bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life is hard: countering definitional pessimism concerning the definition of life
Authors: Smith Kelly C. 
Published: September 2016

AbstractCleland and Chyba published a classic piece in 2002 that began a movement I calldefinitional pessimism,where it is argued that there is no point in attempting anything like a general definition of life. This paper offers a critical response to the pessimist position in general and the influential arguments offered by Cleland and her collaborators in particular. One such argument is that all definitions of life fall short of an ideal in which necessary and sufficient conditions produce unambiguous categorizations that dispose of all counterexamples. But this concept of definition is controversial within philosophy; a fact that greatly diminishes the force of the admonition that biologists should conform to such an ideal. Moreover, biology may well be fundamentally different from logic and the physical sciences from which this ideal is drawn, to the point where definitional conformitymisrepresentsbiological reality. Another idea often pushed is that the prospects for definitional success concerning life are on a par with medieval alchemy's attempts to define matter – that is, doomed to fail for lack of a unifying scientific theory. But this comparison to alchemy is both historically inaccurate and unfair. Planetary science before the discovery of the first exoplanets offers a much better analogy, with much more optimistic conclusions. The pessimists also make much of the desirability of using microbes as models for any universal concept of life, from which they conclude that certain types of ‘Darwinian’ evolutionary definitions are inadequate. But this argument posits an unrealistic ideal, as no account of life can both be universal and do justice to the sorts of precise causal mechanisms microbes exemplify. The character of biology and the demand for universality in definitions of life thus probably accords better with functional rather than structural categories. The bottom line is that there is simply no viablealternative,either pragmatically or theoretically, to the pursuit of definitions. If nothing else, the empirical data the pessimists demand will be a very long time coming and scientists will of necessity continue to employ definitions of life in the interim. Chastising them for this will only drive their ideas underground where they can escape critical analysis, making the problems caused by problematic conceptions of life worse.
Crystal nuclei templated nanostructured membranes prepared by solvent crystallization and polymer migration
Authors: Wang Bo , Ji Jing , Li Kang 
Published: September 2016

AbstractCurrently, production of porous polymeric membranes for filtration is predominated by the phase-separation process. However, this method has reached its technological limit, and there have been no significant breakthrough over the last decade. Here we show, using polyvinylidene fluoride as a sample polymer, a new concept of membrane manufacturing by combining oriented green solvent crystallization and polymer migration is able to obtain high performance membranes with pure water permeation flux substantially higher than those with similar pore size prepared by conventional phase-separation processes. The new manufacturing procedure is governed by fewer operating parameters and is, thus, easier to control with reproducible results. Apart from the high water permeation flux, the prepared membranes also show excellent stable flux after fouling and superior mechanical properties of high pressure load and better abrasion resistance. These findings demonstrate the promise of a new concept for green manufacturing nanostructured polymeric membranes with high performances.
Local microRNA delivery targets Palladin and prevents metastatic breast cancer
Authors: Gilam Avital , Conde João , Weissglas-Volkov Daphna , Oliva Nuria , Friedman Eitan , Artzi Natalie , Shomron Noam 
Published: September 2016

AbstractMetastasis is the primary cause for mortality in breast cancer. MicroRNAs, gene expression master regulators, constitute an attractive candidate to control metastasis. Here we show that breast cancer metastasis can be prevented by miR-96 or miR-182 treatment, and decipher the mechanism of action. We found that miR-96/miR-182 downregulate Palladin protein levels, thereby reducing breast cancer cell migration and invasion. A common SNP, rs1071738, at the miR-96/miR-182-binding site within the Palladin 3′-UTR abolishes miRNA:mRNA binding, thus diminishing Palladin regulation by these miRNAs. Regulation is successfully restored by applying complimentary miRNAs. A hydrogel-embedded, gold-nanoparticle-based delivery vehicle provides efficient local, selective, and sustained release of miR-96/miR-182, markedly suppressing metastasis in a breast cancer mouse model. Combined delivery of the miRNAs with a chemotherapy drug, cisplatin, enables significant primary tumour shrinkage and metastasis prevention. Our data corroborate the role of miRNAs in metastasis, and suggest miR-96/miR-182 delivery as a potential anti-metastatic drug.
Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum
Authors: Pyne Michael E. , Liu Xuejia , Moo-Young Murray , Chung Duane A. , Chou C. Perry 
Published: September 2016

AbstractClostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.
Assimilation of virtual legs and perception of floor texture by complete paraplegic patients receiving artificial tactile feedback
Authors: Shokur Solaiman , Gallo Simone , Moioli Renan C. , Donati Ana Rita C. , Morya Edgard , Bleuler Hannes , Nicolelis Miguel A.L. 
Published: September 2016

AbstractSpinal cord injuries disrupt bidirectional communication between the patient’s brain and body. Here, we demonstrate a new approach for reproducing lower limb somatosensory feedback in paraplegics by remapping missing leg/foot tactile sensations onto the skin of patients’ forearms. A portable haptic display was tested in eight patients in a setup where the lower limbs were simulated using immersive virtual reality (VR). For six out of eight patients, the haptic display induced the realistic illusion of walking on three different types of floor surfaces: beach sand, a paved street or grass. Additionally, patients experienced the movements of the virtual legs during the swing phase or the sensation of the foot rolling on the floor while walking. Relying solely on this tactile feedback, patients reported the position of the avatar leg during virtual walking. Crossmodal interference between vision of the virtual legs and tactile feedback revealed that patients assimilated the virtual lower limbs as if they were their own legs. We propose that the addition of tactile feedback to neuroprosthetic devices is essential to restore a full lower limb perceptual experience in spinal cord injury (SCI) patients, and will ultimately, lead to a higher rate of prosthetic acceptance/use and a better level of motor proficiency.
Determination by near infrared microscopy of the nitrogen and carbon content of tomato (Solanum lycopersicum L.) leaf powder
Authors: Lequeue Gauthier , Draye Xavier , Baeten Vincent 
Published: September 2016

AbstractNear infrared microscopy (NIRM) has been developed as a rapid technique to predict the chemical composition of foods, reduce analytical costs and time and ease sample preparation. In this study, NIRM has been evaluated as an alternative to classical chemical analysis to determine the nitrogen and carbon content of small samples of tomato (Solanum lycopersicum L.) leaf powder. Near infrared spectra were obtained by NIRM for independent leaf samples collected on 216 plants grown under six different levels of nitrogen. From these, 30 calibration and 30 validation samples covering the spectral range of the whole set were selected and their nitrogen and carbon contents were determined by a reference method. The calibration model obtained for nitrogen content proved to be excellent, with a coefficient of determination in calibration (R2c) higher than 0.9 and a ratio of performance to deviation (RPDc) higher than 3. Statistical indicators of prediction using the validation set were also very high (R2p values > 0.90). However, the calibration model obtained for carbon content was much less satisfactory (R2c < 0.50). NIRM appears as a promising and suitable tool for a rapid, non-destructive and reliable determination of nitrogen content of tiny samples of tomato leaf powder.
PAH contamination in Beijing’s topsoil: A unique indicator of the megacity’s evolving energy consumption and overall environmental quality
Authors: Li Jinguo , Zheng Yi , Luo Xiaolin , Lin Zhongrong , Zhang Wei , Wang Xuejun 
Published: September 2016

AbstractTo improve its air quality, Beijing, the capital of China, has implemented high-cost pollution control measures mainly focused on shifting its energy mix. However, the effectiveness of these measures has long been questioned, especially given the recent problem of severe haze. The main study objectives are to achieve independent, although indirect, information on Beijing’s air pollution by measuring the level of polycyclic aromatic hydrocarbon (PAH) contamination in topsoil and to examine how soil contamination reflects energy consumption. Soil sampling data from two years, 2004 and 2013, were used. The key findings are as follows: 1) although the total PAH content in the topsoil did not significantly decrease from 2004 to 2013, the composition changed considerably; 2) as of 2013, vehicle emissions replaced coal combustion as the leading source of soil PAHs, which validates the existing policy measures regarding vehicle purchasing and traffic volume; 3) the regional transport of atmospheric pollutants, as indicated by the contribution of coking sources in 2013, is not negligible; and 4) appropriate policy measures are needed to control the growing practice of burning biomass. Overall, this study demonstrates that the PAH contamination in topsoil represents an informative indicator of Beijing’s energy consumption and overall environmental quality.
Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples
Authors: Wang Jingwen , Skoog Tiina , Einarsdottir Elisabet , Kaartokallio Tea , Laivuori Hannele , Grauers Anna , Gerdhem Paul , Hytönen Marjo , Lohi Hannes , Kere Juha , Jiao Hong 
Published: September 2016

AbstractHigh-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r = 0.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r = 0.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.
Evaluation of Glutathione Peroxidase 4 role in Preeclampsia
Authors: Peng Xinguo , Lin Yan , Li Jinling , Liu Mengchun , Wang Jingli , Li Xueying , Liu Jingjing , Jia Xuewen , Jing Zhongcui , Huang Zuzhou , Chu Kaiqiu , Liu Shiguo 
Published: September 2016

AbstractPreeclampsia (PE) is a pregnancy-specific syndrome that may be lifethreatening to pregnancies and fetus. Glutathione Peroxidase 4 (GPx4) is a powerful antioxidant enzyme that can provide protection from oxidative stress damage which plays a pivotal role in the pathology of PE. Therefore, this study aims to investigate the association between Gpx4 polymorphisms and the susceptibility to PE in Chinese Han women. TaqMan allelic discrimination real-time PCR was used to perform the genotyping of rs713041 and rs4807542 in 1008 PE patients and 1386 normotensive pregnancies. Obviously statistical difference of genotypic and allelic frequencies were found of rs713041 in GPx4 between PE patients and controls and the C allele has the higher risk for pathogenesis of PE (χ2 = 12.292, P = 0.002 by genotype; χ2 = 11.035, P = 0.001, OR = 1.216, 95% CI 1.084–1.365 by allele). Additionally, when subdividing these samples into CC + CT and TT groups, we found a significant difference between the two groups (χ2 = 11.241, P = 0.001, OR = 1.417, 95% CI 1.155–1.738). Furthermore, the genotype of rs713041 was found to be associated with the mild, severe and early-onset PE. Our results suggest that rs713041 in GPx4 may play a key role in the pathogenesis of PE.
Amino-Fe3O4 Microspheres Directed Synthesis of a Series of Polyaniline Hierarchical Nanostructures with Different Wettability
Authors: Ma Yong , Chen Yanhui , Hou Chunping , Zhang Hao , Qiao Mingtao , Zhang Hepeng , Zhang Qiuyu 
Published: September 2016

AbstractWe demonstrated polyaniline (PANI) dimensional transformation by adding trace amino-Fe3O4 microspheres to aniline polymerization. Different PANI nanostructures (i.e., flowers, tentacles, and nanofibers) could be produced by controlling the nucleation position and number on the surface of Fe3O4 microspheres, where hydrogen bonding were spontaneously formed between amino groups of Fe3O4 microspheres and aniline molecules. By additionally introducing an external magnetic field, PANI towers were obtained. These PANI nanostructures displayed distinctly different surface wettability in the range from hydrophobicity to hydrophilicity, which was ascribed to the synergistic effect of their dimension, hierarchy, and size. Therefore, the dimension and property of PANI nanostructures can be largely rationalized and predicted by adjusting the PANI nucleation and growth. Using PANI as a model system, the strategies presented here provide insight into the general scheme of dimension and structure control for other conducting polymers.
Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy
Authors: Fröhlich Thomas , Kemter Elisabeth , Flenkenthaler Florian , Klymiuk Nikolai , Otte Kathrin A. , Blutke Andreas , Krause Sabine , Walter Maggie C. , Wanke Rüdiger , Wolf Eckhard , Arnold Georg J. 
Published: September 2016

AbstractDuchenne muscular dystrophy (DMD) is caused by genetic deficiency of dystrophin and characterized by massive structural and functional changes of skeletal muscle tissue, leading to terminal muscle failure. We recently generated a novel genetically engineered pig model reflecting pathological hallmarks of human DMD better than the widely used mdx mouse. To get insight into the hierarchy of molecular derangements during DMD progression, we performed a proteome analysis of biceps femoris muscle samples from 2-day-old and 3-month-old DMD and wild-type (WT) pigs. The extent of proteome changes in DMD vs. WT muscle increased markedly with age, reflecting progression of the pathological changes. In 3-month-old DMD muscle, proteins related to muscle repair such as vimentin, nestin, desmin and tenascin C were found to be increased, whereas a large number of respiratory chain proteins were decreased in abundance in DMD muscle, indicating serious disturbances in aerobic energy production and a reduction of functional muscle tissue. The combination of proteome data for fiber type specific myosin heavy chain proteins and immunohistochemistry showed preferential degeneration of fast-twitch fiber types in DMD muscle. The stage-specific proteome changes detected in this large animal model of clinically severe muscular dystrophy provide novel molecular readouts for future treatment trials.
Experimental Trapped-ion Quantum Simulation of the Kibble-Zurek dynamics in momentum space
Authors: Cui Jin-Ming , Huang Yun-Feng , Wang Zhao , Cao Dong-Yang , Wang Jian , Lv Wei-Min , Luo Le , del Campo Adolfo , Han Yong-Jian , Li Chuan-Feng , Guo Guang-Can 
Published: September 2016

AbstractThe Kibble-Zurek mechanism is the paradigm to account for the nonadiabatic dynamics of a system across a continuous phase transition. Its study in the quantum regime is hindered by the requisite of ground state cooling. We report the experimental quantum simulation of critical dynamics in the transverse-field Ising model by a set of Landau-Zener crossings in pseudo-momentum space, that can be probed with high accuracy using a single trapped ion. We test the Kibble-Zurek mechanism in the quantum regime in the momentum space and find the measured scaling of excitations is in accordance with the theoretical prediction.
Biochemical and structural characterization of the interface mediating interaction between the influenza A virus non-structural protein-1 and a monoclonal antibody
Authors: Wu Jianping , Mok Chee-Keng , Chow Vincent Tak Kwong , Yuan Y. Adam , Tan Yee-Joo 
Published: September 2016

AbstractWe have previously shown that a non-structural protein 1 (NS1)-binding monoclonal antibody, termed as 2H6, can significantly reduce influenza A virus (IAV) replication when expressed intracellularly. In this study, we further showed that 2H6 binds stronger to the NS1 of H5N1 than A/Puerto Rico/8/1934(H1N1) because of an amino acid difference at residue 48. A crystal structure of 2H6 fragment antigen-binding (Fab) has also been solved and docked onto the NS1 structure to reveal the contacts between specific residues at the interface of antibody-antigen complex. In one of the models, the predicted molecular contacts between residues in NS1 and 2H6-Fab correlate well with biochemical results. Taken together, residues N48 and T49 in H5N1 NS1 act cooperatively to maintain a strong interaction with mAb 2H6 by forming hydrogen bonds with residues found in the heavy chain of the antibody. Interestingly, the pandemic H1N1-2009 and the majority of seasonal H3N2 circulating in humans since 1968 has N48 in NS1, suggesting that mAb 2H6 could bind to most of the currently circulating seasonal influenza A virus strains. Consistent with the involvement of residue T49, which is well-conserved, in RNA binding, mAb 2H6 was also found to inhibit the interaction between NS1 and double-stranded RNA.
Controlling Directionality and Dimensionality of Radiation by Perturbing Separable Bound States in the Continuum
Authors: Rivera Nicholas , Hsu Chia Wei , Zhen Bo , Buljan Hrvoje , Joannopoulos John D. , Soljačić Marin 
Published: September 2016

AbstractA bound state in the continuum (BIC) is an unusual localized state that is embedded in a continuum of extended states. Here, we present the general condition for BICs to arise from wave equation separability. Then we show that by exploiting perturbations of certain symmetry such BICs can be turned into resonances that radiate with a tailorable directionality and dimensionality. Using this general framework, we construct new examples of separable BICs and resonances that can exist in optical potentials for ultracold atoms, photonic systems, and systems described by tight binding. Such resonances with easily reconfigurable radiation allow for applications such as the storage and release of waves at a controllable rate and direction, as well systems that switch between different dimensions of confinement.
Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos
Authors: Ye Youqiong , Gu Liang , Chen Xiaolong , Shi Jiejun , Zhang Xiaobai , Jiang Cizhong 
Published: September 2016

AbstractChromatin remodeling plays a critical role in gene regulation and impacts many biological processes. However, little is known about the relationship between chromatin remodeling dynamics and in vivo cell lineage commitment. Here, we reveal the patterns of histone modification change and nucleosome positioning dynamics and their epigenetic regulatory roles during the in vivo glial differentiation in early Drosophila embryos. The genome-wide average H3K9ac signals in promoter regions are decreased in the glial cells compared to the neural progenitor cells. However, H3K9ac signals are increased in a group of genes that are up-regulated in glial cells and involved in gliogenesis. There occurs extensive nucleosome remodeling including shift, loss, and gain. Nucleosome depletion regions (NDRs) form in both promoters and enhancers. As a result, the associated genes are up-regulated. Intriguingly, NDRs form in two fashions: nucleosome shift and eviction. Moreover, the mode of NDR formation is independent of the original chromatin state of enhancers in the neural progenitor cells.
Discovery and Optimization of N-Substituted 2-(4-pyridinyl)thiazole carboxamides against Tumor Growth through Regulating Angiogenesis Signaling Pathways
Authors: Zhou Wenbo , Tang Wenshu , Sun Zhenliang , Li Yunqi , Dong Yanmin , Pei Haixiang , Peng Yangrui , Wang Jinhua , Shao Ting , Jiang Zhenran , Yi Zhengfang , Chen Yihua 
Published: September 2016

AbstractInhibition of angiogenesis is considered as one of the desirable pathways for the treatment of tumor growth and metastasis. Herein we demonstrated that a series of pyridinyl-thiazolyl carboxamide derivatives were designed, synthesized and examined against angiogenesis through a colony formation and migration assays of human umbilical vein endothelial cells (HUVECs) in vitro. A structure-activity relationship (SAR) study was carried out and optimization toward this series of compounds resulted in the discovery of N-(3-methoxyphenyl)-4-methyl-2-(2-propyl-4-pyridinyl)thiazole-5-carboxamide (3k). The results indicated that compound 3k showed similar or better effects compared to Vandetanib in suppressing HUVECs colony formation and migration as well as VEGF-induced angiogenesis in the aortic ring spreading model and chick embryo chorioallantoic membrane (CAM) model. More importantly, compound 3k also strongly blocked tumor growth with the dosage of 30 mg/kg/day, and subsequent mechanism exploration suggested that this series of compounds took effect mainly through angiogenesis signaling pathways. Together, these results suggested compound 3k may serve as a lead for a novel class of angiogenesis inhibitors for cancer treatments.