bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycyrrhiza uralensis water extract enhances dendritic cell maturation and antitumor efficacy of HPV dendritic cell-based vaccine
Authors: Aipire Adila , Li Jinyu , Yuan Pengfei , He Jiang , Hu Yelang , Liu Lu , Feng Xiaoli , Li Yijie , Zhang Fuchun , Yang Jianhua , Li Jinyao
Published: March 2017

Licorice has been used as herbal medicine and natural sweetener. Here, we prepared Glycyrrhiza uralensis water extract (GUWE) and investigated the effect of GUWE on the maturation and function of dendritic cells (DCs) and its adjuvant effect on DC-based vaccine. We observed that GUWE dose-dependently promoted DC maturation and cytokine secretion through TLR4 signaling pathway. The capacity of DC to stimulate allogenic splenocyte proliferation was also enhanced by GUWE treatment. Compared with control group, GUWE treated DCs pulsed with human papillomavirus (HPV)-16 E6/E7 peptides significantly inhibited the tumor growth in both early and late therapeutic groups. In early therapeutic group, the frequencies of induced regulatory T cells (iTregs: CD4+CD25−Fopx3+) and CD4+ and CD8+ T cells were significantly decreased and increased, respectively. HPV-16-specific CD8+ T cell responses were significantly induced and negatively correlated with iTreg frequencies and tumor weight. These results indicated the immunoregulatory activities of licorice.
SLC22A3 polymorphisms do not modify pancreatic cancer risk, but may influence overall patient survival
Authors: Mohelnikova-Duchonova Beatrice , Strouhal Ondrej , Hughes David J. , Holcatova Ivana , Oliverius Martin , Kala Zdenek , Campa Daniele , Rizzato Cosmeri , Canzian Federico , Pezzilli Raffaele , Talar-Wojnarowska Renata , Malecka-Panas Ewa , Sperti Cosimo , Federico Zambon Carlo , Pedrazzoli Sergio , Fogar Paola , Milanetto Anna Caterina , Capurso Gabriele , Delle Fave Gianfranco , Valente Roberto , Gazouli Maria , Malleo Giuseppe , Teresa Lawlor Rita , Strobel Oliver , Hackert Thilo , Giese Nathalia , Vodicka Pavel , Vodickova Ludmila , Landi Stefano , Tavano Francesca , Gioffreda Domenica , Piepoli Ada , Pazienza Valerio , Mambrini Andrea , Pedata Mariangela , Cantore Maurizio , Bambi Franco , Ermini Stefano , Funel Niccola , Lemstrova Radmila , Soucek Pavel
Published: March 2017

Expression of the solute carrier (SLC) transporter SLC22A3 gene is associated with overall survival of pancreatic cancer patients. This study tested whether genetic variability in SLC22A3 associates with pancreatic cancer risk and prognosis. Twenty four single nucleotide polymorphisms (SNPs) tagging the SLC22A3 gene sequence and regulatory elements were selected for analysis. Of these, 22 were successfully evaluated in the discovery phase while six significant or suggestive variants entered the validation phase, comprising a total study number of 1,518 cases and 3,908 controls. In the discovery phase, rs2504938, rs9364554, and rs2457571 SNPs were significantly associated with pancreatic cancer risk. Moreover, rs7758229 associated with the presence of distant metastases, while rs512077 and rs2504956 correlated with overall survival of patients. Although replicated, the association for rs9364554 did not pass multiple testing corrections in the validation phase. Contrary to the discovery stage, rs2504938 associated with survival in the validation cohort, which was more pronounced in stage IV patients. In conclusion, common variation in the SLC22A3 gene is unlikely to significantly contribute to pancreatic cancer risk. The rs2504938 SNP in SLC22A3 significantly associates with an unfavorable prognosis of pancreatic cancer patients. Further investigation of this SNP effect on the molecular and clinical phenotype is warranted.
Efficient and reliable establishment of lymphoblastoid cell lines by Epstein-Barr virus transformation from a limited amount of peripheral blood
Authors: Omi Natsue , Tokuda Yuichi , Ikeda Yoko , Ueno Morio , Mori Kazuhiko , Sotozono Chie , Kinoshita Shigeru , Nakano Masakazu , Tashiro Kei
Published: March 2017

Lymphoblastoid cell lines (LCLs) transformed by Epstein-Barr virus (EBV) serve as an unlimited resource of human genomic DNA. The protocol that is widely used to establish LCLs involves peripheral blood mononuclear cell isolation by density gradient centrifugation, however, that method requires as much as 5 ml of peripheral blood. In this study, in order to provide a more simple and efficient method for the generation of LCLs, we developed a new protocol using hemolytic reaction to enrich white blood cells for EBV transformation and found that the hemolytic protocol successfully generated LCLs from a small volume (i.e., 0.1 ml) of peripheral blood. To assess the quality of genomic DNA extracted from LCLs established by the hemolytic protocol (LCL-hemolytic), we performed single nucleotide polymorphism (SNP) microarray genotyping using the GeneChip® 100 K Array Set (Affymetrix, Inc.). The concordances of the SNP genotyping resulting from genomic DNA from LCL-hemolytic (99.92%) were found to be as good as the technical replicate (99.90%), and Kappa statistics results confirmed the reliability. The findings of this study reveal that the hemolytic protocol is a simple and reliable method for the generation of LCLs, even from a small volume of peripheral blood.
Effects of the TLR4 signaling pathway on apoptosis of neuronal cells in diabetes mellitus complicated with cerebral infarction in a rat model
Authors: Li Chao , Che Li-He , Ji Tie-Feng , Shi Lei , Yu Jin-Lu
Published: March 2017

This study aims to explore the effects of the TLR4 signaling pathway on the apoptosis of neuronal cells in rats with diabetes mellitus complicated with cerebral infarction (DMCI). A DMCI model was established with 40 Sprague Dawley rats, which were assigned into blank, sham, DM + middle cerebral artery occlusion (MCAO) and DM + MCAO + TAK242 groups. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were measured. A TUNEL assay was applied for detecting cell apoptosis, and Western blotting was used for detecting the expression of TLR4, TNF-α, IL-1β and apoptosis-related proteins. Compared with the blank and sham groups, there was an increase in cell apoptosis, expression of Bcl-2, Bax, cleaved caspase-3, TNF-α, IL-1β and TLR4 proteins and MDA content and a decrease in SOD activity in the DM + MCAO and DM + MCAO + TAK242 groups. Compared with those in the DM + MCAO group, rats in the DM + MCAO + TAK242 group exhibited an increase in SOD activity and a decrease in cell apoptosis, expression of Bcl-2, Bax, cleaved caspase-3, TNF-α, IL-1β and TLR4 proteins and MDA content. Inhibition of the TLR4 signaling pathway reduces neuronal cell apoptosis and nerve injury to protect the brain.
Emergence of linguistic laws in human voice
Authors: Torre Iván González , Luque Bartolo , Lacasa Lucas , Luque Jordi , Hernández-Fernández Antoni
Published: March 2017

Linguistic laws constitute one of the quantitative cornerstones of modern cognitive sciences and have been routinely investigated in written corpora, or in the equivalent transcription of oral corpora. This means that inferences of statistical patterns of language in acoustics are biased by the arbitrary, language-dependent segmentation of the signal, and virtually precludes the possibility of making comparative studies between human voice and other animal communication systems. Here we bridge this gap by proposing a method that allows to measure such patterns in acoustic signals of arbitrary origin, without needs to have access to the language corpus underneath. The method has been applied to sixteen different human languages, recovering successfully some well-known laws of human communication at timescales even below the phoneme and finding yet another link between complexity and criticality in a biological system. These methods further pave the way for new comparative studies in animal communication or the analysis of signals of unknown code.
Design and Functional Characterization of a Novel Abscisic Acid Analog
Authors: Han Xiaoqiang , Jiang Lun , Che Chuanliang , Wan Chuan , Lu Huizhe , Xiao Yumei , Xu Yanjun , Chen Zhongzhou , Qin Zhaohai
Published: March 2017

The phytohormone abscisic acid (ABA) plays a crucial role in mediating plant growth and development by recruiting genetically redundant ABA receptors. To overcome its oxidation inactivation, we developed a novel ABA analog named 2′,3′-benzo-iso-ABA (iso-PhABA) and studied its function and structural characterization with A. thaliana ABA receptors. The (+)-iso-PhABA form showed much higher ABA-like activities than (+)-ABA including inhibitory effects on the seed germination of lettuce and A. thaliana, wheat embryo germination and rice seedling elongation. The PP2C (protein phosphatases 2C) activity assay showed that (+)-iso-PhABA acted as a potent and selective ABA receptor agonist, which is preferred to PYL10. In some cases, (−)-iso-PhABA showed moderate to high activity for the PYL protein inhibiting PP2C activity, suggesting different mechanisms of action of iso-PhABA and ABA. The complex crystal structure of iso-PhABA with PYL10 was determined and elucidated successfully, revealing that (+)-iso-PhABA was better coordinated in the same binding pocket compared to (+)-ABA. Moreover, the detailed interaction network of iso-PhABA/PYL10 was disclosed and involves hydrogen bonds and multiple hydrophobic interactions that provide a robust framework for the design of novel ABA receptor agonists/antagonists.
A millisecond micro-RNA separation technique by a hybrid structure of nanopillars and nanoslits
Authors: Wu Qiong , Kaji Noritada , Yasui Takao , Rahong Sakon , Yanagida Takeshi , Kanai Masaki , Nagashima Kazuki , Tokeshi Manabu , Kawai Tomoji , Baba Yoshinobu
Published: March 2017

A millisecond micro-RNA separation of a mixture of total RNA and genomic DNA, extracted from cultured HeLa cells, was successfully achieved using a hybrid structure of nanopillars and nanoslits contained inside a microchannel. The nanopillars, 250-nm in diameter and 100-nm in height, were fabricated with a 750-nm space inside the nanoslits, which were 100-nm in height and 25-μm in width; the nanopillars were then applied as a new sieve matrix. This ultra-fast technique for the separation of miRNA can be an effective pretreatment for semiconductor nanopore DNA sequencing, which has an optimum reading speed of 1 base/ms to obtain effective signal-to-noise ratio and discriminate each base by ion or tunneling current during the passage of nucleic acids.
Acid phosphatase 2 (ACP2) is required for membrane fusion during influenza virus entry
Authors: Lee Jihye , Kim Jinhee , Son Kidong , d’Alexandry d’Orengiani Anne-Laure Pham Humg , Min Ji-Young
Published: March 2017

Influenza viruses exploit host factors to successfully replicate in infected cells. Using small interfering RNA (siRNA) technology, we identified six human genes required for influenza A virus (IAV) replication. Here we focused on the role of acid phosphatase 2 (ACP2), as its knockdown showed the greatest inhibition of IAV replication. In IAV-infected cells, depletion of ACP2 resulted in a significant reduction in the expression of viral proteins and mRNA, and led to the attenuation of virus multi-cycle growth. ACP2 knockdown also decreased replication of seasonal influenza A and B viruses and avian IAVs of the H7 subtype. Interestingly, ACP2 depletion had no effect on the replication of Ebola or hepatitis C virus. Because ACP2 is known to be a lysosomal acid phosphatase, we assessed the role of ACP2 in influenza virus entry. While neither binding of the viral particle to the cell surface nor endosomal acidification was affected in ACP2-depleted cells, fusion of the endosomal and viral membranes was impaired. As a result, downstream steps in viral entry were blocked, including nucleocapsid uncoating and nuclear import of viral ribonucleoproteins. Our results established ACP2 as a necessary host factor for regulating the fusion step of influenza virus entry.
Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι
Authors: Jain Rinku , Choudhury Jayati Roy , Buku Angeliki , Johnson Robert E. , Prakash Louise , Prakash Satya , Aggarwal Aneel K.
Published: March 2017

N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-ι (Polι) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Polι is ~100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Polι bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a “foothold” and is largely disordered. Together, our kinetic and structural studies show how Polι maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.
Characterizing Biochar as Alternative Sorbent for Oil Spill Remediation
Authors: Silvani Ludovica , Vrchotova Blanka , Kastanek Petr , Demnerova Katerina , Pettiti Ida , Papini Marco Petrangeli
Published: March 2017

Biochar (BC) was characterized as a new carbonaceous material for the adsorption of toluene from water. The tested BC was produced from pine wood gasification, and its sorption ability was compared with that of more common carbonaceous materials such as activated carbon (AC). Both materials were characterized in terms of textural features and sorption abilities by kinetic and equilibrium tests. AC and BC showed high toluene removal from water. Kinetic tests demonstrated that BC is characterized by faster toluene removal than AC is. Textural features demonstrated that the porosity of AC is double that of BC. Nevertheless, equilibrium tests demonstrated that the sorption ability of BC is comparable with that of AC, so the materials’ porosity is not the only parameter that drives toluene adsorption. The specific adsorption ability (mg sorbed m−2 of surface) of the BC is higher than that of AC: toluene is more highly sorbed onto the biochar surface. Biochar is furthermore obtained from biomaterial thermally treated for making energy; this also makes the use of BC economically and environmentally convenient compared with AC, which, as a manufactured material, must be obtained in selected conditions for this type of application.
Genetically-directed Sparse Neuronal Labeling in BAC Transgenic Mice through Mononucleotide Repeat Frameshift
Authors: Lu Xiao-Hong , Yang X. William
Published: March 2017

Mosaicism with Repeat Frameshift (MORF) allows a single Bacterial Artificial Chromosome (BAC) transgene to direct sparse labeling of genetically-defined neuronal populations in mice. The BAC transgene drives cell-type-specific transcription of an out-of-frame mononucleotide repeat that is placed between a translational start codon and a membrane-bound fluorescent protein lacking its start codon. The stochastic frameshift of the unstable repeat DNA in a subset of BAC-expressing neurons results in the in-frame translation of the reporter protein hence the sparse neuronal labeling. As a proof-of-concept, we generated D1-dopamine receptor (D1) BAC MORF mice that label about 1% striatal D1-expressing medium spiny neurons and allow visualization of their dendrites. These mice enable the study of D1-MSN dendrite development in wildtype mice, and its degeneration in a mouse model of Huntington’s disease.
Plasmalogen biosynthesis is spatiotemporally regulated by sensing plasmalogens in the inner leaflet of plasma membranes
Authors: Honsho Masanori , Abe Yuichi , Fujiki Yukio
Published: March 2017

Alkenyl ether phospholipids are a major sub-class of ethanolamine- and choline-phospholipids in which a long chain fatty alcohol is attached at the sn-1 position through a vinyl ether bond. Biosynthesis of ethanolamine-containing alkenyl ether phospholipids, plasmalogens, is regulated by modulating the stability of fatty acyl-CoA reductase 1 (Far1) in a manner dependent on the level of cellular plasmalogens. However, precise molecular mechanisms underlying the regulation of plasmalogen synthesis remain poorly understood. Here we show that degradation of Far1 is accelerated by inhibiting dynamin-, Src kinase-, or flotillin-1-mediated endocytosis without increasing the cellular level of plasmalogens. By contrast, Far1 is stabilized by sequestering cholesterol with nystatin. Moreover, abrogation of the asymmetric distribution of plasmalogens in the plasma membrane by reducing the expression of CDC50A encoding a β-subunit of flippase elevates the expression level of Far1 and plasmalogen synthesis without reducing the total cellular level of plasmalogens. Together, these results support a model that plasmalogens localised in the inner leaflet of the plasma membranes are sensed for plasmalogen homeostasis in cells, thereby suggesting that plasmalogen synthesis is spatiotemporally regulated by monitoring cellular level of plasmalogens.
Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups
Authors: Martin Adam D. , Wojciechowski Jonathan P. , Robinson Andrew B. , Heu Celine , Garvey Christopher J. , Ratcliffe Julian , Waddington Lynne J. , Gardiner James , Thordarson Pall
Published: March 2017

Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy.
Amplified centrosomes and mitotic index display poor concordance between patient tumors and cultured cancer cells
Authors: Mittal Karuna , Choi Da Hoon , Ogden Angela , Donthamsetty Shashi , Melton Brian D. , Gupta Meenakshi. V. , Pannu Vaishali , Cantuaria Guilherme , Varambally Sooryanarayana , Reid Michelle D. , Jonsdottir Kristin , Janssen Emiel A. M. , Aleskandarany Mohammad A. , Ellis Ian O. , Rakha Emad A. , Rida Padmashree C. G. , Aneja Ritu
Published: March 2017

Centrosome aberrations (CA) and abnormal mitoses are considered beacons of malignancy. Cancer cell doubling times in patient tumors are longer than in cultures, but differences in CA between tumors and cultured cells are uncharacterized. We compare mitoses and CA in patient tumors, xenografts, and tumor cell lines. We find that mitoses are rare in patient tumors compared with xenografts and cell lines. Contrastingly, CA is more extensive in patient tumors and xenografts (~35–50% cells) than cell lines (~5–15%), although CA declines in patient-derived tumor cells over time. Intratumoral hypoxia may explain elevated CA in vivo because exposure of cultured cells to hypoxia or mimicking hypoxia pharmacologically or genetically increases CA, and HIF-1α and hypoxic gene signature expression correlate with CA and centrosomal gene signature expression in breast tumors. These results highlight the importance of utilizing low-passage-number patient-derived cell lines in studying CA to more faithfully recapitulate in vivo cellular phenotypes.
Geographical variation in morphology of Chaetosiphella stipae stipae Hille Ris Lambers, 1947 (Hemiptera: Aphididae: Chaitophorinae)
Authors: Wieczorek Karina , Bugaj-Nawrocka Agnieszka , Kanturski Mariusz , Miller Gary L.
Published: March 2017

Chaetosiphella stipae stipaeis a xerothermophilous aphid, associated with Palaearctic temperate steppe zones or dry mountain valleys, where there are grasses from the genusStipa. Its geographical distribution shows several populations that are spread from Spain, across Europe and Asia Minor, to Mongolia and China. Geographical variation in chaetotaxy and other morphological features were the basis to consider whether individuals from different populations are still the same species. Moreover, usingCh. stipae stipaeandStipaspecies occurrences, as well as climatic variables, we predict potential geographical distributions of the aphid and its steppe habitat. Additionally, forStipaspecies we projected current climatic conditions under four climate change scenarios for 2050 and 2070. While highly variable, our results of morphometric analysis demonstrates that allCh. stipae stipaepopulations are one very variable subspecies. And in view of predicted climate change, we expect reduction ofStipagrasslands. The disappearance of these ecosystems could result in stronger separation of the East-European and Asian steppes as well as European ‘warm-stage’ refuges. Therefore, the geographic morphological variability that we see today in the aphid subspeciesCh. stipae stipaemay in the future lead to speciation and creation of separate subspecies or species.
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle
Authors: Guo Yuntao , Zhang Xiuxiu , Huang Wanlong , Miao Xiangyang
Published: March 2017

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.
CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
Authors: Zhang Sijia , Wang Yihan , Chen Meijun , Sun Lulu , Han Jun , Elena V. Kazakova , Qiao Hong
Published: March 2017

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer, and its incidence rate is rapidly growing. It is necessary to understand the pathogenesis of PTC to develop effective diagnosis methods. Promoter methylation has been recognized to contribute to the alterations in gene expression observed in tumorigenesis. Our RNA-seq data identified 1191 differentially expressed mRNAs and 147 differentially expressed lncRNAs in PTC. Next, promoter methylation of these genes was detected by reduced representation bisulfite sequencing (RRBS) technology and comprehensively analyzed to identify differential methylation. In total, 14 genes (13 mRNAs and 1 lncRNA), in which methylation was intimately involved in regulating gene expression, were proposed as novel diagnostic biomarkers. To gain insights into the relationships among these 14 genes, a core co-function network was constructed based on co-expression, co-function and co-methylation data. Notably, CXCL12 was identified as an essential gene in the network that was closely connected with the other genes. These data suggested that CXCL12 down-regulation in PTC may be caused by promoter hypermethylation. Our study was the first to perform an RRBS analysis for PTC and suggested that CXCL12 may contribute to PTC development by methylation-mediated epigenetic regulation of gene expression.
Robustness and Uncertainties of the “Temperature and Greenness” Model for Estimating Terrestrial Gross Primary Production
Authors: Dong Jiaqi , Li Longhui , Shi Hao , Chen Xi , Luo Geping , Yu Qiang
Published: March 2017

Terrestrial gross primary production (GPP) plays a vital role in offsetting anthropogenic CO2 emission and regulating global carbon cycle. Various remote sensing approaches for estimating GPP have attracted considerable scientific attentions, yet their robustness and uncertainties remain unclear. Here we evaluate the performance of the “temperature and greenness” (TG) model, a representative remote sensing model in estimating GPP, using the global FLUXNET GPP based on parameter sensitive analysis and optimization strategies. The results show that the minimum (xn) and optimum (xo) temperatures for photosynthesis are sensitive parameters but maximum temperature (xm) not. Optimized xn and xo differ largely from their defaults for more than half of 12 plant functional types (PFTs). Parameter optimization significantly improves the TG’s performance in forest ecosystems where temperature or solar radiation has significant contribution to GPP. For water-limited ecosystems where GPP are strongly dependent of EVI and EVI are sensitive to precipitation, parameter optimization has limited effects. These results imply that the TG model, and most likely for other kind of GPP models using same methodology, can’t be significantly improved for all PFTs through parameter optimization only, and other key climatic variables should be incorporated into the model for better predicting terrestrial ecosystem GPP.
Computer vision and machine learning for robust phenotyping in genome-wide studies
Authors: Zhang Jiaoping , Naik Hsiang Sing , Assefa Teshale , Sarkar Soumik , Reddy R. V. Chowda , Singh Arti , Ganapathysubramanian Baskar , Singh Asheesh K.
Published: March 2017

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems.
Individual Movement Strategies Revealed through Novel Clustering of Emergent Movement Patterns
Authors: Valle Denis , Cvetojevic Sreten , Robertson Ellen P. , Reichert Brian E. , Hochmair Hartwig H. , Fletcher Robert J.
Published: March 2017

Understanding movement is critical in several disciplines but analysis methods often neglect key information by adopting each location as sampling unit, rather than each individual. We introduce a novel statistical method that, by focusing on individuals, enables better identification of temporal dynamics of connectivity, traits of individuals that explain emergent movement patterns, and sites that play a critical role in connecting subpopulations. We apply this method to two examples that span movement networks that vary considerably in size and questions: movements of an endangered raptor, the snail kite (Rostrhamus sociabilis plumbeus), and human movement in Florida inferred from Twitter. For snail kites, our method reveals substantial differences in movement strategies for different bird cohorts and temporal changes in connectivity driven by the invasion of an exotic food resource, illustrating the challenge of identifying critical connectivity sites for conservation in the presence of global change. For human movement, our method is able to reliably determine the origin of Florida visitors and identify distinct movement patterns within Florida for visitors from different places, providing near real-time information on the spatial and temporal patterns of tourists. These results emphasize the need to integrate individual variation to generate new insights when modeling movement data.
CNT Enabled Co-braided Smart Fabrics: A New Route for Non-invasive, Highly Sensitive & Large-area Monitoring of Composites
Authors: Luo Sida , Wang Yong , Wang Guantao , Wang Kan , Wang Zhibin , Zhang Chuck , Wang Ben , Luo Yun , Li Liuhe , Liu Tao
Published: March 2017

The next-generation of hierarchical composites needs to have built-in functionality to continually monitor and diagnose their own health states. This paper includes a novel strategy forin-situmonitoring the processing stages of composites by co-braiding CNT-enabled fiber sensors into the reinforcing fiber fabrics. This would present a tremendous improvement over the present methods that excessively focus on detecting mechanical deformations and cracks. The CNT enabled smart fabrics, fabricated by a cost-effective and scalable method, are highly sensitive to monitor and quantify various events of composite processing including resin infusion, onset of crosslinking, gel time, degree and rate of curing. By varying curing temperature and resin formulation, the clear trends derived from the systematic study confirm the reliability and accuracy of the method, which is further verified by rheological and DSC tests. More importantly, upon wisely configuring the smart fabrics with a scalable sensor network, localized processing information of composites can be achieved in real time. In addition, the smart fabrics that are readily and non-invasively integrated into composites can provide life-long structural health monitoring of the composites, including detection of deformations and cracks.
Sound Insulation in a Hollow Pipe with Subwavelength Thickness
Authors: Zhang Hai-Long , Zhu Yi-Fan , Liang Bin , Yang Jing , Yang Jun , Cheng Jian-Chun
Published: March 2017

Suppression of the transmission of undesired sound in ducts is a fundamental issue with wide applications in a great variety of scenarios. Yet the conventional ways of duct noise control have to rely on mismatched impedance or viscous dissipation, leading the ducts to have ventilation capability weakened by inserted absorbers or a thick shell to accommodate bulky resonators. Here we present a mechanism for insulating sound transmission in a hollow pipe with subwavelength thickness, by directly reversing its propagating direction via anomalous reflection at the flat inner boundary with well-designed phase profile. A metamaterial-based implementation is demonstrated both in simulation and in experiment, verifying the theoretical prediction on high-efficient sound insulation at the desired frequencies by the resulting device, which has a shell as thin as 1/8 wavelength and an entirely open passage that maintains the continuity of the background medium. We have also investigated the potential of our scheme to work in broadband by simply cascading different metamaterial unit cells. Without the defects of blocked path and bulky size of existing sound insulators, we envision our design will open new route to sound insulation in ducts and have deep implication in practical applications such as designs of ventilation fans and vehicle silencers.
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY
Authors: Shi Jade , Nobrega R. Paul , Schwantes Christian , Kathuria Sagar V. , Bilsel Osman , Matthews C. Robert , Lane T. J. , Pande Vijay S.
Published: March 2017

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
An Innovative Approach for Enhancing Bone Defect Healing Using PLGA Scaffolds Seeded with Extracorporeal-shock-wave-treated Bone Marrow Mesenchymal Stem Cells (BMSCs)
Authors: Chen Youbin , Xu Jiankun , Huang Zhonglian , Yu Menglei , Zhang Yuantao , Chen Hongjiang , Ma Zebin , Liao Haojie , Hu Jun
Published: March 2017

Although great efforts are being made using growth factors and gene therapy, the repair of bone defects remains a major challenge in modern medicine that has resulted in an increased burden on both healthcare and the economy. Emerging tissue engineering techniques that use of combination of biodegradable poly-lactic-co-glycolic acid (PLGA) and mesenchymal stem cells have shed light on improving bone defect healing; however, additional growth factors are also required with these methods. Therefore, the development of novel and cost-effective approaches is of great importance. Our in vitro results demonstrated that ESW treatment (10 kV, 500 pulses) has a stimulatory effect on the proliferation and osteogenic differentiation of bone marrow-derived MSCs (BMSCs). Histological and micro-CT results showed that PLGA scaffolds seeded with ESW-treated BMSCs produced more bone-like tissue with commitment to the osteogenic lineage when subcutaneously implanted in vivo, as compared to control group. Significantly greater bone formation with a faster mineral apposition rate inside the defect site was observed in the ESW group compared to control group. Biomechanical parameters, including ultimate load and stress at failure, improved over time and were superior to those of the control group. Taken together, this innovative approach shows significant potential in bone tissue regeneration.
Colour-crafted phosphor-free white light emitters via in-situ nanostructure engineering
Authors: Min Daehong , Park Donghwy , Lee Kyuseung , Nam Okhyun
Published: March 2017

Colour-temperature (Tc) is a crucial specification of white light-emitting diodes (WLEDs) used in a variety of smart-lighting applications. Commonly, Tc is controlled by distributing various phosphors on top of the blue or ultra violet LED chip in conventional phosphor-conversion WLEDs (PC-WLEDs). Unfortunately, the high cost of phosphors, additional packaging processes required, and phosphor degradation by internal thermal damage must be resolved to obtain higher-quality PC-WLEDs. Here, we suggest a practical in-situ nanostructure engineering strategy for fabricating Tc-controlled phosphor-free white light-emitting diodes (PF-WLEDs) using metal-organic chemical vapour deposition. The dimension controls of in-situ nanofacets on gallium nitride nanostructures, and the growth temperature of quantum wells on these materials, were key factors for Tc control. Warm, true, and cold white emissions were successfully demonstrated in this study without any external processing.
Fluorescence and Magnetic Resonance Dual-Modality Imaging-Guided Photothermal and Photodynamic Dual-Therapy with Magnetic Porphyrin-Metal Organic Framework Nanocomposites
Authors: Zhang Hui , Li Yu-Hao , Chen Yang , Wang Man-Man , Wang Xue-Sheng , Yin Xue-Bo
Published: March 2017

Phototherapy shows some unique advantages in clinical application, such as remote controllability, improved selectivity, and low bio-toxicity, than chemotherapy. In order to improve the safety and therapeutic efficacy, imaging-guided therapy seems particularly important because it integrates visible information to speculate the distribution and metabolism of the probe. Here we prepare biocompatible core-shell nanocomposites for dual-modality imaging-guided photothermal and photodynamic dual-therapy by the in situ growth of porphyrin-metal organic framework (PMOF) on Fe3O4@C core. Fe3O4@C core was used as T2-weighted magnetic resonance (MR) imaging and photothermal therapy (PTT) agent. The optical properties of porphyrin were well remained in PMOF, and PMOF was therefore selected for photodynamic therapy (PDT) and fluorescence imaging. Fluorescence and MR dual-modality imaging-guided PTT and PDT dual-therapy was confirmed with tumour-bearing mice as model. The high tumour accumulation of Fe3O4@C@PMOF and controllable light excitation at the tumour site achieved efficient cancer therapy, but low toxicity was observed to the normal tissues. The results demonstrated that Fe3O4@C@PMOF was a promising dual-imaging guided PTT and PDT dual-therapy platform for tumour diagnosis and treatment with low cytotoxicity and negligible in vivo toxicity.
The effect of diurnal distribution of carbohydrates and fat on glycaemic control in humans: a randomized controlled trial
Authors: Kessler Katharina , Hornemann Silke , Petzke Klaus J. , Kemper Margrit , Kramer Achim , Pfeiffer Andreas F. H. , Pivovarova Olga , Rudovich Natalia
Published: March 2017

Diurnal carbohydrate and fat distribution modulates glycaemic control in rodents. In humans, the optimal timing of both macronutrients and its effects on glycaemic control after prolonged consumption are not studied in detail. In this cross-over trial, 29 non-obese men were randomized to two four-week diets: (1) carbohydrate-rich meals until 13.30 and fat-rich meals between 16.30 and 22.00 (HC/HF) versus (2) inverse sequence of meals (HF/HC). After each trial period two meal tolerance tests were performed, at 09.00 and 15.40, respectively, according to the previous intervention. On the HF/HC diet, whole-day glucose level was increased by 7.9% (p = 0.026) in subjects with impaired fasting glucose and/or impaired glucose tolerance (IFG/IGT, n = 11), and GLP-1 by 10.2% (p = 0.041) in normal glucose-tolerant subjects (NGT, n = 18). Diet effects on fasting GLP-1 (p = 0.009) and PYY (p = 0.034) levels were observed in IFG/IGT, but not in NGT. Afternoon decline of glucose tolerance was more pronounced in IFG/IGT and associated with a stronger decrease of postprandial GLP-1 and PYY levels, but not with changes of cortisol rhythm. In conclusion, the HF/HC diet shows an unfavourable effect on glycaemic control in IFG/IGT, but not in NGT subjects. Consequently, large, carbohydrate-rich dinners should be avoided, primarily by subjects with impaired glucose metabolism.
PD-1 inhibitors increase the incidence and risk of pneumonitis in cancer patients in a dose-independent manner: a meta-analysis
Authors: Wu Jiaying , Hong Dongsheng , Zhang Xiangnan , Lu Xiaoyang , Miao Jing
Published: March 2017

Therapies that targeted PD-1 have shown remarkable rates of durable clinical responses in patients with various tumor types. However, the extent and knowledge of pulmonary toxicities associated with PD-1 blockade, mainly manifested as pneumonitis, remains obscure. In this study, a total of 6360 subjects from 16 phase II/III clinical trials were pooled for meta-analysis to evaluate the overall incidence and risk of PD-1 inhibitors-related pneumonitis in cancer patients. The incidence of pneumonitis during anti-PD-1 immunotherapy was 2.92% (95%CI: 2.18–3.90%) for all-grade and 1.53% (95%CI: 1.15–2.04%) for high-grade pneumonitis. Compared with routine chemotherapy, PD-1 inhibitors were associated with a significant increased risk of pneumonitis. Moreover, among the types of tumor treated with PD-1 inhibitors, the melanoma patients have the lowest incidence of pneumonitis, while the non-small cell lung cancer (NSCLC) and renal cell carcinoma (RCC) patients have the highest. Furthermore, no significant differences were detected in the incidences of all- and high-grade pneumonitis between high-dose and low-dose groups of PD-1 inhibitors. In conclusion, PD-1 inhibitors were probably associated with an increased risk of pneumonitis in a dose-independent manner, compared with routine chemotherapeutic agents. The frequency and severity of treatment-mediated pneumonitis was quite different in patients with various tumor types.
The correlation between osteopontin adsorption and cell adhesion to mixed self-assembled monolayers of varying charges and wettability
Authors: Hao Lijing , Li Tianjie , Yang Fan , Zhao Naru , Cui Fuzhai , Shi Xuetao , Du Chang , Wang Yingjun
Published: March 2017

Mixed SAMs of varying charges and wettability were used as model surfaces to study OPN adsorption and subsequent MSCs adhesion.
Anion exchange: a novel way of preparing hierarchical porous structure in poly(ionic liquid)s
Authors: Qin Li , Wang Binshen , Zhang Yongya , Chen Li , Gao Guohua
Published: March 2017

The exchange of bulky salicylate and its dimers/clusters in PILs by other smaller anions increased specific surface area and fabricated a hierarchical porous structure.
Effects of synthetic iron and aluminium oxide surface charge and hydrophobicity on the formation of bacterial biofilm
Authors: Pouran Hamid M. , Banwart Steve A. , Romero-Gonzalez Maria
Published: March 2017

In this research, bacterial cell attachments to hematite, goethite and aluminium hydroxide were investigated.
Photodegradation of polymer-CNT nanocomposites: effect of CNT loading and CNT release characteristics
Authors: Lankone Ronald S. , Wang Jingjing , Ranville James F. , Fairbrother D. Howard
Published: March 2017

Single particle ICP-MS is used to characterize the evolving magnitude, rate, and form of CNT release from photodegrading polymer nanocomposites.
Facile synthesis of Pd-decorated Pt/Ru networks with highly improved activity for methanol electrooxidation in alkaline media
Authors: Xu Hui , Zhang Ke , Yan Bo , Zhong Jiatai , Li Shumin , Du Yukou
Published: March 2017

Electrocatalytic activity toward methanol oxidation is greatly enhanced after partial replacement of Ru with Pd in Pt/Ru/Pd networks.
LnIII–CoII heterometallic chains based on pyridine substituted nitronyl nitroxides
Authors: Wang Xiufeng , Li Hongdao , Sun Juan , Yang Meng , Li Cun , Li Licun
Published: March 2017

Unprecedented nitronyl nitroxide bridged LnIII–CoII compounds have been obtained. Different magnetic relaxation behaviors were observed for two Dy complexes.
First trial and physicochemical studies on the loading of basic fuchsin, crystal violet and Black Eriochrome T on HKUST-1
Authors: Loera-Serna S. , Ortiz Elba , Beltrán Hiram I.
Published: March 2017

We study the possibility of loading and retaining neutral (basic fuchsin), anionic (Black Eriochrome T) and cationic (crystal violet) molecules on HKUST-1.
Tuning the fluorescence emission in mononuclear heteroleptic trigonal silver(i) complexes
Authors: Durini Sara , Ardizzoia G. Attilio , Therrien Bruno , Brenna Stefano
Published: March 2017

Mononuclear heteroleptic trigonal planar silver(i) complexes have been prepared and characterized, both in solution and in the solid state. Their luminescent behavior was investigated, showing a tunable emission maxima according to the electronic properties of the phosphorous ligand, in the solid state.
Bovine serum albumin as a nanocarrier for the efficient delivery of ginsenoside compound K: preparation, physicochemical characterizations and in vitro biological studies
Authors: Singh Priyanka , Singh Hina , Castro-Aceituno Verónica , Ahn Sungeun , Kim Yeon Ju , Yang Deok Chun
Published: March 2017

Study on the preparation of BSA–CK NPs by a desolvation method and their application as delivery vehicles in cancer and inflammatory cell lines.
Electronic properties of the boroxine–gold interface: evidence of ultra-fast charge delocalization
Authors: Toffoli Daniele , Stredansky Matus , Feng Zhijing , Balducci Gabriele , Furlan Sara , Stener Mauro , Ustunel Hande , Cvetko Dean , Kladnik Gregor , Morgante Alberto , Verdini Alberto , Dri Carlo , Comelli Giovanni , Fronzoni Giovanna , Cossaro Albano
Published: March 2017

A combined theoretical and experimental study of the assembly of triphenylboroxines on Au(111) reveals the charge delocalization properties of the interface.
A two-volt aqueous supercapacitor from porous dehalogenated carbon
Authors: Wang Lin , Zhang Guoxin , Han Biao , Chang Yingna , Li Haoyuan , Wang Jindi , Hu Cejun , Chang Zheng , Huo Ziyang , Sun Xiaoming
Published: March 2017

Safe/long operation of symmetric aqueous supercapacitor at 2 V was achieved using highly porous non-doped carbon from polymer dehalogenation.
The structure and opto–thermo electronic properties of a new (Bi(Bi2S3)9I3)2/3 hexagonal nano-/micro-rod
Authors: Ho Ching-Hwa , Chen Ya-Han , Kuo Yung-Kang , Liu C. W.
Published: March 2017

The structure and opto–thermo electronic properties of a new (Bi(Bi2S3)9I3)2/3 hexagonal nano-/micro-rod have been studied by HRTEM, thermoreflectance, and hot-probe experiments.
A modular platform to develop peptoid-based selective fluorescent metal sensors
Authors: Knight Abigail S. , Kulkarni Rishikesh U. , Zhou Effie Y. , Franke Jenna M. , Miller Evan W. , Francis Matthew B.
Published: March 2017

Peptoid ligands were conjugated to fluorescent pyrene yielding a platform for the selective detection of metal ions in complex samples.
Design, construction, and testing of a supercapacitive swing adsorption module for CO2 separation
Authors: Liu Cong , Landskron Kai
Published: March 2017

We present a device which is able to separate gases from a gas stream using supercapacitive energy.
Porous MoO2 nanowires as stable and high-rate negative electrodes for electrochemical capacitors
Authors: Zheng Dezhou , Feng Haobin , Zhang Xiyue , He Xinjun , Yu Minghao , Lu Xihong , Tong Yexiang
Published: March 2017

Free-standing porous MoO2 nanowires with extraordinary capacitive performance are developed as high-performance electrodes for electrochemical capacitors.
Contrasting diffusion behaviors of O and F atoms on graphene and within bilayer graphene
Authors: Yi Seho , Choi Jin-Ho , Kim Hyun-Jung , Park Chul Hong , Cho Jun-Hyung
Published: March 2017

Our DFT calculations reveal the origin of the contrasting diffusion behaviors of O and F atoms within bilayer graphene.