bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient graphene saturable absorbers on D-shaped optical fiber for ultrashort pulse generation
Authors: Zapata J. D. , Steinberg D. , Saito L. A. M. , de Oliveira R. E. P. , Cárdenas A. M. , de Souza E. A. Thoroh 
Published: February 2016

AbstractWe demonstrated a method to construct high efficiency saturable absorbers based on the evanescent light field interaction of CVD monolayer graphene deposited on side-polished D-shaped optical fiber. A set of samples was fabricated with two different core-graphene distances (0 and 1 μm), covered with graphene ranging between 10 and 25 mm length. The mode-locking was achieved and the best pulse duration was 256 fs, the shortest pulse reported in the literature with CVD monolayer graphene in EDFL. As result, we find a criterion between the polarization relative extinction ratio in the samples and the pulse duration, which relates the better mode-locking performance with the higher polarization extinction ratio of the samples. This criterion also provides a better understanding of the graphene distributed saturable absorbers and their reproducible performance as optoelectronic devices for optical applications.
Functional transcription factor target discovery via compendia of binding and expression profiles
Authors: Banks Christopher J. , Joshi Anagha , Michoel Tom 
Published: February 2016

AbstractGenome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from non-functional binding is therefore a major challenge in the study of transcriptional regulation. We hypothesized that functional targets can be discovered by correlating binding and expression profiles across multiple experimental conditions. To test this hypothesis, we obtained ChIP-seq and RNA-seq data from matching cell types from the human ENCODE resource, considered promoter-proximal and distal cumulative regulatory models to map binding sites to genes and used a combination of linear and non-linear measures to correlate binding and expression data. We found that a high degree of correlation between a gene’s TF-binding and expression profiles was significantly more predictive of the gene being differentially expressed upon knockdown of that TF, compared to using binding sites in the cell type of interest only. Remarkably, TF targets predicted from correlation across a compendium of cell types were also predictive of functional targets in other cell types. Finally, correlation across a time course of ChIP-seq and RNA-seq experiments was also predictive of functional TF targets in that tissue.
Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts
Authors: Scholz Christian F. P. , Brüggemann Holger , Lomholt Hans B. , Tettelin Hervé , Kilian Mogens 
Published: February 2016

AbstractWe present a species-wide comparative analysis of 90 genomes of Propionibacterium acnes that represent the known diversity of the species. Our results are augmented by six high-quality genomes and a manual investigation of all gene-sized indels found in the strains. Overall, the order of genes is conserved throughout the species. A public sybil database for easy comparative analysis of the 90 genomes was established. The analysis of indels revealed a total of 66 loci of non-core genes that correlate with phylogenetic clades. No gene was strain-specific in agreement with our conclusion that the P. acnes pan-genome is closed. An exhaustive search for homopolymeric tracts (HPTs) identified a total of 54 variable-length HPTs almost exclusively of guanine/cytosines located between genes or affecting the reading frame of genes. The repeat variation was consistent with phylogenetic clades suggesting slow accumulation over time rather than active modification. By transcriptome analysis we demonstrate how an HPT variation can affect the gene expression levels. Selected cases of both indels and HPTs are described. The catalogued data and the public P. acnes Sybil database provide a solid foundation for generating hypotheses and facilitate comparative genetic analyses in future P. acnes research.
Pentiptycene-Based Luminescent Cu (II) MOF Exhibiting Selective Gas Adsorption and Unprecedentedly High-Sensitivity Detection of Nitroaromatic Compounds (NACs)
Authors: Zhang Minghui , Zhang Liangliang , Xiao Zhenyu , Zhang Qinhui , Wang Rongming , Dai Fangna , Sun Daofeng 
Published: February 2016

AbstractThe assembly of a fluorescent pentiptycene-based ligand with copper ion resulted in the formation of a 3D porous metal-organic framework (UPC-21) based on well-known paddlewheel SBUs. UPC-21 exhibits selective adsorption of CO2 over CH4 and N2 at 273 K and 295 K, C2H2 over CH4 at 273 K. The most significant performance of UPC-21 is its highly efficient detection of NACs such as 4-NP, 1,4-DNB, NB and 1,3-DNB with the calculated quenching constants, Ksv, being 3.097 × 106, 1.406 × 106, 4.420 × 105 and 1.498 × 105 M−1 for 4-NP, 1,4-DNB, NB, 1,3-DNB, respectively, which keeps a record on the fluorescence detection of NACs. This is the first porous Cu(II) MOF that exhibits fluorescent detection of NACs with high sensitivities.
Cerebral white matter lesions – associations with Aβ isoforms and amyloid PET
Authors: van Westen Danielle , Lindqvist Daniel , Blennow Kaj , Minthon Lennart , Nägga Katarina , Stomrud Erik , Zetterberg Henrik , Hansson Oskar 
Published: February 2016

AbstractSmall vessel disease (SVD) and amyloid deposition may promote each other, with a potential association between SVD and altered production or clearance of β-amyloid (Aβ) affecting its cleavage products. We investigated the relationship between SVD, multiple isoforms of Aβ in cerebrospinal fluid (CSF) and cortical Aβ in 831 subjects with cognitive performance ranging from normal to Alzheimer’s disease (AD) (the Swedish BioFINDER study). SVD was estimated as white matter lesions (WML) and lacunes. 18F-flutemetamol PET was performed in 321 subjects. Lower CSF levels of Aβ38 and Aβ40 were consistently associated with increased WML in all subgroups, while lower levels of CSF Aβ42 were associated with WML mainly in AD. CSF Aβ38 and Aβ40 were associated with regional WML in all regions, while CSF Aβ42 was associated with temporal WML only. A composite measure of 18F-flutemetamol uptake was not associated with WML, and regional 18F-flutemetamol uptake only with temporal WML. Lacunes were not associated with Aβ isoforms nor 18F-flutemetamol uptake. Our results suggest that WML may be associated with alterations in the production or clearance of Aβ species, particularly of Aβ38 and Aβ40. However, in AD cases, Aβ42 pathology might be associated with WML, especially in the temporal lobe.
A molecular nanodevice for targeted degradation of mRNA during protein synthesis
Authors: Lee Kyung-Ho , Min Seung-Eui , Kim Haseong , Lee Seung-Goo , Kim Dong-Myung 
Published: February 2016

AbstractRNase H is an endonuclease that catalyzes the cleavage of RNA. Because it only acts on RNA in RNA:DNA hybrids, RNase H can be used for targeted degradation of RNA when used in combination with antisense oligodeoxyribonucleotides (ASODNs) designed against a specific sequence of the target RNA. In this study, ASODN and RNase H were co-conjugated on magnetic nanoparticles. The resulting nanoparticles, having integrated functions of probing and processing target RNA, were able to remove target mRNA sequences more effectively than free ASODNs. The paramagnetic property of the nanoparticles also enabled timed engagement and disengagement of the RNA-degrading components in a given system, and these nanoparticles were able to be used for ON/OFF control of gene expression during cell-free protein synthesis reactions.
Plumericin inhibits proliferation of vascular smooth muscle cells by blocking STAT3 signaling via S-glutathionylation
Authors: Heiss Elke H , Liu Rongxia , Waltenberger Birgit , Khan Shafaat , Schachner Daniel , Kollmann Paul , Zimmermann Kristin , Cabaravdic Muris , Uhrin Pavel , Stuppner Hermann , Breuss Johannes M , Atanasov Atanas G , Dirsch Verena M 
Published: February 2016

AbstractThe etiology of atherosclerosis and restenosis involves aberrant inflammation and proliferation, rendering compounds with both anti-inflammatory and anti-mitogenic properties as promising candidates for combatting vascular diseases. A recent study identified the iridoid plumericin as a new scaffold inhibitor of the pro-inflammatory NF-κB pathway in endothelial cells. We here examined the impact of plumericin on the proliferation of primary vascular smooth muscle cells (VSMC). Plumericin inhibited serum-stimulated proliferation of rat VSMC. It arrested VSMC in the G1/G0-phase of the cell cycle accompanied by abrogated cyclin D1 expression and hindered Ser 807/811-phosphorylation of retinoblastoma protein. Transient depletion of glutathione by the electrophilic plumericin led to S-glutathionylation as well as hampered Tyr705-phosphorylation and activation of the transcription factor signal transducer and activator of transcription 3 (Stat3). Exogenous addition of glutathione markedly prevented this inhibitory effect of plumericin on Stat3. It also overcame downregulation of cyclin D1 expression and the reduction of biomass increase upon serum exposure. This study revealed an anti-proliferative property of plumericin towards VSMC which depends on plumericin’s thiol reactivity and S-glutathionylation of Stat3. Hence, plumericin, by targeting at least two culprits of vascular dysfunction –inflammation and smooth muscle cell proliferation -might become a promising electrophilic lead compound for vascular disease therapy.
Constitutive expression of a novel antimicrobial protein, Hcm1, confers resistance to both Verticillium and Fusarium wilts in cotton
Authors: Zhang Zhiyuan , Zhao Jun , Ding Lingyun , Zou Lifang , Li Yurong , Chen Gongyou , Zhang Tianzhen 
Published: February 2016

AbstractFusarium and Verticillium wilts, two of the most important diseases in cotton, pose serious threats to cotton production. Here we introduced a novel antimicrobial proteinHcm1, which comprisedharpin protein fromXanthomonas oryzaepv.oryzicola(Xoc), and the chimeric protein, cecropin A-melittin, into cotton. The transgenic cotton lines with stableHcm1expression showed a higher resistance to Verticillium and Fusarium wilts both in greenhouse and field trials compared to controls.Hcm1enabled the transgenic cotton to produced a microscopic hypersensitive response (micro-HR), reactive oxygen species (ROS) burst, and caused the activation of pathogenesis-related (PR) genes in response to biotic stress, indicating that the transgenic cotton was in a primed state and ready to protect the host from pathogenic infection. Simultaneously, Hcm1 protein inhibited the growth ofVerticillium dahliae(V. dahliae) andFusarium oxysporum(F. oxysporum)in vitro. The spread of fungal biomass was also inhibitedin vivosince theV. dahliaebiomass was decreased dramatically in transgenic cotton plants after inoculation withV. dahliae. Together, these results demonstrate thatHcm1could activate innate immunity and inhibit the growth ofV. dahliaeandF. oxysporumto protect cotton against Verticillium and Fusarium wilts.
Spin-orbit torque in Pt/CoNiCo/Pt symmetric devices
Authors: Yang Meiyin , Cai Kaiming , Ju Hailang , Edmonds Kevin William , Yang Guang , Liu Shuai , Li Baohe , Zhang Bao , Sheng Yu , Wang Shouguo , Ji Yang , Wang Kaiyou 
Published: February 2016

AbstractCurrent induced magnetization switching by spin-orbit torques offers an energy-efficient means of writing information in heavy metal/ferromagnet (FM) multilayer systems. The relative contributions of field-like torques and damping-like torques to the magnetization switching induced by the electrical current are still under debate. Here, we describe a device based on a symmetric Pt/FM/Pt structure, in which we demonstrate a strong damping-like torque from the spin Hall effect and unmeasurable field-like torque from Rashba effect. The spin-orbit effective fields due to the spin Hall effect were investigated quantitatively and were found to be consistent with the switching effective fields after accounting for the switching current reduction due to thermal fluctuations from the current pulse. A non-linear dependence of deterministic switching of average Mz on the in-plane magnetic field was revealed, which could be explained and understood by micromagnetic simulation.
Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region
Authors: Faraj Santiago E. , González-Lebrero Rodolfo M. , Roman Ernesto A. , Santos Javier 
Published: February 2016

AbstractThe aim of this study is to investigate the folding reaction of human frataxin, whose deficiency causes the neurodegenerative disease Friedreich’s Ataxia (FRDA). The characterization of different conformational states would provide knowledge about how frataxin can be stabilized without altering its functionality. Wild-type human frataxin and a set of mutants, including two highly destabilized FRDA-associated variants were studied by urea-induced folding/unfolding in a rapid mixing device and followed by circular dichroism. The analysis clearly indicates the existence of an intermediate state (I) in the folding route with significant secondary structure content but relatively low compactness, compared with the native ensemble. However, at high NaCl concentrations I-state gains substantial compaction and the unfolding barrier is strongly affected, revealing the importance of electrostatics in the folding mechanism. The role of the C-terminal region (CTR), the key determinant of frataxin stability, was also studied. Simulations consistently with experiments revealed that this stretch is essentially unstructured, in the most compact transition state ensemble (TSE2). The complete truncation of the CTR drastically destabilizes the native state without altering TSE2. Results presented here shed light on the folding mechanism of frataxin, opening the possibility of mutating it to generate hyperstable variants without altering their folding kinetics.
Tracing amino acid exchange during host-pathogen interaction by combined stable-isotope time-resolved Raman spectral imaging
Authors: Naemat Abida , Elsheikha Hany M. , Boitor Radu A. , Notingher Ioan 
Published: February 2016

AbstractThis study investigates the temporal and spatial interchange of the aromatic amino acid phenylalanine (Phe) between human retinal pigment epithelial cell line (ARPE-19) and tachyzoites of the apicomplexan protozoan parasite Toxoplasma gondii (T. gondii). Stable isotope labelling by amino acids in cell culture (SILAC) is combined with Raman micro-spectroscopy to selectively monitor the incorporation of deuterium-labelled Phe into proteins in individual live tachyzoites. Our results show a very rapid uptake of l-Phe(D8) by the intracellular growing parasite. T. gondii tachyzoites are capable of extracting l-Phe(D8) from host cells as soon as it invades the cell. l-Phe(D8) from the host cell completely replaces the l-Phe within T. gondii tachyzoites 7–9 hours after infection. A quantitative model based on Raman spectra allowed an estimation of the exchange rate of Phe as 0.5–1.6 × 104 molecules/s. On the other hand, extracellular tachyzoites were not able to consume l-Phe(D8) after 24 hours of infection. These findings further our understanding of the amino acid trafficking between host cells and this strictly intracellular parasite. In particular, this study highlights new aspects of the metabolism of amino acid Phe operative during the interaction between T. gondii and its host cell.
Using a Machine Learning Approach to Predict Outcomes after Radiosurgery for Cerebral Arteriovenous Malformations
Authors: Oermann Eric Karl , Rubinsteyn Alex , Ding Dale , Mascitelli Justin , Starke Robert M. , Bederson Joshua B. , Kano Hideyuki , Lunsford L. Dade , Sheehan Jason P. , Hammerbacher Jeffrey , Kondziolka Douglas 
Published: February 2016

AbstractPredictions of patient outcomes after a given therapy are fundamental to medical practice. We employ a machine learning approach towards predicting the outcomes after stereotactic radiosurgery for cerebral arteriovenous malformations (AVMs). Using three prospective databases, a machine learning approach of feature engineering and model optimization was implemented to create the most accurate predictor of AVM outcomes. Existing prognostic systems were scored for purposes of comparison. The final predictor was secondarily validated on an independent site’s dataset not utilized for initial construction. Out of 1,810 patients, 1,674 to 1,291 patients depending upon time threshold, with 23 features were included for analysis and divided into training and validation sets. The best predictor had an average area under the curve (AUC) of 0.71 compared to existing clinical systems of 0.63 across all time points. On the heldout dataset, the predictor had an accuracy of around 0.74 at across all time thresholds with a specificity and sensitivity of 62% and 85% respectively. This machine learning approach was able to provide the best possible predictions of AVM radiosurgery outcomes of any method to date, identify a novel radiobiological feature (3D surface dose), and demonstrate a paradigm for further development of prognostic tools in medical care.
Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species
Authors: Xie Jianbo , Shi Haowen , Du Zhenglin , Wang Tianshu , Liu Xiaomeng , Chen Sanfeng 
Published: February 2016

AbstractPaenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.
Next-generation sequencing-based molecular diagnosis of 12 inherited retinal disease probands of Uyghur ethnicity
Authors: Tajiguli Abulikemu , Xu Mingchu , Fu Qing , Yiming Rouzimaimaiti , Wang Keqing , Li Yumei , Eblimit Aiden , Sui Ruifang , Chen Rui , Aisa Haji Akber 
Published: February 2016

AbstractInherited retinal disease (IRD) is a category of genetic disorders affecting retina. Understanding the molecular basis of IRD is vital for clinical and genetic classification of patients. Uyghur people is an isolated ethnic group mainly residing in northwestern China with genetic admixture from Europeans and East Asians. The genetic etiology of IRD in this specific population still remains unknown. Here, by next-generation sequencing (NGS), we screened mutations in over 200 known retinal disease genes in a cohort of 12 unrelated Uyghur IRD probands. Out of the 12 probands, six are solved with high confidence, two with low confidence, while the remaining four are unsolved. We identified known disease-causing alleles in this cohort that suggest ancient Uyghur migration and also discovered eight novel disease-associated variants. Our results showed NGS-based mutation screening as a reliable approach for molecular diagnosis. In addition, this approach can also be applied to reveal the genetic history of a specific ethnic group.
Sonar sound groups and increased terminal buzz duration reflect task complexity in hunting bats
Authors: Hulgard Katrine , Ratcliffe John M. 
Published: February 2016

AbstractMore difficult tasks are generally regarded as such because they demand greater attention. Echolocators provide rare insight into this relationship because biosonar signals can be monitored. Here we show that bats produce longer terminal buzzes and more sonar sound groups during their approach to prey under presumably more difficult conditions. Specifically, we found Daubenton’s bats,Myotis daubentonii, produced longer buzzes when aerial-hawking versus water-trawling prey, but that bats taking revolving air- and water-borne prey produced more sonar sound groups than did the bats when taking stationary prey. Buzz duration and sonar sound groups have been suggested to be independent means by which bats attend to would-be targets and other objects of interest. We suggest that for attacking bats both should be considered as indicators of task difficulty and that the buzz is, essentially, an extended sonar sound group.
Metabolic/Proteomic Signature Defines Two Glioblastoma Subtypes With Different Clinical Outcome
Authors: Marziali G. , Signore M. , Buccarelli M. , Grande S. , Palma A. , Biffoni M. , Rosi A. , D’Alessandris Q.G. , Martini M. , Larocca L. M. , De Maria R. , Pallini R. , Ricci-Vitiani L. 
Published: February 2016

AbstractGlioblastoma (GBM) is one of the deadliest human cancers. Because of the extremely unfavorable prognosis of GBM, it is important to develop more effective diagnostic and therapeutic strategies based on biologically and clinically relevant subclassification systems. Analyzing a collection of seventeen patient-derived glioblastoma stem-like cells (GSCs) by gene expression profiling, NMR spectroscopy and signal transduction pathway activation, we identified two GSC clusters, one characterized by a pro-neural-like phenotype and the other showing a mesenchymal-like phenotype. Evaluating the levels of proteins differentially expressed by the two GSC clusters in the TCGA GBM sample collection, we found that SRC activation is associated with a GBM subgroup showing better prognosis whereas activation of RPS6, an effector of mTOR pathway, identifies a subgroup with a worse prognosis. The two clusters are also differentiated by NMR spectroscopy profiles suggesting a potential prognostic stratification based on metabolic evaluation. Our data show that the metabolic/proteomic profile of GSCs is informative of the genomic/proteomic GBM landscape, which differs among tumor subtypes and is associated with clinical outcome.