bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcriptional coregulator GRIP1 controls macrophage polarization and metabolic homeostasis
Authors: Coppo Maddalena , Chinenov Yurii , Sacta Maria A. , Rogatsky Inez 
Published: July 2016

AbstractDiet-induced obesity causes chronic macrophage-driven inflammation in white adipose tissue (WAT) leading to insulin resistance. WAT macrophages, however, differ in their origin, gene expression and activities: unlike infiltrating monocyte-derived inflammatory macrophages, WAT-resident macrophages counteract inflammation and insulin resistance, yet, the mechanisms underlying their transcriptional programming remain poorly understood. We recently reported that a nuclear receptor cofactor—glucocorticoid receptor (GR)-interacting protein (GRIP)1—cooperates with GR to repress inflammatory genes. Here, we show that GRIP1 facilitates macrophage programming in response to IL4 via a GR-independent pathway by serving as a coactivator for Kruppel-like factor (KLF)4—a driver of tissue-resident macrophage differentiation. Moreover, obese mice conditionally lacking GRIP1 in macrophages develop massive macrophage infiltration and inflammation in metabolic tissues, fatty livers, hyperglycaemia and insulin resistance recapitulating metabolic disease. Thus, GRIP1 is a critical regulator of immunometabolism, which engages distinct transcriptional mechanisms to coordinate the balance between macrophage populations and ultimately promote metabolic homeostasis.
M2 tumour-associated macrophages contribute to tumour progression via legumain remodelling the extracellular matrix in diffuse large B cell lymphoma
Authors: Shen Long , Li Honghao , Shi Yuzhi , Wang Dekun , Gong Junbo , Xun Jing , Zhou Sifan , Xiang Rong , Tan Xiaoyue 
Published: July 2016

AbstractEffects of M2 tumour-associated macrophages on the pathogenesis of diffuse large B cell lymphoma (DLBCL) are still controversial. Our data showed that the number of CD163-positive M2 macrophages correlated negatively with DLBCL prognosis. Macrophage depletion by clodronate liposomes significantly suppressed tumour growth in a xenograft mouse model of DLBCL using OCI-Ly3 cells. Moreover, M2 polarization of macrophages induced legumain expression in U937 cells. Exogenous legumain promoted degradation of fibronectin and collagen I, which was abolished by administration of a legumain inhibitor RR-11a. Overexpression of legumain in Raw 264.7 cells also induced tube formation of endothelial cells in matrigel. In the xenograft mouse model of DLBCL, decreased fibronectin and collagen I, as well as increased legumain expression and angiogenesis were found at the late stage tumours compared with early stage tumours. Co-localization of legumain and fibronectin was observed in the extracellular matrix of tumour tissues. Administration of the legumain inhibitor to the xenograft DLBCL model suppressed tumour growth, angiogenesis and collagen deposition compared with the control. Taken together, our results suggest that M2 tumour-associated macrophages affect degradation of the extracellular matrix and angiogenesis via overexpression of legumain and therefore play an active role in the progression of DLBCL.
Reinforcement of integrin-mediated T-Lymphocyte adhesion by TNF-induced Inside-out Signaling
Authors: Li Qian , Huth Steven , Adam Dieter , Selhuber-Unkel Christine 
Published: July 2016

AbstractIntegrin-mediated leukocyte adhesion to endothelial cells is a crucial step in immunity against pathogens. Whereas the outside-in signaling pathway in response to the pro-inflammatory cytokine tumour necrosis factor (TNF) has already been studied in detail, little knowledge exists about a supposed TNF-mediated inside-out signaling pathway. In contrast to the outside-in signaling pathway, which relies on the TNF-induced upregulation of surface molecules on endothelium, inside-out signaling should also be present in an endothelium-free environment. Using single-cell force spectroscopy, we show here that stimulating Jurkat cells with TNF significantly reinforces their adhesion to fibronectin in a biomimetic in vitro assay for cell-surface contact times of about 1.5 seconds, whereas for larger contact times the effect disappears. Analysis of single-molecule ruptures further demonstrates that TNF strengthens sub-cellular single rupture events at short cell-surface contact times. Hence, our results provide quantitative evidence for the significant impact of TNF-induced inside-out signaling in the T-lymphocyte initial adhesion machinery.
Real time and label free profiling of clinically relevant exosomes
Authors: Sina Abu Ali Ibn , Vaidyanathan Ramanathan , Dey Shuvashis , Carrascosa Laura G. , Shiddiky Muhammad J. A. , Trau Matt 
Published: July 2016

AbstractTumor-derived exosomes possess significant clinical relevance due to their unique composition of genetic and protein material that is representative of the parent tumor. Specific isolation as well as identification of proportions of these clinically relevant exosomes (CREs) from biological samples could help to better understand their clinical significance as cancer biomarkers. Herein, we present a simple approach for quantification of the proportion of CREs within the bulk exosome population isolated from patient serum. This proportion of CREs can potentially inform on the disease stage and enable non-invasive monitoring of inter-individual variations in tumor-receptor expression levels. Our approach utilises a Surface Plasmon Resonance (SPR) platform to quantify the proportion of CREs in a two-step strategy that involves (i) initial isolation of bulk exosome population using tetraspanin biomarkers (i.e., CD9, CD63), and (ii) subsequent detection of CREs within the captured bulk exosomes using tumor-specific markers (e.g., human epidermal growth factor receptor 2 (HER2)). We demonstrate the isolation of bulk exosome population and detection of as low as 10% HER2(+) exosomes from samples containing designated proportions of HER2(+) BT474 and HER2(−) MDA-MB-231 cell derived exosomes. We also demonstrate the successful isolation of exosomes from a small cohort of breast cancer patient samples and identified that approximately 14–35% of their bulk population express HER2.
Swarm dynamics may give rise to Lévy flights
Authors: Reynolds Andrew M. , Ouellette Nicholas T. 
Published: July 2016

Abstract“Continuous-time correlated random walks” are now gaining traction as models of scale-finite animal movement patterns because they overcome inherent shortcomings with the prevailing paradigm - discrete random walk models. Continuous-time correlated random walk models are founded on the classic Langevin equation that is driven by purely additive noise. The Langevin equation is, however, changed fundamentally by the smallest of multiplicative noises. The inclusion of such noises gives rise to Lévy flights, a popular but controversial model of scale-free movement patterns. Multiplicative noises have not featured prominently in the literature on biological Lévy flights, being seen, perhaps, as no more than a mathematical contrivance. Here we show how Langevin equations driven by multiplicative noises and incumbent Lévy flights arise naturally in the modelling of swarms. Model predictions find some support in three-dimensional, time-resolved measurements of the positions of individual insects in laboratory swarms of the midgeChironomus riparius.We hereby provide a new window on Lévy flights as models of movement pattern data, linking patterns to generative processes.
Discovery of midgut genes for the RNA interference control of corn rootworm
Authors: Hu Xu , Richtman Nina M. , Zhao Jian-Zhou , Duncan Keith E. , Niu Xiping , Procyk Lisa A. , Oneal Meghan A. , Kernodle Bliss M. , Steimel Joseph P. , Crane Virginia C. , Sandahl Gary , Ritland Julie L. , Howard Richard J. , Presnail James K. , Lu Albert L. , Wu Gusui 
Published: July 2016

AbstractRNA interference (RNAi) is a promising new technology for corn rootworm control. This paper presents the discovery of new gene targets - dvssj1 and dvssj2, in western corn rootworm (WCR). Dvssj1 and dvssj2 are orthologs of the Drosophila genes snakeskin (ssk) and mesh, respectively. These genes encode membrane proteins associated with smooth septate junctions (SSJ) which are required for intestinal barrier function. Based on bioinformatics analysis, dvssj1 appears to be an arthropod-specific gene. Diet based insect feeding assays using double-stranded RNA (dsRNA) targeting dvssj1 and dvssj2 demonstrate targeted mRNA suppression, larval growth inhibition, and mortality. In RNAi treated WCR, injury to the midgut was manifested by “blebbing” of the midgut epithelium into the gut lumen. Ultrastructural examination of midgut epithelial cells revealed apoptosis and regenerative activities. Transgenic plants expressing dsRNA targeting dvssj1 show insecticidal activity and significant plant protection from WCR damage. The data indicate that dvssj1 and dvssj2 are effective gene targets for the control of WCR using RNAi technology, by apparent suppression of production of their respective smooth septate junction membrane proteins located within the intestinal lining, leading to growth inhibition and mortality.
Physical activity, body composition and lipids changes in adolescents: analysis from the MyHeART Study
Authors: Majid Hazreen Abdul , Amiri Mohammadreza , Mohd Azmi Nahar , Su Tin Tin , Jalaludin Muhammad Yazid , Al-Sadat Nabilla 
Published: July 2016

AbstractInsufficient physical activity and growing obesity levels among Malaysian adolescents are becoming a public health concern. Our study is to identify the trends of self-reported physical activity (PA) levels, blood lipid profiles, and body composition (BC) indices from a cohort of 820 adolescents. The self-reported PA was assessed using a validated Malay version of the PA Questionnaire for Older Children (PAQ-C). Fasting blood samples were collected to investigate their lipid profiles. Height, weight, waist and hip circumferences as well as body fat percentage were measured. The baseline and the first follow-up were conducted in 2012 and 2014, respectively. A downward trend in the PA level was seen in all categories with a significant reduction among all rural adolescents (P = 0.013) and more specifically, PA among girls residing in rural areas dropped significantly (P = 0.006). Either a significant reduction in high-density lipoprotein (HDL) or a significant increment in BC indices (i.e., body mass index [BMI], waist circumference [WC], hip circumference, and body fat percentage [BF %]) were seen in this group. Female adolescents experienced more body fat increment with the reduction of physical activity. If not intervened early, adolescents from rural areas may increase their risk of developing cardiovascular diseases earlier.
A Fossilized Energy Distribution of Lightning
Authors: Pasek Matthew A. , Hurst Marc 
Published: July 2016

AbstractWhen lightning strikes soil, it may generate a cylindrical tube of glass known as a fulgurite. The morphology of a fulgurite is ultimately a consequence of the energy of the lightning strike that formed it and hence fulgurites may be useful in elucidating the energy distribution frequency of cloud-to-ground lightning. Fulgurites from sand mines in Polk County, Florida, USA were collected and analyzed to determine morphologic properties. Here we show that the energy per unit length of lightning strikes within quartz sand has a geometric mean of ~1.0 MJ/m and that the distribution is lognormal with respect to energy per length and frequency. Energy per length is determined from fulgurites as a function of diameter and frequency is determined both by cumulative number and by cumulative length. This distribution parallels those determined for a number of lightning parameters measured in actual atmospheric discharge events, such as charge transferred, voltage and action integral. This methodology suggests a potential useful pathway for elucidating lightning energy and damage potential of strikes.
Excessive collagen turnover products are released during colorectal cancer progression and elevated in serum from metastatic colorectal cancer patients
Authors: Kehlet S. N. , Sanz-Pamplona R. , Brix S. , Leeming D. J. , Karsdal M. A. , Moreno V. 
Published: July 2016

AbstractDuring cancer progression, the homeostasis of the extracellular matrix becomes imbalanced with an excessive collagen remodeling by matrix metalloproteinases. As a consequence, small protein fragments of degraded collagens are released into the circulation. We have investigated the potential of protein fragments of collagen type I, III and IV as novel biomarkers for colorectal cancer. Specific fragments of degraded type I, III and IV collagen (C1M, C3M, C4M) and type III collagen formation (Pro-C3) were assessed in serum from colorectal cancer patients, subjects with adenomas and matched healthy controls using well-characterized and validated ELISAs. Serum levels of the biomarkers were significantly elevated in colorectal cancer patients compared to subjects with adenomas (C1M, Pro-C3, C3M) and controls (C1M, Pro-C3). When patients were stratified according to their tumour stage, all four biomarkers were able to differentiate stage IV metastatic patients from all other stages. Combination of all markers with age and gender in a logistic regression model discriminated between metastatic and non-metastatic patients with an AUROC of 0.80. The data suggest that the levels of these collagen remodeling biomarkers may be a measure of tumour activity and invasiveness and may provide new clinical tools for monitoring of patients with advanced stage colorectal cancer.
Growth of epitaxial silicon nanowires on a Si substrate by a metal-catalyst-free process
Authors: Ishiyama Takeshi , Nakagawa Shuhei , Wakamatsu Toshiki 
Published: July 2016

AbstractThe growth of epitaxial Si nanowires by a metal-catalyst-free process has been investigated as an alternative to the more common metal-catalyzed vapor–liquid–solid process. The well-aligned Si nanowires are successfully grown on a (111)-oriented Si substrate without any metal catalysts by a thermal treatment using silicon sulfide as a Si source at approximately 1200 °C. The needle-shaped Si nanowires, which have a core–shell structure that consists of a single-crystalline Si core along the <111> direction consistent with the substrate direction and a surface coating of silicon oxide, are grown by a metal-catalyst-free process. In this process, the silicon sulfide in the liquid phase facilitates the nucleation and nanowire growth. In contrast, oxygen-rich nanowires that consist of crystalline Si at the tip and lumpy silicon oxide on the body are observed in a sample grown at 1300 °C, which disturbs the epitaxial growth of Si nanowires.
Cooperative effect of silicon and other alloying elements on creep resistance of titanium alloys: insight from first-principles calculations
Authors: Li Yang , Chen Yue , Liu Jian-Rong , Hu Qing-Miao , Yang Rui 
Published: July 2016

AbstractCreep resistance is one of the key properties of titanium (Ti) alloys for high temperature applications such as in aero engines and gas turbines. It has been widely recognized that moderate addition of Si, especially when added together with some other elements (X), e.g., Mo, significantly improves the creep resistance of Ti alloys. To provide some fundamental understandings on such a cooperative effect, the interactions between Si and X in both hexagonal close-packed α and body-centered cubic β phases are systematically investigated by using a first-principles method. We show that the transition metal (TM) atoms with the number of d electrons (Nd) from 3 to 7 are attractive to Si in α phase whereas those with Nd > 8 and simple metal (SM) alloying atoms are repulsive to Si. All the alloying atoms repel Si in the β phase except for the ones with fewer d electrons than Ti. The electronic structure origin underlying the Si-X interaction is discussed based on the calculated electronic density of states and Bader charge. Our calculations suggest that the beneficial X-Si cooperative effect on the creep resistance is attributable to the strong X-Si attraction.
DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins
Authors: Baek Kwangryul , Kim Duk Hyoung , Jeong Jooyeon , Sim Sang Jun , Melis Anastasios , Kim Jin-Soo , Jin EonSeon , Bae Sangsu 
Published: July 2016

AbstractMicroalgae are versatile organisms capable of converting CO2, H2O and sunlight into fuel and chemicals for domestic and industrial consumption. Thus, genetic modifications of microalgae for enhancing photosynthetic productivity and biomass and bio-products generation are crucial for both academic and industrial applications. However, targeted mutagenesis in microalgae with CRISPR-Cas9 is limited. Here we report, a one-step transformation of Chlamydomonas reinhardtii by the DNA-free CRISPR-Cas9 method rather than plasmids that encode Cas9 and guide RNAs. Outcome was the sequential CpFTSY and ZEP two-gene knockout and the generation of a strain constitutively producing zeaxanthin and showing improved photosynthetic productivity.
Light-induced negative differential resistance in graphene/Si-quantum-dot tunneling diodes
Authors: Lee Kyeong Won , Jang Chan Wook , Shin Dong Hee , Kim Jong Min , Kang Soo Seok , Lee Dae Hun , Kim Sung , Choi Suk-Ho , Hwang Euyheon 
Published: July 2016

AbstractOne of the interesing tunneling phenomena is negative differential resistance (NDR), the basic principle of resonant-tunneling diodes. NDR has been utilized in various semiconductor devices such as frequency multipliers, oscillators, relfection amplifiers, logic switches, and memories. The NDR in graphene has been also reported theoretically as well as experimentally, but should be further studied to fully understand its mechanism, useful for practical device applications. Especially, there has been no observation about light-induced NDR (LNDR) in graphene-related structures despite very few reports on the LNDR in GaAs-based heterostructures. Here, we report first observation of LNDR in graphene/Si quantum dots-embedded SiO2 (SQDs:SiO2) multilayers (MLs) tunneling diodes. The LNDR strongly depends on temperature (T) as well as on SQD size, and the T dependence is consistent with photocurrent (PC)-decay behaviors. With increasing light power, the PC-voltage curves are more structured with peak-to-valley ratios over 2 at room temperature. The physical mechanism of the LNDR, governed by resonant tunneling of charge carriers through the minibands formed across the graphene/SQDs:SiO2 MLs and by their nonresonant phonon-assisted tunneling, is discussed based on theoretical considerations.
Laboratory medicine in pediatric lupus
Authors: La Cava Antonio 
Published: July 2016

AbstractPediatric lupus encompasses a broad variety of clinical manifestations of a systemic disease. Routine laboratory testing, autoantibodies, and complement levels can confirm the diagnosis and help monitoring and therapy of the disease, to ultimately improve outcomes. Additionally, tests can help to identify subsets of patients with specific risk factors and/or the involvement of selected organs/systems. The availability, refinement and accuracy of laboratory tests are instrumental to improve the diagnosis, treatment and prognosis of pediatric lupus patients.
SIM key comparison for luminous flux. SIM.PR-K4
Authors: Matamoros Carlos H , Ohno Yoshi , Zwinkels Joanne , Cogno Jorge A , Couceiro Iakyra B 
Published: July 2016

In compliance with the established BIPM and CCPR policies and guidelines on comparisons, the SIM Photometry and Radiometry Working Group decided to conduct a key comparison on total luminous flux in order to provide an opportunity for its member National Metrology Institutes (NMIs) that did not participate in the CCPR-K4 comparison, to get a link to the reference value obtained for this quantity (the lumen) and to derive the corresponding degrees of equivalence.
This SIM.PR-K4 was piloted by Centro Nacional de Metrología (CENAM), the NMI of Mexico and included the participation of five laboratories: CENAM (Mexico), INTI (Argentina), INMETRO (Brazil), NIST (USA, linking lab), and NRC (Canada, linking lab).
The comparison, conducted in star type scheme, was run using three to four lamps per participant, and results are given in this report, including the unilateral degrees of equivalence.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Narrative and poetry working together
Authors: Linafelt Tod 
Published: July 2016

Abstract
“Narrative and poetry working together” shows how the Bible brings narrative and poetry together as complementary forms to maintain and make use of the distinctive literary resources of each. The poetic insets in narrative contexts can be used as markers of structure; to add certain weight, gravitas, or solemnity to the speech of the characters; to introduce both figurative language and the expression of thought and passion into a literary form where it is otherwise mostly absent; or as an expression of interiority—the expression or intensification of a character’s emotional life, his or her thoughts, feelings, and commitments. Examples from the book of Job are given.
Joint sparse canonical correlation analysis for detecting differential imaging genetics modules
Authors: Fang Jian , Lin Dongdong , Schulz S. Charles , Xu Zongben , Calhoun Vince D. , Wang Yu-Ping 
Published: July 2016

Motivation: Imaging genetics combines brain imaging and genetic information to identify the relationships between genetic variants and brain activities. When the data samples belong to different classes (e.g. disease status), the relationships may exhibit class-specific patterns that can be used to facilitate the understanding of a disease. Conventional approaches often perform separate analysis on each class and report the differences, but ignore important shared patterns.
Results: In this paper, we develop a multivariate method to analyze the differential dependency across multiple classes. We propose a joint sparse canonical correlation analysis method, which uses a generalized fused lasso penalty to jointly estimate multiple pairs of canonical vectors with both shared and class-specific patterns. Using a data fusion approach, the method is able to detect differentially correlated modules effectively and efficiently. The results from simulation studies demonstrate its higher accuracy in discovering both common and differential canonical correlations compared to conventional sparse CCA. Using a schizophrenia dataset with 92 cases and 116 controls including a single nucleotide polymorphism (SNP) array and functional magnetic resonance imaging data, the proposed method reveals a set of distinct SNP-voxel interaction modules for the schizophrenia patients, which are verified to be both statistically and biologically significant.
Availability and Implementation: The Matlab code is available at https://sites.google.com/site/jianfang86/JSCCA.
Contact: wyp@tulane.edu
Supplementary information: Supplementary data are available at Bioinformatics online.