bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional cooling caused recent New Zealand glacier advances in a period of global warming
Authors: Mackintosh Andrew N. , Anderson Brian M. , Lorrey Andrew M. , Renwick James A. , Frei Prisco , Dean Sam M. 
Published: February 2017

AbstractGlaciers experienced worldwide retreat during the twentieth and early twenty first centuries, and the negative trend in global glacier mass balance since the early 1990s is predominantly a response to anthropogenic climate warming. The exceptional terminus advance of some glaciers during recent global warming is thought to relate to locally specific climate conditions, such as increased precipitation. In New Zealand, at least 58 glaciers advanced between 1983 and 2008, and Franz Josef and Fox glaciers advanced nearly continuously during this time. Here we show that the glacier advance phase resulted predominantly from discrete periods of reduced air temperature, rather than increased precipitation. The lower temperatures were associated with anomalous southerly winds and low sea surface temperature in the Tasman Sea region. These conditions result from variability in the structure of the extratropical atmospheric circulation over the South Pacific. While this sequence of climate variability and its effect on New Zealand glaciers is unusual on a global scale, it remains consistent with a climate system that is being modified by humans.
Pervasive translational regulation of the cell signalling circuitry underlies mammalian development
Authors: Fujii Kotaro , Shi Zhen , Zhulyn Olena , Denans Nicolas , Barna Maria 
Published: February 2017

AbstractThe degree and dynamics of translational control during mammalian development remain poorly understood. Here we monitored translation of the mammalian genome as cells become specified and organize into tissues in vivo. This identified unexpected and pervasive translational regulation of most of the core signalling circuitry including Shh, Wnt, Hippo, PI3K and MAPK pathways. We further identify and functionally characterize a complex landscape of upstream open reading frames (uORFs) across 5′-untranslated regions (UTRs) of key signalling components. Focusing on the Shh pathway, we demonstrate the importance of uORFs within the major SHH receptor, Ptch1, in control of cell signalling and neuronal differentiation. Finally, we show that the expression of hundreds of mRNAs underlying critical tissue-specific developmental processes is largely regulated at the translation but not transcript levels. Altogether, this work reveals a new layer of translational control to major signalling components and gene regulatory networks that diversifies gene expression spatially across developing tissues.
RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles
Authors: Cardoso T. F. , Cánovas A. , Canela-Xandri O. , González-Prendes R. , Amills M. , Quintanilla R. 
Published: February 2017

AbstractWe have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively. At the nominal level of significance (P-value ≤ 0.05), we detected 1,430 mRNA and 12 non-coding RNA (ncRNA) transcripts as differentially expressed (DE) in the gluteus medius muscle of HIGH vs LOW pigs. This smaller contribution of ncRNAs to differential expression may have biological and technical reasons. We performed a second analysis, that was more stringent (P-value ≤ 0.01 and fold-change ≥ 1.5), and only 96 and 0 mRNA-and ncRNA-encoding genes happened to be DE, respectively. The subset of DE mRNA genes was enriched in pathways related with lipid (lipogenesis and triacylglycerol degradation) and glucose metabolism. Moreover, HIGH pigs showed a more lipogenic profile than their LOW counterparts.
The nexus between forest fragmentation in Africa and Ebola virus disease outbreaks
Authors: Rulli Maria Cristina , Santini Monia , Hayman David T. S. , D’Odorico Paolo 
Published: February 2017

AbstractTropical forests are undergoing land use change in many regions of the world, including the African continent. Human populations living close to forest margins fragmented and disturbed by deforestation may be particularly exposed to zoonotic infections because of the higher likelihood for humans to be in contact with disease reservoirs. Quantitative analysis of the nexus between deforestation and the emergence of Ebola virus disease (EVD), however, is still missing. Here we use land cover change data in conjunction with EVD outbreak records to investigate the association between recent (2004–2014) outbreaks in West and Central Africa, and patterns of land use change in the region. We show how in these EVD outbreaks the index cases in humans (i.e. spillover from wildlife reservoirs) occurred mostly in hotspots of forest fragmentation.
Bioproduction, characterization, anticancer and antioxidant activities of extracellular melanin pigment produced by newly isolated microbial cell factories Streptomyces glaucescens NEAE-H
Authors: El-Naggar Noura El-Ahmady , El-Ewasy Sara M. 
Published: February 2017

AbstractIn this present study, a newly isolated strain,Streptomycessp. NEAE-H, capable of producing high amount of black extracellular melanin pigment on peptone-yeast extract iron agar and identified asStreptomyces glaucescensNEAE-H. Plackett–Burman statistical design was conducted for initial screening of 17 independent (assigned) variables for their significances on melanin pigment production byStreptomyces glaucescensNEAE-H. The most significant factors affecting melanin production are incubation period, protease-peptone and ferric ammonium citrate. The levels of these significant variables and their interaction effects were optimized by using face-centered central composite design. The maximum melanin production (31.650 μg/0.1 ml) and tyrosinase activity (6089.10 U/ml) were achieved in the central point runs under the conditions of incubation period (6 days), protease-peptone (5 g/L) and ferric ammonium citrate (0.5 g/L). Melanin pigment was recovered by acid-treatment. Higher absorption of the purified melanin pigment was observed in the UV region at 250 nm. It appeared to have defined small spheres by scanning electron microscopy imaging. The maximum melanin yield was 350 mg dry wt/L of production medium.In vitroanticancer activity of melanin pigment was assayed against skin cancer cell line using MTT assay. The IC50value was 16.34 ± 1.31 μg/ml for melanin and 8.8 ± 0.5 μg/ml for standard 5-fluorouracil.
Protective effect of maternal uteroplacental insufficiency on oxygen-induced retinopathy in offspring: removing bias of premature birth
Authors: Becker Silke , Wang Haibo , Yu Baifeng , Brown Randy , Han Xiaokun , Lane Robert H. , Hartnett M. Elizabeth 
Published: February 2017

AbstractTo address the hypothesis that maternal uteroplacental insufficiency (UPI) increases severity of retinopathy of prematurity, we developed a composite rat model of UPI and oxygen-fluctuations and removed premature birth as a confounding factor. Timed-pregnant Sprague-Dawley dams underwent bilateral uterine artery ligation or anesthesia (control) at e19.5. Full-term pups developed in room air (RA) or an oxygen-induced retinopathy (OIR) model. Isolectin-stained retinal flat-mounts were analyzed for percent of areas of avascular/total retina (AVA) and of intravitreal neovascular/total retina (IVNV). Pup weights and serum and mRNA of liver and kidney VEGF, IGF-1, and erythropoietin (EPO) were determined. Multivariable mixed effects linear regressions and Pearson correlations were performed using STATA14. Postnatal growth restriction occurred in pups in UPI/RA, but not in UPI/OIR. Weight gain was similar between UPI/OIR and control/OIR pups. AVA was reduced and a trend toward reduced IVNV was seen in UPI/OIR compared to control/OIR. No difference in birth weights of UPI/OIR vs. control/OIR pups occurred. Serum and renal IGF-1 and EPO were significantly increased in UPI/OIR compared to control/OIR pups. In the absence of prematurity, UPI increased angiogenic factors in association with reduced OIR severity, suggesting that ischemia from UPI could yield protective angiogenic effects by offspring.
Peptoids successfully inhibit the growth of gram negative E. coli causing substantial membrane damage
Authors: Mojsoska Biljana , Carretero Gustavo , Larsen Sylvester , Mateiu Ramona Valentina , Jenssen Håvard 
Published: February 2017

AbstractPeptoids are an alternative approach to antimicrobial peptides that offer higher stability towards enzymatic degradation. It is essential when developing new types of peptoids, that mimic the function of antimicrobial peptides, to understand their mechanism of action. Few studies on the specific mechanism of action of antimicrobial peptoids have been described in the literature, despite the plethora of studies on the mode of action of antimicrobial peptides. Here, we investigate the mechanism of action of two short cationic peptoids, rich in lysine and tryptophan side chain functionalities. We demonstrate that both peptoids are able to cause loss of viability in E. coli susceptible cells at their MIC (16–32 μg/ml) concentrations. Dye leakage assays demonstrate slow and low membrane permeabilization for peptoid 1, that is still higher for lipid compositions mimicking bacterial membranes than lipid compositions containing Cholesterol. At concentrations of 4 × MIC (64–128 μg/ml), pore formation, leakage of cytoplasmic content and filamentation were the most commonly observed morphological changes seen by SEM in E. coli treated with both peptoids. Flow cytometry data supports the increase of cell size as observed in the quantification analysis from the SEM images and suggests overall decrease of DNA per cell mass over time.
Energy dissipation in flows through curved spaces
Authors: Debus J.-D. , Mendoza M. , Succi S. , Herrmann H. J. 
Published: February 2017

AbstractFluid dynamics in intrinsically curved geometries is encountered in many physical systems in nature, ranging from microscopic bio-membranes all the way up to general relativity at cosmological scales. Despite the diversity of applications, all of these systems share a common feature: the free motion of particles is affected by inertial forces originating from the curvature of the embedding space. Here we reveal a fundamental process underlying fluid dynamics in curved spaces: the free motion of fluids, in the complete absence of solid walls or obstacles, exhibits loss of energy due exclusively to the intrinsic curvature of space. We find that local sources of curvature generate viscous stresses as a result of the inertial forces. The curvature- induced viscous forces are shown to cause hitherto unnoticed and yet appreciable energy dissipation, which might play a significant role for a variety of physical systems involving fluid dynamics in curved spaces.
Effects of drought on leaf carbon source and growth of European beech are modulated by soil type
Authors: Liu Jian-Feng , Arend Matthias , Yang Wen-Juan , Schaub Marcus , Ni Yan-Yan , Gessler Arthur , Jiang Ze-Ping , Rigling Andreas , Li Mai-He 
Published: February 2017

AbstractDrought potentially affects carbon balance and growth of trees, but little is known to what extent soil plays a role in the trade-off between carbon gain and growth investment. In the present study, we analyzed leaf non-structural carbohydrates (NSC) as an indicator of the balance of photosynthetic carbon gain and carbon use, as well as growth of European beech (Fagus sylvatica L.) saplings, which were grown on two different soil types (calcareous and acidic) in model ecosystems and subjected to a severe summer drought. Our results showed that drought led in general to increased total NSC concentrations and to decreased growth rate, and drought reduced shoot and stem growth of plants in acidic soil rather than in calcareous soil. This result indicated that soil type modulated the carbon trade-off between net leaf carbon gain and carbon investment to growth. In drought-stressed trees, leaf starch concentration and growth correlated negatively whereas soluble sugar:starch ratio and growth correlated positively, which may contribute to a better understanding of growth regulation under drought conditions. Our results emphasize the role of soil in determining the trade-off between the balance of carbon gain and carbon use on the leaf level and growth under stress (e.g. drought).
In patients with chronic aplastic anemia, bone marrow–derived MSCs regulate the Treg/Th17 balance by influencing the Notch/RBP-J/FOXP3/RORγt pathway
Authors: Li Hongbo , Wang Lin , Pang Yan , Jiang Zujun , Liu Zenghui , Xiao Haowen , Chen Haijia , Ge Xiaohu , Lan Hai , Xiao Yang 
Published: February 2017

AbstractThe standard treatment for aplastic anemia (AA) in young patients is a matched sibling hematopoietic stem cell transplant. Transfusion of a chronic AA patient with allogeneic bone marrow–derived mesenchymal stromal cells (BMMSCs) is currently being developed as a cell-based therapy, and the safety and efficacy of such transfusions are being continuously improved. Nevertheless, the mechanisms by which BMMSCs exert their therapeutic effects remain to be elucidated. In this study, mesenchymal stromal cells (MSCs) obtained from bone marrow donors were concentrated and intravenously injected into 15 chronic AA patients who had been refractory to prior immunosuppressive therapy. We showed that BMMSCs modulate the levels of Th1, Th2, Th17 and Treg cells, as well as their related cytokines in chronic AA patients. Furthermore, the percentages of Th1 and Th17 cells among the H-MSCs decreased significantly, while the percentage Treg cells increased. The Notch/RBP-J/FOXP3/RORγt pathway was involved in modulating the Treg/Th17 balance after MSCs were transfused in vitro. Additionally, the role played by transfused MSCs in regulating the Treg/Th17 balance via the Notch/RBP-J/FOXP3/RORγt pathway was further confirmed in an AA mouse model. In summary, in humans with chronic AA, BMMSCs regulate the Treg/Th17 balance by affecting the Notch/RBP-J/FOXP3/RORγt pathway.
Harvesting pre-polarized macrophages using thermo-responsive substrates
Authors: Malheiro Vera , Elbs-Glatz Yvonne , Obarzanek-Fojt Magdalena , Maniura-Weber Katharina , Bruinink Arie 
Published: February 2017

AbstractIn the cell culture environment macrophages are highly adherent cells. Currently used methods to harvest macrophages have the disadvantage of reducing cell viability and their ability to re-attach after seeding. Although thermo-responsive surfaces have been employed to harvest cell sheets no reports are available to use these to harvest (pre-polarized) macrophages. We show that this method significantly improves the yield of living macrophages and percentage of subsequent cell reattachment, whilst having a minimal effect on the cell phenotype.
Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor
Authors: Kumar Amit , Delogu Francesco 
Published: February 2017

AbstractThe present work focuses on the dynamical aspects of cross-reactivity between myelin based protein (MBP) self-peptide and two microbial peptides (UL15, PMM) for Hy.1B11 T-cell receptor (TCR). This same TCR was isolated from a patient suffering from multiple sclerosis (MS). The study aims at highlighting the chemical interactions underlying recognition mechanisms between TCR and the peptides presented by Major Histocompatibility Complex (MHC) proteins, which form a crucial component in adaptive immune response against foreign antigens. Since the ability of a TCR to recognize different peptide antigens presented by MHC depends on its cross-reactivity, we used molecular dynamics methods to obtain atomistic detail on TCR-peptide-MHC complexes. Our results show how the dynamical basis of Hy.1B11 TCR’s cross-reactivity is rooted in a similar bridging interaction pattern across the TCR-peptide-MHC interface. Our simulations confirm the importance of TCR CDR3α E98 residue interaction with MHC and a predominant role of P6 peptide residue in MHC binding affinity. Altogether, our study provides energetic and dynamical insights into factors governing peptide recognition by the cross-reactive Hy.1B11 TCR, found in MS patient.
Let-7e modulates the inflammatory response in vascular endothelial cells through ceRNA crosstalk
Authors: Lin Zongwei , Ge Junfeng , Wang Zhe , Ren Jianwei , Wang Xiaowei , Xiong Hui , Gao Jing , Zhang Yan , Zhang Qunye 
Published: February 2017

AbstractThe inflammatory responses of vascular endothelial cells (VECs) are critical in the development of many cardio-cerebrovascular diseases. Let-7e is an important regulator of endothelial function and inflammation. However, the effects and mechanisms of let-7e on VECs inflammation have not been studied until recently. Thus, we investigated these issues and found that in addition to proliferation, apoptosis and cell adhesion, let-7e was also implicated in the regulation of inflammatory responses through a complex network, including IκBβ and lncRNA lnc-MKI67IP-3. Let-7e promoted NF-κB activation and translocation to the nucleus by inhibiting its target gene (IκBβ) expression and subsequently increased the expression of inflammatory and adhesion molecules. Meanwhile, lnc-MKI67IP-3 acted as a sponge or competing endogenous RNA (ceRNA) for let-7e, suppressing its pro-inflammatory effects, and let-7e decreased lnc-MKI67IP-3 expression, thereby forming a positive feedback loop to aggravate inflammation. Moreover, let-7e, lnc-MKI67IP-3 and IκBβ were also abnormal in oxLDL-treated VECs and atherosclerotic plaques. The present study revealed let-7e as a pro-inflammatory mediator and a novel regulatory mechanism for the NF-κB pathway through ceRNA crosstalk, comprising let-7e and its target IκBβ and the ceRNA lnc-MKI67IP-3. Thus, this molecule might play important roles in the inflammatory responses of VECs and development of atherosclerosis.
The alternative complement pathway is dysregulated in patients with chronic heart failure
Authors: Shahini Negar , Michelsen Annika E. , Nilsson Per H. , Ekholt Karin , Gullestad Lars , Broch Kaspar , Dahl Christen P. , Aukrust Pål , Ueland Thor , Mollnes Tom Eirik , Yndestad Arne , Louwe Mieke C. 
Published: February 2017

AbstractThe complement system, an important arm of the innate immune system, is activated in heart failure (HF). We hypothesized that HF patients are characterized by an imbalance of alternative amplification loop components; including properdin and complement factor D and the alternative pathway inhibitor factor H. These components and the activation product, terminal complement complex (TCC), were measured in plasma from 188 HF patients and 67 age- and sex- matched healthy controls by enzyme immunoassay. Our main findings were: (i) Compared to controls, patients with HF had significantly increased levels of factor D and TCC, and decreased levels of properdin, particularly patients with advanced clinical disorder (i.e., NYHA functional class IV), (ii) Levels of factor D and properdin in HF patients were correlated with measures of systemic inflammation (i.e., C-reactive protein), neurohormonal deterioration (i.e., Nt-proBNP), cardiac function, and deteriorated diastolic function, (iii) Low levels of factor H and properdin were associated with adverse outcome in univariate analysis and for factor H, this was also seen in an adjusted model. Our results indicate that dysregulation of circulating components of the alternative pathway explain the increased degree of complement activation and is related to disease severity in HF patients.
A pupal transcriptomic screen identifies Ral as a target of store-operated calcium entry in Drosophila neurons
Authors: Richhariya Shlesha , Jayakumar Siddharth , Abruzzi Katharine , Rosbash Michael , Hasan Gaiti 
Published: February 2017

AbstractTranscriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement for SOCE in neurons that regulate Drosophila flight bouts. We refine this requirement temporally to the early pupal stage and use RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. Down regulation of dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system, altered the expression of 131 genes including Ral, a small GTPase. Disruption of Ral function in neurons impaired flight, whereas ectopic expression of Ral in SOCE-compromised neurons restored flight. Through live imaging of calcium transients from cultured pupal neurons, we confirmed that Ral does not participate in SOCE, but acts downstream of it. These results identify neuronal SOCE as a mechanism that regulates expression of specific genes during development of the pupal nervous system and emphasizes the relevance of SOCE-regulated gene expression to flight circuit maturation.
Aging and serum exomiR content in women-effects of estrogenic hormone replacement therapy
Authors: Kangas Reeta , Törmäkangas Timo , Fey Vidal , Pursiheimo Juha , Miinalainen Ilkka , Alen Markku , Kaprio Jaakko , Sipilä Sarianna , Säämänen Anna-Marja , Kovanen Vuokko , Laakkonen Eija K. 
Published: February 2017

AbstractExosomes participate in intercellular messaging by transporting bioactive lipid-, protein- and RNA-molecules and -complexes. The contents of the exosomes reflect the physiological status of an individual making exosomes promising targets for biomarker analyses. In the present study we extracted exosome microRNAs (exomiRs) from serum samples of premenopausal women (n = 8) and monozygotic postmenopausal twins (n = 10 female pairs), discordant for the use of estrogenic hormone replacement therapy (HRT), in order to see whether the age or/and the use of HRT associates with exomiR content. A total of 241 exomiRs were detected by next generation sequencing, 10 showing age, 14 HRT and 10 age +HRT -related differences. When comparing the groups, differentially expressed miRs were predicted to affect cell proliferation processes showing inactivation with younger age and HRT usage. MiR-106-5p, -148a-3p, -27-3p, -126-5p, -28-3p and -30a-5p were significantly associated with serum 17β-estradiol. MiRs formed two hierarchical clusters being indicative of positive or negative health outcomes involving associations with body composition, serum 17β-estradiol, fat-, glucose- and inflammatory markers. Circulating exomiR clusters, obtained by NGS, could be used as indicators of metabolic and inflammatory status affected by hormonal changes at menopause. Furthermore, the individual effects of HRT-usage could be evaluated based on the serum exomiR signature.