bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial genetic structure ofManilkara maxima(Sapotaceae), a tree species from the Brazilian Atlantic forest
Authors: Ganzhorn S. M. , Thomas W. W. , Gaiotto F. A. , Lewis J. D. 
Published: June 2015

Abstract:Habitat fragmentation may lead to spatial genetic structuring of plant populations, but the magnitude of this effect differs among species. In this study, the effects of fragmentation on spatial genetic structure ofManilkara maxima, an ecologically important tree species endemic to the Atlantic forest of southern Bahia, Brazil, were examined. To address this issue, 222 individuals were sampled across two large-forest sites (200 and 400 ha) and one site comprising eight small fragments (5, 10 and 25 ha) roughly 35 y old. Five microsatellite loci were used. In general,M. maximaexhibited limited genetic structuring within and across the sites examined. At the landscape scale, genetic structure was not shaped by isolation by distance. Within individual sites, weak to moderate genetic structure was observed for both adults and saplings, which represented pre- and post-fragmentation, respectively. Sapling genetic structure did not clearly vary among the study sites, suggesting fragmentation has not affected spatial genetic structure. High levels of migration were observed, which would help maintain genetic connectivity. Taken together, these results suggestM. maxima, a long-lived tree that naturally occurs in low densities, may have limited spatial genetic structuring both within and across forest patches.
Early life history traits ofTrematomus scottiin the Bransfield Strait
Authors: La Mesa Mario , Catalano Barbara , Jones Christopher D. 
Published: June 2015

AbstractEarly life history traits of the blackfin notothen,Trematomus scotti, were investigated through otolith microincrement pattern and stomach content analyses. Post-larval specimens of 12–20 mm standard length (SL) were collected in the Bransfield Strait and adjacent waters during the 2010–11 summer. Catches were unevenly distributed across the surveyed area, yielding a relative abundance of 0.3–3.6 specimens per 1000 m3of filtered sea water. Age estimates ranged from 34 to 67 days, with good consistency and no apparent bias between readings. Based on an exponential model fitted to the age-length dataset, the growth rate was 0.17 mm day-1, corresponding to a daily percentage increment in size of 1.07% SL. In agreement with previous studies, larval hatching occurred at a mean size of 9.0 mm and was spread over a relatively short period, lasting from late December to late January. Prey composition consisted exclusively of copepods, mainly larval stages of copepodites. Feeding intensity ranged from 1–14 prey items per stomach, being positively correlated with larval fish size. In summary,T. scottishares a common early life history strategy with several other notothenioids, consisting of small larvae hatching in summer and overwintering as pelagic early juveniles until the following summer season.
Solid State Reaction Mechanism and Microstructure Evolution of Ni-Al Powders during High Energy Ball Milling Revisited by TEM
Authors: Fan Guohua , Geng Lin , Feng Yicheng , Cui Xiping , Yan Xudong 
Published: June 2015

AbstractMicrostructure evolution during the formation of B2–NiAl by high energy ball milling of equiatomic elemental mixtures was studied by X-ray diffractometer, scanning electron microscopy, and transmission electron microscopy (TEM). The crystallite size, lattice defects and ordering of the B2–NiAl were monitored via TEM as function of milling time. The diffusion reaction, Ni+Al→NiAl3or/and Ni2Al3, occurred during high energy ball milling, and to a certain extent offered the stored energy for the explosive exothermic reaction, Ni+Al→B2–NiAl. The fine microstructure of newly formed B2–NiAl after 5 h milling involved high density defects, e.g. antiphase boundary, long range ordering domains, vacancies, and dislocations.
Postmastectomy internal mammary node radiation in women with breast cancer: a long-term follow-up study
Authors: Yadav Budhi S. , Sharma Suresh C. , Ghoshal Sushmita , Kapoor Rakesh K. , Kumar Narendra 
Published: June 2015

AbstractBackgroundTo observe the impact of internal mammary node irradiation (IMNI) on disease-free survival (DFS) and overall survival (OS) in postmastectomy women with breast cancer.Materials and methodsBetween 1978 and 1996, 153 women with stage II–III breast cancer were treated with postmastectomy radiation therapy (RT) with IMNI. Their clinical, pathological and treatment characteristics were matched with 166 patients without IMNI. The RT dose was 35 Gy to the chest wall and 40 Gy to the supraclavicular fossa and IMN in 15 fractions over 3 weeks with photons. All patients were planned with two-dimensional technique. Adjuvant chemotherapy was administered to 41% and endocrine therapy to 52% of the patients. Symptomatic patients were further assessed for late pulmonary and late cardiac effects.ResultsThe median follow-up period was 203 months (range, 182–224), and the median age was 44 years (range 20–73 years). The IMNI group had significantly more right-sided and inner/central quadrant tumours. Other characteristics were comparable between both the groups. DFS at 15 years with and without IMNI was 64 and 49%, respectively (p=0·0001). On multivariate analysis, IMNI was an independent, positive predictor of DFS [hazard ratio (HR), 2·89;p=0·0001]. Benefit of IMNI on DFS was more apparent in inner/central tumours [HR, 1·48; 95% confidence interval (CI), 1·02–2·88], N2–N3 patients (HR, 1·44; 95% CI, 1·09–2·10) and in those who received chemotherapy (HR, 1·70; 95% CI, 1·07–2·71). OS at 15 years with and without IMNI was 68 and 54%, respectively (p=0·0001). Late pulmonary toxicity was 1·5 versus 1% with and without IMNI, respectively. Late cardiac toxicity was 2·6 versus 1·8% with and without IMNI, respectively.ConclusionsIMNI significantly improved DFS and OS in postmastectomy breast cancer patients. Benefit of IMNI was seen in patients with central/inner tumours and N2–N3 disease. Late cardiopulmonary toxicities were comparable between the two groups.
Glycation of vitronectin inhibits VEGF-induced angiogenesis by uncoupling VEGF receptor-2–αvβ3 integrin cross-talk
Authors: Wang L , Zhang X , Pang N , Xiao L , Li Y , Chen N , Ren M , Deng X , Wu J 
Published: June 2015

AbstractGlycation of vessel wall proteins is thought to have an important role in the pathogenesis of vascular complications in diabetes mellitus. However, no previous study has implicated glycated vitronectin (VN) in the control of vascular endothelial growth factor (VEGF) signaling. To explore whether the glycation of VN affects angiogenic signaling and to understand the molecular mechanisms involved, we synthesized glycated VN by incubating VN with methylglyoxal (MGO) in vitro and identified the formation of glycated VN by an LC–ESI–MS/MS-based method. We tested the hypothesis that glycation of VN downregulates VEGF receptor-2 (VEGFR-2) activation by uncoupling the interaction between VEGFR-2 and αvβ3. Unmodified and MGO-glycated VN were used as substrates for human umbilical vein endothelial cells (HUVECs). The effects of glycated VN on VEGF signaling in HUVECs were investigated. The glycation of VN inhibited VEGF-induced phosphorylation of VEGFR-2 and the intracellular signaling pathway downstream of VEGFR-2. Glycated VN inhibited the binding of VEGFR-2 to β3 integrin and inhibited the phosphorylation of β3 integrin. Furthermore, glycation of VN significantly decreased VEGF-induced migration of HUVECs in vitro and vessel outgrowth in an ex vivo angiogenesis model. Collectively, these data indicate that the glycation of VN inhibits VEGF-induced VEGFR-2 activation by uncoupling VEGFR-2–αvβ3 integrin cross-talk. The glycation of VN causes a reduction in the migration of endothelial cells and vessel outgrowth. This may provide a mechanism for the failure of collateral sprouting in diabetic microangiopathy.
IL-1 receptor antagonist-deficient mice develop autoimmune arthritis due to intrinsic activation of IL-17-producing CCR2+Vγ6+γδ T cells
Authors: Akitsu Aoi , Ishigame Harumichi , Kakuta Shigeru , Chung Soo-hyun , Ikeda Satoshi , Shimizu Kenji , Kubo Sachiko , Liu Yang , Umemura Masayuki , Matsuzaki Goro , Yoshikai Yasunobu , Saijo Shinobu , Iwakura Yoichiro 
Published: June 2015

AbstractInterleukin-17 (IL-17)-producing γδ T (γδ17) cells have been implicated in inflammatory diseases, but the underlying pathogenic mechanisms remain unclear. Here, we show that both CD4+ and γδ17 cells are required for the development of autoimmune arthritis in IL-1 receptor antagonist (IL-1Ra)-deficient mice. Specifically, activated CD4+ T cells direct γδ T-cell infiltration by inducing CCL2 expression in joints. Furthermore, IL-17 reporter mice reveal that the Vγ6+ subset of CCR2+ γδ T cells preferentially produces IL-17 in inflamed joints. Importantly, because IL-1Ra normally suppresses IL-1R expression on γδ T cells, IL-1Ra-deficient mice exhibit elevated IL-1R expression on Vγ6+ cells, which play a critical role in inducing them to produce IL-17. Our findings demonstrate a pathogenic mechanism in which adaptive and innate immunity induce an autoimmune disease in a coordinated manner.
Caenorhabditis elegans is a useful model for anthelmintic discovery
Authors: Burns Andrew R. , Luciani Genna M. , Musso Gabriel , Bagg Rachel , Yeo May , Zhang Yuqian , Rajendran Luckshika , Glavin John , Hunter Robert , Redman Elizabeth , Stasiuk Susan , Schertzberg Michael , Angus McQuibban G. , Caffrey Conor R. , Cutler Sean R. , Tyers Mike , Giaever Guri , Nislow Corey , Fraser Andy G. , MacRae Calum A. , Gilleard John , Roy Peter J. 
Published: June 2015

AbstractParasitic nematodes infect one quarter of the world’s population and impact all humans through widespread infection of crops and livestock. Resistance to current anthelmintics has prompted the search for new drugs. Traditional screens that rely on parasitic worms are costly and labour intensive and target-based approaches have failed to yield novel anthelmintics. Here, we present our screen of 67,012 compounds to identify those that kill the non-parasitic nematode Caenorhabditis elegans. We then rescreen our hits in two parasitic nematode species and two vertebrate models (HEK293 cells and zebrafish), and identify 30 structurally distinct anthelmintic lead molecules. Genetic screens of 19 million C. elegans mutants reveal those nematicides for which the generation of resistance is and is not likely. We identify the target of one lead with nematode specificity and nanomolar potency as complex II of the electron transport chain. This work establishes C. elegans as an effective and cost-efficient model system for anthelmintic discovery.
A plastic relationship between vinculin-mediated tension and adhesion complex area defines adhesion size and lifetime
Authors: Hernández-Varas Pablo , Berge Ulrich , Lock John G. , Strömblad Staffan 
Published: June 2015

AbstractCell-matrix adhesions are central mediators of mechanotransduction, yet the interplay between force and adhesion regulation remains unclear. Here we use live cell imaging to map time-dependent cross-correlations between vinculin-mediated tension and adhesion complex area, revealing a plastic, context-dependent relationship. Interestingly, while an expected positive cross-correlation dominated in mid-sized adhesions, small and large adhesions display negative cross-correlation. Furthermore, although large changes in adhesion complex area follow vinculin-mediated tension alterations, small increases in area precede vinculin-mediated tension dynamics. Modelling based on this mapping of the vinculin-mediated tension-adhesion complex area relationship confirms its biological validity, and indicates that this relationship explains adhesion size and lifetime limits, keeping adhesions focal and transient. We also identify a subpopulation of steady-state adhesions whose size and vinculin-mediated tension become stabilized, and whose disassembly may be selectively microtubule-mediated. In conclusion, we define a plastic relationship between vinculin-mediated tension and adhesion complex area that controls fundamental cell-matrix adhesion properties.
Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells
Authors: Chabaud Mélanie , Heuzé Mélina L. , Bretou Marine , Vargas Pablo , Maiuri Paolo , Solanes Paola , Maurin Mathieu , Terriac Emmanuel , Le Berre Maël , Lankar Danielle , Piolot Tristan , Adelstein Robert S. , Zhang Yingfan , Sixt Michael , Jacobelli Jordan , Bénichou Olivier , Voituriez Raphaël , Piel Matthieu , Lennon-Duménil Ana-Maria 
Published: June 2015

AbstractThe immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.
Lifetime Reduction and Enhanced Emission of Single Photon Color Centers in Nanodiamond via Surrounding Refractive Index Modification
Authors: Khalid Asma , Chung Kelvin , Rajasekharan Ranjith , Lau Desmond W.M. , Karle Timothy J. , Gibson Brant C. , Tomljenovic-Hanic Snjezana 
Published: June 2015

AbstractThe negatively-charged nitrogen vacancy (NV−) center in diamond is of great interest for quantum information processing and quantum key distribution applications due to its highly desirable long coherence times at room temperature. One of the challenges for their use in these applications involves the requirement to further optimize the lifetime and emission properties of the centers. Our results demonstrate the reduction of the lifetime of NV− centers and hence an increase in the emission rate, achieved by modifying the refractive index of the environment surrounding the nanodiamond (ND). By coating the NDs in a polymer film, experimental results and numerical calculations show an average of 63% reduction in the lifetime and an average enhancement in the emission rate by a factor of 1.6. This strategy is also applicable for emitters other than diamond color centers where the particle refractive index is greater than the refractive index of the surrounding media.
Individual Differences in Newborn Visual Attention Associate with Temperament and Behavioral Difficulties in Later Childhood
Authors: Papageorgiou Kostas A. , Farroni Teresa , Johnson Mark H. , Smith Tim J. , Ronald Angelica 
Published: June 2015

AbstractRecently it was shown that individual differences in attention style in infants are associated with childhood effortful control, surgency and hyperactivity-inattention. Here we investigated whether effortful control, surgency and behavioral problems in childhood can be predicted even earlier, from individual differences in newborns’ average duration of gaze to stimuli. Eighty newborns participated in visual preference and habituation studies. Parents completed questionnaires at follow up (mean age = 7.5 years, SD = 1.0 year). Newborns’ average dwell time was negatively associated with childhood surgency (β = −.25, R2 = .04, p = .02) and total behavioral difficulties (β = −.28, R2 = .05, p = .04) but not with effortful control (β = .03, R2 = .001, p = .76). Individual differences in newborn visual attention significantly associated with individual variation in childhood surgency and behavioral problems, showing that some of the factors responsible for this variation are present at birth.
Considerably Unfolded Transthyretin Monomers Preceed and Exchange with Dynamically Structured Amyloid Protofibrils
Authors: Groenning Minna , Campos Raul I. , Hirschberg Daniel , Hammarström Per , Vestergaard Bente 
Published: June 2015

AbstractDespite numerous studies, a detailed description of the transthyretin (TTR) self-assembly mechanism and fibril structure in TTR amyloidoses remains unresolved. Here, using a combination of primarily small -angle X-ray scattering (SAXS) and hydrogen exchange mass spectrometry (HXMS) analysis, we describe an unexpectedly dynamic TTR protofibril structure which exchanges protomers with highly unfolded monomers in solution. The protofibrils only grow to an approximate final size of 2,900 kDa and a length of 70 nm and a comparative HXMS analysis of native and aggregated samples revealed a much higher average solvent exposure of TTR upon fibrillation. With SAXS, we reveal the continuous presence of a considerably unfolded TTR monomer throughout the fibrillation process and show that a considerable fraction of the fibrillating protein remains in solution even at a late maturation state. Together, these data reveal that the fibrillar state interchanges with the solution state. Accordingly, we suggest that TTR fibrillation proceeds via addition of considerably unfolded monomers and the continuous presence of amyloidogenic structures near the protofibril surface offers a plausible explanation for secondary nucleation. We argue that the presence of such dynamic structural equilibria must impact future therapeutic development strategies.
Synthesis, characterization and apoptotic activity of quinazolinone Schiff base derivatives toward MCF-7 cells via intrinsic and extrinsic apoptosis pathways
Authors: Zahedifard Maryam , Lafta Faraj Fadhil , Paydar Mohammadjavad , Yeng Looi Chung , Hajrezaei Maryam , Hasanpourghadi Mohadeseh , Kamalidehghan Behnam , Abdul Majid Nazia , Mohd Ali Hapipah , Ameen Abdulla Mahmood 
Published: June 2015

AbstractThe current study investigated the cytotoxic effect of 3-(5-chloro-2-hydroxybenzylideneamino)-2-(5-chloro-2-hydroxyphenyl)-2,3-dihydroquinazolin-41(H)-one (A) and 3-(5-nitro-2-hydroxybenzylideneamino)-2-(5-nitro-2-hydroxyphenyl)-2,3-dihydroquinazolin-4(1H)-one (B) on MCF-7, MDA-MB-231, MCF-10A and WRL-68 cells. The mechanism involved in apoptosis was assessed to evaluate the possible pathways induced by compound A and B. MTT assay results using A and B showed significant inhibition of MCF-7 cell viability, with IC50 values of 3. 27 ± 0.171 and 4.36 ± 0.219 μg/mL, respectively, after a 72 hour treatment period. Compound A and B did not demonstrate significant cytotoxic effects towards MDA-MB-231, WRL-68 and MCF-10A cells. Acute toxicity tests also revealed an absence of toxic effects on mice. Fluorescent microscopic studies confirmed distinct morphological changes (membrane blebbing and chromosome condensation) corresponding to typical apoptotic features in treated MCF-7 cells. Using Cellomics High Content Screening (HCS), we found that compound A and B could trigger the release of cytochrome c from mitochondria to the cytosol. The release of cytochrome c activated the expression of caspases-9 and then stimulated downstream executioner caspase-3/7. In addition, caspase-8 showed remarkable activity, followed by inhibition of NF-κB activation in A-and B-treated MCF-7 cells. The results indicated that A and B could induce apoptosis via a mechanism that involves either extrinsic or intrinsic pathways.
GDC 2: Compression of large collections of genomes
Authors: Deorowicz Sebastian , Danek Agnieszka , Niemiec Marcin 
Published: June 2015

AbstractThe fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.
Identification of cytokine-induced modulation of microRNA expression and secretion as measured by a novel microRNA specific qPCR assay
Authors: Benes Vladimir , Collier Paul , Kordes Claus , Stolte Jens , Rausch Tobias , Muckentaler Martina U. , Häussinger Dieter , Castoldi Mirco 
Published: June 2015

AbstractmicroRNAs are an abundant class of small non-coding RNAs that control gene expression post-transcriptionally. Importantly, microRNA activity participates in the regulation of cellular processes and is a potentially valuable source of biomarkers in the diagnosis and prognosis of human diseases. Here we introduce miQPCR, an innovative method to quantify microRNAs expression by using Real-Time PCR. miQPCR exploits T4 RNA ligase activities to extend uniformly microRNAs’ 3′-ends by addition of a linker-adapter. The adapter is then used as ‘anchor’ to prime cDNA synthesis and throughout qPCR to amplify specifically target amplicons. miQPCR is an open, adaptable and cost-effective procedure, which offers the following advantages; i) universal elongation and reverse transcription of all microRNAs; ii) Tm-adjustment of microRNA-specific primers; iii) high sensitivity and specificity in discriminating among closely related sequences and; iv) suitable for the analysis of cellular and cell-free circulating microRNAs. Analysis of cellular and cell-free circulating microRNAs secreted by rat primary hepatocytes stimulated with cytokines and growth factors identifies for the first time a widespread modulation of both microRNAs expression and secretion. Altogether, our findings suggest that the pleiotropic activity of humoral factors on microRNAs may extensively affect liver function in response to injury and regeneration.