bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited clonal relatedness between gut IgA plasma cells and memory B cells after oral immunization
Authors: Bemark Mats , Hazanov Helena , Strömberg Anneli , Komban Rathan , Holmqvist Joel , Köster Sofia , Mattsson Johan , Sikora Per , Mehr Ramit , Lycke Nils Y. 
Published: September 2016

AbstractUnderstanding how memory B cells are induced and relate to long-lived plasma cells is important for vaccine development. Immunity to oral vaccines has been considered short-lived because of a poor ability to develop IgA B-cell memory. Here we demonstrate that long-lived mucosal IgA memory is readily achieved by oral but not systemic immunization in mouse models with NP hapten conjugated with cholera toxin and transfer of B1-8high/GFP+NP-specific B cells. Unexpectedly, memory B cells are poorly related to long-lived plasma cells and less affinity-matured. They are α4β7-integrin+CD73+PD-L2+CD80+and at systemic sites mostly IgM+, while 80% are IgA+in Peyer’s patches. On reactivation, most memory B cells in Peyer’s patches are GL7−, but expand in germinal centres and acquire higher affinity and more mutations, demonstrating strong clonal selection. CCR9 expression is found only in Peyer’s patches and appears critical for gut homing. Thus, gut mucosal memory possesses unique features not seen after systemic immunization.
Opportunities for biodiversity gains under the world’s largest reforestation programme
Authors: Hua Fangyuan , Wang Xiaoyang , Zheng Xinlei , Fisher Brendan , Wang Lin , Zhu Jianguo , Tang Ya , Yu Douglas W. , Wilcove David S. 
Published: September 2016

AbstractReforestation is a critical means of addressing the environmental and social problems of deforestation. China’s Grain-for-Green Program (GFGP) is the world’s largest reforestation scheme. Here we provide the first nationwide assessment of the tree composition of GFGP forests and the first combined ecological and economic study aimed at understanding GFGP’s biodiversity implications. Across China, GFGP forests are overwhelmingly monocultures or compositionally simple mixed forests. Focusing on birds and bees in Sichuan Province, we find that GFGP reforestation results in modest gains (via mixed forest) and losses (via monocultures) of bird diversity, along with major losses of bee diversity. Moreover, all current modes of GFGP reforestation fall short of restoring biodiversity to levels approximating native forests. However, even within existing modes of reforestation, GFGP can achieve greater biodiversity gains by promoting mixed forests over monocultures; doing so is unlikely to entail major opportunity costs or pose unforeseen economic risks to households.
LECT2 drives haematopoietic stem cell expansion and mobilization via regulating the macrophages and osteolineage cells
Authors: Lu Xin-Jiang , Chen Qiang , Rong Ye-Jing , Yang Guan-Jun , Li Chang-Hong , Xu Ning-Yi , Yu Chao-Hui , Wang Hui-Ying , Zhang Shun , Shi Yu-Hong , Chen Jiong 
Published: September 2016

AbstractHaematopoietic stem cells (HSCs) can differentiate into cells of all lineages in the blood. However, the mechanisms by which cytokines in the blood affect HSC homeostasis remain largely unknown. Here we show that leukocyte cell-derived chemotaxin 2 (LECT2), a multifunctional cytokine, induces HSC expansion and mobilization. Recombinant LECT2 administration results in HSC expansion in the bone marrow and mobilization to the blood via CD209a. The effect of LECT2 on HSCs is reduced after specific depletion of macrophages or reduction of osteolineage cells. LECT2 treatment reduces the tumour necrosis factor (TNF) expression in macrophages and osteolineage cells. In TNF knockout mice, the effect of LECT2 on HSCs is reduced. Moreover, LECT2 induces HSC mobilization in irradiated mice, while granulocyte colony-stimulating factor does not. Our results illustrate that LECT2 is an extramedullar cytokine that contributes to HSC homeostasis and may be useful to induce HSC mobilization.
Colossal Seebeck effect enhanced by quasi-ballistic phonons dragging massive electrons in FeSb2
Authors: Takahashi H. , Okazaki R. , Ishiwata S. , Taniguchi H. , Okutani A. , Hagiwara M. , Terasaki I. 
Published: September 2016

AbstractPhonon transport is an essential property of thermoelectric materials. Although the phonon carries heat, which reduces the thermoelectric efficiency, it contributes positively to the Seebeck coefficient S through the phonon-drag effect, as typified by the high-purity semiconductors, which show fairly large S at cryogenic temperatures. Although such a large S is attractive in terms of Peltier cooling, a clear guiding principle for designing thermoelectric materials enriched by the phonon-drag effect remains to be established. Here we demonstrate that a correlated semiconductor, FeSb2, is a promising thermoelectric material featuring quasi-ballistic phonons dragging d electrons with large effective mass. By changing the sample size within the sub-millimetre order for high-purity single crystals, we succeed in substantially increasing S to as much as −27 mV K−1 at low temperatures. Our results exemplify a strategy for exploring phonon-drag-based thermoelectric materials, the performance of which can be maximized by combining heavy electrons with ballistic phonons.
Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish
Authors: Fruciano Carmelo , Franchini Paolo , Kovacova Viera , Elmer Kathryn R. , Henning Frederico , Meyer Axel 
Published: September 2016

AbstractOur understanding of how biological diversity arises is limited, especially in the case of speciation in the face of gene flow. Here we investigate the genomic basis of adaptive traits, focusing on a sympatrically diverging species pair of crater lake cichlid fishes. We identify the main quantitative trait loci (QTL) for two eco-morphological traits: body shape and pharyngeal jaw morphology. These traits diverge in parallel between benthic and limnetic species in the repeated adaptive radiations of this and other fish lineages. Remarkably, a single chromosomal region contains the highest effect size QTL for both traits. Transcriptomic data show that the QTL regions contain genes putatively under selection. Independent population genomic data corroborate QTL regions as areas of high differentiation between the sympatric sister species. Our results provide empirical support for current theoretical models that emphasize the importance of genetic linkage and pleiotropy in facilitating rapid divergence in sympatry.
Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex
Authors: Mitchell Amanda C. , Javidfar Behnam , Bicks Lucy K. , Neve Rachael , Garbett Krassimira , Lander Sharon S. , Mirnics Karoly , Morishita Hirofumi , Wood Marcelo A. , Jiang Yan , Gaisler-Salomon Inna , Akbarian Schahram 
Published: September 2016

AbstractNeuronal epigenomes, including chromosomal loopings moving distal cis-regulatory elements into proximity of target genes, could serve as molecular proxy linking present-day-behaviour to past exposures. However, longitudinal assessment of chromatin state is challenging, because conventional chromosome conformation capture assays essentially provide single snapshots at a given time point, thus reflecting genome organization at the time of brain harvest and therefore are non-informative about the past. Here we introduce ‘NeuroDam’ to assess epigenome status retrospectively. Short-term expression of the bacterial DNA adenine methyltransferase Dam, tethered to the Gad1 gene promoter in mouse prefrontal cortex neurons, results in stable GmethylATC tags at Gad1-bound chromosomal contacts. We show by NeuroDam that mice with defective cognition 4 months after pharmacological NMDA receptor blockade already were affected by disrupted chromosomal conformations shortly after drug exposure. Retrospective profiling of neuronal epigenomes is likely to illuminate epigenetic determinants of normal and diseased brain development in longitudinal context.
Socio-economic factors, gender and smoking as determinants of COPD in a low-income country of sub-Saharan Africa: FRESH AIR Uganda
Authors: van Gemert Frederik , Chavannes Niels , Kirenga Bruce , Jones Rupert , Williams Sian , Tsiligianni Ioanna , Vonk Judith , Kocks Janwillem , de Jong Corina , van der Molen Thys 
Published: September 2016

AbstractIn Uganda, biomass smoke seems to be the largest risk factor for the development of COPD, but socio-economic factors and gender may have a role. Therefore, more in-depth research is needed to understand the risk factors. The aim of this study was to investigate the impact of socio-economic factors and gender differences on the COPD prevalence in Uganda. The population comprised 588 randomly selected participants (>30 years) who previously completed the FRESH AIR Uganda study. In this post hoc analysis, the impact of several socio-economic characteristics, gender and smoking on the prevalence of COPD was assessed using a logistic regression model. The main risk factors associated with COPD were non-Bantu ethnicity (odds ratio (OR) 1.73, 95% confidence interval (CI) 1.06–2.82, P=0.030), biomass fuel use for heating (OR 1.76, 95% CI 1.03–3.00, P=0.038), former smoker (OR 1.87, 95% CI 0.97–3.60, P=0.063) and being unmarried (OR 0.087, 95% CI 0.93–2.95, P=0.087). A substantial difference in the prevalence of COPD was seen between the two ethnic groups: non-Bantu 20% and Bantu 12.9%. Additional analysis between these two groups showed significant differences in socio-economic circumstances: non-Bantu people smoked more (57.7% vs 10.7%), lived in tobacco-growing areas (72% vs 14.8%) and were less educated (28.5% vs 12.9% had no education). With regard to gender, men with COPD were unmarried (OR 3.09, 95% CI 1.25–7.61, P=0.015) and used more biomass fuel for heating (OR 2.15, 95% CI 1.02–4.54, P=0.045), and women with COPD were former smokers (OR 3.35, 95% CI 1.22–9.22, P=0.019). Only a few socio-economic factors (i.e., smoking, biomass fuel use for heating, marital status and non-Bantu ethnicity) have been found to be associated with COPD. This applied for gender differences as well (i.e., for men, marital status and biomass fuel for heating, and for women being a former smoker). More research is needed to clarify the complexity of the different risk factors.
Characterizing the International Migration Barriers with a Probabilistic Multilateral Migration Model
Authors: Li Xiaomeng , Xu Hongzhong , Chen Jiawei , Chen Qinghua , Zhang Jiang , Di Zengru 
Published: September 2016

AbstractHuman migration is responsible for forming modern civilization and has had an important influence on the development of various countries. There are many issues worth researching, and “the reason to move” is the most basic one. The concept of migration cost in the classical self-selection theory, which was introduced by Roy and Borjas, is useful. However, migration cost cannot address global migration because of the limitations of deterministic and bilateral choice. Following the idea of migration cost, this paper developed a new probabilistic multilateral migration model by introducing the Boltzmann factor from statistical physics. After characterizing the underlying mechanism or driving force of human mobility, we reveal some interesting facts that have provided a deeper understanding of international migration, such as the negative correlation between migration costs for emigrants and immigrants and a global classification with clear regional and economic characteristics, based on clustering of migration cost vectors. In addition, we deconstruct the migration barriers using regression analysis and find that the influencing factors are complicated but can be partly (12.5%) described by several macro indexes, such as the GDP growth of the destination country, the GNI per capita and the HDI of both the source and destination countries.
Circulating Biomarkers of Immune Activation, Oxidative Stress and Inflammation Characterize Severe Canine Visceral Leishmaniasis
Authors: Solcà Manuela S. , Andrade Bruno B. , Abbehusen Melissa Moura Costa , Teixeira Clarissa R. , Khouri Ricardo , Valenzuela Jesus G. , Kamhawi Shaden , Bozza Patrícia Torres , Fraga Deborah Bittencourt Mothé , Borges Valeria Matos , Veras Patrícia Sampaio Tavares , Brodskyn Claudia Ida 
Published: September 2016

AbstractClinical manifestations in canine visceral leishmaniasis (CVL) have not been clearly associated with immunological status or disease progression. We simultaneously assessed biomarkers of inflammation, immune activation, oxidative stress, and anti-sand fly saliva IgG concentrations in dog sera with different clinical manifestations to characterize a biosignature associated with CVL severity. In a cross-sectional exploratory study, a random population of 70 dogs from an endemic area in Brazil was classified according to CVL clinical severity and parasitological evaluation. A panel of biomarkers and anti–sand fly saliva IgG were measured in canine sera. Assessment of protein expression of profile biomarkers identified a distinct biosignature that could cluster separately animal groups with different clinical scores. Increasing severity scores were associated with a gradual decrease of LTB4 and PGE2, and a gradual increase in CXCL1 and CCL2. Discriminant analyses revealed that combined assessment of LTB4, PGE2 and CXCL1 was able to distinguish dogs with different clinical scores. Dogs with the highest clinical score values also exhibited high parasite loads and higher concentrations of anti-saliva antibodies. Our findings suggest CVL clinical severity is tightly associated with a distinct inflammatory profile hallmarked by a differential expression of circulating eicosanoids and chemokines.
Smad4 suppresses the tumorigenesis and aggressiveness of neuroblastoma through repressing the expression of heparanase
Authors: Qu Hongxia , Zheng Liduan , Jiao Wanju , Mei Hong , Li Dan , Song Huajie , Fang Erhu , Wang Xiaojing , Li Shiwang , Huang Kai , Tong Qiangsong 
Published: September 2016

AbstractHeparanase (HPSE) is the only endo-β-D-glucuronidase that is correlated with the progression of neuroblastoma (NB), the most common extracranial malignancy in childhood. However, the mechanisms underlying HPSE expression in NB still remain largely unknown. Herein, through analyzing cis-regulatory elements and mining public microarray datasets, we identified SMAD family member 4 (Smad4) as a crucial transcription regulator of HPSE in NB. We demonstrated that Smad4 repressed the HPSE expression at the transcriptional levels in NB cells. Mechanistically, Smad4 suppressed the HPSE expression through directly binding to its promoter and repressing the lymphoid enhancer binding factor 1 (LEF1)-facilitated transcription of HPSE via physical interaction. Gain- and loss-of-function studies demonstrated that Smad4 inhibited the growth, invasion, metastasis, and angiogenesis of NB cells in vitro and in vivo. Restoration of HPSE expression prevented the NB cells from changes in these biological features induced by Smad4. In clinical NB specimens, Smad4 was under-expressed and inversely correlated with HPSE levels, while LEF1 was highly expressed and positively correlated with HPSE expression. Patients with high Smad4 expression, low LEF1 or HPSE levels had greater survival probability. These results demonstrate that Smad4 suppresses the tumorigenesis and aggressiveness of NB through repressing the HPSE expression.
Genome-wide identification and comparison of legume MLO gene family
Authors: Rispail Nicolas , Rubiales Diego 
Published: September 2016

AbstractMLO proteins are highly conserved proteins with seven trans-membrane domains. Specific MLO genes have been linked to plant disease susceptibility. Others are involved in plant reproduction and in root thigmomorphogenesis. Functions of the remaining MLOs are still unknown. Here we performed a genome-wide survey of the MLO family in eight legume species from different clades of the Papillionoideae sub-family. A total of 118 MLO sequences were identified and characterized. Their deduced protein sequences shared the characteristics of MLO proteins. The total number of MLO genes per legume species varied from 13 to 20 depending on the species. Legume MLOs were evenly distributed over their genomes and tended to localize within syntenic blocks conserved across legume genomes. Phylogenetic analysis indicated that these sequences clustered in seven well-defined clades. Comparison of MLO protein sequences revealed 34 clade-specific motifs in the variable regions of the proteins. Comparative analyses of the MLO family between legume species also uncovered several evolutionary differences between the tropical legume species from the Phaseoloid clades and the other legume species. Altogether, this study provides interesting new features on the evolution of the MLO family. It also provides valuable clues to identify additional MLO genes from non-sequenced species.
One-year Outcomes of Pachymetry and Epithelium Thicknesses after Accelerated (45 mW/cm2) Transepithelial Corneal Collagen Cross-linking for Keratoconus Patients
Authors: Zhang Xiaoyu , Sun Ling , Chen Yingjun , Li Meiyan , Tian Mi , Zhou Xingtao 
Published: September 2016

AbstractThe thickness of corneal pachymetry and the epithelium after accelerated (45 mW/cm2) transepithelial corneal collagen cross-linking (CXL) for keratoconus were assessed in this prospective case series study. Twenty-eight patients were treated for keratoconus. The mean Kmax was 56.18 ± 7.90. The thinnest point, as assessed by optical coherence tomography (OCT), was 443.18 ± 39.75 μm. Accelerated transepithelial CXL was performed, and corrected distance visual acuity (CDVA), corneal topography, and OCT were recorded at 1 week postoperatively as well as at 1, 3, 6, and 12 months. The surgery was uneventful in all eyes. Postoperative epithelial edema was observed and faded in 3 days. The postoperative Kmax was 54.56 ± 8.81, 55.78 ± 8.11, 56.37 ± 8.71, 55.80 ± 7.92, and 55.47 ± 8.24 at 1 week, 1 month, 3 months, 6 months, and 12 months, respectively (all, P > 0.05). The thinnest postoperative corneal point, 439.04 ± 44.99 μm, was observed at 12 months (P = 0.109). The epithelial thickness decreased during the first postoperative week then showed a gradual recovery. Postoperative pachymetry thickness showed no significant changes for up to 12 months. Postoperative epithelial thickness decreased temporarily, then stabilized at month 12. Accelerated transepithelial CXL was shown to be effective and safe for the treatment of keratoconus.
On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli
Authors: van den Berg Jonas , Galbiati Heloisa , Rasmussen Akiko , Miller Samantha , Poolman Bert 
Published: September 2016

AbstractBacterial mechanosensitive channels protect cells from structural damage during hypoosmotic shock. MscS, MscL and MscK are the most abundant channels in E. coli and arguably the most important ones in osmoprotection. By combining physiological assays with quantitative photo-activated localization microscopy (qPALM), we find an almost linear relationship between channel abundance and cell survival. A minimum of 100 MscL (or MscS) channels is needed for protection when a single type of channel is expressed. Under native-like conditions MscL, MscS as well as MscK distribute homogeneously over the cytoplasmic membrane and the lateral diffusion of the channels is in accordance with their relative protein mass. However, we observe cluster formation and a reduced mobility of MscL when the majority of the subunits of the pentameric channel contain the fluorescent mEos3.2 protein. These data provide new insights into the quantitative biology of mechanosensitive channels and emphasizes the need for care in analysing protein complexes even when the fluorescent tag has been optimized for monomeric behaviour.
Biogeography and Adaptive evolution of Streptomyces Strains from saline environments
Authors: Zhao Fei , Qin Yu-Hua , Zheng Xin , Zhao Hong-Wei , Chai Dong-Yan , Li Wei , Pu Ming-Xiang , Zuo Xing-Sheng , Qian Wen , Ni Ping , Zhang Yong , Mei Han , He Song-Tao 
Published: September 2016

AbstractThe genus Streptomyces is a widespread genus within the phylum Actinobacteria and has been isolated from various environments worldwide. However, little is known about whether biogeography affects distributional pattern of Streptomyces in salty environments. Such information is essential for understanding the ecology of Streptomyces. Here we analyzed four house-keeping genes (16S rRNA, rpoB, recA and atpD) and salty-tolerance related genes (ectA-ectD) of 38 Streptomyces strains isolated from saline environments in Yunnan and Xinjiang Provinces of western China. The obtained Streptomyces strains were classified into three operational taxonomic units, each comprising habitat-specific geno- and ecotype STs. In combination with expressional variations of salty-tolerance related genes, the statistical analyses showed that spatial distance and environmental factors substantially influenced Streptomyces distribution in saline environments: the former had stronger influence at large spatial scales (>700 km), whereas the latter was influential at large (>700 km) and small spatial scales (<700 km). Plus, the quantitative analyses of salty-tolerence related genes (ectA-D) indicated that Streptomyces strains from salt lakes have higher expression of ectA-D genes and could accumulate larger quantities of ectoine and hydroxyectoine than strains from salt mines, which could help them resist to salinity in the hypersaline environments.
A 3D Poly(ethylene glycol)-based Tumor Angiogenesis Model to Study the Influence of Vascular Cells on Lung Tumor Cell Behavior
Authors: Roudsari Laila C. , Jeffs Sydney E. , Witt Amber S. , Gill Bartley J. , West Jennifer L. 
Published: September 2016

AbstractTumor angiogenesis is critical to tumor growth and metastasis, yet much is unknown about the role vascular cells play in the tumor microenvironment. In vitro models that mimic in vivo tumor neovascularization facilitate exploration of this role. Here we investigated lung adenocarcinoma cancer cells (344SQ) and endothelial and pericyte vascular cells encapsulated in cell-adhesive, proteolytically-degradable poly(ethylene) glycol-based hydrogels. 344SQ in hydrogels formed spheroids and secreted proangiogenic growth factors that significantly increased with exposure to transforming growth factor beta 1 (TGF-β1), a potent tumor progression-promoting factor. Vascular cells in hydrogels formed tubule networks with localized activated TGF-β1. To study cancer cell-vascular cell interactions, we engineered a 2-layer hydrogel with 344SQ and vascular cell layers. Large, invasive 344SQ clusters (area > 5,000 μm2, circularity < 0.25) developed at the interface between the layers, and were not evident further from the interface or in control hydrogels without vascular cells. A modified model with spatially restricted 344SQ and vascular cell layers confirmed that observed cluster morphological changes required close proximity to vascular cells. Additionally, TGF-β1 inhibition blocked endothelial cell-driven 344SQ migration. Our findings suggest vascular cells contribute to tumor progression and establish this culture system as a platform for studying tumor vascularization.