bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hallmarks of the Mott-metal crossover in the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4
Authors: Cao Yue , Wang Qiang , Waugh Justin A. , Reber Theodore J. , Li Haoxiang , Zhou Xiaoqing , Parham Stephen , Park S.-R. , Plumb Nicholas C. , Rotenberg Eli , Bostwick Aaron , Denlinger Jonathan D. , Qi Tongfei , Hermele Michael A. , Cao Gang , Dessau Daniel S. 
Published: April 2016

AbstractThe physics of doped Mott insulators remains controversial after decades of active research, hindered by the interplay among competing orders and fluctuations. It is thus highly desired to distinguish the intrinsic characters of the Mott-metal crossover from those of other origins. Here we investigate the evolution of electronic structure and dynamics of the hole-doped pseudospin-1/2 Mott insulator Sr2IrO4. The effective hole doping is achieved by replacing Ir with Rh atoms, with the chemical potential immediately jumping to or near the top of the lower Hubbard band. The doped iridates exhibit multiple iconic low-energy features previously observed in doped cuprates—pseudogaps, Fermi arcs and marginal-Fermi-liquid-like electronic scattering rates. We suggest these signatures are most likely an integral part of the material’s proximity to the Mott state, rather than from many of the most claimed mechanisms, including preformed electron pairing, quantum criticality or density-wave formation.
Selective inhibition of the kinase DYRK1A by targeting its folding process
Authors: Kii Isao , Sumida Yuto , Goto Toshiyasu , Sonamoto Rie , Okuno Yukiko , Yoshida Suguru , Kato-Sumida Tomoe , Koike Yuka , Abe Minako , Nonaka Yosuke , Ikura Teikichi , Ito Nobutoshi , Shibuya Hiroshi , Hosoya Takamitsu , Hagiwara Masatoshi 
Published: April 2016

AbstractAutophosphorylation of amino-acid residues is part of the folding process of various protein kinases. Conventional chemical screening of mature kinases has missed inhibitors that selectively interfere with the folding process. Here we report a cell-based assay that evaluates inhibition of a kinase at a transitional state during the folding process and identify a folding intermediate-selective inhibitor of dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), which we refer to as FINDY. FINDY suppresses intramolecular autophosphorylation of Ser97 in DYRK1A in cultured cells, leading to its degradation, but does not inhibit substrate phosphorylation catalysed by the mature kinase. FINDY also suppresses Ser97 autophosphorylation of recombinant DYRK1A, suggesting direct inhibition, and shows high selectivity for DYRK1A over other DYRK family members. In addition, FINDY rescues DYRK1A-induced developmental malformations in Xenopus laevis embryos. Our study demonstrates that transitional folding intermediates of protein kinases can be targeted by small molecules, and paves the way for developing novel types of kinase inhibitors.
Size-Dependent Raman Shifts for nanocrystals
Authors: Gao Yukun , Zhao Xinmei , Yin Penggang , Gao Faming 
Published: April 2016

AbstractRaman spectroscopy is a very sensitive tool for probing semiconductor nanocrystals. The underlying mechanism behind the size-dependent Raman shifts is still quite controversial. Here we offer a new theoretical method for the quantum confinement effects on the Raman spectra of semiconductor nanocrystals. We propose that the shift of Raman spectra in nanocrystals can result from two overlapping effects: the quantum effect shift and surface effect shift. The quantum effect shift is extracted from an extended Kubo formula, the surface effect shift is determined via the first principles calculations. Fairly good prediction of Raman shifts can be obtained without the use of any adjustable parameter. Closer analysis shows that the size-dependent Raman shifts in Si nanocrystals mainly result from the quantum effect shifts. For nanodiamond, the proportion of surface effect shift in Raman shift is up to about 40%. Such model can also provide a good baseline for using Raman spectroscopy as a tool to measure size.
Clonify: unseeded antibody lineage assignment from next-generation sequencing data
Authors: Briney Bryan , Le Khoa , Zhu Jiang , Burton Dennis R. 
Published: April 2016

AbstractDefining the dynamics and maturation processes of antibody clonal lineages is crucial to understanding the humoral response to infection and immunization. Although individual antibody lineages have been previously analyzed in isolation, these studies provide only a narrow view of the total antibody response. Comprehensive study of antibody lineages has been limited by the lack of an accurate clonal lineage assignment algorithm capable of operating on next-generation sequencing datasets. To address this shortcoming, we developed Clonify, which is able to perform unseeded lineage assignment on very large sets of antibody sequences. Application of Clonify to IgG+ memory repertoires from healthy individuals revealed a surprising lack of influence of large extended lineages on the overall repertoire composition, indicating that this composition is driven less by the order and frequency of pathogen encounters than previously thought. Clonify is freely available at www.github.com/briney/clonify-python.
Tobacco control policies and perinatal health: a national quasi-experimental study
Authors: Peelen Myrthe J. , Sheikh Aziz , Kok Marjolein , Hajenius Petra , Zimmermann Luc J. , Kramer Boris W. , Hukkelhoven Chantal W. , Reiss Irwin K. , Mol Ben W. , Been Jasper V. 
Published: April 2016

AbstractWe investigated whether changes in perinatal outcomes occurred following introduction of key tobacco control policies in the Netherlands: smoke-free legislation in workplaces plus a tobacco tax increase and mass media campaign (January-February 2004); and extension of the smoke-free law to the hospitality industry, accompanied by another tax increase and mass media campaign (July 2008). This was a national quasi-experimental study using Netherlands Perinatal Registry data (2000–2011; registration: ClinicalTrials.gov NCT02189265). Primary outcome measures were: perinatal mortality, preterm birth and being small-for-gestational age (SGA). The association with timing of the tobacco control policies was investigated using interrupted time series logistic regression analyses with adjustment for confounders. Among 2,069,695 singleton births, there were 13,027 (0.6%) perinatal deaths, 116,043 (5.6%) preterm live-births and 187,966 (9.1%) SGA live-births. The 2004 policies were not associated with significant changes in the odds of developing any of the primary outcomes. After the 2008 policy change, a -4.4% (95% CI -2.4; -6.4, p < 0.001) decrease in odds of being SGA was observed. A reduction in SGA births, but not preterm birth or perinatal mortality, was observed in the Netherlands after extension of the smoke-free workplace law to bars and restaurants in conjunction with a tax increase and mass media campaign.
A new approach to epitaxially grow high-quality GaN films on Si substrates: the combination of MBE and PLD
Authors: Wang Wenliang , Wang Haiyan , Yang Weijia , Zhu Yunnong , Li Guoqiang 
Published: April 2016

AbstractHigh-quality GaN epitaxial films have been grown on Si substrates with Al buffer layer by the combination of molecular beam epitaxy (MBE) and pulsed laser deposition (PLD) technologies. MBE is used to grow Al buffer layer at first and then PLD is deployed to grow GaN epitaxial films on the Al buffer layer. The surface morphology, crystalline quality and interfacial property of as-grown GaN epitaxial films on Si substrates are studied systematically. The as-grown ~300 nm-thick GaN epitaxial films grown at 850 °C with ~30 nm-thick Al buffer layer on Si substrates show high crystalline quality with the full-width at half-maximum (FWHM) for GaN(0002) and GaN(102) X-ray rocking curves of 0.45° and 0.61°, respectively; very flat GaN surface with the root-mean-square surface roughness of 2.5 nm; as well as the sharp and abrupt GaN/AlGaN/Al/Si hetero-interfaces. Furthermore, the corresponding growth mechanism of GaN epitaxial films grown on Si substrates with Al buffer layer by the combination of MBE and PLD is hence studied in depth. This work provides a novel and simple approach for the epitaxial growth of high-quality GaN epitaxial films on Si substrates.
The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages
Authors: Mariano Rachelle , Wuchty Stefan , Vizoso-Pinto Maria G. , Häuser Roman , Uetz Peter 
Published: April 2016

AbstractAlthough an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such patterns were largely absent in S. pneumoniae. Furthermore, targets in E. coli were mutually strongly intertwined, while targets of Dp-1 and Cp-1 were strongly connected through essential and orthologous proteins in their immediate network vicinity. In both phage-host systems, the impact of phages on their protein targets appears to extend from their network neighbors, since proteins that interact with phage targets were located in central network positions, have a strong topologically disruptive effect and touch complexes with high functional heterogeneity. Such observations suggest that the phages, biological impact is accomplished through a surprisingly limited topological reach of their targets.
Simultaneous hyperthermia-chemotherapy with controlled drug delivery using single-drug nanoparticles
Authors: Sato Itaru , Umemura Masanari , Mitsudo Kenji , Fukumura Hidenobu , Kim Jeong-Hwan , Hoshino Yujiro , Nakashima Hideyuki , Kioi Mitomu , Nakakaji Rina , Sato Motohiko , Fujita Takayuki , Yokoyama Utako , Okumura Satoshi , Oshiro Hisashi , Eguchi Haruki , Tohnai Iwai , Ishikawa Yoshihiro 
Published: April 2016

AbstractWe previously investigated the utility of μ-oxo N,N′- bis(salicylidene)ethylenediamine iron (Fe(Salen)) nanoparticles as a new anti-cancer agent for magnet-guided delivery with anti-cancer activity. Fe(Salen) nanoparticles should rapidly heat up in an alternating magnetic field (AMF) and we hypothesized that these single-drug nanoparticles would be effective for combined hyperthermia-chemotherapy. Conventional hyperthermic particles are usually made of iron oxide and thus cannot exhibit anti-cancer activity in the absence of an AMF. We found that Fe(Salen) nanoparticles induced apoptosis in cultured cancer cells and that AMF exposure enhanced the apoptotic effect. Therefore, we evaluated the combined three-fold strategy, i.e., chemotherapy with Fe(Salen) nanoparticles, magnetically guided delivery of the nanoparticles to the tumor and AMF-induced heating of the nanoparticles to induce local hyperthermia, in a rabbit model of tongue cancer. Intravenous administration of Fe(Salen) nanoparticles per se inhibited tumor growth before the other two modalities were applied. This inhibition was enhanced when a magnet was used to accumulate Fe(Salen) nanoparticles at the tongue. When an AMF was further applied (magnet-guided chemotherapy plus hyperthermia), the tumor masses were dramatically reduced. These results indicate that our strategy of combined hyperthermia-chemotherapy using Fe(Salen) nanoparticles specifically delivered with magnetic guidance represents a powerful new approach for cancer treatment.
Particulate-free porous silicon networks for efficient capacitive deionization water desalination
Authors: Metke Thomas , Westover Andrew S. , Carter Rachel , Oakes Landon , Douglas Anna , Pint Cary L. 
Published: April 2016

AbstractEnergy efficient water desalination processes employing low-cost and earth-abundant materials is a critical step to sustainably manage future human needs for clean water resources. Here we demonstrate that porous silicon – a material harnessing earth abundance, cost and environmental/biological compatibility is a candidate material for water desalination. With appropriate surface passivation of the porous silicon material to prevent surface corrosion in aqueous environments, we show that porous silicon templates can enable salt removal in capacitive deionization (CDI) ranging from 0.36% by mass at the onset from fresh to brackish water (10 mM, or 0.06% salinity) to 0.52% in ocean water salt concentrations (500 mM, or ~0.3% salinity). This is on par with reports of most carbon nanomaterial based CDI systems based on particulate electrodes and covers the full salinity range required of a CDI system with a total ocean-to-fresh water required energy input of ~1.45 Wh/L. The use of porous silicon for CDI enables new routes to directly couple water desalination technology with microfluidic systems and photovoltaics that natively use silicon materials, while mitigating adverse effects of water contamination occurring from nanoparticulate-based CDI electrodes.
Digital Signal Processing and Control for the Study of Gene Networks
Authors: Shin Yong-Jun 
Published: April 2016

AbstractThanks to the digital revolution, digital signal processing and control has been widely used in many areas of science and engineering today. It provides practical and powerful tools to model, simulate, analyze, design, measure and control complex and dynamic systems such as robots and aircrafts. Gene networks are also complex dynamic systems which can be studied via digital signal processing and control. Unlike conventional computational methods, this approach is capable of not only modeling but also controlling gene networks since the experimental environment is mostly digital today. The overall aim of this article is to introduce digital signal processing and control as a useful tool for the study of gene networks.
AtOPR3 specifically inhibits primary root growth in Arabidopsis under phosphate deficiency
Authors: Zheng Hongyan , Pan Xiaoying , Deng Yuxia , Wu Huamao , Liu Pei , Li Xuexian 
Published: April 2016

AbstractThe primary root plays essential roles in root development, nutrient absorption and root architectural establishment. Primary root growth is generally suppressed by phosphate (P) deficiency in A. thaliana; however, the underlying molecular mechanisms are largely elusive to date. We found that AtOPR3 specifically inhibited primary root growth under P deficiency via suppressing root tip growth at the transcriptional level, revealing an important novel function of AtOPR3 in regulating primary root response to the nutrient stress. Importantly, AtOPR3 functioned to down-regulate primary root growth under P limitation mostly by its own, rather than depending on the Jasmonic acid signaling pathway. Further, AtOPR3 interacted with ethylene and gibberellin signaling pathways to regulate primary root growth upon P deficiency. In addition, the AtOPR3’s function in inhibiting primary root growth upon P limitation was also partially dependent on auxin polar transport. Together, our studies provide new insights into how AtOPR3, together with hormone signaling interactions, modulates primary root growth in coping with the environmental stress in Arabidopsis.
Lifecourse socioeconomic status and type 2 diabetes: the role of chronic inflammation in the English Longitudinal Study of Ageing
Authors: Stringhini Silvia , Zaninotto Paola , Kumari Meena , Kivimäki Mika , Batty G. David 
Published: April 2016

AbstractWe examined the association between lifecourse socioeconomic status (SES) and the risk of type 2 diabetes at older ages, ascertaining the extent to which adult lifestyle factors and systemic inflammation explain this relationship. Data were drawn from the English Longitudinal Study of Ageing (ELSA) which, established in 2002, is a representative cohort study of ≥50-year olds individuals living in England. SES indicators were paternal social class, participants’ education, participants’ wealth, and a lifecourse socioeconomic index. Inflammatory markers (C-reactive protein and fibrinogen) and lifestyle factors were measured repeatedly; diabetes incidence (new cases) was monitored over 7.5 years of follow-up. Of the 6218 individuals free from diabetes at baseline (44% women, mean aged 66 years), 423 developed diabetes during follow-up. Relative to the most advantaged people, those in the lowest lifecourse SES group experienced more than double the risk of diabetes (hazard ratio 2.59; 95% Confidence Interval (CI) = 1.81–3.71). Lifestyle factors explained 52% (95%CI:30–85) and inflammatory markers 22% (95%CI:13–37) of this gradient. Similar results were apparent with the separate SES indicators. In a general population sample, socioeconomic inequalities in the risk of type 2 diabetes extend to older ages and appear to partially originate from socioeconomic variations in modifiable factors which include lifestyle and inflammation.
Bone marrow-derived mesenchymal stem cells improve diabetes-induced cognitive impairment by exosome transfer into damaged neurons and astrocytes
Authors: Nakano Masako , Nagaishi Kanna , Konari Naoto , Saito Yuki , Chikenji Takako , Mizue Yuka , Fujimiya Mineko 
Published: April 2016

AbstractThe incidence of dementia is higher in diabetic patients, but no effective treatment has been developed. This study showed that rat bone marrow mesenchymal stem cells (BM-MSCs) can improve the cognitive impairments of STZ-diabetic mice by repairing damaged neurons and astrocytes. The Morris water maze test demonstrated that cognitive impairments induced by diabetes were significantly improved by intravenous injection of BM-MSCs. In the CA1 region of the hippocampus, degeneration of neurons and astrocytes, as well as synaptic loss, were prominent in diabetes and BM-MSC treatment successfully normalized them. Since a limited number of donor BM-MSCs was observed in the brain parenchyma, we hypothesized that humoral factors, especially exosomes released from BM-MSCs, act on damaged neurons and astrocytes. To investigate the effectiveness of exosomes for treatment of diabetes-induced cognitive impairment, exosomes were purified from the culture media and injected intracerebroventricularly into diabetic mice. Recovery of cognitive impairment and histological abnormalities similar to that seen with BM-MSC injection was found following exosome treatment. Use of fluorescence-labeled exosomes demonstrated that injected exosomes were internalized into astrocytes and neurons; these subsequently reversed the dysfunction. The present results indicate that exosomes derived from BM-MSCs might be a promising therapeutic tool for diabetes-induced cognitive impairment.
Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery
Authors: Sun Huiyong , Pan Peichen , Tian Sheng , Xu Lei , Kong Xiaotian , Li Youyong , Dan Li  , Hou Tingjun 
Published: April 2016

AbstractThe MIEC-SVM approach, which combines molecular interaction energy components (MIEC) derived from free energy decomposition and support vector machine (SVM), has been found effective in capturing the energetic patterns of protein-peptide recognition. However, the performance of this approach in identifying small molecule inhibitors of drug targets has not been well assessed and validated by experiments. Thereafter, by combining different model construction protocols, the issues related to developing best MIEC-SVM models were firstly discussed upon three kinase targets (ABL, ALK, and BRAF). As for the investigated targets, the optimized MIEC-SVM models performed much better than the models based on the default SVM parameters and Autodock for the tested datasets. Then, the proposed strategy was utilized to screen the Specs database for discovering potential inhibitors of the ALK kinase. The experimental results showed that the optimized MIEC-SVM model, which identified 7 actives with IC50 < 10 μM from 50 purchased compounds (namely hit rate of 14%, and 4 in nM level) and performed much better than Autodock (3 actives with IC50 < 10 μM from 50 purchased compounds, namely hit rate of 6%, and 2 in nM level), suggesting that the proposed strategy is a powerful tool in structure-based virtual screening.
Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes
Authors: Ahadi Alireza , Brennan Samuel , Kennedy Paul J. , Hutvagner Gyorgy , Tran Nham 
Published: April 2016

AbstractLong non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes. The function of these lncRNAs in cancer biology is not entirely clear, but they appear to be modulators of gene expression. In this study, we characterize the expression of lncRNAs in several prostate cancer exosomes and their parental cell lines. We show that certain lncRNAs are enriched in cancer exosomes with the overall expression signatures varying across cell lines. These exosomal lncRNAs are themselves enriched for miRNA seeds with a preference for let-7 family members as well as miR-17, miR-18a, miR-20a, miR-93 and miR-106b. The enrichment of miRNA seed regions in exosomal lncRNAs is matched with a concomitant high expression of the same miRNA. In addition, the exosomal lncRNAs also showed an over representation of RNA binding protein binding motifs. The two most common motifs belonged to ELAVL1 and RBMX. Given the enrichment of miRNA and RBP sites on exosomal lncRNAs, their interplay may suggest a possible function in prostate cancer carcinogenesis.
Glycoengineered Outer Membrane Vesicles: A Novel Platform for Bacterial Vaccines
Authors: Price Nancy L. , Goyette-Desjardins Guillaume , Nothaft Harald , Valguarnera Ezequiel , Szymanski Christine M. , Segura Mariela , Feldman Mario F. 
Published: April 2016

AbstractThe World Health Organization has indicated that we are entering into a post-antibiotic era in which infections that were routinely and successfully treated with antibiotics can now be lethal due to the global dissemination of multidrug resistant strains. Conjugate vaccines are an effective way to create a long-lasting immune response against bacteria. However, these vaccines present many drawbacks such as slow development, high price and batch-to-batch inconsistencies. Alternate approaches for vaccine development are urgently needed. Here we present a new vaccine consisting of glycoengineered outer membrane vesicles (geOMVs). This platform exploits the fact that the initial steps in the biosynthesis of most bacterial glycans are similar. Therefore, it is possible to easily engineer non-pathogenic Escherichia coli lab strains to produce geOMVs displaying the glycan of the pathogen of interest. In this work we demonstrate the versatility of this platform by showing the efficacy of geOMVs as vaccines against Streptococcus pneumoniae in mice and against Campylobacter jejuni in chicken. This cost-effective platform could be employed to generate vaccines to prevent infections caused by a wide variety of microbial agents in human and animals.