiolarian tests under the microscope [3], [4]. List of species consists of two hundred eight radiolarian taxa. During the routine counting, we made the microphotographs of radiolarians. Our dataset consists of three data files: 1) coordinates of stations, 2) list of the radiolarian taxa with microphotographs, 3) data on the raw counts of the radiolarian tests per 1 slide, and calculated total radiolarian abundances and taxa percentages.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Hongjia Zhang, Antoine Jérusalem, Enrico Salvati, Chrysanthi Papadaki, Kai Soon Fong, Xu Song, Alexander M. Korsunsky〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Diffraction data were collected using synchrotron X-ray scattering (sXRD) and electron back-scattered diffraction (EBSD) during 〈em〉in situ〈/em〉 tensile-compressive deformation of Mg alloy AZ31B dogbone samples. The onset and evolution of twinning and detwinning were monitored based on intensity changes in sXRD 2D scattering patterns (which also provided average elastic strain values through the calculation of orientation-specific lattice spacing changes), and EBSD, that revealed the micro-scale grain morphology changes. The observations were interpreted and analysed with the help of crystal plasticity finite element modelling (CP-FEM), as reported in the published article (https://doi.org/10.1016/j.ijplas.2019.02.018).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Adnan Amin-Safwan, Mohd Pauzi Mardhiyyah, Mohd Affendi Izzah-Syafiah, Harman Muhd-Farouk, Hidayah Manan, Hairul Hafiz Mahsol, Musa Nadirah, Mhd Ikhwanuddin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This article investigated how crabs responded to different culture salinities through ovarian maturation stages using combination of external morphology (ovarian coloration and gonadosomatic index), and histological assessment (oocyte structures and diameter sizes). A total of sixty immature crabs were sampled from coastal water of Setiu Wetlands, Kuala Nerus, Terengganu, Peninsular Malaysia, and were introduced to limb autotomy technique in order to induce molt. Crabs were reared until successfully molted, and leaves prior to hardened shell, before proceed with salinities acclimatization prior to salinity treatments (10, 20 and 30 ppt). Five crabs were randomly selected every 15 days throughout 60-day of culture (Day 15, 30, 45 and 60) for the assessment. The different between each ovarian maturation stages was recorded based on the color appearances, and Kruskal-Wallis analysis were done between gonadosomatic index and oocyte diameter sizes with different salinity treatments. Part of the data is associated with the recent articles [1], [2] and provided here as raw data of Supplementary materials.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Joseph A. Hakim, Casey D. Morrow, Stephen A. Watts, Asim K. Bej〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉We present high-throughput amplicon sequence (HTS) datasets of the microbial metacommunity DNA of the gut tissue and the gut digesta of naturally occurring (〈em〉n〈/em〉 = 3) and laboratory aquaculture (〈em〉n〈/em〉 = 2) green sea urchins, 〈em〉Lytechinus variegatus.〈/em〉 The HTS datasets were generated on an Illumina MiSeq by targeting the amplicons of the V4 region of the 16S rRNA gene. After the raw sequences were quality checked and filtered, 88% of the sequence reads were subjected to bioinformatics analyses to generate operation taxonomic units (OTUs), which were then verified for saturation by using rarefaction analysis at a 3% sequence variation. Further, the OTUs were randomly subsampled to the minimum sequence count values. Then, the FASTA-formatted representative sequences of the microbiota were assigned taxonomic identities through multiple databases using the SILVA ACT: Alignment, Classification and Tree Service (〈a href="http://www.arb-silva.de/aligner" target="_blank"〉www.arb-silva.de/aligner〈/a〉). The HTS datasets of this metagenome can be accessed from the BioSample Submission Portal (〈a href="https://www.ncbi.nlm.nih.gov/bioproject/" target="_blank"〉https://www.ncbi.nlm.nih.gov/bioproject/〈/a〉〈u〉)〈/u〉 under the BioProject IDs PRJNA291441 and PRJNA326427.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Joshua J. Gruber, Justin Chen, Benjamin Geller, Natalie Jäger, Andrew M. Lipchik, Guangwen Wang, Allison W. Kurian, James M. Ford, Michael P. Snyder〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Individuals with a single functional copy of the 〈em〉BRCA2〈/em〉 tumor suppressor have elevated risks for breast, ovarian, and other solid tumor malignancies. The exact mechanisms of carcinogenesis due to 〈em〉BRCA2〈/em〉 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function (“BRCA2-crisis”), which may contribute to disease. Here, we establish an 〈em〉in vitro〈/em〉 model for BRCA2-crisis that demonstrates chromatin remodeling and activation of an NF-κB survival pathway in response to transient BRCA2 depletion. Mechanistically, we identify BRCA2 chromatin binding, histone acetylation, and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis. These chromatin alterations are reflected in transcriptional profiles of pre-malignant tissues from 〈em〉BRCA2〈/em〉 carriers and, therefore, may reflect natural steps in human disease. By modeling BRCA2-crisis 〈em〉in vitro〈/em〉, we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309611-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Adam J. Vogrin, Neil I. Bower, Menachem J. Gunzburg, Sally Roufail, Kazuhide S. Okuda, Scott Paterson, Stephen J. Headey, Steven A. Stacker, Benjamin M. Hogan, Marc G. Achen〈/p〉 〈div〉 〈h6〉Summary〈/h6〉 〈p〉Lymphatic vascular development establishes embryonic and adult tissue fluid balance and is integral in disease. In diverse vertebrate organs, lymphatic vessels display organotypic function and develop in an organ-specific manner. In all settings, developmental lymphangiogenesis is considered driven by vascular endothelial growth factor (VEGF) receptor-3 (VEGFR3), whereas a role for VEGFR2 remains to be fully explored. Here, we define the zebrafish Vegf/Vegfr code in receptor binding studies. We find that while Vegfd directs craniofacial lymphangiogenesis, it binds Kdr (a VEGFR2 homolog) but surprisingly, unlike in mammals, does not bind Flt4 (VEGFR3). Epistatic analyses and characterization of a 〈em〉kdr〈/em〉 mutant confirm receptor-binding analyses, demonstrating that Kdr is indispensible for rostral craniofacial lymphangiogenesis, but not caudal trunk lymphangiogenesis, in which Flt4 is central. We further demonstrate an unexpected yet essential role for Kdr in inducing lymphatic endothelial cell fate. This work reveals evolutionary divergence in the Vegf/Vegfr code that uncovers spatially restricted mechanisms of developmental lymphangiogenesis.〈/p〉 〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309593-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Susan Lindtner, Rinaldo Catta-Preta, Hua Tian, Linda Su-Feher, James D. Price, Diane E. Dickel, Vanille Greiner, Shanni N. Silberberg, Gabriel L. McKinsey, Michael T. McManus, Len A. Pennacchio, Axel Visel, Alex S. Nord, John L.R. Rubenstein〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of 〈em〉Dlx1&2〈/em〉 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with 〈em〉in situ〈/em〉 hybridization (ISH), and 〈em〉in vivo〈/em〉 and 〈em〉in vitro〈/em〉 studies of regulatory element (RE) function. This revealed the DLX-organized gene regulatory network at genomic, cellular, and spatial levels in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to 〈em〉Dlx1&2〈/em〉 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S221112471930912X-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Ilya E. Nifant'ev, Andrey V. Shlyakhtin, Maxim A. Kosarev, Pavel D. Komarov, Stanislav G. Karchevsky, Pavel V. Ivchenkoa〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The data presented in this paper are related to the research article entitled "Mechanistic study of transesterification in TBD-catalyzed ring-opening polymerization of methyl ethylene phosphate" [1]. In this data article, we present 3D molecular information of 76 structures for TBD-catalyzed transformations of methyl ethylene phosphate (MeOEP) and trimethyl phosphate (TMP). We also present 3D molecular information for 24 complexes that model the reaction profile of transesterification of poly(MeOEP) and TMP catalyzed by 2,6-di-〈em〉tert〈/em〉-butyl-4-methylphenoxy magnezium species, complementing the article "Mechanistic insights of BHT-Mg-catalyzed ethylene phosphate’s coordination ring-opening polymerization: DFT modeling and experimental data" [2]. The data contains stationary points and transition states (TS) along the first propagation step of MeOEP ring-opening polymerization (ROP) for alternative amide and donor-acceptor mechanisms, initiated by EtOH in the presence of TBD; stationary points and TS for MeOH and HOCH〈sub〉2〈/sub〉CH〈sub〉2〈/sub〉OP(O)(OMe)〈sub〉2〈/sub〉 initiated ROP of MeOEP; and stationary points and TS for transesterification of poly(MeOEP) and TMP. In addition, the data contains stationary points and transition states for the ROP of MeOEP and transesterification of poly(MeOEP) and TMP catalyzed by 2,6-di-〈em〉tert〈/em〉-butylphenoxy magnesium complex. The data are provided in a PDB format that can be used for further studies.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Shaokun He, Shenglian Guo, Kebing Chen, Lele Deng, Zhen Liao, Feng Xiong, Jiabo Yin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The dataset contains reservoir characteristic parameters, streamflow series of reservoirs in the upper Yangtze River, the standard operating rules (SORs) and the seasonal top of buffer pools (seasonal TBPs) for these reservoirs, which were provided by the Yangtze River Commission. Moreover, annual hydropower of these reservoirs is tested to evaluate operation performance. These research materials are related to the research article in 〈em〉Advances in Water Resources〈/em〉, entitled ‘Optimal impoundment operation for cascade reservoirs coupling parallel dynamic programming with importance sampling and successive approximation’ [1]. The dataset could be used to derive optimal operating rules to explore the potential benefits of water resources via our proposed algorithm (importance sampling – parallel dynamic programming, IS-PDP) in different runoff scenarios. It can also be further applied for water resources management and other potential users.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 28 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Ibrahim Sadek, Penny Chong, Shafiq Ul Rehman, Yuval Elovici, Alexander Binder〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This article presents a dataset for studying the detection of obfuscated malware in volatile computer memory. Several obfuscated reverse remote shells were generated using Metasploit-Framework, Hyperion, and PEScrambler tools. After compromising the host, Memory snapshots of a Windows 10 virtual machine were acquired using the open-source Rekall's WinPmem acquisition tool. The dataset is complemented by memory snapshots of uncompromised virtual machines. The data includes a reference for all running processes as well as a mapping for the designated malware running inside the memory. The datasets are available in the article, for advancing research towards the detection of obfuscated malware from volatile computer memory during a forensic analysis.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 26〈/p〉 〈p〉Author(s): Natal Henrique Cordeiro, Emerson Carlos Pedrino〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This paper presents in detail the methodology for the detection and tracking of dynamic objects from the article in press (A new methodology applied to dynamic object detection and tracking systems for visually impaired people [1]). In order to validate this methodology, four different architectures have been designed in this paper. These architectures have implemented the techniques of pattern recognition, optical flow, background subtraction and color tracking to enable comparison and to see which is the most appropriate in a given environment. In this paper we also present a method created to quantify the effectiveness of each architecture implemented.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Riccardo Mel, Luca Carniello, Luigi D'Alpaos〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉This data article includes the dataset of wind setup in the Venice lagoon computed by means of a 2-D hydrodynamic model. The capability of the model to reproduce the hydrodynamic regime of the lagoon has been extensively investigated, with particular attention to the calibration of the wind shear stress at the water surface, in order to precisely characterize the contribute of wind setup on the water level estimation inside the lagoon.〈/p〉 〈p〉We analyze the wind setup induced considering all the reliable wind speeds (with step of 1 m/s) and wind directions (with step of 30°) potentially blowing over the Venice lagoon, comparing the results obtained considering the present not-regulated configuration of the lagoon (pre-Mo.S.E. scenario) to the regulated configuration (post-Mo.S.E. scenario), which refers to the hydrodynamic regime when the Mo.S.E. movable barriers will be operational. The analysis shows that the wind setup significantly increases when the gates at the three inlets of the Venice lagoon are regulated, up to exceeding four times the pre-Mo.S.E. scenario. We deem this result is of paramount importance for the management of the Mo.S.E. barriers and for the definition of their operating strategy aiming at preventing the flooding at all the urban settlements of the lagoon.〈/p〉 〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 22 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Dalia Daggag, Jovian Lazare, Tandabany Dinadayalane〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this data article, M06-2X/6-31G(d) level optimized geometries of complexes of tyrosine conformers binding with graphene sheets are shown in top and side views with selected non-bonding distances. The images of frontier molecular orbitals from HOMO-15 to LUMO+15 of the complexes involving graphene with tyrosine conformers are presented and the isovalue is 0.003 au. For some complexes involving small graphene, the orbitals are from HOMO-5 to LUMO+5. The molecular orbitals highlighted with frames show obvious overlaps between the fragments. Total energies of small and large graphene (〈strong〉G〈/strong〉〈sub〉〈strong〉S〈/strong〉〈/sub〉 and 〈strong〉G〈/strong〉〈sub〉〈strong〉L〈/strong〉〈/sub〉) and selected tyrosine conformers in gas and aqueous phases obtained at M06-2X/6-31G(d) level are given. The data also include total energies of all complexes in the gas phase and the aqueous phase, binding energies, BSSE (basis set superposition error) correction, and BSSE-corrected binding energies in gas phase and solvation effect on the binding energies obtained at M06-2X/6-31G(d) level. Mulliken charges of tyrosine conformers in gas and aqueous phases, and the deformation energy for tyrosine and graphene in the gas phase complexes are provided. The values of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) and HOMO-LUMO energy gaps for some of graphene-tyrosine complexes that were not reported in the article [1] are given. The data is related to the research article “Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation” [1].〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Luis Andrés Leal, Dayana Donneys-Victoria, Fiderman Machuca-Martínez〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉Electrocoagulation consists of the in-situ generation of the coagulant by the electro dissolution of sacrificial electrodes (Mg and Al). This technique, besides being normally used for water treatment, can be used to synthesize Layered Double Hydroxides (LDH) or Hydrotalcites (HT) such as green rust, MgAlCl/LDH, and other oxides as Magnetite. The HT has a high tendency for water in the interlayer to be replaced by anions, these exchange characteristics generate a high interest in the fields of drug administration, photodegradation, catalyst supports, supercapacitors, and water oxidation. There are several routes of synthesis for these compounds such as co-precipitation, hydrolysis of urea, hydrothermal treatment and a novel route by electrocoagulation (EC).〈/p〉 〈p〉This work discloses the data of the energy consumption at laboratory-scale production in the synthesis of hydrotalcite (HT) or Layered Double Hydroxides (LDH) by electrocoagulation, the values obtained through these experiments are intended to provide support due to the lack of information on the energy consumption of this novel production method. Aluminum and AZ31 electrodes were used as a cations source during two- and four-hours operation, at 50 °C with 5 mA cm〈sup〉−2〈/sup〉 of current density, and 5 minutes of polarity change for Aluminum and 8 minutes for AZ31 (Magnesium alloy).〈/p〉 〈/div〉 〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Patrícia M. Silva, Charles Puerner, Agnese Seminara, Martine Bassilana, Robert A. Arkowitz〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉During symmetry breaking, the highly conserved Rho GTPase Cdc42 becomes stabilized at a defined site via an amplification process. However, little is known about how a new polarity site is established in an already asymmetric cell—a critical process in a changing environment. The human fungal pathogen 〈em〉Candida albicans〈/em〉 switches from budding to filamentous growth in response to external cues, a transition controlled by Cdc42. Here, we have used optogenetic manipulation of cell polarity to reset growth in asymmetric filamentous 〈em〉C. albicans〈/em〉 cells. We show that increasing the level of active Cdc42 on the plasma membrane results in disruption of the exocyst subunit Sec3 localization and a striking 〈em〉de novo〈/em〉 clustering of secretory vesicles. This new cluster of secretory vesicles is highly dynamic, moving by hops and jumps, until a new growth site is established. Our results reveal that secretory vesicle clustering can occur in the absence of directional growth.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309660-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Xiao Yu, Bo Li, Geng-Jen Jang, Shan Jiang, Daohong Jiang, Jyan-Chyun Jang, Shu-Hsing Wu, Libo Shan, Ping He〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Proper transcriptome reprogramming is critical for hosts to launch an effective defense response upon pathogen attack. How immune-related genes are regulated at the posttranscriptional level remains elusive. We demonstrate here that P-bodies, the non-membranous cytoplasmic ribonucleoprotein foci related to 5′-to-3′ mRNA decay, are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns (MAMPs). The DCP1-DCP2 mRNA decapping complex, a hallmark of P-bodies, positively regulates plant MAMP-triggered responses and immunity against pathogenic bacteria. MAMP-activated MAP kinases directly phosphorylate DCP1 at the serine〈sup〉237〈/sup〉 residue, which further stimulates its interaction with XRN4, an exonuclease executing 5′-to-3′ degradation of decapped mRNA. Consequently, MAMP treatment potentiates DCP1-dependent mRNA decay on a specific group of MAMP-downregulated genes. Thus, the conserved 5′-to-3′ mRNA decay elicited by the MAMP-activated MAP kinase cascade is an integral part of plant immunity. This mechanism ensures a rapid posttranscriptional downregulation of certain immune-related genes that may otherwise negatively impact immunity.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309581-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Guanming Wang, Takahisa Kouwaki, Masaaki Okamoto, Hiroyuki Oshiumi〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Excessive innate immune response is harmful to the host, and aberrant activation of the cytoplasmic viral RNA sensors RIG-I and MDA5 leads to autoimmune disorders. ZNF598 is an E3 ubiquitin ligase involved in the ribosome quality control pathway. It is also involved in the suppression of interferon (IFN)-stimulated gene (ISG) expression; however, its underlying mechanism is unclear. In this study, we show that ZNF598 is a negative regulator of the RIG-I-mediated signaling pathway, and endogenous ZNF598 protein binds to RIG-I. ZNF598 ubiquitin ligase activity is dispensable for the suppression of RIG-I signaling. Instead, ZNF598 delivers a ubiquitin-like protein FAT10 to the RIG-I protein, resulting in the inhibition of RIG-I polyubiquitination, which is required for triggering downstream signaling to produce type I IFN. Moreover, ZNF598-mediated suppression is abrogated by FAT10 knockout. Our data elucidate the mechanism by which ZNF598 inhibits RIG-I-mediated innate immune response.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309854-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Amber Tariq, JiaBei Lin, Meredith E. Jackrel, Christina D. Hesketh, Peter J. Carman, Korrie L. Mack, Rachel Weitzman, Craig Gambogi, Oscar A. Hernandez Murillo, Elizabeth A. Sweeny, Esin Gurpinar, Adam L. Yokom, Stephanie N. Gates, Keolamau Yee, Saurabh Sudesh, Jacob Stillman, Alexandra N. Rizo, Daniel R. Southworth, James Shorter〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Hsp104 is an AAA+ protein disaggregase, which can be potentiated via diverse mutations in its autoregulatory middle domain (MD) to mitigate toxic misfolding of TDP-43, FUS, and α-synuclein implicated in fatal neurodegenerative disorders. Problematically, potentiated MD variants can exhibit off-target toxicity. Here, we mine disaggregase sequence space to safely enhance Hsp104 activity via single mutations in nucleotide-binding domain 1 (NBD1) or NBD2. Like MD variants, NBD variants counter TDP-43, FUS, and α-synuclein toxicity and exhibit elevated ATPase and disaggregase activity. Unlike MD variants, non-toxic NBD1 and NBD2 variants emerge that rescue TDP-43, FUS, and α-synuclein toxicity. Potentiating substitutions alter NBD1 residues that contact ATP, ATP-binding residues, or the MD. Mutating the NBD2 protomer interface can also safely ameliorate Hsp104. Thus, we disambiguate allosteric regulation of Hsp104 by several tunable structural contacts, which can be engineered to spawn enhanced therapeutic disaggregases with minimal off-target toxicity.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309738-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Roberto Costa, Roberta Peruzzo, Magdalena Bachmann, Giulia Dalla Montà, Mattia Vicario, Giulia Santinon, Andrea Mattarei, Enrico Moro, Rubén Quintana-Cabrera, Luca Scorrano, Massimo Zeviani, Francesca Vallese, Mario Zoratti, Cristina Paradisi, Francesco Argenton, Marisa Brini, Tito Calì, Sirio Dupont, Ildikò Szabò, Luigi Leanza〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Wnt signaling affects fundamental development pathways and, if aberrantly activated, promotes the development of cancers. Wnt signaling is modulated by different factors, but whether the mitochondrial energetic state affects Wnt signaling is unknown. Here, we show that sublethal concentrations of different compounds that decrease mitochondrial ATP production specifically downregulate Wnt/β-catenin signaling 〈em〉in vitro〈/em〉 in colon cancer cells and 〈em〉in vivo〈/em〉 in zebrafish reporter lines. Accordingly, fibroblasts from a GRACILE syndrome patient and a generated zebrafish model lead to reduced Wnt signaling. We identify a mitochondria-Wnt signaling axis whereby a decrease in mitochondrial ATP reduces calcium uptake into the endoplasmic reticulum (ER), leading to endoplasmic reticulum stress and to impaired Wnt signaling. In turn, the recovery of the ATP level or the inhibition of endoplasmic reticulum stress restores Wnt activity. These findings reveal a mechanism that links mitochondrial energetic metabolism to the control of the Wnt pathway that may be beneficial against several pathologies.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309544-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Roja Babazadeh, Doryaneh Ahmadpour, Song Jia, Xinxin Hao, Per Widlund, Kara Schneider, Frederik Eisele, Laura Dolz Edo, Gertien J. Smits, Beidong Liu, Thomas Nystrom〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Spatial sorting to discrete quality control sites in the cell is a process harnessing the toxicity of aberrant proteins. We show that the yeast t-snare phosphoprotein syntaxin5 (Sed5) acts as a key factor in mitigating proteotoxicity and the spatial deposition and clearance of IPOD (insoluble protein deposit) inclusions associates with the disaggregase Hsp104. Sed5 phosphorylation promotes dynamic movement of COPII-associated Hsp104 and boosts disaggregation by favoring anterograde ER-to-Golgi trafficking. Hsp104-associated aggregates co-localize with Sed5 as well as components of the ER, 〈em〉trans〈/em〉 Golgi network, and endocytic vesicles, transiently during proteostatic stress, explaining mechanistically how misfolded and aggregated proteins formed at the vicinity of the ER can hitchhike toward vacuolar IPOD sites. Many inclusions become associated with mitochondria in a HOPS/vCLAMP-dependent manner and co-localize with Vps39 (HOPS/vCLAMP) and Vps13, which are proteins providing contacts between vacuole and mitochondria. Both Vps39 and Vps13 are required also for efficient Sed5-dependent clearance of aggregates.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S221112471930957X-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Tiffany Wu, Borislav Dejanovic, Vineela D. Gandham, Alvin Gogineni, Rose Edmonds, Stephen Schauer, Karpagam Srinivasan, Melanie A. Huntley, Yuanyuan Wang, Tzu-Ming Wang, Maj Hedehus, Kai H. Barck, Maya Stark, Hai Ngu, Oded Foreman, William J. Meilandt, Justin Elstrott, Michael C. Chang, David V. Hansen, Richard A.D. Carano〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Complement pathway overactivation can lead to neuronal damage in various neurological diseases. Although Alzheimer’s disease (AD) is characterized by β-amyloid plaques and tau tangles, previous work examining complement has largely focused on amyloidosis models. We find that glial cells show increased expression of classical complement components and the central component C3 in mouse models of amyloidosis (PS2APP) and more extensively tauopathy (TauP301S). Blocking complement function by deleting C3 rescues plaque-associated synapse loss in PS2APP mice and ameliorates neuron loss and brain atrophy in TauP301S mice, improving neurophysiological and behavioral measurements. In addition, C3 protein is elevated in AD patient brains, including at synapses, and levels and processing of C3 are increased in AD patient CSF and correlate with tau. These results demonstrate that complement activation contributes to neurodegeneration caused by tau pathology and suggest that blocking C3 function might be protective in AD and other tauopathies.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309647-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 19 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Camilo Montes, Andres Felipe Rodriguez-Corcho, German Bayona, Natalia Hoyos, Sebastian Zapata, Agustin Cardona〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This contribution contains a GPlates digital reconstruction of the northern Andes and southern Caribbean margin for the last 90 Ma. It is built using different strain datasets fully described in “Continental Margin Response to Multiple Arc-Continent Collisions: the Northern Andes-Caribbean Margin” [1]. Two digital reconstructions are included here: one is a rigid block reconstruction, and the other is a continuously closing polygon reconstruction digitized every one -million years. We placed the South and North American plates at the root of the reconstruction tree, so that the Andean blocks move with respect to the former, and the Caribbean Plate, and related intra-oceanic arcs with respect to the latter. These reconstructions can be used as templates to place in palinspastic space any dataset that can be represented by lines or points.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 19 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Han Liu, Peng Li, Jin Liu, Ziqi Lu, Ping Tang, Zhaojia Li, Baoqin Lin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The data presented herein are related to the research article entitled “Danhong Huayu Koufuye prevents venous thrombosis through antiinflammation via Sirtuin 1/NF-κB signaling pathway” [1]. This article describes the effect of Danhong Huayu Koufuye (DHK) on thrombus weight and blood coagulation indexes at the early and late stages of inferior vena cava stenosis-induced deep vein thrombosis in rats. In addition, the effect of DHK on blood cell counts and whole blood viscosity at the early stage were presented. The field dataset is made publicly available to enable critical or extended analyses.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 19 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Jorge Parraga-Alava, Kevin Cusme, Angélica Loor, Esneider Santander〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In this article we introduce a 〈em〉robusta〈/em〉 coffee leaf images dataset called RoCoLe. The dataset contains 1560 leaf images with visible red mites and spots (denoting coffee leaf rust presence) for infection cases and images without such structures for healthy cases. In addition, the data set includes annotations regarding objects (leaves), state (healthy and unhealthy) and the severity of disease (leaf area with spots). Images were all obtained in real-world conditions in the same coffee plants field using a smartphone camera. RoCoLe data set facilitates the evaluation of the performance of machine learning algorithms used in image segmentation and classification problems related to plant diseases recognition. The current dataset is freely and publicly available at 〈a href="https://doi.org/10.17632/c5yvn32dzg.2" target="_blank"〉https://doi.org/10.17632/c5yvn32dzg.2〈/a〉.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 19 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): S. Ghisaura, R. Melis, G. Biosa, D. Pagnozzi, H. Slavski, S. Uzzau, R. Anedda, M.F. Addis〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉We report the proteomic dataset of livers from 〈em〉Sparus aurata〈/em〉 exposed to low temperature during growth. Gilthead sea bream juveniles were reared in Recirculating Aquaculture Systems (RAS) and exposed to a temperature ramp made of two phases of four weeks each: a Cooling phase from 18 °C (t0) to 11 °C (t1) and a Cold Maintenance phase at 11 °C (t1-t2) in a 8 week feeding trial. At the end of the experiment, sea bream livers were collected and analyzed with a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry, peptide identification carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform, and label-free differential analysis.〈/p〉 〈p〉The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011059 [1], [2], [3]. The dataset described here is also related to the research article entitled “Liver proteomics of gilthead sea bream (〈em〉Sparus aurata〈/em〉) exposed to cold stress” [4].〈/p〉 〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 19 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Maria João Rodrigues, Ivo Monteiro, Chloé Placines, Viana Castañeda-Loaiza, Sylwester Ślusarczyk, Adam Matkowski, Catarina Pereira, Pedro Pousão-Ferreira, Luísa Custódio〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This data article includes data and analyses on the effect of different agronomic techniques on the production of 〈em〉Polygonum maritimu〈/em〉m L. (sea knotgrass), namely different salinity irrigation treatments (0, 100, 200, 300 and 600 mM of NaCl) and a multi-harvest regime, and their relation with the chemical profile (ultra-high-resolution mass spectrometry - UHRMS), 〈em〉in vitro〈/em〉 antioxidant [radical-scavenging activity (RSA) of DPPH and ABTS, copper chelating activity and ferric reducing antioxidant power] and anti-inflammatory (nitric oxide reduction on lipopolysaccharide-stimulated macrophages) activities. For further interpretation of the data presented in this work, please see the related research article “The irrigation salinity and harvesting affect the growth, chemical profile and biological activities of 〈em〉Polygonum maritimum〈/em〉 L.” (Rodrigues et al., 2019).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Aldobenedetto Zotti, Simona Zuppolini, Anna Borriello, Mauro Zarrelli〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The following data describe the thermal properties of two different typologies of Hyperbranched Polymers (HBPs): the first one is a polyester (HBPG – Hyperbranched Polymer Glassy) with a glass transition temperature (T〈sub〉g〈/sub〉) higher than room temperature (∼90 °C) whereas the second one is a polyamide ester (HBPR – Hyperbranched Polymer Rubbery) characterized by T〈sub〉g〈/sub〉 of about 20 °C. The nanocomposites manufactured using these HBPs as filler were characterized using Optical Microscopy and Differential Scanning Calorimetry. The raw data for the evaluation of fracture toughness properties are reported for the listed materials. This article provides data related to “The effect of Glassy and Rubbery Hyperbranched Polymers as Modifiers in Epoxy Aeronautical Systems” (Zotti et al.).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Sangyeob Lee, Jiseong Jang, Kyung Soo Cho, Yong-Jun Oh, Ki-Ha Hong, Choong-Heui Chung〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The authors have recently reported silver nanowire based Cu(In,Ga)Se〈sub〉2〈/sub〉 solar cells [1], [2]. Metal mesh based transparent electrodes other than the silver nanowire can be also employed or have a potential to provide a better performance for the solar cells. To select a suitable electrode for a solar cell among metal meshes, it is required to have data on the lateral collection length of charge carriers in the targeted cell. The method to determine the lateral collection has been reported in our previous publication [3]. Here, we report data on the effect of the light intensity during pre-white-light soaking on the lateral charge collection length for metal mesh transparent electrode based Cu(In,Ga)Se〈sub〉2〈/sub〉 solar cells.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Ruoyu Ma, Jianbo Yang, Steven Kelley, Benjamin W. Gung〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The shared data is the unpublished portion of the experimental section for the article with the title “NHC–Au(I) catalyzed enantioselective intramolecular [4 + 3] cycloaddition of furan propargyl esters”.[1] The preparation of the intermediates for chiral NHC-gold(I) complexes and the furan propargyl ester substrates are included in this article. The 〈sup〉1〈/sup〉H NMR and 〈sup〉13〈/sup〉C NMR spectra of the gold complexes 〈strong〉17a-19c〈/strong〉 and the X-ray crystal data of 〈strong〉17a〈/strong〉, 〈strong〉18a〈/strong〉 and cycloaddition product 〈strong〉24〈/strong〉 are also provided in this article or in Mendeley Data. Finally, the chiral HPLC spectra used to determine enantiomeric excess and Cartesian coordinates of the optimized structure of 〈strong〉25〈/strong〉 and 〈strong〉26〈/strong〉 calculated by DFT calculation are also presented in the article.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Sourav Saha, Lewis A. Owen, Elizabeth N. Orr, Marc W. Caffee〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉A comprehensive analysis of the variable temporal and spatial responses of tropical-subtropical high-altitude glaciers to climate change is critical for successful model predictions and environmental risk assessment in the Himalayan-Tibetan orogen. High-frequency Holocene glacier chronostratigraphies are therefore reconstructed in 79 glaciated valleys across the orogen using 519 published and 16 new terrestrial cosmogenic 〈sup〉10〈/sup〉Be exposure age dataset. Published 〈sup〉10〈/sup〉Be ages are compiled only for moraine boulders (excluding bedrock ages). These ages are recalculated using the latest ICE-D production rate calibration database and the scaling scheme models. Outliers for the individual moraine are detected using the Chauvenet's criterion. In addition, past equilibrium-line altitudes (ELAs) are determined using the area-altitude (AA), area accumulation ratio (AAR), and toe-headwall accumulation ratio (THAR) methods for each glacier advance. The modern maximum elevations of lateral moraines (MELM) are also used to estimate modern ELAs and as an independent check on mean ELAs derived using the above three methods. These data may serve as an essential archive for future studies focusing on the cryospheric and environmental changes in the Himalayan-Tibetan orogen. A more comprehensive analysis of the published and new 〈sup〉10〈/sup〉Be ages and ELA results and an exhaustive list of references are presented in Saha et al. (2019, High-frequency Holocene glacier fluctuations in the Himalayan-Tibetan orogen. Quaternary Science Reviews).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Olga Bukato, Olga Pobeguts, Daria Rakitina, Julia Baikova, Ivan Butenko, Artemy Silantyev, Gleb Fisunov, Vadim Govorun〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Crohn's disease (CD) is a type of inflammatory bowel disease (IDB). The endoscopic picture of Crohn's disease includes thickened submucosa, transmural inflammation, fissuring ulceration, and non-caseating granulomas. Intestinal microbiome dysbiosis has been described systematically in patients with IBD. In recent decades it was detailed that 〈em〉Escherichia coli〈/em〉, especially adherent-invasive 〈em〉E. coli〈/em〉 (AIEC) pathotype, has been implicated in the pathogenesis of IBD, including Crohn's disease [1]. In comparison with commensal strains of 〈em〉E. coli〈/em〉, AIEC strains have a large adhesive-invasive potential therefore its surface composition is of great interest. We presented a dataset of the membrane proteins of strains isolated from patients with Crohn's disease. From the set of 〈em〉Escherichia coli〈/em〉 isolated from Crohn's disease patients [2] we chose three isolates with strongest AIEC pathotype. We performed proteome-wide LC-MS analysis of membrane fraction of this isolates after invasion or adhesion-invasion to human intestinal CaCo-2 cell line and prior to this (control). The data including LC-MS/MS raw files and exported MaxQuant search results with fasta files were deposited to the PRIDE repository project accession PXD014250.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 26〈/p〉 〈p〉Author(s): H. Correa, Alvaro Garcia Muriel, D. Peña Lara〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Using the ac-calorimetry technique and the electric modulus formalism for analysis of ionic conductivity relaxation in crystalline 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.svg"〉〈mrow〉〈mi〉γ〈/mi〉〈/mrow〉〈/math〉-RbAg〈sub〉4〈/sub〉I〈sub〉5〈/sub〉, close to the 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.svg"〉〈mrow〉〈mi〉γ〈/mi〉〈/mrow〉〈/math〉 to 〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si3.svg"〉〈mrow〉〈mi〉β〈/mi〉〈/mrow〉〈/math〉 phase transition at 120 K, the temperature derivative of microscopic interaction energy for a single-mobile ion is proportional to the specific heat. The two different experimental techniques show that cooperative behavior drives the phase transition at 120 K (obey the same mechanism).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Tati Suryati Syamsudin, Hafsah Hafsah, Iriawati〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This data informs about the profile of volatile compound of coffee flower (Coffee arabica) from different locations with different annual rainfall by using gas chromatography - mass spectrometry (GC-MS). The volatile compounds were captured by solid phase micro extraction (SPME) methods. The extract then subjected to GC-MS for separation and identification of compounds. The profile of volatile compound was provided in, Table 1, Table 2, Tables 3 and 4.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Adam L. Burrack, Ellen J. Spartz, Jackson F. Raynor, Iris Wang, Margaret Olson, Ingunn M. Stromnes〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer resistant to immunotherapy. We create a PDA mouse model and show that neoantigen expression is required for intratumoral T cell accumulation and response to immune checkpoint blockade. By generating a peptide:MHC tetramer, we identify that PDA induces rapid intratumoral, and progressive systemic, tumor-specific T cell exhaustion. Monotherapy PD-1 or PD-L1 blockade enhances systemic T cell expansion and induces objective responses that require systemic T cells. However, tumor escape variants defective in IFNγ-inducible 〈em〉Tap1〈/em〉 and MHC class I cell surface expression ultimately emerge. Combination PD-1 + PD-L1 blockade synergizes therapeutically by increasing intratumoral KLRG1+Lag3−TNFα+ tumor-specific T cells and generating memory T cells capable of expanding to spontaneous tumor recurrence, thereby prolonging animal survival. Our studies support that PD-1 and PD-L1 are relevant immune checkpoints in PDA and identify a combination for clinical testing in those patients with neoantigen-specific T cells.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309635-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Raquel Buj, Chi-Wei Chen, Erika S. Dahl, Kelly E. Leon, Rostislav Kuskovsky, Natella Maglakelidze, Maithili Navaratnarajah, Gao Zhang, Mary T. Doan, Helen Jiang, Michael Zaleski, Lydia Kutzler, Holly Lacko, Yiling Lu, Gordon B. Mills, Raghavendra Gowda, Gavin P. Robertson, Joshua I. Warrick, Meenhard Herlyn, Yuka Imamura〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Reprogrammed metabolism and cell cycle dysregulation are two cancer hallmarks. p16 is a cell cycle inhibitor and tumor suppressor that is upregulated during oncogene-induced senescence (OIS). Loss of p16 allows for uninhibited cell cycle progression, bypass of OIS, and tumorigenesis. Whether p16 loss affects pro-tumorigenic metabolism is unclear. We report that suppression of p16 plays a central role in reprogramming metabolism by increasing nucleotide synthesis. This occurs by activation of mTORC1 signaling, which directly mediates increased translation of the mRNA encoding ribose-5-phosphate isomerase A (〈em〉RPIA〈/em〉), a pentose phosphate pathway enzyme. p16 loss correlates with activation of the mTORC1-RPIA axis in multiple cancer types. Suppression of RPIA inhibits proliferation only in p16-low cells by inducing senescence both 〈em〉in vitro〈/em〉 and 〈em〉in vivo〈/em〉. These data reveal the molecular basis whereby p16 loss modulates pro-tumorigenic metabolism through mTORC1-mediated upregulation of nucleotide synthesis and reveals a metabolic vulnerability of p16-null cancer cells.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719310009-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Mirunalini Ravichandran, Run Lei, Qin Tang, Yilin Zhao, Joun Lee, Liyang Ma, Stephanie Chrysanthou, Benjamin M. Lorton, Ales Cvekl, David Shechter, Deyou Zheng, Meelad M. Dawlaty〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉The Retinoid inducible nuclear factor (Rinf), also known as CXXC5, is a nuclear protein, but its functions in the context of the chromatin are poorly defined. We find that in mouse embryonic stem cells (mESCs), Rinf binds to the chromatin and is enriched at promoters and enhancers of 〈em〉Tet1〈/em〉, 〈em〉Tet2〈/em〉, and pluripotency genes. The Rinf-bound regions show significant overlapping occupancy of pluripotency factors Nanog, Oct4, and Sox2, as well as Tet1 and Tet2. We found that Rinf forms a complex with Nanog, Oct4, Tet1, and Tet2 and facilitates their proper recruitment to regulatory regions of pluripotency and 〈em〉Tet〈/em〉 genes in ESCs to positively regulate their transcription. Rinf deficiency in ESCs reduces expression of Rinf target genes, including several pluripotency factors and Tet enzymes, and causes aberrant differentiation. Together, our findings establish Rinf as a regulator of the pluripotency network genes and Tet enzymes in ESCs.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309842-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Richard J. Smith, Marilia H. Cordeiro, Norman E. Davey, Giulia Vallardi, Andrea Ciliberto, Fridolin Gross, Adrian T. Saurin〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases localize to an almost identical molecular space and yet they still manage to regulate unique pathways and processes. By switching or modulating the positions of PP1/PP2A-B56 at kinetochores, we show that their unique downstream effects are not due to either the identity of the phosphatase or its precise location. Instead, these phosphatases signal differently because their kinetochore recruitment can be either inhibited (PP1) or enhanced (PP2A) by phosphorylation inputs. Mathematical modeling explains how these inverse phospho-dependencies elicit unique forms of cross-regulation and feedback, which allows otherwise indistinguishable phosphatases to produce distinct network behaviors and control different mitotic processes. Furthermore, our genome-wide analysis suggests that these major phosphatase families may have evolved to respond to phosphorylation inputs in opposite ways because many other PP1 and PP2A-B56-binding motifs are also phospho-regulated.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309714-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Qiuli Liang, Quan Zheng, Yong Zuo, Yalan Chen, Jiao Ma, Peihua Ni, Jinke Cheng〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Brown adipose tissue (BAT) is a thermogenic organ that maintains body temperature and energy homeostasis. Transcriptional regulation plays an important role in the program of brown adipogenesis. However, it remains unclear how the transcriptional events are controlled in this program. In this study, we analyze an SENP2 BAT conditional knockout mouse model and find that SENP2-mediated de-SUMOylation is essential for BAT development. SENP2 catalyzes de-SUMOylation of cAMP response element-binding protein (CREB) to suppress Necdin expression, which induces brown adipocyte differentiation and brown adipogenesis. Mechanistically, we find that SUMOylation enhances CREB interaction with serine/threonine protein phosphatase 2A (PP2A) to de-phosphorylate CREB, which activates Necdin transcription. SENP2 deficiency enhances the expression of Necdin to inhibit brown adipocyte differentiation. Therefore, we reveal a crucial role of SENP2-mediated de-SUMOylation of CREB in suppression of Necdin expression during brown adipose development and brown adipogenesis.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309878-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Nergis Kara, Matthew R. Kent, Dominic Didiano, Kamya Rajaram, Anna Zhao, Emily R. Summerbell, James G. Patton〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Unlike the adult mammalian retina, Müller glia (MG) in the adult zebrafish retina are able to dedifferentiate into a “stem cell”-like state and give rise to multipotent progenitor cells upon retinal damage. We show that 〈em〉miR-216a〈/em〉 is downregulated in MG after constant intense light lesioning and that 〈em〉miR-216a〈/em〉 suppression is necessary and sufficient for MG dedifferentiation and proliferation during retina regeneration. 〈em〉miR-216a〈/em〉 targets the H3K79 methyltransferase Dot1l, which is upregulated in proliferating MG after retinal damage. Loss-of-function experiments show that Dot1l is necessary for MG reprogramming and mediates MG proliferation downstream of 〈em〉miR-216a〈/em〉. We further demonstrate that 〈em〉miR-216a〈/em〉 and Dot1l regulate MG-mediated retina regeneration through canonical Wnt signaling. This article reports a regulatory mechanism upstream of Wnt signaling during retina regeneration and provides potential targets for enhancing regeneration in the adult mammalian retina.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309659-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Hanna Sabelström, Rebecca Petri, Ksenya Shchors, Rahul Jandial, Christin Schmidt, Rohit Sacheva, Selma Masic, Edith Yuan, Trenten Fenster, Michael Martinez, Supna Saxena, Theodore P. Nicolaides, Shirin Ilkhanizadeh, Mitchel S. Berger, Evan Y. Snyder, William A. Weiss, Johan Jakobsson, Anders I. Persson〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Identifying cellular programs that drive cancers to be stem-like and treatment resistant is critical to improving outcomes in patients. Here, we demonstrate that constitutive extracellular signal-regulated kinase 1/2 (ERK1/2) activation sustains a stem-like state in glioblastoma (GBM), the most common primary malignant brain tumor. Pharmacological inhibition of ERK1/2 activation restores neurogenesis during murine astrocytoma formation, inducing neuronal differentiation in tumorspheres. Constitutive ERK1/2 activation globally regulates miRNA expression in murine and human GBMs, while neuronal differentiation of GBM tumorspheres following the inhibition of ERK1/2 activation requires the functional expression of miR-124 and the depletion of its target gene SOX9. Overexpression of miR124 depletes SOX9 〈em〉in vivo〈/em〉 and promotes a stem-like-to-neuronal transition, with reduced tumorigenicity and increased radiation sensitivity. Providing a rationale for reports demonstrating miR-124-induced abrogation of GBM aggressiveness, we conclude that reversal of an ERK1/2-miR-124-SOX9 axis induces a neuronal phenotype and that enforcing neuronal differentiation represents a therapeutic strategy to improve outcomes in GBM.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309751-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Carles Solà-Riera, Shawon Gupta, Kimia T. Maleki, Patricia González-Rodriguez, Dalel Saidi, Christine L. Zimmer, Sindhu Vangeti, Laura Rivino, Yee-Sin Leo, David Chien Lye, Paul A. MacAry, Clas Ahlm, Anna Smed-Sörensen, Bertrand Joseph, Niklas K. Björkström, Hans-Gustaf Ljunggren, Jonas Klingström〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Cytotoxic lymphocytes normally kill virus-infected cells by apoptosis induction. Cytotoxic granule-dependent apoptosis induction engages the intrinsic apoptosis pathway, whereas death receptor (DR)-dependent apoptosis triggers the extrinsic apoptosis pathway. Hantaviruses, single-stranded RNA viruses of the order 〈em〉Bunyavirales〈/em〉, induce strong cytotoxic lymphocyte responses in infected humans. Cytotoxic lymphocytes, however, are largely incapable of eradicating hantavirus-infected cells. Here, we show that the prototypic hantavirus, Hantaan virus (HTNV), induces TRAIL production but strongly inhibits TRAIL-mediated extrinsic apoptosis induction in infected cells by downregulating DR5 cell surface expression. Mechanistic analyses revealed that HTNV triggers both 26S proteasome-dependent degradation of DR5 through direct ubiquitination of DR5 and hampers DR5 transport to the cell surface. These results corroborate earlier findings, demonstrating that hantavirus also inhibits cytotoxic cell granule-dependent apoptosis induction. Together, these findings show that HTNV counteracts intrinsic and extrinsic apoptosis induction pathways, providing a defense mechanism utilized by hantaviruses to inhibit cytotoxic cell-mediated eradication of infected cells.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309702-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Shaun Egolf, Yann Aubert, Miriam Doepner, Amy Anderson, Alexandra Maldonado-Lopez, Gina Pacella, Jessica Lee, Eun Kyung Ko, Jonathan Zou, Yemin Lan, Cory L. Simpson, Todd Ridky, Brian C. Capell〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Self-renewing somatic tissues depend upon the proper balance of chromatin-modifying enzymes to coordinate progenitor cell maintenance and differentiation, disruption of which can promote carcinogenesis. As a result, drugs targeting the epigenome hold significant therapeutic potential. The histone demethylase, LSD1 (KDM1A), is overexpressed in numerous cancers, including epithelial cancers; however, its role in the skin is virtually unknown. Here we show that LSD1 directly represses master epithelial transcription factors that promote differentiation. LSD1 inhibitors block both LSD1 binding to chromatin and its catalytic activity, driving significant increases in H3K4 methylation and gene transcription of these fate-determining transcription factors. This leads to both premature epidermal differentiation and the repression of squamous cell carcinoma. Together these data highlight both LSD1’s role in maintaining the epidermal progenitor state and the potential of LSD1 inhibitors for the treatment of keratinocyte cancers, which collectively outnumber all other cancers combined.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309623-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Khadar Abdi, Gabriel Neves, Joon Pyun, Emre Kiziltug, Angelica Ahrens, Chay T. Kuo〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Specialized microenvironments, called niches, control adult stem cell proliferation and differentiation. The brain lateral ventricular (LV) neurogenic niche is generated from distinct postnatal radial glial progenitors (pRGPs), giving rise to adult neural stem cells (NSCs) and niche ependymal cells (ECs). Cellular-intrinsic programs govern stem versus supporting cell maturation during adult niche assembly, but how they are differentially initiated within a similar microenvironment remains unknown. Using chemical approaches, we discovered that EGFR signaling powerfully inhibits EC differentiation by suppressing multiciliogenesis. We found that EC pRGPs actively terminated EGF activation through receptor redistribution away from CSF-contacting apical domains and that randomized EGFR membrane targeting blocked EC differentiation. Mechanistically, we uncovered spatiotemporal interactions between EGFR and endocytic adaptor protein Numb. Ca〈sup〉2+〈/sup〉-dependent basolateral targeting of Numb is necessary and sufficient for proper EGFR redistribution. These results reveal a previously unknown cellular mechanism for neighboring progenitors to differentially engage environmental signals, initiating adult stem cell niche assembly.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S221112471930960X-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 8〈/p〉 〈p〉Author(s): Thomas Z. Young, Ping Liu, Guste Urbonaite, Murat Acar〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Although double-strand break (DSB) repair is essential for a cell’s survival, little is known about how DSB repair mechanisms are affected by age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a DSB repair mechanism. We measure SSA repair efficiency in young and old yeast cells and report a 23.4% decline in repair efficiency. This decline is not due to increased use of non-homologous end joining. Instead, we identify increased G1 phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. Expression of 3x〈em〉CLN2〈/em〉 leads to higher SSA repair efficiency in old cells compared with expression of 1x〈em〉CLN2〈/em〉, confirming the involvement of cell-cycle regulation in age-associated repair inefficiency. Examining how SSA repair efficiency is affected by sequence heterology, we find that heteroduplex rejection remains high in old cells. Our work provides insights into the links between single-cell aging and DSB repair efficiency.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309866-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 17 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Bo Jiang, Yu Zhang, Huifang Zhao, Tianyu Guo, Wenjuan Wu, Yongcan Jin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The data presented in this article are related to the research article entitled “Structure-antioxidant activity relationship of active oxygen catalytic lignin and lignin-carbohydrate complex” (Jiang et al.). It supplements the article with thermostability of milled wood lignin (MWL) and alkali-oxygen lignin (AOL), main substructures of lignin in rice straw, main products and yield of nitrobenzene oxidation of lignin-carbohydrate complexes (LCCs), Fourier transform infrared spectroscopy of LCCs, radical (ABTS·) scavenging ability of lignins and signal assignment of lignins and LCCs in nuclear magnetic resonance spectra (〈sup〉1〈/sup〉H, 〈sup〉13〈/sup〉C, 2D HSQC NMR). The dataset is made publicly available and can be useful for extending the structural and bioactive research and critical analyses of lignin and LCC.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 17 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Po-Chih Kuo, Yi-Li Tseng, Karl Zilles, Summit Suen, Simon B. Eickhoff, Juin-Der Lee, Philip E. Cheng, Michelle Liou〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉There is a growing interest in functional magnetic resonance imaging (fMRI) studies on connectivity networks in the brain when subjects are under exposure to natural sensory stimulation. Because of a complicated coupling between spontaneous and evoked brain activity under real-world stimulation, there is no critical mapping between the experimental inputs and corresponding brain responses. The dataset contains auditory fMRI scans and T1-weighted anatomical scans acquired under eyes-closed and eyes-open conditions. Within each scanning condition, the subject was presented 12 different sound clips, including human voices followed by animal vocalizations. The dataset is meant to be used to assess brain dynamics and connectivity networks under natural sound stimulation; it also allows for empirical investigation of changes in fMRI responses between eyes-closed and eyes-open conditions, between animal vocalizations and human voices, as well as between the 12 different sound clips during auditory stimulation. The dataset is a supplement to the research findings in the paper “Brain dynamics and connectivity networks under natural auditory stimulation” published in NeuroImage.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 14 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Tarek Sedki, Shehata Ali, Haroun A. Mohamed〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The Sol Hamed (SH) area is a part of the Arabian-Nubian Shield (ANS) ophiolites occurred within Onib-Sol Hamed suture zone in the southern Eastern Desert of Egypt. The ophiolitic assemblages in this area are represented by serpentinite, metagabbro and arc assemblages represented by metavolcanics. They later intruded by gabbroes and granites. The compatible trace elements (Cr = 2426–2709 ppm, Ni = 1657–2377 ppm and Co = 117–167 ppm) enrichment in SH serpentinites indicate derivation from a depleted mantle peridotite source. They show affinity to the typical metamorphic peridotites. The normative compositions reflect harzburgitic mantle source. Their Al〈sub〉2〈/sub〉O〈sub〉3〈/sub〉 contents (0.05–1.02 wt %) are akin to oceanic and active margin peridotites and Pan-African serpentinites. The Cr and TiO〈sub〉2〈/sub〉 contents indicate supra-subduction zone (SSZ) environment. Their Al〈sub〉2〈/sub〉O〈sub〉3〈/sub〉/SiO〈sub〉2〈/sub〉 and MgO/SiO〈sub〉2〈/sub〉 ratios support the SSZ affinity and are similar to ANS peridotites with fore-arc setting. Moreover, their Al〈sub〉2〈/sub〉O〈sub〉3〈/sub〉 and CaO depletion is typical of fore-arc peridotites.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 15 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Omar Narvaez-Delgado, Gilberto Rojas-Vite, Ricardo Coronado-Leija, Alonso Ramirez-Manzanares, José Luis Marroquın, Ramses Noguez-Imm, Marcos L. Aranda, Benoit Scherrer, Jorge Larriva-Sahd, Luis Concha〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to infer microstructural characteristics of tissue, particularly in cerebral white matter. Histological validation of the metrics derived from dMRI methods are needed to fully characterize their ability to capture biologically-relevant histological features non-invasively. The data described here were used to correlate metrics derived from dMRI and quantitative histology in an animal model of axonal degeneration (“Histological validation of per-bundle water diffusion metrics within a region of fiber crossing following axonal degeneration” [1]). Unilateral retinal ischemia/reperfusion was induced in 10 rats, by the elevation of pressure of the anterior chamber of the eye for 90 min. Five rats were used as controls. After five weeks, injured animals were intracardially perfused to analyze the optic nerves and chiasm with dMRI and histology. This resulted in 15 brain scans, each with 80 diffusion-sensitizing gradient directions with b = 2000 and 2500 s/mm〈sup〉2〈/sup〉 and 20 non-diffusion-weighted images (b = 0 s/mm〈sup〉2〈/sup〉), with isometric voxel resolution of 125 μm〈sup〉3〈/sup〉. Histological sections were obtained after dMRI. Optical microscopy photomicrographs of the optic nerves (stained with toluidine blue) are available, as well as their corresponding automatic segmentations of axons and myelin.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Sarbajeet Nagdas, Jennifer A. Kashatus, Aldo Nascimento, Syed S. Hussain, Riley E. Trainor, Sarah R. Pollock, Sara J. Adair, Alex D. Michaels, Hiromi Sesaki, Edward B. Stelow, Todd W. Bauer, David F. Kashatus〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Mitochondria undergo fission and fusion to maintain homeostasis, and tumors exhibit the dysregulation of mitochondrial dynamics. We recently demonstrated that ectopic HRas〈sup〉G12V〈/sup〉 promotes mitochondrial fragmentation and tumor growth through Erk phosphorylation of the mitochondrial fission GTPase Dynamin-related protein 1 (Drp1). However, the role of Drp1 in the setting of endogenous oncogenic KRas remains unknown. Here, we show that Drp1 is required for KRas-driven anchorage-independent growth in fibroblasts and patient-derived pancreatic cancer cell lines, and it promotes glycolytic flux, in part through the regulation of hexokinase 2 (HK2). Furthermore, Drp1 deletion imparts a significant survival advantage in a model of KRas-driven pancreatic cancer, and tumors exhibit a strong selective pressure against complete Drp1 deletion. Rare tumors that arise in the absence of Drp1 have restored glycolysis but exhibit defective mitochondrial metabolism. This work demonstrates that Drp1 plays dual roles in KRas-driven tumor growth: supporting both glycolysis and mitochondrial function through independent mechanisms.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309283-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Shamsideen A. Ojelade, Tom V. Lee, Nikolaos Giagtzoglou, Lei Yu, Berrak Ugur, Yarong Li, Lita Duraine, Zhongyuan Zuo, Vlad Petyuk, Philip L. De Jager, David A. Bennett, Benjamin R. Arenkiel, Hugo J. Bellen, Joshua M. Shulman〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉The Alzheimer’s disease (AD) susceptibility gene, CD2-associated protein (〈em〉CD2AP〈/em〉), encodes an actin binding adaptor protein, but its function in the nervous system is largely unknown. Loss of the 〈em〉Drosophila〈/em〉 ortholog 〈em〉cindr〈/em〉 enhances neurotoxicity of human Tau, which forms neurofibrillary tangle pathology in AD. We show that Cindr is expressed in neurons and present at synaptic terminals. 〈em〉cindr〈/em〉 mutants show impairments in synapse maturation and both synaptic vesicle recycling and release. Cindr associates and genetically interacts with 14-3-3ζ, regulates the ubiquitin-proteasome system, and affects turnover of Synapsin and the plasma membrane calcium ATPase (PMCA). Loss of 〈em〉cindr〈/em〉 elevates PMCA levels and reduces cytosolic calcium. Studies of 〈em〉Cd2ap〈/em〉 null mice support a conserved role in synaptic proteostasis, and CD2AP protein levels are inversely related to Synapsin abundance in human postmortem brains. Our results reveal CD2AP neuronal requirements with relevance to AD susceptibility, including for proteostasis, calcium handling, and synaptic structure and function.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309386-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Cornelia N. Stacher Hörndli, Eleanor Wong, Elliott Ferris, Kathleen Bennett, Susan Steinwand, Alexis Nikole Rhodes, P. Thomas Fletcher, Christopher Gregg〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Complex ethological behaviors could be constructed from finite modules that are reproducible functional units of behavior. Here, we test this idea for foraging and develop methods to dissect rich behavior patterns in mice. We uncover discrete modules of foraging behavior reproducible across different strains and ages, as well as nonmodular behavioral sequences. Modules differ in terms of form, expression frequency, and expression timing and are expressed in a probabilistically determined order. Modules shape economic patterns of feeding, exposure, activity, and perseveration responses. The modular architecture of foraging changes developmentally, and different developmental, genetic, and parental effects are found to shape the expression of specific modules. Dissecting modules from complex patterns is powerful for phenotype analysis. We discover that both parental alleles of the imprinted Prader-Willi syndrome gene 〈em〉Magel2〈/em〉 are functional in mice but regulate different modules. Our study found that complex economic patterns are built from finite, genetically controlled modules.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309350-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Matthew A. Huggins, Frances V. Sjaastad, Mark Pierson, Tamara A. Kucaba, Whitney Swanson, Christopher Staley, Alexa R. Weingarden, Isaac J. Jensen, Derek B. Danahy, Vladimir P. Badovinac, Stephen C. Jameson, Vaiva Vezys, David Masopust, Alexander Khoruts, Thomas S. Griffith, Sara E. Hamilton〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Microbial exposures can define an individual’s basal immune state. Cohousing specific pathogen-free (SPF) mice with pet store mice, which harbor numerous infectious microbes, results in global changes to the immune system, including increased circulating phagocytes and elevated inflammatory cytokines. How these differences in the basal immune state influence the acute response to systemic infection is unclear. Cohoused mice exhibit enhanced protection from virulent 〈em〉Listeria monocytogenes〈/em〉 (LM) infection, but increased morbidity and mortality to polymicrobial sepsis. Cohoused mice have more TLR2〈sup〉+〈/sup〉 and TLR4〈sup〉+〈/sup〉 phagocytes, enhancing recognition of microbes through pattern-recognition receptors. However, the response to a TLR2 ligand is muted in cohoused mice, whereas the response to a TLR4 ligand is greatly amplified, suggesting a basis for the distinct response to 〈em〉Listeria monocytogenes〈/em〉 and sepsis. Our data illustrate how microbial exposure can enhance the immune response to unrelated challenges but also increase the risk of immunopathology from a severe cytokine storm.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309258-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Yasir S. Elhassan, Katarina Kluckova, Rachel S. Fletcher, Mark S. Schmidt, Antje Garten, Craig L. Doig, David M. Cartwright, Lucy Oakey, Claire V. Burley, Ned Jenkinson, Martin Wilson, Samuel J.E. Lucas, Ildem Akerman, Alex Seabright, Yu-Chiang Lai, Daniel A. Tennant, Peter Nightingale, Gareth A. Wallis, Konstantinos N. Manolopoulos, Charles Brenner〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Nicotinamide adenine dinucleotide (NAD〈sup〉+〈/sup〉) is modulated by conditions of metabolic stress and has been reported to decline with aging in preclinical models, but human data are sparse. Nicotinamide riboside (NR) supplementation ameliorates metabolic dysfunction in rodents. We aimed to establish whether oral NR supplementation in aged participants can increase the skeletal muscle NAD〈sup〉+〈/sup〉 metabolome and if it can alter muscle mitochondrial bioenergetics. We supplemented 12 aged men with 1 g NR per day for 21 days in a placebo-controlled, randomized, double-blind, crossover trial. Targeted metabolomics showed that NR elevated the muscle NAD〈sup〉+〈/sup〉 metabolome, evident by increased nicotinic acid adenine dinucleotide and nicotinamide clearance products. Muscle RNA sequencing revealed NR-mediated downregulation of energy metabolism and mitochondria pathways, without altering mitochondrial bioenergetics. NR also depressed levels of circulating inflammatory cytokines. Our data establish that oral NR is available to aged human muscle and identify anti-inflammatory effects of NR.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309404-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Alexander J. Baker-Williams, Fiza Hashmi, Marek A. Budzyński, Mark R. Woodford, Stephanie Gleicher, Samu V. Himanen, Alan M. Makedon, Derek Friedman, Stephanie Cortes, Sara Namek, William G. Stetler-Stevenson, Gennady Bratslavsky, Alaji Bah, Mehdi Mollapour, Lea Sistonen, Dimitra Bourboulia〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉The extracellular molecular chaperone heat shock protein 90 (eHSP90) stabilizes protease client the matrix metalloproteinase 2 (MMP2), leading to tumor cell invasion. Although co-chaperones are critical modulators of intracellular HSP90:client function, how the eHSP90:MMP2 complex is regulated remains speculative. Here, we report that the tissue inhibitor of metalloproteinases-2 (TIMP2) is a stress-inducible extracellular co-chaperone that binds to eHSP90, increases eHSP90 binding to ATP, and inhibits its ATPase activity. In addition to disrupting the eHSP90:MMP2 complex and terminally inactivating MMP2, TIMP2 loads the client to eHSP90, keeping the protease in a transient inhibitory state. Secreted activating co-chaperone AHA1 displaces TIMP2 from the complex, providing a “reactivating” mechanism for MMP2. Gene knockout or blocking antibodies targeting TIMP2 and AHA1 released by HT1080 cancer cells modify their gelatinolytic activity. Our data suggest that TIMP2 and AHA1 co-chaperones function as a molecular switch that determines the inhibition and reactivation of the eHSP90 client protein MMP2.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309490-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Jakob Neuser, Caroline C. Metzen, Bernd H. Dreyer, Claudio Feulner, Joost T. van Dongen, Romy R. Schmidt, Jos H.M. Schippers〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Plants continuously need to adapt to their environment and prioritize either growth or defense responses to secure survival and reproduction. Trade-offs between growth and defense are often attributed to the allocation of energy for growth to adaptation responses. Still, the exact mechanisms underlying growth and defense trade-offs are poorly understood. Here, we demonstrate that the growth-related transcription factor HOMOLOG OF BEE2 INTERACTING WITH IBH 1 (HBI1) regulates apoplastic reactive oxygen species (ROS) homeostasis by differentially controlling the expression of NADPH oxidases (NOXs) and peroxidases (POXs). The HBI1 target genes 〈em〉RESPIRATORY BURST OXIDASE HOMOLOG A〈/em〉 (〈em〉RbohA〈/em〉) and 〈em〉RbohC〈/em〉 have contrasting effects on the regulation of cell size. In addition, the HBI1-controlled 〈em〉NOX〈/em〉s and 〈em〉POX〈/em〉s oppositely regulate susceptibility toward 〈em〉Pseudomonas syringae〈/em〉. Our findings reveal that the incompatibility between growth and defense programs can be attributed to the way apoplastic ROS homeostasis is modulated during both processes.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S221112471930926X-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Melanie Korbelius, Nemanja Vujic, Vinay Sachdev, Sascha Obrowsky, Silvia Rainer, Benjamin Gottschalk, Wolfgang F. Graier, Dagmar Kratky〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉As circulating lipid levels are balanced by the rate of lipoprotein release and clearance from the plasma, lipid absorption in the small intestine critically contributes to the maintenance of whole-body lipid homeostasis. Within enterocytes, excessive triglycerides are transiently stored as cytosolic lipid droplets (cLDs), and their mobilization sustains lipid supply during interprandial periods. Using mice lacking adipose triglyceride lipase (ATGL) and its coactivator comparative gene identification-58 (CGI-58) exclusively in the intestine (intestine-specific double KO [iDKO]), we show that ATGL/CGI-58 are not involved in providing substrates for chylomicron synthesis. Massive intestinal cLD accumulation in iDKO mice independent of dietary lipids together with inefficient lipid incorporation into cLDs in the early absorption phase demonstrate the existence of a secretion/re-uptake cycle, corroborating the availability of two diverse cLD pools. This study identified ATGL/CGI-58 as critical players in the catabolism of basolaterally (blood) derived lipids and highlights the necessity to modify the current model of intestinal lipid metabolism.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309271-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Penelope Kroustallaki, Lisa Lirussi, Sergio Carracedo, Panpan You, Q. Ying Esbensen, Alexandra Götz, Laure Jobert, Lene Alsøe, Pål Sætrom, Sarantis Gagos, Hilde Nilsen〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Telomerase biogenesis is a complex process where several steps remain poorly understood. Single-strand-selective uracil-DNA glycosylase (SMUG1) associates with the DKC1-containing H/ACA ribonucleoprotein complex, which is essential for telomerase biogenesis. Herein, we show that SMUG1 interacts with the telomeric RNA component (〈em〉hTERC〈/em〉) and is required for co-transcriptional processing of the nascent transcript into mature 〈em〉hTERC〈/em〉. We demonstrate that SMUG1 regulates the presence of base modifications in 〈em〉hTERC〈/em〉, in a region between the CR4/CR5 domain and the H box. Increased levels of 〈em〉hTERC〈/em〉 base modifications are accompanied by reduced DKC1 binding. Loss of SMUG1 leads to an imbalance between mature 〈em〉hTERC〈/em〉 and its processing intermediates, leading to the accumulation of 3′-polyadenylated and 3′-extended intermediates that are degraded in an EXOSC10-independent RNA degradation pathway. Consequently, SMUG1-deprived cells exhibit telomerase deficiency, leading to impaired bone marrow proliferation in 〈em〉Smug1〈/em〉-knockout mice.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309374-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 7〈/p〉 〈p〉Author(s): Yuanming Cheng, Hanzhi Luo, Franco Izzo, Brian F. Pickering, Diu Nguyen, Robert Myers, Alexandra Schurer, Saroj Gourkanti, Jens C. Brüning, Ly P. Vu, Samie R. Jaffrey, Dan A. Landau, Michael G. Kharas〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Stem cells balance cellular fates through asymmetric and symmetric divisions in order to self-renew or to generate downstream progenitors. Symmetric commitment divisions in stem cells are required for rapid regeneration during tissue damage and stress. The control of symmetric commitment remains poorly defined. Using single-cell RNA sequencing (scRNA-seq) in combination with transcriptomic profiling of HSPCs (hematopoietic stem and progenitor cells) from control and m〈sup〉6〈/sup〉A methyltransferase 〈em〉Mettl3〈/em〉 conditional knockout mice, we found that m〈sup〉6〈/sup〉A-deficient hematopoietic stem cells (HSCs) fail to symmetrically differentiate. Dividing HSCs are expanded and are blocked in an intermediate state that molecularly and functionally resembles multipotent progenitors. Mechanistically, RNA methylation controls 〈em〉Myc〈/em〉 mRNA abundance in differentiating HSCs. We identified MYC as a marker for HSC asymmetric and symmetric commitment. Overall, our results indicate that RNA methylation controls symmetric commitment and cell identity of HSCs and may provide a general mechanism for how stem cells regulate differentiation fate choice.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309295-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 12 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Debabrata Panda, Swati S. Mishra, Sangram K. Mohanty, Prafulla K. Behera, Sangram K. Lenka〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Precise physiological and molecular marker-based assessment provides information about the extent of genetic diversity, which helps for effective breeding programmes. We have conducted detailed physiological and molecular marker-based assessment of selected eight indigenous rice landraces from Koraput, India along with tolerant (N22) and susceptible (IR64) check varieties under control and simulated drought stress using polyethylene glycol (PEG) 6000. After exposure to different levels of drought stress, relative germination performance (RGP), seedling vigour index (SVI) and relative growth index (RGI) were significantly declined in all the rice landraces compared to the control plants and significant varietal differences were observed. Genetic relationship among the studied rice landraces was assessed with 24 previously reported drought tolerance linked Simple Sequence Repeat (SSR) markers. A total of 53 alleles were detected at the loci of the 24 markers across the 10 rice accessions〈strong〉.〈/strong〉 The Nei's gene diversity (〈em〉He〈/em〉) and the polymorphism information content (〈em〉PIC〈/em〉) ranged from 0 to 0.665 and 0 to 0.687, respectively. Six SSR loci, RM276, RM411, RM3, RM263, RM216 and RM28199, provided the highest 〈em〉PIC〈/em〉 values and are potential for exploring the genetic diversity of studied rice lines for drought tolerance. Four rice genotypes (Butkichudi, Haldichudi, Machakanta and Kalajeera) showed the highest genetic distance with tolerant check variety (N22) and can be considered as valuable genetic resources for drought breeding program.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 12 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): R.H. de Boer, C.P. de Campos〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The International Collegiate Programming Contest〈sup〉1〈/sup〉 is an annual, multi-tier competition held amongst college students on a global scale, with world championships every year. Last year alone, around fifty thousand students from three thousand universities participated in ICPC regional competitions [1]. Because of its significant size involving a lot of talent and skillful people, multiple stakeholders are interested in the competition. Each of the competitions results in scoreboards, containing valuable data about the performance of teams. This data however is, up till now, never collected and stored in an open and free repository. The ICPC does keep track of the basic information such as teams' names and their final scores, but more detailed information has remained scattered across the internet. This paper describes the data collected and cleaned from the European, Latin-American, North American, South Pacific and World Finals from 2012 to 2018, opening up research opportunities for an in-depth look into the programming competitions.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 9 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Affandi Omar, Julaina A. Jalil, Norashareena M. Shakrin, Lock H. Ngu, Zabedah M. Yunus〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This article contains information related to a recent study “Selective screening for detection of mucopolysaccharidoses (MPS) in Malaysia; A Two-year Study” [1]. Any patient registered under government healthcare facilities in Malaysia and fit at least two inclusion criteria were included in this selective screening. Urine and blood from these high risk patients were obtained and analysed for glycosaminoglycans (GAGs) level before characterization using high resolution electrophoresis (HRE). Thereafter, enzyme assay for different types of MPS based on result of HRE were determined using specific substrate. Demographic data as well as laboratory findings were tabulated and analysed. The data of this study demonstrate between clinical presentation and laboratory findings among high risk patients of MPS and can be employed to improve diagnosis of MPS.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 9 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Woong-Hee Kim, Pyeonghwa Jeong, Seon-Wook Kim, Haaglim Cho, Jeong-min Lee, Shinae Seo, Haihong Shen, Youngkeun Ahn, Da-Woon Jung, Yong-Chul Kim, Darren R. Williams〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This article contains chemical characterization and biological activity data for a novel indirubin derivative, termed LDD-1819. The detailed synthesis procedure and associated NMR data are presented. The concentration-dependent inhibition data of two biological targets, glycogen synthase kinase-3〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"〉〈mrow〉〈mi mathvariant="normal"〉β〈/mi〉〈/mrow〉〈/math〉 and aurora A kinase are described. The following biological data are also contained in this article: 1) the cellularization of skeletal muscle myotubes by LDD-1819 or two small molecule inhibitors of glycogen synthase kinase-3〈math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"〉〈mrow〉〈mi mathvariant="normal"〉β〈/mi〉〈/mrow〉〈/math〉 and aurora kinase A (BIO and reversine) and gene expression data for the myoblast markers Pax-7 and Myf5, 2) Cell viability of hTERT human immortalized fibroblasts, colon cancer cells and breast cancer cells, and 3) Western blotting analysis of full length and cleaved caspse-7, and cleaved poly (ADP-ribose) polymerase (PARP) in hTERT fibroblasts treated with LDD-1819. A schematic diagram of the biological activities of LDD-1819 is also presented. Further interpretation and discussion of these data are provided in the associated research article ‘A novel indirubin derivative that increases somatic cell plasticity and inhibits tumorigenicity’ (Kim et al., 2019).〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief, Volume 25〈/p〉 〈p〉Author(s): Wei Peng, Zhiyun Jia, Xiaoqi Huang, Su Lui, Weihong Kuang, John A. Sweeney, Qiyong Gong〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉This data article provided additional data related to the research article entitled “Brain structural abnormalities in emotional regulation and sensory processing regions associated with anxious depression” Peng et al.,2019. Correlation analyses were conducted for clinical information (HAMD total, anxiety/somatization scores, HAMA total and illness duration) and identified regional gray matter volumes in all patients with anxious depression and non-anxious depression. More detailed correlation analysis was applied for each item of anxiety factor and reginal gray matter volumes to find which items were more associated with structural alterations in patients. Data showed that mean values of regional gray matter volumes in left postcentral gyrus (PCG) were positively associated with HAMD total and anxiety factor scores in anxious depression group. More detailed correlation analysis considering each item of anxiety factor revealed that, item 10 (psychic anxiety) and Item15 (hypochondriasis) were most significantly and positively associated with regional gray matter volumes in left PCG in anxious group. While HAMA scores and illness duration showed no significant correlation with any regional gray matter volume in both patient groups. Sample size matched groups were selected to explore possible replicability of imaging results. It revealed that different gray matter volumes in right inferior frontal gyrus were most robust findings among three groups. And anxious group had larger gray matter volumes in left PCG than non-anxious depression, despite of not survived after multiple comparisons corrections.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Andrea Tassi, Ioannis Mavromatis, Robert J. Robert Piechocki〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉A dataset of measurements of ETSI ITS-G5 Dedicated Short Range Communications (DSRC) is presented. Our dataset consists of network interactions happening between two On-Board Units (OBUs) and four Road Side Units (RSUs). Each OBU was fitted onto a vehicle driven across the FLOURISH Test Track in Bristol, UK. Each RSU and OBU was equipped with two transceivers operating at different frequencies. During our experiments, each transceiver broadcasts Cooperative Awareness Messages (CAMs) over the licensed DSRC band, and over the unlicensed Industrial, Scientific, and Medical radio (ISM) bands 2.4 GHz-2.5 GHz and 5.725 GHz-5.875 GHz.〈/p〉 〈p〉Each transmitted and received CAM is logged along with its Received Signal Strength Indicator (RSSI) value and accurate positioning information. The Media Access Control layer (MAC) layer Packet Delivery Rates (PDRs) and RSSI values are also empirically calculated across the whole length of the track for any transceiver. The dataset can be used to derive realistic approximations of the PDR as a function of RSSI values under urban environments and for both the DSRC and ISM bands – thus, the dataset is suitable to calibrate (simplified) physical layers of full-stack vehicular simulators where the MAC layer PDR is a direct function of the RSSI. The dataset is not intended to be used for signal propagation modelling.〈/p〉 〈p〉The dataset can be found at https://doi.org/10.5523/bris.eupowp7h3jl525yxhm3521f57, and it has been analyzed in the following paper: I. Mavromatis, A. Tassi, and R. J. Piechocki, “Operating ITS-G5 DSRC over Unlicensed Bands: A City-Scale Performance Evaluation,” IEEE PIMRC 2019. [Online]. Available: https://arxiv.org/abs/1904.00464.〈/p〉 〈/div〉 〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Ishmail Abdus-Saboor, Nathan T. Fried, Mark Lay, Justin Burdge, Kathryn Swanson, Roman Fischer, Jessica Jones, Peter Dong, Weihua Cai, Xinying Guo, Yuan-Xiang Tao, John Bethea, Minghong Ma, Xinzhong Dong, Long Ding, Wenqin Luo〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Rodents are the main model systems for pain research, but determining their pain state is challenging. To develop an objective method to assess pain sensation in mice, we adopt high-speed videography to capture sub-second behavioral features following hind paw stimulation with both noxious and innocuous stimuli and identify several differentiating parameters indicating the affective and reflexive aspects of nociception. Using statistical modeling and machine learning, we integrate these parameters into a single index and create a “mouse pain scale,” which allows us to assess pain sensation in a graded manner for each withdrawal. We demonstrate the utility of this method by determining sensations triggered by three different von Frey hairs and optogenetic activation of two different nociceptor populations. Our behavior-based “pain scale” approach will help improve the rigor and reproducibility of using withdrawal reflex assays to assess pain sensation in mice.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309076-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Miyuki Suzawa, Nigel M. Muhammad, Bradley S. Joseph, Michelle L. Bland〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Chronic enteropathogen infection in early childhood reduces circulating insulin-like growth factor 1 (IGF1) levels and restricts growth. Pathogen-derived molecules activate host Toll-like receptors to initiate the immune response, but whether this pathway contributes to growth inhibition is unclear. In 〈em〉Drosophila〈/em〉, activation of Toll receptors in larval fat body suppresses whole-animal growth. Here, using a transcriptomic approach, we identify 〈em〉Drosophila insulin-like peptide 6〈/em〉 (〈em〉Dilp6〈/em〉), a fat-body-derived IGF1 ortholog, as a selective target of Toll signaling induced by infection or genetic activation of the pathway. Using a tagged allele that we generated to measure endogenous Dilp6, we find a marked reduction in circulating hormone levels. Restoring Dilp6 expression in fat body rescues growth in animals with active Toll signaling. Our results establish that Toll signaling reduces growth by inducing hormone insufficiency, implying a mechanistic link between innate immune signaling and endocrine regulation of growth.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309052-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Chi-Jung Liang, Zih-Wun Wang, Yi-Wen Chang, Ko-Chuan Lee, Wei-Hsin Lin, Jia-Lin Lee〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Secreted frizzled-related proteins (SFRPs) are mainly known for their role as extracellular modulators and tumor suppressors that downregulate Wnt signaling. Using the established (CRISPR/Cas9 targeting promoters of SFRPs and targeting SFRPs transcript) system, we find that nuclear SFRPs interact with β-catenin and either promote or suppress TCF4 recruitment. SFRPs bind with β-catenin on both their N and C termini, which the repressive effects caused by SFRP-β-catenin-N-terminus binding overpower the promoting effects of their binding at the C terminus. By high Wnt activity, β-catenin and SFRPs only bind with their C termini, which results in the upregulation of β-catenin transcriptional activity and cancer stem cell (CSC)-related genes. Furthermore, we identify disulfide bonds of the cysteine-rich domain (CRD) and two threonine phosphorylation events of the netrin-related motif (NTR) domain of SFRPs that are essential for their role as biphasic modulators, suggesting that SFRPs are biphasic modulators of Wnt signaling-elicited CSC properties beyond extracellular control.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309131-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Aditya Mojumdar, Kyle Sorenson, Marcel Hohl, Mathias Toulouze, Susan P. Lees-Miller, Karine Dubrana, John H.J. Petrini, Jennifer A. Cobb〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Non-homologous end joining (NHEJ) and homologous recombination (HR) are the two major pathways of DNA double-strand break (DSB) repair and both are highly conserved from yeast to mammals. Nej1 has a role in DNA end-tethering at a DSB, and the Mre11/Rad50/Xrs2 (MRX) complex is important for its recruitment to the break. Nej1 and Dna2-Sgs1 interact with the C-terminal end of Mre11, which also includes the region where Rad50 binds. By characterizing the functionality of Nej1 in two 〈em〉rad50〈/em〉 mutants, which alter the structural features of MRX, we demonstrate that Nej1 inhibits the binding of Dna2 to Mre11 and Sgs1. Nej1 interactions with Mre11 promote tethering and inhibit hyper-resection, and when these events are compromised, large deletions develop at a DSB. The work indicates that Nej1 provides a layer of regulation to repair pathway choice and is consistent with its role in NHEJ.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309088-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Grit Bornschein, Jens Eilers, Hartmut Schmidt〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Coupling distances between Ca〈sup〉2+〈/sup〉 channels and release sensors regulate vesicular release probability (〈em〉p〈/em〉〈sub〉v〈/sub〉). Tight coupling is thought to provide a framework for high 〈em〉p〈/em〉〈sub〉v〈/sub〉 and loose coupling for high plasticity at low 〈em〉p〈/em〉〈sub〉v〈/sub〉. At synapses investigated during development, coupling distances decrease, thereby increasing 〈em〉p〈/em〉〈sub〉v〈/sub〉 and transmission fidelity. We find that neocortical high-fidelity synapses deviate from these rules. Paired recordings from pyramidal neurons with “slow” and “fast” Ca〈sup〉2+〈/sup〉 chelators combined with experimentally constrained simulations suggest that coupling tightens significantly during development. However, fluctuation analysis revealed that neither 〈em〉p〈/em〉〈sub〉v〈/sub〉 (∼0.63) nor the number of release sites (∼8) changes concomitantly. Moreover, the amplitude and time course of presynaptic Ca〈sup〉2+〈/sup〉 transients are not different between age groups. These results are explained by high-〈em〉p〈/em〉〈sub〉v〈/sub〉 release sites with Ca〈sup〉2+〈/sup〉 microdomains in young synapses and nanodomains in mature synapses. Thus, at neocortical synapses, a developmental reorganization of the active zone leaves 〈em〉p〈/em〉〈sub〉v〈/sub〉 unaffected, emphasizing developmental and functional synaptic diversity.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719308988-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Erin E. Talbert, Maria C. Cuitiño, Katherine J. Ladner, Priyani V. Rajasekerea, Melissa Siebert, Reena Shakya, Gustavo W. Leone, Michael C. Ostrowski, Brian Paleo, Noah Weisleder, Peter J. Reiser, Amy Webb, Cynthia D. Timmers, Daniel S. Eiferman, David C. Evans, Mary E. Dillhoff, Carl R. Schmidt, Denis C. Guttridge〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Cachexia is a wasting syndrome characterized by pronounced skeletal muscle loss. In cancer, cachexia is associated with increased morbidity and mortality and decreased treatment tolerance. Although advances have been made in understanding the mechanisms of cachexia, translating these advances to the clinic has been challenging. One reason for this shortcoming may be the current animal models, which fail to fully recapitulate the etiology of human cancer-induced tissue wasting. Because pancreatic ductal adenocarcinoma (PDA) presents with a high incidence of cachexia, we engineered a mouse model of PDA that we named KPP. KPP mice, similar to PDA patients, progressively lose skeletal and adipose mass as a consequence of their tumors. In addition, KPP muscles exhibit a similar gene ontology as cachectic patients. We envision that the KPP model will be a useful resource for advancing our mechanistic understanding and ability to treat cancer cachexia.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309064-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Runrui Zhang, Marcelo Boareto, Anna Engler, Angeliki Louvi, Claudio Giachino, Dagmar Iber, Verdon Taylor〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Neural stem cells (NSCs) in the adult mouse hippocampal dentate gyrus (DG) are mostly quiescent, and only a few are in cell cycle at any point in time. DG NSCs become increasingly dormant with age and enter mitosis less frequently, which impinges on neurogenesis. How NSC inactivity is maintained is largely unknown. Here, we found that 〈em〉Id4〈/em〉 is a downstream target of Notch2 signaling and maintains DG NSC quiescence by blocking cell-cycle entry. Id4 expression is sufficient to promote DG NSC quiescence and Id4 knockdown rescues Notch2-induced inhibition of NSC proliferation. 〈em〉Id4〈/em〉 deletion activates NSC proliferation in the DG without evoking neuron generation, and overexpression increases NSC maintenance while promoting astrogliogenesis at the expense of neurogenesis. Together, our findings indicate that Id4 is a major effector of Notch2 signaling in NSCs and a Notch2-Id4 axis promotes NSC quiescence in the adult DG, uncoupling NSC activation from neuronal differentiation.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719309040-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: 6 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Cell Reports, Volume 28, Issue 6〈/p〉 〈p〉Author(s): Katie M. Campbell, Kathleen A. O’Leary, Debra E. Rugowski, William A. Mulligan, Erica K. Barnell, Zachary L. Skidmore, Kilannin Krysiak, Malachi Griffith, Linda A. Schuler, Obi L. Griffith〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉The NRL-PRL murine model, defined by mammary-selective transgenic rat prolactin ligand 〈em〉rPrl〈/em〉 expression, establishes spontaneous ER+ mammary tumors in nulliparous females, mimicking the association between elevated prolactin (PRL) and risk for development of ER+ breast cancer in postmenopausal women. Whole-genome and exome sequencing in a discovery cohort (n = 5) of end-stage tumors revealed canonical activating mutations and copy number amplifications of 〈em〉Kras〈/em〉. The frequent mutations in this pathway were validated in an extension cohort, identifying activating 〈em〉Ras〈/em〉 alterations in 79% of tumors (23 of 29). Transcriptome analyses over the course of oncogenesis revealed marked alterations associated with Ras activity in established tumors compared with preneoplastic tissues; in cell-intrinsic processes associated with mitosis, cell adhesion, and invasion; as well as in the surrounding tumor environment. These genomic analyses suggest that PRL induces a selective bottleneck for spontaneous Ras-driven tumors that may model a subset of aggressive clinical ER+ breast cancers.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2211124719308848-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 5 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Johannes Lutzenkirchen, Antun Barisic, Gregory Lefevre, Tajana Preocanin〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The Data in Brief contains data on the electrokinetic mobility of PTFE and silica particles in aqueous suspensions as a function of pH and temperature. Furthermore, the concomitant conductivities and pH values are reported both for systems in the absence and presence of PTFE particles as a function of temperature and are compatible with the associated research paper “The influence of temperature on the charging of Polytetrafluoroethylene surfaces in electrolyte solutions” (Barisic et al.). The trend of the electrokinetic charging with temperature can be inferred from this for both kinds of particles. The data on the evolution of the pH and the measured conductivities are valuable input for future models that simulate the charge of inert surfaces at variable temperature.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 2 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Data in Brief〈/p〉 〈p〉Author(s): Seok Hyun Eom, Jong-Kuk Na〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The data presented in this article are associated to the research articles, “DOI: 10.1007/s11295-019-1348-3”, [1]; and “DOI: 10.1007/s13205-018-1162-x” [2]. 〈em〉Clausena excavata〈/em〉 Burm. f. and 〈em〉Sterculia lanceolata〈/em〉 Cav. are medicinal tree plants [3], [4] native to Southeast Asia and China, and most members of both the genus 〈em〉Clausena〈/em〉 and the genus 〈em〉Sterculia〈/em〉 contain various valuable secondary metabolites with a great potential for drug development. Though many phytochemical studies have been conducted using plant extracts from various parts of these plants [4], [5], there are very limited genetic resources available. RNA sequencing of 〈em〉C. excavata〈/em〉 and 〈em〉S. lanceolata〈/em〉 was conducted using pair-end Illumina HiSeq2500 sequencing system, from which the first 〈em〉de novo〈/em〉 transcriptome data were produced for both genus 〈em〉Clausena〈/em〉 and 〈em〉Sterculia〈/em〉. Transcriptome shotgun assembly using three different assembly tools [2] generated a total of 16,638 non-redundant contigs (N50, 900 bp) from 〈em〉C. excavata〈/em〉 and 7,857 (N50, 423 bp) from 〈em〉S. lanceolata〈/em〉. The data are accessible at NCBI BioProject: PRJNA428402 for 〈em〉C. excavata〈/em〉 or PRJNA435648 for 〈em〉S. lanceolata〈/em〉.〈/p〉〈/div〉 〈/div〉