bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiCASA is a new method for quantifying cellular organization
Authors: Sornborger Andrew , Li Jie , Timmons Cullen , Lupu Floria , Eggenschwiler Jonathan , Takahama Yousuke , Manley Nancy R. 
Published: May 2017

AbstractWhile many tools exist for identifying and quantifying individual cell types, few methods are available to assess the relationships between cell types in organs and tissues and how these relationships change during aging or disease states. We present a quantitative method for evaluating cellular organization, using the mouse thymus as a test organ. The thymus is the primary lymphoid organ responsible for generating T cells in vertebrates, and its proper structure and organization is essential for optimal function. Our method, Multitaper Circularly Averaged Spectral Analysis (MiCASA), identifies differences in the tissue-level organization with high sensitivity, including defining a novel type of phenotype by measuring variability as a specific parameter. MiCASA provides a novel and easily implemented quantitative tool for assessing cellular organization.
A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers
Authors: Pisignano Giuseppina , Napoli Sara , Magistri Marco , Mapelli Sarah N. , Pastori Chiara , Di Marco Stefano , Civenni Gianluca , Albino Domenico , Enriquez Claudia , Allegrini Sara , Mitra Abhishek , D’Ambrosio Gioacchino , Mello-Grand Maurizia , Chiorino Giovanna , Garcia-Escudero Ramon , Varani Gabriele , Carbone Giuseppina M. , Catapano Carlo V. 
Published: May 2017

AbstractLong noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.
Rapid mass production of two-dimensional metal oxides and hydroxides via the molten salts method
Authors: Hu Zhimi , Xiao Xu , Jin Huanyu , Li Tianqi , Chen Ming , Liang Zhun , Guo Zhengfeng , Li Jia , Wan Jun , Huang Liang , Zhang Yanrong , Feng Guang , Zhou Jun 
Published: May 2017

AbstractBecause of their exotic electronic properties and abundant active sites, two-dimensional (2D) materials have potential in various fields. Pursuing a general synthesis methodology of 2D materials and advancing it from the laboratory to industry is of great importance. This type of method should be low cost, rapid and highly efficient. Here, we report the high-yield synthesis of 2D metal oxides and hydroxides via a molten salts method. We obtained a high-yield of 2D ion-intercalated metal oxides and hydroxides, such as cation-intercalated manganese oxides (Na0.55Mn2O4·1.5H2O and K0.27MnO2·0.54H2O), cation-intercalated tungsten oxides (Li2WO4 and Na2W4O13), and anion-intercalated metal hydroxides (Zn5(OH)8(NO3)2·2H2O and Cu2(OH)3NO3), with a large lateral size and nanometre thickness in a short time. Using 2D Na2W4O13 as an electrode, a high performance electrochemical supercapacitor is achieved. We anticipate that our method will enable new path to the high-yield synthesis of 2D materials for applications in energy-related fields and beyond.
Conjugation of squalene to gemcitabine as unique approach exploiting endogenous lipoproteins for drug delivery
Authors: Sobot Dunja , Mura Simona , Yesylevskyy Semen O. , Dalbin Laura , Cayre Fanny , Bort Guillaume , Mougin Julie , Desmaële Didier , Lepetre-Mouelhi Sinda , Pieters Grégory , Andreiuk Bohdan , Klymchenko Andrey S. , Paul Jean-Louis , Ramseyer Christophe , Couvreur Patrick 
Published: May 2017

AbstractOnce introduced in the organism, the interaction of nanoparticles with various biomolecules strongly impacts their fate. Here we show that nanoparticles made of the squalene derivative of gemcitabine (SQGem) interact with lipoproteins (LPs), indirectly enabling the targeting of cancer cells with high LP receptors expression. In vitro and in vivo experiments reveal preeminent affinity of the squalene-gemcitabine bioconjugates towards LP particles with the highest cholesterol content and in silico simulations further display their incorporation into the hydrophobic core of LPs. To the best of our knowledge, the use of squalene to induce drug insertion into LPs for indirect cancer cell targeting is a novel concept in drug delivery. Interestingly, not only SQGem but also other squalene derivatives interact similarly with lipoproteins while such interaction is not observed with liposomes. The conjugation to squalene represents a versatile platform that would enable efficient drug delivery by simply exploiting endogenous lipoproteins.
Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
Authors: Schuenemann Verena J. , Peltzer Alexander , Welte Beatrix , van Pelt W. Paul , Molak Martyna , Wang Chuan-Chao , Furtwängler Anja , Urban Christian , Reiter Ella , Nieselt Kay , Teßmann Barbara , Francken Michael , Harvati Katerina , Haak Wolfgang , Schiffels Stephan , Krause Johannes 
Published: May 2017

AbstractEgypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.
Genome-wide association study of 1,5-anhydroglucitol identifies novel genetic loci linked to glucose metabolism
Authors: Li Man , Maruthur Nisa M. , Loomis Stephanie J. , Pietzner Maik , North Kari E. , Mei Hao , Morrison Alanna C. , Friedrich Nele , Pankow James S. , Nauck Matthias , Boerwinkle Eric , Teumer Alexander , Selvin Elizabeth , Köttgen Anna 
Published: May 2017

Abstract1,5-anhydroglucitol (1,5-AG) is a biomarker of hyperglycemic excursions associated with diabetic complications. Because of its structural similarity to glucose, genetic studies of 1,5-AG can deliver complementary insights into glucose metabolism. We conducted genome-wide association studies of serum 1,5-AG concentrations in 7,550 European ancestry (EA) and 2,030 African American participants (AA) free of diagnosed diabetes from the ARIC Study. Seven loci in/near EFNA1/SLC50A1, MCM6/LCT, SI, MGAM, MGAM2, SLC5A10, and SLC5A1 showed genome-wide significant associations (P < 5 × 10−8) among EA participants, five of which were novel. Six of the seven loci were successfully replicated in 8,790 independent EA individuals, and MCM6/LCT and SLC5A10 were also associated among AA. Most of 1,5-AG-associated index SNPs were not associated with the clinical glycemic markers fasting glucose or the HbA1c, and vice versa. Only the index variant in SLC5A1 showed a significant association with fasting glucose in the expected opposing direction. Products of genes in all 1,5-AG-associated loci have known roles in carbohydrate digestion and enteral or renal glucose transport, suggesting that genetic variants associated with 1,5-AG influence its concentration via effects on glucose metabolism and handling.
The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures
Authors: Mir B. , Solés X. , González C. , Escaja N. 
Published: May 2017

AbstractIncorporation of pseudoisocytidine (psC), a neutral analogue of protonated cytidine, in i-motifs has been studied by spectroscopic methods. Our results show that neutral psC:C base pairs can stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C+ stacks. When psC occupies central positions, the resulting i-motifs are only observed at low pH and psC:C+ or psC:psC+ hemiprotonated base pairs are formed instead of their neutral analogs. Overall, our results suggest that positively charged base pairs are necessary to stabilize this non-canonical DNA structure.
Inhibition of Steel Corrosion and Alkaline Zinc Oxide Dissolution by Dicarboxylate Bola-Amphiphiles: Self-Assembly Supersedes Host-Guest Conception
Authors: Schmelter Dirk , Langry Arthur , Koenig Andrej , Keil Patrick , Leroux Fabrice , Hintze-Bruening Horst 
Published: May 2017

AbstractFor many decorative applications like industrial and architectural paints, prevention of metal substrates from corrosion is a primary function of organic coatings. Triggered release of inhibitor species is generally accepted as a remedy for starting corrosion in case of coatings damage. A polyurethane based coating, doped with bola-amphiphiles of varying molecular weight but with a common head group motif that stems from ring-opened alkenyl succinic anhydride, enables passivation of the defect and mitigates cathodic delamination, if applied on cold rolled steel. An antagonistic effect results from the intercalation of the bola-amphiphiles into layered double hydroxide Zn2Al(OH)6 and subsequent incorporation of the hybrid phase into the organic matrix. In particular higher molecular weight bola-amphiphiles get immobilized through alkaline degradation of the layered framework in the basic milieu at the cathode. By means of sediments from colloidal states it is demonstrated that in-situ formed zinc oxide encapsulates the hybrid phase, evidenced by impeded dissolution of the ZnO based shell into caustic soda. While inhibition of steel corrosion results from a Donnan barrier layer, impeded zinc oxide dissolution is rooted in zinc catalyzed bola-amphiphile hydrolysis and layered deposition of the crystalline spacer diol hydrogenated bisphenol-A.
Photobiomodulation of human dermal fibroblasts in vitro: decisive role of cell culture conditions and treatment protocols on experimental outcome
Authors: Mignon C. , Uzunbajakava N. E. , Raafs B. , Botchkareva N. V. , Tobin D. J. 
Published: May 2017

AbstractPhotobiomodulation-based (LLLT) therapies show tantalizing promise for treatment of skin diseases. Confidence in this approach is blighted however by lamentable inconsistency in published experimental designs, and so complicates interpretation. Here we interrogate the appropriateness of a range of previously-reported treatment parameters, including light wavelength, irradiance and radiant exposure, as well as cell culture conditions (e.g., serum concentration, cell confluency, medium refreshment, direct/indirect treatment, oxygen concentration, etc.), in primary cultures of normal human dermal fibroblasts exposed to visible and near infra-red (NIR) light. Apart from irradiance, all study parameters impacted significantly on fibroblast metabolic activity. Moreover, when cells were grown at atmospheric O2 levels (i.e. 20%) short wavelength light inhibited cell metabolism, while negligible effects were seen with long visible and NIR wavelength. By contrast, NIR stimulated cells when exposed to dermal tissue oxygen levels (approx. 2%). The impact of culture conditions was further seen when inhibitory effects of short wavelength light were reduced with increasing serum concentration and cell confluency. We conclude that a significant source of problematic interpretations in photobiomodulation reports derives from poor optimization of study design. Further development of this field using in vitro/ex vivo models should embrace significant standardization of study design, ideally within a design-of-experiment setting.
Synthetic surfactant- and cross-linker-free preparation of highly stable lipid-polymer hybrid nanoparticles as potential oral delivery vehicles
Authors: Wang Taoran , Xue Jingyi , Hu Qiaobin , Zhou Mingyong , Chang Chao , Luo Yangchao 
Published: May 2017

AbstractThe toxicity associated with concentrated synthetic surfactants and the poor stability at gastrointestinal condition are two major constraints for practical applications of solid lipid nanoparticles (SLN) as oral delivery vehicles. In this study, a synthetic surfactant-free and cross-linker-free method was developed to fabricate effective, safe, and ultra-stable lipid-polymer hybrid nanoparticles (LPN). Bovine serum albumin (BSA) and dextran varying in molecular weights were first conjugated through Maillard reaction and the conjugates were exploited to emulsify solid lipid by a solvent diffusion and sonication method. The multilayer structure was formed by self-assembly of BSA-dextran micelles to envelope solid lipid via a pH- and heating-induced facile process with simultaneous surface deposition of pectin. The efficiency of different BSA-dextran conjugates was systematically studied to prepare LPN with the smallest size, the most homogeneous distribution and the greatest stability. The molecular interactions were characterized by Fourier transform infrared and fluorescence spectroscopies. Both nano spray drying and freeze-drying methods were tested to produce spherical and uniform pectin-coated LPN powders that were able to re-assemble nanoscale structure when redispersed in water. The results demonstrated the promise of a synthetic surfactant- and cross-linker-free technique to prepare highly stable pectin-coated LPN from all natural biomaterials as potential oral delivery vehicles.
Phytohormone ethylene-responsive Arabidopsis organ growth under light is in the fine regulation of Photosystem II deficiency-inducible AKIN10 expression
Authors: Kim Geun-Don , Cho Young-Hee , Yoo Sang-Dong 
Published: May 2017

AbstractFor photoautotrophic plants, light-dependent photosynthesis plays an important role in organismal growth and development. Under light, Arabidopsis hypocotyl growth is promoted by the phytohormone ethylene. Despite well-characterized ethylene signaling pathways, the functions of light in the hormone-inducible growth response still remain elusive. Our cell-based functional and plant-system-based genetic analyses with biophysical and chemical tools showed that a chemical blockade of photosystem (PS) II activity affects ethylene-induced hypocotyl response under light. Interestingly, ethylene responsiveness modulates PSII activity in retrospect. The lack of ethylene responsiveness-inducible PSII inefficiency correlates with the induction of AKIN10 expression. Consistently, overexpression of AKIN10 in transgenic plants suppresses ethylene-inducible hypocotyl growth promotion under illumination as in other ethylene-insensitive mutants. Our findings provide information on how ethylene responsiveness-dependent photosynthetic activity controls evolutionarily conserved energy sensor AKIN10 that fine-tunes EIN3-mediated ethylene signaling responses in organ growth under light.
Integration of vibrotactile frequency information beyond the mechanoreceptor channel and somatotopy
Authors: Kuroki Scinob , Watanabe Junji , Nishida Shin’ya 
Published: May 2017

AbstractA wide variety of tactile sensations arise from the activation of several types of mechanoreceptor-afferent channels scattered all over the body, and their projections create a somatotopic map in the somatosensory cortex. Recent findings challenge the traditional view that tactile signals from different mechanoreceptor-channels/locations are independently processed in the brain, though the contribution of signal integration to perception remains obscure. Here we show that vibrotactile frequency perception is functionally enriched by signal integration across different mechanoreceptor channels and separate skin locations. When participants touched two sinusoidal vibrations of far-different frequency, which dominantly activated separate channels with the neighboring fingers or the different hand and judged the frequency of one vibration, the perceived frequency shifted toward the other (assimilation effect). Furthermore, when the participants judged the frequency of the pair as a whole, they consistently reported an intensity-based interpolation of the two vibrations (averaging effect). Both effects were similar in magnitude between the same and different hand conditions and significantly diminished by asynchronous presentation of the vibration pair. These findings indicate that human tactile processing is global and flexible in that it can estimate the ensemble property of a large-scale tactile event sensed by various receptors distributed over the body.
Solution-Processed Cu2Se Nanocrystal Films with Bulk-Like Thermoelectric Performance
Authors: Forster Jason D. , Lynch Jared J. , Coates Nelson E. , Liu Jun , Jang Hyejin , Zaia Edmond , Gordon Madeleine P. , Szybowski Maxime , Sahu Ayaskanta , Cahill David G. , Urban Jeffrey J. 
Published: May 2017

AbstractThermoelectric power generation can play a key role in a sustainable energy future by converting waste heat from power plants and other industrial processes into usable electrical power. Current thermoelectric devices, however, require energy intensive manufacturing processes such as alloying and spark plasma sintering. Here, we describe the fabrication of a p-type thermoelectric material, copper selenide (Cu2Se), utilizing solution-processing and thermal annealing to produce a thin film that achieves a figure of merit, ZT, which is as high as its traditionally processed counterpart, a value of 0.14 at room temperature. This is the first report of a fully solution-processed nanomaterial achieving performance equivalent to its bulk form and represents a general strategy to reduce the energy required to manufacture advanced energy conversion and harvesting materials.
Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions
Authors: Wang Qing , Wang Xu , Zhang Weijia , Li Xianyu , Zhou Yuan , Li Dan , Wang Yinjia , Tian Jiesheng , Jiang Wei , Zhang Ziding , Peng Youliang , Wang Lei , Li Ying , Li Jilun 
Published: May 2017

AbstractMagnetosome formation by Magnetospirillum gryphiswaldense MSR-1 is dependent on iron and oxygen levels. We used transcriptome to evaluate transcriptional profiles of magnetic and non-magnetic MSR-1 cells cultured under high-iron and low-iron conditions. A total of 80 differentially expressed genes (DEGs) were identified, including 53 upregulated and 27 downregulated under high-iron condition. These DEGs belonged to the functional categories of biological regulation, oxidation-reduction process, and ion binding and transport, and were involved in sulfur metabolism and cysteine/methionine metabolism. Comparison with our previous results from transcriptome data under oxygen-controlled conditions indicated that transcription of mam or mms was not regulated by oxygen or iron signals. 17 common DEGs in iron- and oxygen-transcriptomes were involved in energy production, iron transport, and iron metabolism. Some unknown-function DEGs participate in iron transport and metabolism, and some are potential biomarkers for identification of Magnetospirillum strains. IrrA and IrrB regulate iron transport in response to low-oxygen and high-iron signals, respectively. Six transcription factors were predicted to regulate DEGs. Fur and Crp particularly co-regulate DEGs in response to changes in iron or oxygen levels, in a proposed joint regulatory network of DEGs. Our findings provide new insights into biomineralization processes under high- vs. low-iron conditions in magnetotactic bacteria.
The evaluation of land consolidation policy in improving agricultural productivity in China
Authors: Jin Xiaobin , Shao Yang , Zhang Zhihong , Resler Lynn M. , Campbell James B. , Chen Guo , Zhou Yinkang 
Published: May 2017

AbstractChina is presently undergoing rapid economic development and unprecedented urbanization. Concerns over food security have prompted the Chinese government to implement large-scale land consolidation projects. However, no formal evaluation has been conducted on such projects. Thus, effectiveness of land consolidation policy remains uncertain. We obtained detailed geo-spatial information for 5328 land consolidation projects implemented between 2006 and 2010, and used time-series MODIS NDVI (2006–2016) data to assess effectiveness of China’s land consolidation policy in improving agricultural productivity. Our results show that the overall effectiveness of land consolidation in improving agricultural productivity is low, which lies in contrast to optimistic estimates based on regional statistical analysis and theoretical approaches. For projects (n = 560) implemented in 2006, about 29.5% showed significant (p < 0.05) increasing trends of MODIS NDVI after implementation of land consolidation. For 2007–2010, lower percentages (e.g., 25.9% in 2007 and 13.5% in 2010) of projects showed significant increasing trends. Furthermore, we found effectiveness of land consolidation projects displayed clear regional differences and driving factors are inconsistent with policy design. We anticipate our research to be a starting point for a more comprehensive evaluation involving longer time-series and higher spatial resolution data.
The progression pattern of male hyrax songs and the role of climactic ending
Authors: Demartsev Vlad , Ilany Amiyaal , Kershenbaum Arik , Geva Yair , Margalit Ori , Schnitzer Inbar , Barocas Adi , Bar-Ziv Einat , Koren Lee , Geffen Eli 
Published: May 2017

AbstractThe study of animal vocal signals can either focus on the properties of distinct vocal elements or address the signal as a whole. Although some attention has been given to the continuous progression patterns of bird songs, such patterns in mammalian vocalisations have been largely overlooked. We examined temporal changes in structural and acoustic parameters in male rock hyrax songs. We found a gradual increase in call frequency and amplitude towards the song ending, as well as an abrupt increase in bout syntactic complexity, peaking in the last quintile of a song. In musical terms, such a pattern can be described as a crescendo (amplitude increase) with a terminal climax. In Western music, crescendos are used to maintain attention and direct the listeners towards a memorable highpoint of the musical piece. This structure may have an analogous function in animal communication, recruiting audience attention towards the climactic and potentially most informative part of the signal. Our playback experiments revealed that hyrax males tend to reply more to songs with a climactic ending, indicating that this progression pattern is important for hyrax communication. We suggest that animal vocal communication research can benefit from adding musical concepts to the analysis toolbox.