bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution African population projections from radiative forcing and socio-economic models, 2000 to 2100
Authors: Boke-Olén Niklas , Abdi Abdulhakim M. , Hall Ola , Lehsten Veiko 
Published: January 2017

AbstractFor its fifth assessment report, the Intergovernmental Panel on Climate Change divided future scenario projections (2005–2100) into two groups: Socio-Economic Pathways (SSPs) and Representative Concentration Pathways (RCPs). Each SSP has country-level urban and rural population projections, while the RCPs are based on radiative forcing caused by greenhouse gases, aerosols and associated land-use change. In order for these projections to be applicable in earth system models, SSP and RCP population projections must be at the same spatial scale. Thus, a gridded population dataset that takes into account both RCP-based urban fractions and SSP-based population projection is needed. To support this need, an annual (2000–2100) high resolution (approximately 1km at the equator) gridded population dataset conforming to both RCPs (urban land use) and SSPs (population) country level scenario data were created.
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens
Authors: Blande Daniel , Halimaa Pauliina , Tervahauta Arja I , Aarts Mark G.M. , Kärenlampi Sirpa O 
Published: January 2017

AbstractNoccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies. The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.
Phantom vortices: hidden angular momentum in ultracold dilute Bose-Einstein condensates
Authors: Weiner Storm E. , Tsatsos Marios C. , Cederbaum Lorenz S. , Lode Axel U. J. 
Published: January 2017

AbstractVortices are essential to angular momentum in quantum systems such as ultracold atomic gases. The existence of quantized vorticity in bosonic systems stimulated the development of the Gross-Pitaevskii mean-field approximation. However, the true dynamics of angular momentum in finite, interacting many-body systems like trapped Bose-Einstein condensates is enriched by the emergence of quantum correlations whose description demands more elaborate methods. Herein we theoretically investigate the full many-body dynamics of the acquisition of angular momentum by a gas of ultracold bosons in two dimensions using a standard rotation procedure. We demonstrate the existence of a novel mode of quantized vorticity, which we term the phantom vortex. Contrary to the conventional mean-field vortex, can be detected as a topological defect of spatial coherence, but not of the density. We describe previously unknown many-body mechanisms of vortex nucleation and show that angular momentum is hidden in phantom vortices modes which so far seem to have evaded experimental detection. This phenomenon is likely important in the formation of the Abrikosov lattice and the onset of turbulence in superfluids.
Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties
Authors: Tyuryaeva Irina I. , Lyublinskaya Olga G. , Podkorytov Ivan S. , Skrynnikov Nikolai R. 
Published: January 2017

AbstractAntitumor GO peptides have been designed as dimerization inhibitors of prominent oncoprotein mucin 1. In this study we demonstrate that activity of GO peptides is independent of the level of cellular expression of mucin 1. Furthermore, these peptides prove to be broadly cytotoxic, causing cell death also in normal cells such as dermal fibroblasts and endometrial mesenchymal stem cells. To explore molecular mechanism of their cytotoxicity, we have designed and tested a number of new peptide sequences containing the key CxC or CxxC motifs. Of note, these sequences bear no similarity to mucin 1 except that they also contain a pair of proximal cysteines. Several of the new peptides turned out to be significantly more potent than their GO prototypes. The results suggest that cytotoxicity of these peptides stems from their (moderate) activity as disulfide oxidoreductases. It is expected that such peptides, which we have termed DO peptides, are involved in disulfide-dithiol exchange reaction, resulting in formation of adventitious disulfide bridges in cell proteins. In turn, this leads to a partial loss of protein function and rapid onset of apoptosis. We anticipate that coupling DO sequences with tumor-homing transduction domains can create a potentially valuable new class of tumoricidal peptides.
A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic
Authors: Patrascu Orlane , Béguet-Crespel Fabienne , Marinelli Ludovica , Le Chatelier Emmanuelle , Abraham Anne-Laure , Leclerc Marion , Klopp Christophe , Terrapon Nicolas , Henrissat Bernard , Blottière Hervé M. , Doré Joël , Béra-Maillet Christel 
Published: January 2017

AbstractThe digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.
Osteopontin regulates macrophage activation and osteoclast formation in hypertensive patients with vascular calcification
Authors: Ge Qian , Ruan Cheng-Chao , Ma Yu , Tang Xiao-Feng , Wu Qi-Hong , Wang Ji-Guang , Zhu Ding-Liang , Gao Ping-Jin 
Published: January 2017

AbstractVascular calcification (VC) is a highly regulated ectopic mineral deposition process involving immune cell infiltration in the vasculatures, which has been recognized to be promoted by hypertension. The matricellular glycoprotein osteopontin (OPN) is strongly induced in myeloid cells as a potential inflammatory mediator of vascular injury. This study aims to examine whether OPN is involved in the regulation of macrophage activation and osteoclast formation in hypertensive subjects with VC. We firstly found an increased proportion of CD11c+CD163- pro-inflammatory peripheral monocytes in hypertensive subjects with VC compared to those without VC by flow cytometric analysis. Primary cultured macrophages from hypertensive subjects with VC also showed altered expression profile of inflammatory factors and higher serum OPN level. Exogenous OPN promoted the differentiation of peripheral monocytes into an alternative, anti-inflammatory phenotype, and inhibited macrophage-to-osteoclast differentiation from these VC patients. In addition, calcified vessels showed increased osteoclasts accumulation accompanied with decreased macrophages infiltration in the of hypertensive subjects. Taken together, these demonstrated that OPN exerts an important role in the monocytes/macrophage phenotypic differentiation from hypertensive patients with VC, which includes reducing inflammatory factor expression and attenuating osteoclast formation.
Identification of wood-boring beetles (Cerambycidae and Buprestidae) intercepted in trade-associated solid wood packaging material using DNA barcoding and morphology
Authors: Wu Yunke , Trepanowski Nevada F. , Molongoski John J. , Reagel Peter F. , Lingafelter Steven W. , Nadel Hannah , Myers Scott W. , Ray Ann M. 
Published: January 2017

AbstractGlobal trade facilitates the inadvertent movement of insect pests and subsequent establishment of populations outside their native ranges. Despite phytosanitary measures, nonnative insects arrive at United States (U.S.) ports of entry as larvae in solid wood packaging material (SWPM). Identification of wood-boring larval insects is important for pest risk analysis and management, but is difficult beyond family level due to highly conserved morphology. Therefore, we integrated DNA barcoding and rearing of larvae to identify wood-boring insects in SWPM. From 2012 to 2015, we obtained larvae of 338 longhorned beetles (Cerambycidae) and 38 metallic wood boring beetles (Buprestidae) intercepted in SWPM associated with imported products at six U.S. ports. We identified 265 specimens to species or genus using DNA barcodes. Ninety-three larvae were reared to adults and identified morphologically. No conflict was found between the two approaches, which together identified 275 cerambycids (23 genera) and 16 buprestids (4 genera). Our integrated approach confirmed novel DNA barcodes for seven species (10 specimens) of woodborers not in public databases. This study demonstrates the utility of DNA barcoding as a tool for regulatory agencies. We provide important documentation of potential beetle pests that may cross country borders through the SWPM pathway.
Impact of age and vaccination history on long-term serological responses after symptomatic B. pertussis infection, a high dimensional data analysis
Authors: van Twillert Inonge , Bonačić Marinović Axel A. , Kuipers Betsy , van Gaans-van den Brink Jacqueline A. M. , Sanders Elisabeth A. M. , van Els Cécile A. C. M. 
Published: January 2017

AbstractCapturing the complexity and waning patterns of co-occurring immunoglobulin (Ig) responses after clinical B. pertussis infection may help understand how the human host gradually loses protection against whooping cough. We applied bi-exponential modelling to characterise and compare B. pertussis specific serological dynamics in a comprehensive database of IgG, IgG subclass and IgA responses to Ptx, FHA, Prn, Fim2/3 and OMV antigens of (ex-) symptomatic pertussis cases across all age groups. The decay model revealed that antigen type and age group were major factors determining differences in levels and kinetics of Ig (sub) classes. IgG-Ptx waned fastest in all age groups, while IgA to Ptx, FHA, Prn and Fim2/3 decreased fast in the younger but remained high in older (ex-) cases, indicating an age-effect. While IgG1 was the main IgG subclass in response to most antigens, IgG2 and IgG3 dominated the anti-OMV response. Moreover, vaccination history plays an important role in post-infection Ig responses, demonstrated by low responsiveness to Fim2/3 in unvaccinated elderly and by elevated IgG4 responses to multiple antigens only in children primed with acellular pertussis vaccine (aP). This work highlights the complexity of the immune response to this re-emerging pathogen and factors determining its Ig quantity and quality.
Dual sources of water overprinting on the low zircon δ18O metamorphic country rocks: Disequilibrium constrained through inverse modelling of partial reequilibration
Authors: Wei Chun-Sheng , Zhao Zi-Fu 
Published: January 2017

AbstractSince water is only composed of oxygen and hydrogen, δ18O and δ2H values are thus utilized to trace the origin of water(s) and quantify the water-rock interactions. While Triassic high pressure (HP) and ultrahigh pressure (UHP) metamorphic rocks across the Dabie-Sulu orogen in central-eastern China have been well documented, postcollisional magmatism driven hydrothermal systems are little known. Here we show that two sources of externally derived water interactions were revealed by oxygen isotopes for the gneissic country rocks intruded by the early Cretaceous postcollisional granitoids. Inverse modellings indicate that the degree of disequilibrium (doD) of meteoric water interactions was more evident than that of magmatic one (−65 ± 1o vs. −20 ± 2°); the partial reequilibration between quartz and alkali feldspar oxygen isotopes with magmatic water was achieved at 340 °C with a water/rock (W/R) ratio of about 1.2 for an open-hydrothermal system; two-stage meteoric water interactions were unraveled with reequilibration temperatures less than 300 °C and W/R ratios around 0.4. The lifetime of fossil magmatic hydrothermal system overprinted on the low zircon δ18O orthogneissic country rocks was estimated to maintain up to 50 thousand years (Kyr) through oxygen exchange modellings. Four-stage isotopic evolutions were proposed for the magmatic water interacted gneiss.
Spatio-temporal analysis of malaria incidence in the Peruvian Amazon Region between 2002 and 2013
Authors: Soto-Calle Veronica , Rosas-Aguirre Angel , Llanos-Cuentas Alejandro , Abatih Emmanuel , DeDeken Redgi , Rodriguez Hugo , Rosanas-Urgell Anna , Gamboa Dionicia , D´Alessandro Umberto , Erhart Annette , Speybroeck Niko 
Published: January 2017

AbstractMalaria remains a major public health problem in the Peruvian Amazon where the persistence of high-risk transmission areas (hotspots) challenges the current malaria control strategies. This study aimed at identifying significant space-time clusters of malaria incidence in Loreto region 2002–2013 and to determine significant changes across years in relation to the control measures applied. Poisson regression and purely temporal, spatial, and space-time analyses were conducted. Three significantly different periods in terms of annual incidence rates (AIR) were identified, overlapping respectively with the pre-, during, and post- implementation control activities supported by PAMAFRO project. The most likely space-time clusters of malaria incidence for P. vivax and P. falciparum corresponded to the pre- and first two years of the PAMAFRO project and were situated in the northern districts of Loreto, while secondary clusters were identified in eastern and southern districts with the latest onset and the shortest duration of PAMAFRO interventions. Malaria in Loreto was highly heterogeneous at geographical level and over time. Importantly, the excellent achievements obtained during 5 years of intensified control efforts totally vanished in only 2 to 3 years after the end of the program, calling for sustained political and financial commitment for the success of malaria elimination as ultimate goal.
Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion
Authors: Kallehauge Thomas Beuchert , Li Shangzhong , Pedersen Lasse Ebdrup , Ha Tae Kwang , Ley Daniel , Andersen Mikael Rørdam , Kildegaard Helene Faustrup , Lee Gyun Min , Lewis Nathan E. 
Published: January 2017

AbstractRecombinant protein production coopts the host cell machinery to provide high protein yields of industrial enzymes or biotherapeutics. However, since protein translation is energetically expensive and tightly controlled, it is unclear if highly expressed recombinant genes are translated as efficiently as host genes. Furthermore, it is unclear how the high expression impacts global translation. Here, we present the first genome-wide view of protein translation in an IgG-producing CHO cell line, measured with ribosome profiling. Through this we found that our recombinant mRNAs were translated as efficiently as the host cell transcriptome, and sequestered up to 15% of the total ribosome occupancy. During cell culture, changes in recombinant mRNA translation were consistent with changes in transcription, demonstrating that transcript levels influence specific productivity. Using this information, we identified the unnecessary resistance marker NeoR to be a highly transcribed and translated gene. Through siRNA knock-down of NeoR, we improved the production- and growth capacity of the host cell. Thus, ribosomal profiling provides valuable insights into translation in CHO cells and can guide efforts to enhance protein production.
Ultrasound prediction of abnormal infant development in hypertensive pregnant women in the second and third trimester
Authors: Shen Guofang , Huang Yajuan , Jiang Lixin , Gu Jinghong , Wang Yaxin , Hu Bing 
Published: January 2017

AbstractThe objective was to assess the sensitivities and accuracies of Doppler ultrasound parameters in the second and third trimester of hypertensive pregnancies in determining perinatal outcomes. 1,054 pregnancies were retrospectively categorized into three groups (healthy pregnancies (HP, n = 988), pregnancies of hypertensive women (HypP, n = 30) and high-risk hypertension pregnancies (HRHypP, n = 36), depending on gestational hypertension as well as fetal birth weights and pregnancy outcomes. Systolic/diastolic ratio (S/D), resistance index (RI), pulsatility index (PI) of the bilateral uterine artery, umbilical artery and vein as well as venous flow velocity data were monitored by Doppler ultrasound. At 20–27 and 28–32 gestational weeks, uterine artery PIs and RIs were significantly higher in the HRHypP group than in the HP and HypP patients. At gestational weeks 20–27 and 28–32 left plus right PI data with cut-off values of 2.35 and 1.73 indicated a risk of stillbirth, premature pregnancy termination and a birth weight of less than 2,500 g with sensitivities of 94.4% and 93.1% as well as specificities of 95.2% and 90.1%, respectively.
Fluctuations in Evolutionary Integration Allow for Big Brains and Disparate Faces
Authors: Evans Kory M. , Waltz Brandon T. , Tagliacollo Victor A. , Sidlauskas Brian L. , Albert James S. 
Published: January 2017

AbstractIn theory, evolutionary modularity allows anatomical structures to respond differently to selective regimes, thus promoting morphological diversification. These differences can then influence the rate and direction of phenotypic evolution among structures. Here we use geometric morphometrics and phenotypic matrix statistics to compare rates of craniofacial evolution and estimate evolvability in the face and braincase modules of a clade of teleost fishes (Gymnotiformes) and a clade of mammals (Carnivora), both of which exhibit substantial craniofacial diversity. We find that the face and braincase regions of both clades display different degrees of integration. We find that the face and braincase evolve at similar rates in Gymnotiformes and the reverse in Carnivora with the braincase evolving twice as fast as the face. Estimates of evolvability and constraints in these modules suggest differential responses to selection arising from fluctuations in phylogenetic integration, thus influencing differential rates of skull-shape evolution in these two clades.
Visualization of the role of host heme on the virulence of the heme auxotroph Streptococcus agalactiae
Authors: Joubert Laetitia , Dagieu Jean-Baptiste , Fernandez Annabelle , Derré-Bobillot Aurélie , Borezée-Durant Elise , Fleurot Isabelle , Gruss Alexandra , Lechardeur Delphine 
Published: January 2017

AbstractHeme is essential for several cellular key functions but is also toxic. Whereas most bacterial pathogens utilize heme as a metabolic cofactor and iron source, the impact of host heme during bacterial infection remains elusive. The opportunist pathogen Streptococcus agalactiae does not synthesize heme but still uses it to activate a respiration metabolism. Concomitantly, heme toxicity is mainly controlled by the HrtBA efflux transporter. Here we investigate how S. agalactiae manages heme toxicity versus benefits in the living host. Using bioluminescent bacteria and heme-responsive reporters for in vivo imaging, we show that the capacity of S. agalactiae to overcome heme toxicity is required for successful infection, particularly in blood-rich organs. Host heme is simultaneously required, as visualized by a generalized infection defect of a respiration-negative mutant. In S. agalactiae, HrtBA expression responds to an intracellular heme signal via activation of the two-component system HssRS. A hssRS promoter-driven intracellular luminescent heme sensor was designed to identify host compartments that supply S. agalactiae with heme. S. agalactiae acquires heme in heart, kidneys, and liver, but not in the brain. We conclude that S. agalactiae response to heme is organ-dependent, and its efflux may be particularly relevant in late stages of infection.
Spatio-temporal coordination among functional residues in protein
Authors: Dutta Sutapa , Ghosh Mahua , Chakrabarti J. 
Published: January 2017

AbstractThe microscopic basis of communication among the functional sites in bio-macromolecules is a fundamental challenge in uncovering their functions. We study the communication through temporal cross-correlation among the binding sites. We illustrate via Molecular Dynamics simulations the properties of the temporal cross-correlation between the dihedrals of a small protein, ubiquitin which participates in protein degradation in eukaryotes. We show that the dihedral angles of the residues possess non-trivial temporal cross-correlations with asymmetry with respect to exchange of the dihedrals, having peaks at low frequencies with time scales in nano-seconds and an algebraic tail with a universal exponent for large frequencies. We show the existence of path for temporally correlated degrees of freedom among the functional residues. We explain the qualitative features of the cross-correlations through a general mathematical model. The generality of our analysis suggests that temporal cross-correlation functions may provide convenient theoretical framework to understand bio-molecular functions on microscopic basis.