bluuebunny/crossref_metadata_2025 huggingface dataset:
Have burrowing petrels recovered on Marion Island two decades after cats were eradicated? Evidence from sub-Antarctic skua prey remains
Authors: Cerfonteyn Mia , Ryan Peter G.
Published: October 2015

In the 1980s, penguins dominated the prey remains of sub-Antarctic skuasStercorarius antarcticusbreeding on Marion Island, whereas on neighbouring Prince Edward Island burrowing petrels made up >95% of prey remains in nest middens. This difference resulted at least in part from the impact of introduced catsFelis catuson Marion Island’s burrowing petrel populations. Cats were introduced to Marion Island in 1949, and prior to their eradication in 1991, they killed an estimated 450 000 petrels each year, greatly reducing the densities of petrels breeding on the island. A repeat survey of skua prey remains showed that penguins still dominated the prey of breeding sub-Antarctic skuas on Marion Island in the summer of 2010–11, two decades after cats were eradicated from the island. The proportion of penguin remains decreased slightly compared to 1987–88, but this might be expected given the decreases in penguin numbers on Marion Island over this period. Regurgitated pellets confirmed the dominance of penguin prey on Marion Island. Taken together with the decrease in skua numbers on Marion Island over the last two decades, our results suggest that there has been little recovery in the population of at least summer-breeding burrowing petrels since cats were eradicated.
Predictive value of red blood cell distribution width for coronary artery lesions in patients with Kawasaki disease
Authors: Xu Haiyan , Fu Songling , Wang Wei , Zhang Qing , Hu Jian , Gao Lichao , Zhu Weihua , Gong Fangqi
Published: October 2015

Recent studies have shown that elevated red blood cell distribution width is associated with poor outcome in cardiovascular diseases. In order to assess the predictive value of red blood cell distribution width, before treatment with intravenous immunoglobulins, for coronary artery lesions in patient with Kawasaki disease, we compared 83 patients with coronary artery lesions and 339 patients without coronary artery lesions before treatment with intravenous immunoglobulin. Clinical, echocardiographic, and biochemical values were evaluated along with red blood cell distribution width. A total of 422 consecutive patients with Kawasaki disease were enrolled into our study. According to receiver operating characteristic curve analysis, the optimal red blood cell distribution width cut-off value for predicting coronary artery lesions was 14.55% (area under the curve was 0.721; p=0.000); eighty-three patients (19.7%) had coronary artery lesions, and 70% of the patients with coronary artery lesions had red blood cell distribution width level >14.55%. Logistic regression analysis revealed that fever duration >14 days (odds ratio was 3.42, 95% confidence interval was 1.27–9.22; p=0.015), intravenous immunoglobulin resistance (odds ratio was 2.33, 95% confidence interval was 1.02–5.29; p=0.04), and red blood cell distribution width >14.55% (odds ratio was 3.49, 95% confidence interval was 2.01–6.05; p=0.000) were independent predictors of coronary artery lesions in patients with Kawasaki disease. In Conclusion, red blood cell distribution width may be helpful for predicting coronary artery lesions in patients with Kawasaki disease.
The relation between aspect and inversion in English
Authors: DE WIT ASTRID
Published: October 2015

This article discusses the peculiar use of the simple present/past in full-verb inversion (i.e. locative inversion, directional inversion, quotative inversion, presentational there), and the corresponding scarcity of progressive aspect in these contexts. While it is normally ungrammatical in English to use the simplex tenses to report events that are ongoing at reference time, inversion seems to defy this restriction. Building on a combination of insights from analyses of aspect and of full-verb inversion in English, this study presents a cognitive-functional explanation for this exceptional characteristic of inversion that has gone largely unnoticed in previous accounts. I argue that there exists a canonical relationship between the preposed ground and the postposed figure in full-verb inversion and that this meaning of canonicity ties in perfectly with the perfective value that I deem constitutive of the English simple tenses. In addition, some cases of directional inversion involve a ‘deictic effect’ (Drubig 1988): in these instances, the conceptualizer's vantage point is anchored within the ground and the denoted (dis)appearance of the figure is construed as inevitable. On the basis of a large sample of corpus data and native-speaker elicitations, I demonstrate that the use of the progressive is disallowed in inverted contexts that involve a deictic effect, while its use is dispreferred but not excluded in other cases of inversion. This study thus brings together insights from the domains of information structure and aspect in English, and merges these into a comprehensive cognitive account.
Decline in the prevalence of anaemia among children of pre-school age after implementation of wheat flour fortification with multiple micronutrients in Jordan
Authors: Al Rifai Rami , Nakamura Keiko , Seino Kaoruko
Published: October 2015

Objective

To examine changes in the prevalence of anaemia and its correlates among children of pre-school age after implementation of wheat flour fortification with multiple micronutrients in Jordan.

Design

Retrospective analysis of the data from two repeated national cross-sectional panels of pre-school children.

Setting

The two surveys were conducted in 2007 and 2009, 16–20 months and 34–36 months, respectively, after implementation of wheat flour fortification with multiple micronutrients in Jordan. Anaemia was considered if Hb level was <11 g/dl. An anaemia prevalence of ≥40 % was considered a severe public health problem, while that of 20–39·9 % was considered a moderate public health problem.

Subjects

A total of 3789 and 3447 children aged 6–59 months tested in 2007 and 2009, respectively.

Results

The prevalence of anaemia in pre-school children declined from 40·4 % in 2007 to 33·9 % in 2009 (adjusted OR=0·74;P<0·001). The decline in the prevalence in 2009 as compared with 2007 was more pronounced among children aged >24 months (−13·7 points), children living in urban areas (−8·0 points), children from rich households (−9·0 points), children who had never been breast-fed (−17·0 points) and well-nourished children (−6·8 points). In both surveys, presence of childhood anaemia was strongly associated with child age ≤24 months, living in poor households, breast-feeding for ≥6 months, malnourishment, poor maternal education and maternal anaemia.

Conclusions

The public health problem of childhood anaemia declined from severe in 2007 to moderate in 2009, after the implementation of wheat flour fortification with multiple micronutrients in Jordan.
The global history of Latin America
Authors: Brown Matthew
Published: October 2015

This article explains why historians of Latin America have been disinclined to engage with global history, and how global history has yet to successfully integrate Latin America into its debates. It analyses research patterns and identifies instances of parallel developments in the two fields, which have operated until recently in relative isolation from one another, shrouded and disconnected. It outlines a framework for engagement between Latin American history and global history, focusing particularly on the significant transformations of the understudied nineteenth century. It suggests that both global history and Latin American history will benefit from recognition of the existing work that has pioneered a path between the two, and from enhanced and sustained dialogue.
Caribbean ginger and Atlantic trade, 1570–1648
Authors: Aram Bethany
Published: October 2015

Ginger smuggled out of Asia flourished on the Caribbean islands of Hispaniola and Puerto Rico during the late sixteenth and early seventeenth centuries. The oriental root, whose migration and transplantation Spanish sovereigns sought to stimulate, enjoyed more of a market in England and the Low Countries than in Castile. A differentiated demand for ginger in northern and southern Europe, documented in archival and literary sources, reflected the principles of humoral medicine and influenced trade. Ginger’s poor adaptation to the Spanish fleet system, exacerbated by armed conflicts, including the revolt of the Low Countries (1568–1648) and the Anglo-Spanish War (1585–1604), fomented rather than inhibited a continuum of prohibited practices from privateering to contraband, with English and Dutch merchant-privateers in the ‘Spanish’ Caribbean interested in ginger, sugar, and hides, among other commodities.
Nemerteans in an Irish marine reserve: synopsis of current and historical records
Authors: Trowbridge Cynthia D. , Hiebert Laurel S. , Junoy Juan , Little Colin , Stirling Penny , Dlouhy-Massengale Brittney , McAllen Rob
Published: October 2015

The under-rock guild of nemerteans from Lough Hyne, south-west Ireland was recorded during a long-term benthic survey of the marine reserve. From 2004 to 2014, common nemerteans were recorded annually in late summer for ten historical monitoring sites (each 10 m of shoreline); more comprehensive surveys were completed in 2012 (4126 low-intertidal to shallow-subtidal rocks were turned) and 2014 (1289 rocks turned) with supplementary information in 2015. The bootlace worm,Lineus longissimus,was the most abundant nemertean species. It was significantly more abundant at the extremely shallow East Castle site than the other nine sites; peak populations (across all ten sites) occurred in 2012. The Lusitanian nemerteanParadrepanophorus crassuswas abundant after 2007. To date, 13 nemertean species were recorded with numerous new records for the lough, includingTubulanus annulatus, Micrura purpurea, Ramphogordius sanguineus, Micrella rufaandEmplectonema gracile. Three additional nemertean species were previously recorded, indicating that at least 16 species occur in the lough. Given the low densities and paucity of comprehensive earlier records, we are not able to ascertain definitely whether these species are new incursions or if sparsely distributed residents have increased.
Brightness-equalized quantum dots
Authors: Lim Sung Jun , Zahid Mohammad U. , Le Phuong , Ma Liang , Entenberg David , Harney Allison S. , Condeelis John , Smith Andrew M.
Published: October 2015

As molecular labels for cells and tissues, fluorescent probes have shaped our understanding of biological structures and processes. However, their capacity for quantitative analysis is limited because photon emission rates from multicolour fluorophores are dissimilar, unstable and often unpredictable, which obscures correlations between measured fluorescence and molecular concentration. Here we introduce a new class of light-emitting quantum dots with tunable and equalized fluorescence brightness across a broad range of colours. The key feature is independent tunability of emission wavelength, extinction coefficient and quantum yield through distinct structural domains in the nanocrystal. Precise tuning eliminates a 100-fold red-to-green brightness mismatch of size-tuned quantum dots at the ensemble and single-particle levels, which substantially improves quantitative imaging accuracy in biological tissue. We anticipate that these materials engineering principles will vastly expand the optical engineering landscape of fluorescent probes, facilitate quantitative multicolour imaging in living tissue and improve colour tuning in light-emitting devices.
Exploring three-dimensional orbital imaging with energy-dependent photoemission tomography
Authors: Weiß S. , Lüftner D. , Ules T. , Reinisch E. M. , Kaser H. , Gottwald A. , Richter M. , Soubatch S. , Koller G. , Ramsey M. G. , Tautz F. S. , Puschnig P.
Published: October 2015

Recently, it has been shown that experimental data from angle-resolved photoemission spectroscopy on oriented molecular films can be utilized to retrieve real-space images of molecular orbitals in two dimensions. Here, we extend this orbital tomography technique by performing photoemission initial state scans as a function of photon energy on the example of the brickwall monolayer of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on Ag(110). The overall dependence of the photocurrent on the photon energy can be well accounted for by assuming a plane wave for the final state. However, the experimental data, both for the highest occupied and the lowest unoccupied molecular orbital of PTCDA, exhibits an additional modulation attributed to final state scattering effects. Nevertheless, as these effects beyond a plane wave final state are comparably small, we are able, with extrapolations beyond the attainable photon energy range, to reconstruct three-dimensional images for both orbitals in agreement with calculations for the adsorbed molecule.
Observing the overall rocking motion of a protein in a crystal
Authors: Ma Peixiang , Xue Yi , Coquelle Nicolas , Haller Jens D. , Yuwen Tairan , Ayala Isabel , Mikhailovskii Oleg , Willbold Dieter , Colletier Jacques-Philippe , Skrynnikov Nikolai R. , Schanda Paul
Published: October 2015

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.
Electrical behaviour of dendritic spines as revealed by voltage imaging
Authors: Popovic Marko A. , Carnevale Nicholas , Rozsa Balazs , Zecevic Dejan
Published: October 2015

Thousands of dendritic spines on individual neurons process information and mediate plasticity by generating electrical input signals using a sophisticated assembly of transmitter receptors and voltage-sensitive ion channel molecules. Our understanding, however, of the electrical behaviour of spines is limited because it has not been possible to record input signals from these structures with adequate sensitivity and spatiotemporal resolution. Current interpretation of indirect data and speculations based on theoretical considerations are inconclusive. Here we use an electrochromic voltage-sensitive dye which acts as a transmembrane optical voltmeter with a linear scale to directly monitor electrical signals from individual spines on thin basal dendrites. The results show that synapses on these spines are not electrically isolated by the spine neck to a significant extent. Electrically, they behave as if they are located directly on dendrites.
A quantum dot single-photon source with on-the-fly all-optical polarization control and timed emission
Authors: Heinze Dirk , Breddermann Dominik , Zrenner Artur , Schumacher Stefan
Published: October 2015

Sources of single photons are key elements for applications in quantum information science. Among the different sources available, semiconductor quantum dots excel with their integrability in semiconductor on-chip solutions and the potential that photon emission can be triggered on demand. Usually, the photon is emitted from a single-exciton ground state. Polarization of the photon and time of emission are either probabilistic or pre-determined by electronic properties of the system. Here, we study the direct two-photon emission from the biexciton. The two-photon emission is enabled by a laser pulse driving the system into a virtual state inside the band gap. From this intermediate state, the single photon of interest is then spontaneously emitted. We show that emission through this higher-order transition provides a versatile approach to generate a single photon. Through the driving laser pulse, polarization state, frequency and emission time of the photon can be controlled on-the-fly.
A nanobuffer reporter library for fine-scale imaging and perturbation of endocytic organelles
Authors: Wang Chensu , Wang Yiguang , Li Yang , Bodemann Brian , Zhao Tian , Ma Xinpeng , Huang Gang , Hu Zeping , DeBerardinis Ralph J. , White Michael A. , Gao Jinming
Published: October 2015

Endosomes, lysosomes and related catabolic organelles are a dynamic continuum of vacuolar structures that impact a number of cell physiological processes such as protein/lipid metabolism, nutrient sensing and cell survival. Here we develop a library of ultra-pH-sensitive fluorescent nanoparticles with chemical properties that allow fine-scale, multiplexed, spatio-temporal perturbation and quantification of catabolic organelle maturation at single organelle resolution to support quantitative investigation of these processes in living cells. Deployment in cells allows quantification of the proton accumulation rate in endosomes; illumination of previously unrecognized regulatory mechanisms coupling pH transitions to endosomal coat protein exchange; discovery of distinct pH thresholds required for mTORC1 activation by free amino acids versus proteins; broad-scale characterization of the consequence of endosomal pH transitions on cellular metabolomic profiles; and functionalization of a context-specific metabolic vulnerability in lung cancer cells. Together, these biological applications indicate the robustness and adaptability of this nanotechnology-enabled ‘detection and perturbation’ strategy.
Self-assembled hybrid metal oxide base catalysts prepared by simply mixing with organic modifiers
Authors: Tamura Masazumi , Kishi Ryota , Nakagawa Yoshinao , Tomishige Keiichi
Published: October 2015

Multidentate materials formed by simply mixing heterogeneous and homogeneous components are promising for construction of versatile active sites on the surface of heterogeneous compounds, however, to the best of our knowledge, there are no reports on such materials. Self-assembly of hetero-hybrid catalytic materials occurs when heterogeneous catalysts having adjacent Lewis acid-Lewis base sites are mixed with an organic modifier that contains at least two Lewis base functional groups. Here we demonstrate the strategy by combining cerium oxide and 2-cyanopyridine that self-assembles to form a charge-transfer complex in methanol that exhibits a 2,000-fold increase in reaction rate for hydromethoxylation of acrylonitrile with high selectivity compared with cerium oxide or 2-cyanopyridine alone. The catalytic system is applied to the transesterification and Knoevenagel condensation affording 14-fold and 11-fold higher activity, respectively, than cerium oxide alone. These results demonstrate the potential versatility of the catalytic system and the generality of the catalyst preparation strategy.
Atypical role of sprouty in colorectal cancer: sprouty repression inhibits epithelial–mesenchymal transition
Authors: Zhang Q , Wei T , Shim K , Wright K , Xu K , Palka-Hamblin H L , Jurkevich A , Khare S
Published: October 2015

Sprouty (SPRY) appears to act as a tumor suppressor in cancer, whereas we demonstrated that SPRY2 functions as a putative oncogene in colorectal cancer (CRC) (Oncogene, 2010, 29: 5241–5253). We investigated the mechanisms by which SPRY regulates epithelial–mesenchymal transition (EMT) in CRC. SPRY1 and SPRY2 mRNA transcripts were significantly upregulated in human CRC. Suppression of SPRY2 repressed AKT2 and EMT-inducing transcription factors and significantly increased E-cadherin expression. Concurrent downregulation of SPRY1 and SPRY2 also increased E-cadherin and suppressed mesenchymal markers in colon cancer cells. An inverse expression pattern between AKT2 and E-cadherin was established in a human CRC tissue microarray. SPRY2 negatively regulated miR-194-5p that interacts with AKT2 3′ untranslated region. Mir-194 mimics increased E-cadherin expression and suppressed cancer cell migration and invasion. By confocal microscopy, we demonstrated redistribution of E-cadherin to plasma membrane in colon cancer cells transfected with miR-194. Spry1

−/−
and Spry2

−/−
double mutant mouse embryonic fibroblasts exhibited decreased cell migration while acquiring several epithelial markers. In CRC, SPRY drive EMT and may serve as a biomarker of poor prognosis.
PIK3CA mutations can initiate pancreatic tumorigenesis and are targetable with PI3K inhibitors
Authors: Payne S N , Maher M E , Tran N H , Van De Hey D R , Foley T M , Yueh A E , Leystra A A , Pasch C A , Jeffrey J J , Clipson L , Matkowskyj K A , Deming D A
Published: October 2015

Aberrations in the phosphoinositide 3-kinase (PI3K) signaling pathway have a key role in the pathogenesis of numerous cancers by altering cell growth, metabolism, proliferation and apoptosis. Interest in targeting the PI3K signaling cascade continues, as new agents are being clinically evaluated. PIK3CA mutations result in a constitutively active PI3K and are present in a subset of pancreatic cancers. Here we examine mutant PIK3CA-mediated pancreatic tumorigenesis and the response of PIK3CA mutant pancreatic cancers to dual PI3K/mammalian target of rapamycin (mTOR) inhibition. Two murine models were generated expressing a constitutively active PI3K within the pancreas. An increase in acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasms (PanINs) was identified. In one model these lesions were detected as early as 10 days of age. Invasive pancreatic ductal adenocarcinoma developed in these mice as early as 20 days of age. These cancers were highly sensitive to treatment with dual PI3K/mTOR inhibition. In the second model, PanINs and invasive cancer develop with a greater latency owing to a lesser degree of PI3K pathway activation in this murine model. In addition to PI3K pathway activation, increased ERK1/2 signaling is common in human pancreatic cancers. Phosphorylation of ERK1/2 was also investigated in these models. Phosphorylation of ERK1/2 is demonstrated in the pre-neoplastic lesions and invasive cancers. This activation of ERK1/2 is diminished with dual PI3K/mTOR inhibition. In summary, PIK3CA mutations can initiate pancreatic tumorigenesis and these cancers are particularly sensitive to dual PI3K/mTOR inhibition. Future studies of PI3K pathway inhibitors for patients with PIK3CA mutant pancreatic cancers are warranted.
Azobenzene Modified Imidacloprid Derivatives as Photoswitchable Insecticides: Steering Molecular Activity in a Controllable Manner
Authors: Xu Zhiping , Shi Lina , Jiang Danping , Cheng Jiagao , Shao Xusheng , Li Zhong
Published: October 2015

Incorporating the photoisomerizable azobenzene into imidacloprid produced a photoswitchable insecticidal molecule as the first neonicotinoid example of remote control insecticide performance with spatiotemporal resolution. The designed photoswitchable insecticides showed distinguishable activity against Musca both in vivo and in vitro upon irradiation. Molecular docking study further suggested the binding difference of the two photoisomers. The generation of these photomediated insecticides provides novel insight into the insecticidal activity facilitating further investigation on the functions of insect nicotinic acetylcholine receptors and opens a novel way to control and study insect behavior on insecticide poisoning using light.
Real-time Detection of Breast Cancer Cells Using Peptide-functionalized Microcantilever Arrays
Authors: Etayash Hashem , Jiang Keren , Azmi Sarfuddin , Thundat Thomas , Kaur Kamaljit
Published: October 2015

Ligand-directed targeting and capturing of cancer cells is a new approach for detecting circulating tumor cells (CTCs). Ligands such as antibodies have been successfully used for capturing cancer cells and an antibody based system (CellSearch®) is currently used clinically to enumerate CTCs. Here we report the use of a peptide moiety in conjunction with a microcantilever array system to selectively detect CTCs resulting from cancer, specifically breast cancer. A sensing microcantilever, functionalized with a breast cancer specific peptide 18-4 (WxEAAYQrFL), showed significant deflection on cancer cell (MCF7 and MDA-MB-231) binding compared to when exposed to noncancerous (MCF10A and HUVEC) cells. The peptide-functionalized microcantilever allowed efficient capture and detection of cancer cells in MCF7 spiked human blood samples emulating CTCs in human blood. A detection limit of 50–100 cancer cells mL−1 from blood samples was achieved with a capture yield of 80% from spiked whole blood samples. The results emphasize the potential of peptide 18-4 as a novel peptide for capturing and detecting cancer cells in conjunction with nanomechanical cantilever platform. The reported peptide-based cantilever platform represents a new analytical approach that can lead to an alternative to the various detection platforms and can be leveraged to further study CTCs.
The role of putrescine in the regulation of proteins and fatty acids of thylakoid membranes under salt stress
Authors: Shu Sheng , Yuan Yinghui , Chen Jie , Sun Jin , Zhang Wenhua , Tang Yuanyuan , Zhong Min , Guo Shirong
Published: October 2015

Polyamines can alleviate the inhibitory effects of salinity on plant growth by regulating photosynthetic efficiency. However, little information is available to explain the specific mechanisms underlying the contribution of polyamines to salt tolerance of the photosynthetic apparatus. Here, we investigated the role of putrescine (Put) on the photosynthetic apparatus of cucumber seedlings under salt stress. We found that NaCl stress resulted in severe ion toxicity and oxidative stress in cucumber chloroplasts. In addition, salinity caused a significant increase in the saturated fatty acid contents of thylakoid membranes. Put altered unsaturated fatty acid content, thereby alleviating the disintegration of thylakoid grana lamellae and reducing the number of plastoglobuli in thylakoid membranes. BN-PAGE revealed Put up-regulated the expression of ATP synthase, CP47, D1, Qb and psbA proteins and down-regulated CP24, D2 and LHCII type III in NaCl-stressed thylakoid membranes. qRT-PCR analysis of gene expression was used to compare transcript and protein accumulation among 10 candidate proteins. For five of these proteins, induced transcript accumulation was consistent with the pattern of induced protein accumulation. Our results suggest that Put regulates protein expression at transcriptional and translational levels by increasing endogenous polyamines levels in thylakoid membranes, which may stabilise photosynthetic apparatus under salt stress.
Analysis of a transgenic Oct4 enhancer reveals high fidelity long-range chromosomal interactions
Authors: Cai Mingyang , Gao Fan , Zhang Peilin , An Woojin , Shi Jiandang , Wang Kai , Lu Wange
Published: October 2015

Genome structure or nuclear organization has fascinated researchers investigating genome function. Recently, much effort has gone into defining relationships between specific genome structures and gene expression in pluripotent cells. We previously analyzed chromosomal interactions of the endogenous Oct4 distal enhancer in pluripotent cells. Here, we derive ES and iPS cells from a transgenic Oct4 distal enhancer reporter mouse. Using sonication-based Circularized Chromosome Conformation Capture (4C) coupled with next generation sequencing, we determined and compared the genome-wide interactome of the endogenous and transgenic Oct4 distal enhancers. Integrative genomic analysis indicated that the transgenic enhancer binds to a similar set of loci and shares similar key enrichment profiles with its endogenous counterpart. Both the endogenous and transgenic Oct4 enhancer interacting loci were enriched in the open nucleus compartment, which is associated with active histone marks (H3K4me1, H3K27ac, H3K4me3 and H3K9ac), active cis-regulatory sequences (DNA hypersensitivity sites (DHS)), 5-hydroxymethylcytosine (5-hmc) and early DNA replication domains. In addition, binding of some pluripotency-related transcription factors was consistently enriched in our 4C sites and genes in those sites were generally more highly expressed. Overall, our work reveals critical features that may function in gene expression regulation in mouse pluripotent cells.
Correction: Corrigendum: A Novel Role of Numb as A Regulator of Pro-inflammatory Cytokine Production in Macrophages in Response to Toll-like Receptor 4
Authors: Kueanjinda Patipark , Roytrakul Sittiruk , Palaga Tanapat
Published: October 2015

Activation of macrophages triggers the release of pro-inflammatory cytokines leading to inflammation. Numb is a negative regulator of Notch signaling, but the role of Numb in macrophages is not fully understood. In this study, the role of Numb as a regulator of inflammatory responses in macrophages was investigated. Murine bone marrow-derived macrophages, in which expression of Numb was silenced, secreted significantly less TNFα, IL-6 and IL-12 and more IL-10 upon activation by lipopolysaccharide (LPS), a ligand for Toll-like receptor 4 (TLR4), despite increased Notch signaling. The Tnfα mRNA levels both in Numb-deficient and wild-type macrophages were not significantly different, unlike those of Il6 and Il12-p40. In Numb-deficient macrophages, the Tnfα mRNAs were degraded at faster rate, compared to those in control macrophages. Activation of p38 MAPK and NF-κΒ p65 were compromised in activated Numb deficient macrophages. Numb was found to interact with the E3 ubiquitin ligase, Itch, which reportedly regulates p38 MAPK. In addition, blocking the Notch signaling pathway in activated, Numb-deficient macrophages did not further reduce TNFα levels, suggesting a Notch-independent role for Numb. A proteomics approach revealed a novel funciton for Numb in regulating complex signaling cascades downstream of TLRs, partially involving Akt/NF-κB p65/p38 MAPK in macrophages.
Correction: Corrigendum: Sound Packing DNA: packing open circular DNA with low-intensity ultrasound
Authors: Park DongHee , Jung Bong-Kwang , Park Hyunjin , Lee Hyungbeen , Lee Gyudo , Park Jingam , Shin Unchul , Won Jong Ho , Jo Yong Jun , Chang Jin Woo , Lee Sangwoo , Yoon Daesung , Seo Jongbum , Kim Chul-Woo
Published: October 2015

Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm2 intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery.
Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection
Authors: Mooney Jason P. , Lokken Kristen L. , Byndloss Mariana X. , George Michael D. , Velazquez Eric M. , Faber Franziska , Butler Brian P. , Walker Gregory T. , Ali Mohamed M. , Potts Rashaun , Tiffany Caitlin , Ahmer Brian M. M. , Luckhart Shirley , Tsolis Renée M.
Published: October 2015

Childhood malaria is a risk factor for disseminated infections with non-typhoidal Salmonella (NTS) in sub-Saharan Africa. While hemolytic anemia and an altered cytokine environment have been implicated in increased susceptibility to NTS, it is not known whether malaria affects resistance to intestinal colonization with NTS. To address this question, we utilized a murine model of co-infection. Infection of mice with Plasmodium yoelii elicited infiltration of inflammatory macrophages and T cells into the intestinal mucosa and increased expression of inflammatory cytokines. These mucosal responses were also observed in germ-free mice, showing that they are independent of the resident microbiota. Remarkably, P. yoelii infection reduced colonization resistance of mice against S. enterica serotype Typhimurium. Further, 16S rRNA sequence analysis of the intestinal microbiota revealed marked changes in the community structure. Shifts in the microbiota increased susceptibility to intestinal colonization by S. Typhimurium, as demonstrated by microbiota reconstitution of germ-free mice. These results show that P. yoelii infection, via alterations to the microbial community in the intestine, decreases resistance to intestinal colonization with NTS. Further they raise the possibility that decreased colonization resistance may synergize with effects of malaria on systemic immunity to increase susceptibility to disseminated NTS infections.
mirPRo–a novel standalone program for differential expression and variation analysis of miRNAs
Authors: Shi Jieming , Dong Min , Li Lei , Liu Lin , Luz-Madrigal Agustin , Tsonis Panagiotis A. , Del Rio-Tsonis Katia , Liang Chun
Published: October 2015

Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and “arm switching” are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called “mirPRo” to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization and “arm switching” detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).
Control of a chemical reaction (photodegradation of the p3ht polymer) with nonlocal dielectric environments
Authors: Peters V. N. , Tumkur T. U. , Zhu G. , Noginov M. A.
Published: October 2015

Proximity to metallic surfaces, plasmonic structures, cavities and other inhomogeneous dielectric environments is known to control spontaneous emission, energy transfer, scattering and many other phenomena of practical importance. The aim of the present study was to demonstrate that, in spirit of the Marcus theory, the rates of chemical reactions can, too, be influenced by nonlocal dielectric environments, such as metallic films and metal/dielectric bilayer or multilayer structures. We have experimentally shown that metallic, composite metal/dielectric substrates can, indeed, control ordering as well as photodegradation of thin poly-3-hexylthiophene (p3ht) films. In many particular experiments, p3ht films were separated from metal by a dielectric spacer, excluding conventional catalysis facilitated by metals and making modification of the nonlocal dielectric environment a plausible explanation for the observed phenomena. This first step toward understanding of a complex relationship between chemical reactions and nonlocal dielectric environments is to be followed by the theory development and a broader scope of thorough experimental studies.
An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life
Authors: Barry Roche Daniel , Brüls Thomas
Published: October 2015

Previous studies of protein fold space suggest that fold coverage is plateauing. However, sequence sampling has been -and remains to a large extent- heavily biased, focusing on culturable phyla. Sustained technological developments have fuelled the advent of metagenomics and single-cell sequencing, which might correct the current sequencing bias. The extent to which these efforts affect structural diversity remains unclear, although preliminary results suggest that uncultured organisms could constitute a source of new folds. We investigate to what extent genomes from uncultured and under-sampled phyla accessed through single cell sequencing, metagenomics and high-throughput culturing efforts have the potential to increase protein fold space and conclude that i) genomes from under-sampled phyla appear enriched in sequences not covered by current protein family and fold profile libraries, ii) this enrichment is linked to an excess of short (and possibly partly spurious) sequences in some of the datasets, iii) the discovery rate of novel folds among sequences uncovered by current fold and family profile libraries may be as high as 36%, but would ultimately translate into a marginal increase in global discovery of novel folds. Thus, genomes from under-sampled phyla should have a rather limited impact on increasing coarse grained tertiary structure level novelty.
USP15 regulates SMURF2 kinetics through C-lobe mediated deubiquitination
Authors: Iyengar Prasanna Vasudevan , Jaynes Patrick , Rodon Laura , Lama Dilraj , Law Kai Pong , Lim Yoon Pin , Verma Chandra , Seoane Joan , Eichhorn Pieter Johan Adam
Published: October 2015

Ubiquitin modification of the TGF-β pathway components is emerging as a key mechanism of TGF-β pathway regulation. To limit TGF-β responses, TGF-β signaling is regulated through a negative feedback loop whereby the E3 ligase SMURF2 targets the TGF-β receptor (TβR) complex for ubiquitin-mediated degradation. Counteracting this process, a number of deubiquitinating (DUBs) enzymes have recently been identified that deubiquitinate and stabilize the TβR. However the precise mechanism by which these DUBs act on TβR function remains poorly defined. Here, we demonstrate that apart from targeting the TβR complex directly, USP15 also deubiquitinates SMURF2 resulting in enhanced TβR stability and downstream pathway activation. Through proteomic analysis, we show that USP15 modulates the ubiquitination of Lys734, a residue required for SMURF2 catalytic activity. Our results show that SMURF2 is a critical target of USP15 in the TGF-β pathway and may also explain how USP15 and SMURF2 target multiple complementary protein complexes in other pathways.
Distinguishing time-delayed causal interactions using convergent cross mapping
Authors: Ye Hao , Deyle Ethan R. , Gilarranz Luis J. , Sugihara George
Published: October 2015

An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made substantial progress on this problem by applying the idea of nonlinear attractor reconstruction to time series data. Here, we expand upon the technique of CCM by explicitly considering time lags. Applying this extended method to representative examples (model simulations, a laboratory predator-prey experiment, temperature and greenhouse gas reconstructions from the Vostok ice core and long-term ecological time series collected in the Southern California Bight), we demonstrate the ability to identify different time-delayed interactions, distinguish between synchrony induced by strong unidirectional-forcing and true bidirectional causality and resolve transitive causal chains.
Determination of the hyperfine magnetic field in magnetic carbon-based materials: DFT calculations and NMR experiments
Authors: Freitas Jair C. C. , Scopel Wanderlã L. , Paz Wendel S. , Bernardes Leandro V. , Cunha-Filho Francisco E. , Speglich Carlos , Araújo-Moreira Fernando M. , Pelc Damjan , Cvitanić Tonči , Požek Miroslav
Published: October 2015

The prospect of carbon-based magnetic materials is of immense fundamental and practical importance and information on atomic-scale features is required for a better understanding of the mechanisms leading to carbon magnetism. Here we report the first direct detection of the microscopic magnetic field produced at 13C nuclei in a ferromagnetic carbon material by zero-field nuclear magnetic resonance (NMR). Electronic structure calculations carried out in nanosized model systems with different classes of structural defects show a similar range of magnetic field values (18–21 T) for all investigated systems, in agreement with the NMR experiments. Our results are strong evidence of the intrinsic nature of defect-induced magnetism in magnetic carbons and establish the magnitude of the hyperfine magnetic field created in the neighbourhood of the defects that lead to magnetic order in these materials.
Remote calorimetric detection of urea via flow injection analysis
Authors: Gaddes David E. , Demirel Melik C. , Reeves W. Brian , Tadigadapa Srinivas
Published: October 2015

A continuous flow calorimetric sensing system for biochemical measurements is demonstrated using a highly temperature sensitive Y-cut quartz resonator.
DNA-scaffolded silver nanoclusters as an on–off label-free fluorescence probe for the selective detection of endonuclease activity and inhibition
Authors: Yang Wen , Tian Jianniao , Wang Lijun , Zhao Yanchun , Zhao Shulin
Published: October 2015

A label-free platform method to selectively detect the activity and inhibition of EcoRI has been developed.
A novel cross-linked co-polymeric ionic liquid as a potential adsorbent for highly efficient adsorption of curcuminoids
Authors: Wang Xiao-Feng , Hai Xin , Shu Yang , Chen Xu-Wei , Wang Jian-Hua
Published: October 2015

A novel cross-linked co-polymeric ionic liquid is prepared via mini-emulsion polymerization and it exhibits promising potential in the adsorption of curcuminoids.
Hydrophilic non-precious metal nitrogen-doped carbon electrocatalysts for enhanced efficiency in oxygen reduction reaction
Authors: Hao Guang-Ping , Sahraie Nastaran Ranjbar , Zhang Qiang , Krause Simon , Oschatz Martin , Bachmatiuk Alicja , Strasser Peter , Kaskel Stefan
Published: October 2015

The role of surface hydrophilicity of non-precious metal N-doped carbon electrocatalysts is found to be positive in enhancing catalysis efficiency for oxygen reduction reaction.
The rational design of a gemcitabine prodrug with AIE-based intracellular light-up characteristics for selective suppression of pancreatic cancer cells
Authors: Han Haijie , Jin Qiao , Wang Yin , Chen Yangjun , Ji Jian
Published: October 2015

An enzyme and reduction-activatable gemcitabine prodrug with AIE properties was designed for targeted and image-guided pancreatic cancer therapy.
Functional shakeup of metal–organic frameworks: the rise of the sidekick
Authors: He Jun , Zeller Matthias , Hunter Allen D. , Xu Zhengtao
Published: October 2015

The ever more versatile side groups, from labile weak donors to strong-binding thiol and dendritic functions, sulfur-enabled framework chemistry heralds a rising trend in the design of solid-state materials.
Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges
Authors: Martínez-Araya Jorge Ignacio , Grand André , Glossman-Mitnik Daniel
Published: October 2015

The Spin-Polarized Conceptual Density Functional Theory (SP-CDFT) provides a local reactivity descriptor that after being assessed on the catalytic site (Fe) tends to be proportional to catalytic activity in a better way than the net electric charge computed on the same site. For this aim three 2,6-bis(imino)pyridil iron(iii) cationic catalysts, used for the polymerization of ethylene, were studied.
pH-responsive ion transport in polyelectrolyte multilayers of poly(diallyldimethylammonium chloride) (PDADMAC) and poly(4-styrenesulfonic acid-co-maleic acid) (PSS-MA) bearing strong- and weak anionic groups
Authors: Maza Eliana , Tuninetti Jimena S. , Politakos Nikolaos , Knoll Wolfgang , Moya Sergio , Azzaroni Omar
Published: October 2015

We describe the creation of interfacial architectures displaying pH-dependent ionic transport properties which until now have not been observed in polyelectrolyte multilayers.
Computational modeling of self-trapped electrons in rutile TiO2
Authors: Yan Likai , Elenewski Justin E. , Jiang Wei , Chen Hanning
Published: October 2015

Anionic polaron migration in rutile TiO2 is modeled by the valence bond representation in conjunction with the constrained density functional theory.
Probing zeolites by vibrational spectroscopies
Authors: Bordiga Silvia , Lamberti Carlo , Bonino Francesca , Travert Arnaud , Thibault-Starzyk Frédéric
Published: October 2015

This review addresses the most relevant aspects of vibrational spectroscopies (IR, Raman and INS) applied to zeolites and zeotype materials: acidity, basicity and site accessibility investigated by probes molecules; precise determination of the IR absorption coefficients; thermodynamic aspects of molecular adsorption; space and time resolved experiments.
Metal carbonyl complexes of phosphaamidines. Coordinative integrity detected in C-amino(λ3,σ2)-phosphaalkene isomers coordinated through n(P) HOMO−1 donor orbitals
Authors: Masuda Jason D. , Boeré René T.
Published: October 2015

L(Cr,Mo,W)(CO)5coordination ofN,P-disubstituted phosphaamidines stabilizes molecules prone to isomerization. NMR spectra are consistent with the average mirror symmetry.
A urea-assisted template method to synthesize mesoporous N-doped CeO2 for CO2 capture
Authors: Wang Yangang , Yin Chaochuang , Qin Hengfei , Wang Yunzhu , Li Yaguang , Li Xi , Zuo Yuanhui , Kang Shifei , Cui Lifeng
Published: October 2015

Novel mesoporous nitrogen doped CeO2 has been prepared via a simple urea-assisted template method. The synthesized N-doped mesoporous CeO2 exhibits significantly enhanced CO2 adsorption capacity compared to undoped mesoporous CeO2.
Long-chain polyunsaturated fatty acids amend palmitate-induced inflammation and insulin resistance in mouse C2C12 myotubes
Authors: Chen Shiuan-Chih , Chen Pei-Yin , Wu Yu-Ling , Chen Ching-Wen , Chen Haw-Wen , Lii Chong-Kuei , Sun Hai-Lun , Liu Kai-Li
Published: October 2015

Long-chain PUFAs inhibit inflammation and insulin resistance in mouse C2C12 myotubes.
Evaluation of sample preparation methods for single cell quantitative elemental imaging using proton or synchrotron radiation focused beams
Authors: Perrin Laura , Carmona Asuncion , Roudeau Stéphane , Ortega Richard
Published: October 2015

Sample preparation protocols for single cell quantitative elemental imaging using micro-PIXE or micro-SXRF have been compared and optimized for neuronal cells.
Use of a new enrichment nanosorbent for speciation of mercury by FI-CV-ICP-MS
Authors: Sánchez Trujillo I. , Vereda Alonso E. , Cano Pavón J. M. , García de Torres A.
Published: October 2015

The FI-CV-ICP-MS system using a PMTH-mesoporous sorbent is demonstrated to be promising for the routine determination of mercury species in sea-water samples.
Syntheses and biological evaluations of highly functionalized hydroxamate containing and N-methylthio monobactams as anti-tuberculosis and β-lactamase inhibitory agents
Authors: Majewski Mark W. , Watson Kyle D. , Cho Sanghyun , Miller Patricia A. , Franzblau Scott G. , Miller Marvin J.
Published: October 2015

Described are the syntheses and evaluations of hydroxamate containing and N-methylthiolated monobactams as a class of potent β-lactamase inhibitors.