bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD25+Bcl6low T follicular helper cells provide help to maturing B cells in germinal centers of human tonsil
Authors: Li Haishan , Pauza C. David 
Published: September 2014

The majority of CXCR5+PD1+CD4+ T follicular helper (Tfh) cells (>90%) are CD25−Bcl6hi, while a small subpopulation (<10%) are CD25+Bcl6low but do not express FoxP3 and are not T regulatory cells. We purified T:B‐cell conjugates from tonsils and found they were enriched for the CD25+Bcl6low Tfh‐cell subpopulation. In response to IL‐2, these CD25+ Tfh cells increased expression of costimulatory molecules ICOS or OX40, upregulated transcription factor cMaf, produced cytokines IL‐21, IL‐17, and IL‐10, and raised the levels of antiapoptotic protein Bcl2. Conjugates formed with CD25+BCl6low Tfh cells included B cells expressing higher levels of activation‐induced cytidine deaminase (AID), memory marker CD45RO, surface IgG or IgA, and MHC class II compared to B‐cell conjugates including CD25−Bcl6hi Tfh cells. While IL‐2 suppresses early Tfh‐cell differentiation, Tfh‐cell recognition of antigen‐presenting B cells and signaling through the T‐cell receptor likely triggers expression of the high‐affinity IL‐2 receptor and responses to IL‐2 including downregulation of Bcl6. CD25 expression on Tfh cells and local production of IL‐2 in tonsil or lymph node may support B helper T‐cell function during later stages of B‐cell maturation and the development of immune memory.
Modulation of exogenous selenium in cadmium-induced changes in antioxidative metabolism, cadmium uptake, and photosynthetic performance in the 2 tobacco genotypes differing in cadmium tolerance
Authors: Liu Wenxing , Shang Shenghua , Feng Xue , Zhang Guoping , Wu Feibo 
Published: September 2014

Abstract

Hydroponic experiments were conducted using cadmium (Cd)–sensitive (cv Guiyan 1) and Cd-tolerant (Yunyan 2) tobacco cultivars to evaluate cultivar differences in response to Cd toxicity in the presence of selenium (Se). The results showed that addition of 3 µM Se in 50 µM Cd solution markedly reduced Cd accumulation in plants, alleviated Cd-induced growth inhibition, and increased nitrogen and chlorophyll contents as well as photosynthetic performance (i.e., net photosynthetic rate, stomatal conductance, and transpiration rate). External Se dramatically depressed Cd-induced O2•−, H2O2, and malondialdehyde accumulation, especially in the sensitive cultivar. Selenium significantly elevated Cd-depressed activities of superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, glutathione-peroxidase, and glutathione reductase in the both cultivars after 7-d treatments. Meanwhile, Se counteracted Cd-induced alterations in certain nutrient elements; for example, it significantly increased Zn and Ca concentrations and reduced Mg concentration in both cultivars. Furthermore, Se significantly elevated Cd-depressed H+-K+-adenosine triphosphatase (ATPase), Na+-K+-ATPase, and Ca2+-Mg2+-ATPase activities. The beneficial effect of Se under Cd stress may be related mainly to the increased ATPase activity and reduced Cd uptake and reactive oxygen species accumulation, thus reducing the negative consequences of oxidative stress caused by Cd toxicity. Environ Toxicol Chem 2015;34:92–99. © 2014 SETAC
Application of a redox-proteomics toolbox to Daphnia magna challenged with model pro-oxidants copper and paraquat
Authors: Rainville Louis-Charles , Coelho Ana Varela , Sheehan David 
Published: September 2014

Abstract

The redox status of cells is involved in the regulation of several cellular stress–response pathways. It is frequently altered by xenobiotics, as well as by environmental stressors. As such, there is an increasing interest in understanding the redox status of proteins in different scenarios. Recent advances in proteomics enable researchers to measure oxidative lesions in a wide range of proteins. This opens the door to the sensitive detection of toxicity targets and helps decipher the molecular impact of pollutants and environmental stressors. The present study applies the measurement of protein carbonyls, the most common oxidative lesion of proteins, to gel-based proteomics in Daphnia magna. Daphnids were exposed to copper and paraquat, 2 well-known pro-oxidants. Catalase activity was decreased by paraquat, whereas global measurement of protein carbonyls and thiols indicated no change with treatment. Despite the absence of observed oxidative stress, 2-dimensional electrophoresis of the daphnid proteins and measurement of their carbonylation status revealed that 32 features were significantly affected by the treatments, showing higher sensitivity than single measurements. Identified proteins affected by copper indicated a decrease in the heat-shock response, whereas paraquat affected glycolysis. The present study demonstrates the applicability of redox-proteomics in daphnids, and indicates that the heat-shock response plays a counterintuitive role in metal resistance in daphnids. Environ Toxicol Chem 2015;34:84–91. © 2014 SETAC
Linking Organic Carbon, Water Content, and Nitrous Oxide Emission in a Reclaimed Coal Mine Soil
Authors: Dutta Tanushree , Stehouwer Richard C. , Dell Curtis J. 
Published: September 2014

AbstractMine‐land reclamation for biomass production is often achieved by means of large applications of N and organic C with amendments that could create soil conditions favorable for N2O production and emissions. To investigate this possibility, we conducted a laboratory experiment using mine soil collected from an active surface coal mine site near Philipsburg, Pennsylvania. During a 37‐d incubation period, we measured N2O and CO2fluxes from non‐amended soil and from soil amended with ammonium nitrate (L + F), composted poultry manure (Comp), poultry manure alone (Man) and mixed with 3 rates of paper mill sludge (PMS) to obtain carbon to nitrogen ratios of 14, 20 and 27 (Man + PMS14, 20 and 27), each at 60% and 80% water filled pore space (WFPS). Results showed that manure alone leads to a greater emission of N2O under laboratory conditions than with L + F. However, composting manure effectively reduced the emissions compared to that of L + F despite a large addition of organic C and N. Composted manure‐treated soil emitted less than all other manure‐based treatments at both 60% and 80% WFPS. The emissions were greater from soil amended with the Man + PMS treatments compared to non‐amended and L + F‐amended soil, and it increased during periods of intense microbial activity created by the application of manure and PMS. Higher water content increased emissions particularly during periods of intense microbial activity coupled with inorganic N availability. Cumulative N2O emissions from manure‐treated soils represented less than 0·1% loss of total applied N. Copyright © 2014 John Wiley & Sons, Ltd.
Synthesis of unsaturation containing P(VDF‐co‐TrFE‐co‐CTFE) from P(VDF‐co‐CTFE) in one‐pot catalyzed with Cu(0)‐based single electron transfer living radical polymerization system
Authors: Hu Xin , Tan Shaobo , Gao Guoxin , Xie Yunchuan , Wang Qinzhuo , Li Na , Zhang Zhicheng 
Published: September 2014

ABSTRACTPoly(vinylidene fluoride‐co‐trifluoroethylene‐co‐chlorotrifluoroethylene) (P(VDF‐co‐TrFE‐co‐CTFE)) with internal double bond has been reported with high dielectric constant and energy density at room temperature, which is expected to serve as a promising dielectric film in high pulse discharge capacitors. An environmentally friendly one‐pot route, including the controllable hydrogenation via Cu(0) mediated single electron transfer radical chain transfer reaction (SET‐CTR) and dehydrochlorination catalyzed with N‐containing reagent, is successfully developed to synthesize P(VDF‐co‐TrFE‐co‐CTFE) containing unsaturation. The resultant polymer was carefully characterized with 1H NMR, 19F NMR, and FTIR. The composition of the resultant copolymer is strongly influenced by reaction conditions, including the reaction temperature, catalyst concentration, the types of ligands and solvents. The kinetics data of the chain transfer and elimination reaction demonstrate their well‐controlled feature of the strategy. By shifting the equilibrium between the CTR and elimination reactions dominated by N‐compounds serving as ligands in SET‐CTR and catalyst in the dehydrochlorination of P(VDF‐co‐CTFE), P(VDF‐co‐TrFE‐co‐CTFE) with tunable TrFE and double‐bond content could be synthesized in this one‐pot route. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 3429–3440
Protected hinge in the immunoglobulin G2‐A2 disulfide isoform
Authors: Liu Yaoqing Diana , Chou Robert Y.‐T. , Dillon Thomas M. , Poppe Leszek , Spahr Chris , Shi Stone D. H. , Flynn Gregory C. 
Published: September 2014

AbstractHuman IgG2 consists of disulfide‐mediated structural isoforms, classified by the number of Fab arms disulfide‐linked to the heavy chain hinge. In the IgG2‐B isoform, both Fab arms are linked to the hinge region, and in IgG2‐A, neither Fab arm are linked to the hinge. IgG2‐A/B is a hybrid between these two forms, with only one Fab arm disulfide‐linked to the hinge. Within each of these isoform types are subtypes, with subtle disulfide‐linkage differences. Here we explored the structural basis for the A1 and A2 isoform subtypes. Whereas A1 isoform converts into the A/B and B isoforms under mild redox conditions, A2 does not. Characterization of the disulfide connectivities of A2 isoform revealed a similar structure to A1 isoform, with parallel inter heavy chain disulfide linkages in the hinge region. However, the hinge disulfides in A2 isoform were resistant to reduction under conditions where A1 isoform hinge disulfides became reduced and they required thermal treatment (>55°C) to obtain thiol‐dependent disulfide reduction. Structural analysis of the hinge region indicated that the protected disulfides were restricted to cysteines 219 and 220 of the upper hinge. Disruption of the upper hinge through insertion mutagenesis eliminated A2 isoform behavior. 1H NMR studies showed that the A1 isoform Fc glycan was more dynamic than that on A2 isoform and showed some other conformational differences. Results point to an IgG2‐A2 upper hinge region that is more akin to the interior of a globular protein than the flexible hinge region expected on an IgG.
Novel fermentation process strengthening strategy for production of propionic acid and vitamin B12 by Propionibacterium freudenreichii
Authors: Wang Peng , Jiao Youjing , Liu Shouxin 
Published: September 2014

Abstract
An efficient fermentation-strengthening approach was developed to improve the anaerobic production of propionic acid and vitamin B12 by co-fermentation with Propionibacterium freudenreichii. Vitamin B12 production from glucose resulted in relatively high productivity (0.35 mg/L h) but a low propionic acid yield (0.55 g/g). By contrast, glycerol gave a high propionic acid yield (0.63 g/g) but low productivity (0.16 g/L h). Co-fermentation of glycerol and glucose with a gradual addition strategy gave high yields (propionic acid: 0.71 g/g; vitamin B12: 0.72 mg/g) and productivities (propionic acid: 0.36 g/L h; vitamin B12: 0.36 mg/L h). Finally, the integrated feedstock and fermentation system strengthening strategy was demonstrated as an efficient method for the economic production of bio-based propionic acid and vitamin B12.
The transition to adulthood around the Mediterranean: Contributions of the special issue
Authors: Tagliabue Semira , Lanz Margherita , Beyers Wim 
Published: September 2014

ABSTRACTThis analysis of the papers in the special issue on the transition to adulthood around the Mediterranean calls attention to the role of the family of origin in the transition itself. All the papers analyzed a specific aspect of family relationships, focusing especially on the parent–child relationship. Moreover, several outcomes were considered, such as identity, psychological well‐being, life satisfaction, and criteria of adulthood, highlighting the multidimensional features of the transitional phase young people are facing. Together, these papers make a great contribution to the current literature, especially for the ones linked to the Mediterranean area, and provide both foundation and new paths for future research.
Neonatal hypoxic–ischemic encephalopathy reduces c‐Fos activation in the rat hippocampus: evidence of a long‐lasting effect
Authors: Souza Andressa , Dussan‐Sarria Jairo Alberto , Medeiros Liciane Fernandes , Souza Ana Cláudia , Oliveira Carla , Scarabelot Vanessa Leal , Adachi Lauren Naomi , Winkelmann‐Duarte Elisa Cristiana , Philippi‐Martins Bárbara Beatriz , Netto Carlos Alexandre , Caumo Wolnei , Torres Iraci L.S. 
Published: September 2014

AbstractThe effect of neonatal hypoxic–ischemic encephalopathy (HIE) on maturation of nociceptive pathways has been sparsely explored. To investigate whether neonatal HIE alters neuronal activity, nociceptive behavior, and serum neuroplasticity mediators (brain‐derived neurotrophic factor [BDNF] and tumor necrosis factor‐α [TNF]) in the short, medium, and long term. Neonate male Wistar rats were randomized to receive a brain insult that could be either ischemic (left carotid artery ligation [LCAL]), hypoxic (8% oxygen chamber), hypoxic–ischemic (LCAL and hypoxic chamber), sham‐ischemic, or sham‐hypoxic. Neuronal activity (c‐Fos activation at region CA1 and dentate gyrus of the hippocampus), nociceptive behavior (von Frey, tail‐flick, and hot‐plate tests), neuroplasticity mediators (BDNF, TNF), and a cellular injury marker (lactase dehydrogenase [LDH]) were assessed in blood serum 14, 30, and 60 days after birth. Neonatal HIE persistently reduced c‐Fos activation in the ipsilateral hippocampal region CA1; however, contralateral c‐Fos reduction appeared only 7 weeks after the event. Neonatal HIE acutely reduced the paw withdrawal threshold (von Frey test), but this returned to normal by the 30th postnatal day. Hypoxia reduced serum LDH levels. Serum neuroplasticity mediators increased with age, and neonatal HIE did not affect their ontogeny. Neonatal HIE‐induced reduction in neuronal activity occurs acutely in the ipsilateral hippocampal region CA1 and persists for at least 60 days, but the contralateral effect of the insult is delayed. Alterations in the nociceptive response are acute and self‐limited. Serum neuroplasticity mediators increase with age, and remain unaffected by HIE.
EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data
Authors: Winkler Thomas W. , Kutalik Zoltan , Gorski Mathias , Lottaz Claudio , Kronenberg Florian , Heid Iris M. 
Published: September 2014

AbstractSummary: The R package EasyStrata facilitates the evaluation and visualization of stratified genome-wide association meta-analyses (GWAMAs) results. It provides (i) statistical methods to test and account for between-strata difference as a means to tackle gene–strata interaction effects and (ii) extended graphical features tailored for stratified GWAMA results. The software provides further features also suitable for general GWAMAs including functions to annotate, exclude or highlight specific loci in plots or to extract independent subsets of loci from genome-wide datasets. It is freely available and includes a user-friendly scripting interface that simplifies data handling and allows for combining statistical and graphical functions in a flexible fashion.Availability: EasyStrata is available for free (under the GNU General Public License v3) from our Web site www.genepi-regensburg.de/easystrata and from the CRAN R package repository cran.r-project.org/web/packages/EasyStrata/.Contact: thomas.winkler@ukr.de or iris.heid@ukr.deSupplementary information: Supplementary data are available at Bioinformatics online.
PINBPA: Cytoscape app for network analysis of GWAS data
Authors: Wang Lili , Matsushita Takuya , Madireddy Lohith , Mousavi Parvin , Baranzini Sergio E. 
Published: September 2014

Abstract
Summary: Protein interaction network-based pathway analysis (PINBPA) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion. Users can easily import GWAS summary-level data, draw Manhattan plots, define blocks, prioritize genes with random walk with restart, detect enriched subnetworks and test the significance of subnetworks via a user-friendly interface.
Availability and implementation: PINBPA app is freely available in Cytoscape app store.
Contact: pmousavi@cs.queensu.ca and sebaran@cgl.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CO (J = 3 → 2) observations of the starburst galaxy NGC 1808 with ASTE
Authors: Salak Dragan , Nakai Naomasa , Kitamoto Shoko 
Published: September 2014

Abstract
We present the first map of 12CO (J = 3 → 2) and the first detection of 13CO (J = 3 → 2) in the nearby starburst galaxy with a superwind, NGC 1808. The molecular gas is concentrated in the inner 2 kpc region of the galaxy with extended structure along the galactic bar and along the minor galactic axis. The minor-axis structure can be explained as molecular gas entrained in a galactic wind observed as a dust outflow at optical wavelengths. We have carried out a radiative transfer analysis of the excitation conditions of molecular gas in the starburst region (radius 550 pc) by using the ratios of J = 1 → 0, J = 2 → 1, and J = 3 → 2 emission lines of 12CO and 13CO, and the large velocity gradient approximation. The beam-averaged density and kinetic temperature of molecular gas can be fitted at n H2 ≃ 103.5 cm−3 and Tk ≃ 35 K, indicating the presence of warm molecular gas, close to the estimated dust temperature of Td ≃ 34–37 K. The abundance ratio of the CO isotopologues is found to be [12CO]/[13CO] ≃ 34. The calculations show that, for the derived physical parameters, J = 2 → 1 and J = 3 → 2 transitions of 12CO are optically thick, 12CO J = 1 → 0 is moderately optically thick, and all transitions of 13CO are optically thin. We have estimated an average CO–H2 conversion factor of XCO ≃ 0.8 × 1020 cm−2 (K km s−1)−1 in the central 550 pc by using a simple theoretical model assuming homogeneous, gravitationally bound gas clouds with turbulent velocities. In the same region the molecular gas mass is 3.0 × 108 M⊙ available to fuel the nuclear starburst.
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
Authors: Quick Joshua , Quinlan Aaron , Loman Nicholas J 
Published: September 2014

AbstractBackgroundThe MinION™ is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and is powered from the USB 3.0 port of a laptop computer. By measuring the change in current produced when DNA strands translocate through and interact with a charged protein nanopore the device is able to deduce the underlying nucleotide sequence.FindingsWe present a read dataset from whole-genome shotgun sequencing of the model organismEscherichia coliK-12 substr. MG1655 generated on a MinION™ device during the early-access MinION Access Program (MAP). Sequencing runs of the MinION™ are presented, one generated using R7 chemistry (released in July 2014) and one using R7.3 (released in September 2014).ConclusionsBase-called sequence data are provided to demonstrate the nature of data produced by the MinION™ platform and to encourage the development of customised methods for alignment, consensus and variant calling, de novo assembly and scaffolding. FAST5 files containing event data within the HDF5 container format are provided to assist with the development of improved base-calling methods. Datasets are provided through the GigaDB databasehttp://gigadb.org/dataset/100102
Cooperative riboregulation in living cells through allosteric programming of toehold activation
Authors: Rodrigo Guillermo , Prakash Satya , Shen Shensi , Majer Eszter , Daròs José-Antonio , Jaramillo Alfonso 
Published: September 2014

AbstractLiving cells rely on small non-coding RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. Contrary to most protein-based activators of transcription, all known riboregulators do not exploit cooperative binding mechanisms to activate gene expression. We conceived a general strategy to design cooperative riboregulation by programming a hierarchical toehold activation cascade, which we implemented into ade novosequence design algorithm. We engineered different riboregulatory systems relying on the conditional formation of a heterotrimeric species. We characterized the specificity of each RNA-RNA interactionin vitroand the cooperative activation of gene expression inEscherichia coli. As we only rely on a biochemical model to compute allosteric regulation, our strategy could be applied to reach more complex RNA-based nanostructures regulating gene expression for synthetic biology applications.
15 Transforming Lessons from the Past into Lessons for the Future
Authors: van der Leeuw Sander E. 
Published: September 2014

ABSTRACTThis paper argues that we would massively increase the value of our archaeological understanding of the past for the present if we cast it differently. Rather than use a reductionist, ex‐post approach (which explains the present by invoking the past, looking for origins), we should be using an “ex ante” approach that looks at the emergence of change, linking past and present to the future. This would allow us to learn from the past for the future. The paper examines some of the difficulties encountered in implementing such a different approach, at the level of our cognition, our scientific practices, and our paradigms, and then illustrates some of the changes in perspective such a shift would bring about by referring to the different discussions of Maya archaeology presented in this volume.
Biomarkers and insulin sensitivity in women with Polycystic Ovary Syndrome: Characteristics and predictive capacity
Authors: Cassar Samantha , Teede Helena J. , Harrison Cheryce L. , Joham Anju E. , Moran Lisa J. , Stepto Nigel K. 
Published: September 2014

SummaryObjectivePolycystic ovary syndrome (PCOS) is a common endocrine disorder associated with metabolic complications. Metabolic biomarkers with roles in obesity, glycaemic control and lipid metabolism are potentially relevant in PCOS. The aim was to investigate metabolic biomarkers in lean and overweight women with and without PCOS and to determine whether any biomarker was able to predict insulin resistance in PCOS.DesignCross‐sectional study.PatientsEighty‐four women (22 overweight and 22 lean women with PCOS, 18 overweight and 22 lean women without PCOS) were recruited from the community and categorized based on PCOS and BMI status.MeasurementsPrimary outcomes were metabolic biomarkers [ghrelin, resistin, visfatin, glucagon‐like peptide‐1 (GLP‐1), leptin, plasminogen activator inhibitor ‐1 (PAI‐1), glucose‐dependent insulinotropic polypeptide (GIP) and C‐Peptide] measured using the Bio‐Plex Pro Diabetes assay and insulin sensitivity as assessed by glucose infusion rate on euglycaemic–hyperinsulinaemic clamp.ResultsThe biomarkers C‐peptide, leptin, ghrelin and visfatin were different between overweight and lean women, irrespective of PCOS status. The concentration of circulating biomarkers did not differ between women with PCOS diagnosed by the Rotterdam criteria or National Institute of Health criteria. PAI‐1 was the only biomarker that significantly predicted insulin resistance in both control women (P = 0·04) and women with PCOS (P = 0·01).ConclusionsBiomarkers associated with metabolic diseases appear more strongly associated with obesity rather than PCOS status. PAI‐1 may also be a novel independent biomarker and predictor of insulin resistance in women with and without PCOS.