SwePub - sökning: WFRF:(Xiao Jun)

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1.	Klionsky, Daniel J., et al. (författare) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Forskningsöversikt (refereegranskat)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
2.	Li, Lili, et al. (författare) Heparanase overexpression reduces carrageenan-induced mechanical and cold hypersensitivity in mice 2012 Ingår i: Neuroscience Letters. - : Elsevier BV. - 0304-3940 .- 1872-7972. ; 511:1, s. 4-7 Tidskriftsartikel (refereegranskat)abstract Heparanase controls the structure and functions of extracellular matrix (ECM) by degrading heparan sulfate proteoglycans. Heparanase is involved in inflammatory process through modulating the functions of inflammatory cytokines. The present study aimed to find out whether overexpression of heparanase in mice affects carrageenan-induced localized inflammation and inflammatory hyperalgesia. Without challenge, the heparanase overexpression did not significantly affect the mice in response to mechanical, cold and heat stimulation. Unilateral subcutaneous administration of carrageenan produced hypersensitivity to mechanical and cold in both wildtype and the heparanase overexpression (Hpa-tg) mice 24h after treatment. In comparison to wildtype animals, the Hpa-tg mice showed significantly reduced mechanical and cold hypersensitivity. This may, at least partially, due to the reduced mast cell infiltration at the site of inflammation in Hpa-tg mice. These data support a role for heparanase that reduces localized inflammation and inflammatory hyperalgesia in mice.
3.	Zhang, Xiao-Dong, et al. (författare) Establishment and assessments of a new model for the postoperative fatigue syndrome by major small intestinal resection in rats 2011 Ingår i: Scandinavian Journal of Gastroenterology. - : Informa UK Limited. - 1502-7708 .- 0036-5521. ; 46:11, s. 1302-1309 Tidskriftsartikel (refereegranskat)abstract Objective. Postoperative fatigue syndrome (POFS) is a general and main complication after surgery. However, there is no stable and standardized animal model for POFS. The aim of the present study was to establish a rodent model of POFS by small intestinal resection, with POFS evaluated by acknowledged physical and behavioral methods. Material and Methods. Forty-two Sprague-Dawley rats were randomly divided into four groups according to the length of a "middle" small intestinal resection: 0% (sham group; i.e., laparotomy alone), 10%, 40% and 70% groups, with corresponding lengths of small intestinal resections. Following surgery, the general state of health was evaluated. Tail suspension test, open field test and Morris water maze test were used to evaluate the degree of POFS. Serum albumin, transferrin, prealbumin and fibronectin were measured to assess the nutritional status, and superoxide dismutase (SOD) and malondialdehyde (MDA) were also measured. Results. As compared with the other three groups, the 70% small intestinal resection group showed the worst general state of health, decreased strength of the tail suspension test and decreased score of Morris water maze test (p < 0.05) after operation. All rats in whom the small intestinal resection was done demonstrated a certain degree of malnutrition and behavior of depression, and the 70% resection group had the lowest levels of transferrin, prealbumin and fibronectin as compared with the other groups (p < 0.05), as well as decreased SOD and increased MDA in serum (p < 0.05). Conclusions. Resection of 70% of the small intestine resulted in typical characteristics of POFS. As this procedure is simple, stable and easily reproducible, it may serve as a model for research on POFS.
4.	Zhou, Xiang-Yu, et al. (författare) TRAF6 as the Key Adaptor of TLR4 Signaling Pathway Is Involved in Acute Pancreatitis 2010 Ingår i: PANCREAS. - 0885-3177. ; 39:3, s. 359-366 Tidskriftsartikel (refereegranskat)abstract Objectives: To study the potential role of tumor necrosis factor receptor-associated factor 6 (TRAF6) as the key adaptor of the toll-like receptor 4 (TLR4) signaling pathway in acute pancreatitis (AP) in mice. Methods: Acute pancreatitis was induced by 7 intraperitoneal injections of cerulein in TLR4-deficient (TLR4-Def) and TLR4 wild-type (TLR4-WT) mice. Inflammatory severity was scored and evaluated based on pathological study. TRAF6 expression was determined by reverse transcriptase polymerase chain reaction, Western blot, and immunohistochemistry. Results: Acute pancreatitis was successfully induced in both mice strains, but the inflammatory progression was different. In TLR4-Def mice, pancreatic inflammation was blunt and mild first, then became increasingly intensive and peaked at the later stage, whereas in the TLR4-WT mice, the response was fast initiated and peaked at the early stage of AP, then alleviated gradually. TRAF6 expression in TLR4-Def mice was significantly higher than that in the TLR4-WT mice. Immunohistochemistry located TRAF6 expressed mainly in the pancreatic acinar cells. Conclusions: The TLR4-TRAF6 signaling pathway is critically involved in AP. Other signaling pathways beyond TLR4 may participate in the pancreatic inflammatory process via TRAF6. As a convergence point of the TLR4-dependent and the TLR4-independent signaling pathways, TRAF6 plays an important role in AP.
5.	An, Junghwa, et al. (författare) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009 2010 Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408 Tidskriftsartikel (refereegranskat)abstract This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
6.	Carlsson-Jonsson, Anna, et al. (författare) N-terminal truncations of substance P1-7 amide affect its action on spinal cord injury-induced mechanical allodynia in rats 2014 Ingår i: European Journal of Pharmacology. - : Elsevier BV. - 0014-2999 .- 1879-0712. ; 738, s. 319-325 Tidskriftsartikel (refereegranskat)abstract Central neuropathic pain can arise from injury of the spinal cord and can become chronic. Treatment is difficult and, because complete pain relief is currently very hard to achieve, there is a need for new, more effective treatment options. In this study we used an animal model of spinal cord injury to evaluate the potency of a bioactive fragment of substance P (SP), i.e. SP1-7, in alleviating signs of allodynia and acute pain. SP1-7 is known from earlier studies to possess antinociceptive properties. We also studied the effects of intraperitoneal injection of an amidated analog of this heptapeptide and of its truncated analogs, all of which had high affinity to the SP1-7 binding site, to evaluate the importance of the removed amino acids for the bioclistribution and stability of the peptides. Most of the examined compounds alleviated mechanical alloclynia without any signs of sedation or motor impairment in the rats. In contrast, the response threshold to acute nociceptive stimulation was not affected by arty of the compounds tested. Most of the amino acids in the heptapepticle structure were essential for retaining the biological effect after peripheral injection. These observations suggest that the heptapepticle and its N-Lerminal truncated hexa- and pentapeptide analogs could be of interest for further development of analgesics in the management of mechanical allodynia.
7.	Cho, Yoon Shin, et al. (författare) Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. 2012 Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:1 Tidskriftsartikel (refereegranskat)abstract We conducted a three-stage genetic study to identify susceptibility loci for type 2 diabetes (T2D) in east Asian populations. We followed our stage 1 meta-analysis of eight T2D genome-wide association studies (6,952 cases with T2D and 11,865 controls) with a stage 2 in silico replication analysis (5,843 cases and 4,574 controls) and a stage 3 de novo replication analysis (12,284 cases and 13,172 controls). The combined analysis identified eight new T2D loci reaching genome-wide significance, which mapped in or near GLIS3, PEPD, FITM2-R3HDML-HNF4A, KCNK16, MAEA, GCC1-PAX4, PSMD6 and ZFAND3. GLIS3, which is involved in pancreatic beta cell development and insulin gene expression, is known for its association with fasting glucose levels. The evidence of an association with T2D for PEPD and HNF4A has been shown in previous studies. KCNK16 may regulate glucose-dependent insulin secretion in the pancreas. These findings, derived from an east Asian population, provide new perspectives on the etiology of T2D.
8.	Ding, Jun-Li, et al. (författare) Attenuation of Acute Pancreatitis by Peroxisome Proliferator-Activated Receptor-α in Rats: The Effect on Toll-Like Receptor Signaling Pathways 2013 Ingår i: Pancreas. - : Lippincott, Williams and Wilkins. - 0885-3177 .- 1536-4828. ; 42:1, s. 114-122 Tidskriftsartikel (refereegranskat)abstract Objectives: The peroxisome proliferator-activated receptor-α (PPAR-α) has attracted considerable attention for its anti-inflammatory properties; however, Toll-like receptor (TLR) pathways have an essential proinflammatory role in acute pancreatitis (AP). This study aimed to evaluate the attenuation of inflammation by PPAR-α and to investigate the interaction between PPAR-α and TLR pathways in AP.Methods: Acute pancreatitis was induced in rats by administration of cerulein. The PPAR-α agonist WY14643 and/or antagonist MK886 was administered. The severity of AP was determined by measuring serum amylase, lipase, Ca2+, pathological changes, myeloperoxidase activity, serum levels of interleukin (IL)-6, and intercellular adhesion molecule-1 (ICAM-1). The TLR2 and TLR4 messenger RNA (mRNA) and proteins were determined by real-time reverse transcriptase polymerase chain reaction and Western blotting, respectively. The mRNA expressions of target molecules of TLR pathways, including IL-6, IL-10, ICAM-1, and tumor necrosis factor α were also measured.Results: Treatment with WY14643 significantly decreased amylase, lipase, myeloperoxidase activity, pathological scores, IL-6, and ICAM-1 levels. The TLR2 and TLR4 mRNA and proteins were markedly decreased after treatment with WY14643, along with IL-6, ICAM-1, and tumor necrosis factor α mRNA levels. However, these effects were completely reversed by the coadministration of MK886.Conclusions: Activation of PPAR-α played a protective role in AP, partially mediated by modulation of TLR pathways.
9.	Ding, Zong-Ling, et al. (författare) Effect of Electrodes on Geometric and Transport Properties of the Graphene-Based Nanomolecular Devices 2011 Ingår i: Journal of Nanoscience and Nanotechnology. - : American Scientific Publishers. - 1533-4880 .- 1533-4899. ; 11:12, s. 10778-10781 Tidskriftsartikel (refereegranskat)abstract Graphene-based nanomolecular devices are formed by connecting one of the prototype molecular materials of graphene nanoribbons to two Au electrodes. The geometric structure and electronic properties are calculated by using density functional theory. Basing on the optimized structure and the electronic distributions, we obtain the transport properties of the devices by using the Green's functional method. It is found that that the geometry structures of the molecule and the transport properties are sensitive to the distance between source and drain electrodes. With increasing the distances, the curvature radius of the atomic plane is increased, and the deformation energy is decreased. The current versus voltage curves have almost same threshold voltage with different distances between the electrodes. The transmission probability, the density of states and the external bias voltage play important role in determining the transport properties of the molecular devices.
10.	Ellinghaus, David, et al. (författare) Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies 2013 Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 145:2, s. 339-347 Tidskriftsartikel (refereegranskat)abstract BACKGROUND & AIMS: Genome-wide association studies (GWAS) have identified 140 Crohn's disease (CD) susceptibility loci. For most loci, the variants that cause disease are not known and the genes affected by these variants have not been identified. We aimed to identify variants that cause CD through detailed sequencing, genetic association, expression, and functional studies.METHODS: We sequenced whole exomes of 42 unrelated subjects with CD and 5 healthy subjects (controls) and then filtered single nucleotide variants by incorporating association results from meta-analyses of CD GWAS and in silico mutation effect prediction algorithms. We then genotyped 9348 subjects with CD, 2868 subjects with ulcerative colitis, and 14,567 control subjects and associated variants analyzed in functional studies using materials from subjects and controls and in vitro model systems.RESULTS: We identified rare missense mutations in PR domain-containing 1 (PRDM1) and associated these with CD. These mutations increased proliferation of T cells and secretion of cytokines on activation and increased expression of the adhesion molecule L-selectin. A common CD risk allele, identified in GWAS, correlated with reduced expression of PRDM1 in ileal biopsy specimens and peripheral blood mononuclear cells (combined P = 1.6 x 10(-8)). We identified an association between CD and a common missense variant, Val248Ala, in nuclear domain 10 protein 52 (NDP52) (P = 4.83 x 10(-9)). We found that this variant impairs the regulatory functions of NDP52 to inhibit nuclear factor kappa B activation of genes that regulate inflammation and affect the stability of proteins in Toll-like receptor pathways.CONCLUSIONS: We have extended the results of GWAS and provide evidence that variants in PRDM1 and NDP52 determine susceptibility to CD. PRDM1 maps adjacent to a CD interval identified in GWAS and encodes a transcription factor expressed by T and B cells. NDP52 is an adaptor protein that functions in selective autophagy of intracellular bacteria and signaling molecules, supporting the role of autophagy in the pathogenesis of CD.
11.	Fernández Galván, Ignacio, et al. (författare) S0 → S3 transition in recombination products of photodissociated dihalomethanes 2014 Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 112:5-6, s. 575-582 Tidskriftsartikel (refereegranskat)abstract Species of the form CH2X–Y (X, Y = Br, I) have been proposed and identified as recombination products of the photodissociation of the parent dihalomethanes. Second-order complete active space perturbation theory (CASPT2) calculations of the vertical absorption energies considerably overestimate the experimental transient absorption band maxima, while the computationally cheaper time-dependent density functional theory (TD-DFT) method yields results with a reasonable agreement. In this work, we try to find the reason for this unexpected performance difference. In an initial study of the I2 molecule, we establish that CASPT2 is capable of providing quantitatively accurate results and that the TD-DFT values are only valid at first sight, but are qualitatively flawed. In the CASPT2 calculations for the CH2X–Y molecules, we include relativistic corrections, spin–orbit coupling, vibrational and thermal effects, and the solvent polarisation. Unfortunately, the results do not improve appreciably compared to the experimental measurements. We conclude that the good agreement of TD-DFT results is very likely fortuitous in this case as well, and that further theoretical and experimental investigations are probably needed to resolve the current discrepancy between CASPT2 and experiments.
12.	Jarvis, Erich D., et al. (författare) Whole-genome analyses resolve early branches in the tree of life of modern birds 2014 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331 Tidskriftsartikel (refereegranskat)abstract To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
13.	Kotz, Kenneth T., et al. (författare) Clinical microfluidics for neutrophil genomics and proteomics 2010 Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 16:9, s. 1042-U142 Tidskriftsartikel (refereegranskat)abstract Neutrophils have key roles in modulating the immune response. We present a robust methodology for rapidly isolating neutrophils directly from whole blood with 'on-chip' processing for mRNA and protein isolation for genomics and proteomics. We validate this device with an ex vivo stimulation experiment and by comparison with standard bulk isolation methodologies. Last, we implement this tool as part of a near-patient blood processing system within a multi-center clinical study of the immune response to severe trauma and burn injury. The preliminary results from a small cohort of subjects in our study and healthy controls show a unique time-dependent gene expression pattern clearly demonstrating the ability of this tool to discriminate temporal transcriptional events of neutrophils within a clinical setting.
14.	Li, Fay-Wei, et al. (författare) Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns 2014 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:18, s. 6672-6677 Tidskriftsartikel (refereegranskat)abstract Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
15.	Li, Jun, et al. (författare) An efficient and reliable approach for quality-of-service-aware service composition 2014 Ingår i: Information Sciences. - : Elsevier. - 0020-0255 .- 1872-6291. ; 269, s. 238-254 Tidskriftsartikel (refereegranskat)abstract With the rapidly increasing number of independently developed Web services that provide similar functionalities with varied quality of service (QoS), service composition is considered as a problem in the selection of component services that are in accordance with users' QoS requirements; a practice known as the QoS-aware service composition problem. However, current solutions are unsuitable for most real-time decision-making service composition applications required to obtain a relatively optimal result within a reasonable amount of time. These services are also unreliable (or even risky) given the open service-oriented environment. In this paper, we address these problems and propose a novel heuristic algorithm for an efficient and reliable selection of trustworthy services in a service composition. The proposed algorithm consists of three steps. First, a trust-based selection method is used to filter untrustworthy component services. Second, convex hulls are constructed to reduce the search space in the process of service composition. Finally, a heuristic global optimization approach is used to obtain the near-optimal solution. The results demonstrate that our approach obtains a close-to-optimal and reliable solution within a reasonable computation time.
16.	Li, Jun, et al. (författare) Full-Diversity Binary Frame-Wise Network Coding for Multiple-Source Multiple-Relay Networks Over Slow-Fading Channels 2012 Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 61:3, s. 1346-1360 Tidskriftsartikel (refereegranskat)abstract We study the design of network codes for M-source N-relay (M - N - 1) wireless networks over slow-fading channels. Binary frame-wise network coding (BFNC) based on cyclic-shifting matrices is developed to achieve full diversity and good coding gain. We develop a criterion in the context of BFNC that if satisfied guarantees to achieve full diversity gain. Based on this criterion, we propose an algorithm to design low-complexity encoders for a BFNC scheme by exploiting quasi-cyclic low-density parity-check (LDPC) code structures. We also design practical decoders based on the belief propagation decoding principle with a focus on large block lengths. Numerical results demonstrate that our BFNC schemes have substantial benefits over previous complex field and Galois field network coding schemes in the sense that our BFNC schemes can achieve full diversity gain and high coding gain for arbitrary block lengths with low encoding/decoding complexity.
17.	Li, Jun, et al. (författare) Network Coded LDPC Code Design for a Multi-Source Relaying System 2011 Ingår i: IEEE Transactions on Wireless Communications. - 1536-1276 .- 1558-2248. ; 10:5, s. 1538-1551 Tidskriftsartikel (refereegranskat)abstract We investigate LDPC code design for a multi-source single-relay system, with uniform phase-fading Gaussian channels. We specifically consider the asymmetric channels for multiple sources, where the channel condition for each source in the system is different. We focus on LDPC code design when network coding (NC) at the relay is utilized. For the asymmetric sources, we firstly introduce a binary field rate splitting theorem which is used to discover an appropriate NC scheme at the relay. This NC scheme is then used to determine the achievable rates of each source and the whole system. These steps assist us in the development of the main contribution of our work, namely, network coded multi-edge type LDPC (NCMET-LDPC) code design. Extrinsic mutual information transfer (EXIT) chart analysis is utilized to optimize the code profiles. Our results demonstrate two key points. (1) From the whole system point of view, our NCMET-LDPC codes achieve better error performance than that of LDPC codes designed for the system without NC. (2) As a consequence of the binary field rate-splitting theorem, our NCMET-LDPC codes also guarantee better error performance of each asymmetric source. The improvement in error performance is typically about 0.3 dB relative to a system without NC.
18.	Li, Jun, et al. (författare) Threshold-Based One-Bit Soft Forwarding for a Network Coded Multi-Source Single-Relay System 2014 Ingår i: IEEE Transactions on Communications. - 0090-6778 .- 1558-0857. ; 62:5, s. 1604-1620 Tidskriftsartikel (refereegranskat)abstract In this paper, we propose a threshold-based one-bit soft forwarding (TOB-SF) protocol for a multi-source relaying system with network coding, where two sources communicate with the destination with the help of a relay. Specifically in the TOB-SF protocol, the relay calculates the log-likelihood ratio (LLR) value of each network coded symbol, compares this LLR value with a pre-optimized threshold, and determines whether to transmit or keep silent. We are interested in optimizing the TOB-SF protocol in fading channels, and consider both the uncoded and low-density parity check coded systems. In the uncoded system, we first derive the bit error rate (BER) expressions at the destination, based on which, we derive the optimal threshold. Then we theoretically prove that the system can achieve the full diversity gain by using this threshold. Further, we optimize the power allocation at the relay to achieve a higher coding gain. In the coded system, we first optimize the LLR threshold. Then we develop a methodology to track the BER evolution at the destination by using Gaussian approximations. Based on the BER evolution, we further optimize the power allocation at the relay which minimizes the system BER. Simulation results show that the proposed TOB-SF protocol outperforms other conventional relaying protocols in terms of error performance.
19.	Li, Xiao, et al. (författare) The A55T and K153R polymorphisms of MSTN gene are associated with the strength training-induced muscle hypertrophy among Han Chinese men. 2014 Ingår i: Journal of Sports Sciences. - : Informa UK Limited. - 0264-0414 .- 1466-447X. ; 32:9, s. 883-91 Tidskriftsartikel (refereegranskat)abstract Myostatin, encoded by the MSTN gene, is a strong regulator of skeletal muscle growth. The present study aimed to investigate whether the A55T and K153R polymorphisms of MSTN were associated with the strength training-induced muscle hypertrophy among Han Chinese men. A total of 94 healthy, untrained men were recruited for an 8-week strength training programme. The thicknesses of biceps and quadriceps, along with anthropometric measurements of the participants, were assessed before and after the programme. The MSTN polymorphisms were subsequently genotyped employing polymerase chain reaction-restriction fragment length polymorphism technique and confirmed by DNA sequencing. One-way analysis of variance was used to compare the pre- and post-training measurements between carriers of different polymorphic genotypes. Our results indicated that individuals with AT + TT genotype of the A55T polymorphism showed a significant increase in the thickness of biceps (0.292 ± 0.210 cm, P = 0.03), but not quadriceps (0.254 ± 0.198 cm, P = 0.07), compared to carriers of AA genotype. For the K153R polymorphism, the increases in the thicknesses of both biceps (0.300 ± 0.131 cm) and quadriceps (0.421 ± 0.281 cm) were significantly higher among individuals with KR than those with KK genotypes (P < 0.01 for both muscles). The results obtained therefore suggested a possible association between the two polymorphisms and the strength training-induced muscle hypertrophy among men of Han Chinese ethnicity.
20.	Lian, Ke-Yan, et al. (författare) Big Bandgap in Highly Reduced Graphene Oxides 2013 Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:12, s. 6049-6054 Tidskriftsartikel (refereegranskat)abstract It is generally believed that the bandgap of the graphene oxide is proportional to the concentration of the oxygen atoms and a highly reduced graphene oxide (rGO) without vacancy defects should be gapless. We show here from first principles calculations that the bandgap can be effectively opened even in low oxidation level with the absorption of oxygen atoms either symmetrically or asymmetrically. The properly arranged absorption can induce a bandgap up to 1.19 eV for a C/O ratio of 16/1 in a symmetric system and a bandgap up to 1.58 eV for a C/O ratio of 32/3 in an asymmetric system, at generalized gradient approximation (GGA) level. The hybridization between the in-plane p(xy) orbitals of oxygen atoms and the out-of-plane p(z) frontier orbital of graphene is responsible for the opening of the bandgap. This finding sheds new light on the bandgap engineering of graphene.
21.	Lian, Ke-Yan, et al. (författare) Tuning electronic and magnetic properties of armchair vertical bar zigzag hybrid graphene nanoribbons by the choice of supercell model of grain boundaries 2014 Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 115:10, s. 104303- Tidskriftsartikel (refereegranskat)abstract Grain boundaries (GBs) attract much interest for its ability to tune the property of hybrid materials. Theoretically predicting the properties of hybrid graphene with GBs, even a linear GB remains challenging due to its inhomogeneous structure, which makes supercell model tough to choose in theoretic studies. For the first time, the applicability of supercells with different GBs and lattice-mismatches for describing armchair-zigzag hybrid graphene nanoribbons was validated by ab initio molecular dynamic simulations and first principles electronic structure calculations. And to what extent the electronic properties can be tuned by the strain effects resulting from the lattice-mismatch and the GBs distortion in supercells was demonstrated. This work showed that the intrinsic strain in such system plays a decisive role in determining the band structure and spin polarization properties. Hybrid graphene nanoribbon was found to be ferromagnetic in the ground state, especially for the case of using the supercell with nearly-perfect lattice match. Its high Curie temperature suggests the potential applications of this material in spintronics.
22.	Lind, Mårten, et al. (författare) A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection 2014 Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:7, s. e101049- Tidskriftsartikel (refereegranskat)abstract A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F-1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.
23.	Navizet, Isabelle, et al. (författare) Color-Tuning Mechanism of Firefly Investigated by Multi-Configurational Perturbation Method 2010 Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 132:2, s. 706-712 Tidskriftsartikel (refereegranskat)abstract This is the first report on a multiconfigurational reference second-order perturbation theory−molecular mechanics study of the color modulation of the observed bioluminescence of the oxyluciferin−luciferase complex of the Japanese genji-botaru firefly using structures according to recent X-ray data. Our theoretical results do not support the experimentally deduced conclusion that the color modulation of the emitted light primarily depends on the size of the compact luciferase protein cavity embedding the excited oxyluciferin molecule. Rather, we find, in agreement with recent experimental observations, that the wavelength of the emitted light depends on the polarity of the microenvironment at the phenol/phenolate terminal of the benzothiazole fragment in oxyluciferin.
24.	Navizet, Isabelle, et al. (författare) Light emission in firefly : a theoretical study 2012 Ingår i: Luminescence (Chichester, England Print). - 1522-7235 .- 1522-7243. ; 27 Tidskriftsartikel (refereegranskat)
25.	Proletov, Ian, et al. (författare) Primary and secondary glomerulonephritides 1. 2014 Ingår i: Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. - : Oxford University Press (OUP). - 1460-2385. ; 29 Suppl 3:May, s. 186-200 Tidskriftsartikel (refereegranskat)
26.	Shi, Zhan, et al. (författare) A portable high-resolution soft x-ray and extreme ultraviolet spectrometer designed for the Shanghai EBIT and the Shanghai low energy EBITs 2014 Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 1089-7623 .- 0034-6748. ; 85:6 Tidskriftsartikel (refereegranskat)abstract A portable high resolution soft x-ray and extreme ultraviolet (EUV) spectrometer has been developed for spectroscopic research at the Shanghai Electron Beam Ion Trap (EBIT) laboratory. A unique way of aligning the grazing incidence spectrometer using the zero order of the grating is introduced. This method is realized by extending the range of the movement of the CCD detector to cover the zero order. The alignment can be done in a few minutes, thus leading to a portable spectrometer. The high vacuum needed to be compatible with the EBITs is reached by mounting most of the translation and rotation stages outside the chamber. Only one high vacuum compatible linear guide is mounted inside the chamber. This is to ensure the convenient interchange of the gratings needed to enable wavelength coverage of the whole range of 10 to 500 angstrom. Spectra recorded with one of our low energy EBITs shows that a resolving power of above 800 can be achieved. In the slitless configuration used in this work, we found the resolving power to be limited by the width of the EBIT plasma. When mounted on the Shanghai EBIT which is a high energy EBIT and has a narrower EBIT plasma width, the estimated resolving power will be around 1400 at 221.15 angstrom. (C) 2014 AIP Publishing LLC.
27.	Tang, Ting-Ting, et al. (författare) Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure. 2011 Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272- Tidskriftsartikel (refereegranskat)abstract Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
28.	Wang, Zhaoming, et al. (författare) Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33 2014 Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633 Tidskriftsartikel (refereegranskat)abstract Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
29.	Zang, Xiao-Ying, et al. (författare) Pivotal factors interfering in 24-hour blood pressure fluctuation and arterial stiffness in a community of Chinese elderly hypertensive patients 2013 Ingår i: Journal of Clinical Nursing. - : Wiley. - 0962-1067 .- 1365-2702. ; 22:3/4, s. 379-388 Tidskriftsartikel (refereegranskat)abstract Aims and objectives: To explore which sociodemographic and clinical factors could interfere in the parameters of ambulatory blood pressure monitoring and determine the affecting factors of Ambulatory Arterial Stiffness Index.Background: Although the clinical relevance of ambulatory blood pressure monitoring and Ambulatory Arterial Stiffness Index have been studied, the explanation of their role and related interfering factors remains controversial in patients with different disease or age, etc.Design: Cross-sectional study.Methods: The study was carried out between October 2008–October 2009. A convenience sample of hypertensive patients over 60 years old was recruited in China. Twenty-four hour ambulatory blood pressure monitoring was carried out on the non-dominant arm using an oscillometric device.Results: (1) All 95 patients completed the study and their ages ranged from 60–76 years. (2) There were statistical differences for certain parameters of ambulatory blood pressure monitoring between different characteristics of patients. Financial status was an important factor interfering in patients’ BP fluctuation, especially daytime and 24 hours systolic pressure. The higher body mass index the patients had, the higher the pressure was. (3) Multiple variants logistic analysis of Ambulatory Arterial Stiffness Index showed statistical differences only in coefficient variation of 24-hour diastolic pressure and daytime systolic blood pressure.Conclusions: There are more factors that interfered with systolic pressure and diastolic pressure during the day than nigh. Patients who have less nocturnal dipping may have a higher night time systolic pressure and diastolic pressure. The coefficient of variation of 24 hours diastolic pressure and daytime systolic pressure contribute more to Ambulatory Arterial Stiffness Index which should arouse practitioners’ attention.Relevance to clinical practice: Ambulatory blood pressure monitoring should be used as a routine procedure, as well as Ambulatory Arterial Stiffness Index calculated for older hypertensive patients. The findings may be used to guide community health providers to pay more attention to the factors that may influence BP fluctuation and Ambulatory Arterial Stiffness Index according to individual’s characteristics.
30.	Zhang, Guojie, et al. (författare) Comparative genomics reveals insights into avian genome evolution and adaptation 2014 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320 Tidskriftsartikel (refereegranskat)abstract Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
31.	Zhang, Mei, et al. (författare) Discovery and Structural Modification of 1-Phenyl-3-(1-phenylethyl)urea Derivatives as Inhibitors of Complement 2012 Ingår i: ACS Medicinal Chemistry Letters. - : American Chemical Society (ACS). - 1948-5875. ; 3:4, s. 317-321 Tidskriftsartikel (refereegranskat)abstract A series of 1-phenyl-3-(1-phenylethyl)urea derivatives were identified as novel and potent complement inhibitors through structural modification of the original compound from high-throughput screening. Various analogues (7 and 13-15) were synthesized and identified as complement inhibitors, with the introduction of a five- or six-carbon chain (7c, 7d, 7k, 7I, and 7o) greatly improving their activity. Optimized compound 7I has an excellent inhibition activity with IC50 values as low as 13 nM. We demonstrated that the compound 7I inhibited C9 deposition through the classical, the lectin, and the alternative pathways but had no influence on C3 and C4 depositions.
32.	Zhang, Wei, et al. (författare) Activation of nuclear factor-kappa B pathway is responsible for tumor necrosis factor-a-induced up-regulation of endothelin B2 receptor expression in vascular smooth muscle cells in vitro 2012 Ingår i: Toxicology Letters. - : Elsevier BV. - 1879-3169 .- 0378-4274. ; 209:2, s. 107-112 Tidskriftsartikel (refereegranskat)abstract The endothelin B2 (ETB2) receptors are induced in vascular smooth muscle cells (VSMCs) in cardiovascular diseases. We tested if in vitro short-term exposure to the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) could up-regulate ETB2 receptors in rat mesenteric arteries, and if this effect is through activation of intracellular nuclear factor-kappa B (NF-kappa B) pathway. The mesenteric arteries were dissected from male Sprague-Dawley rats and the endothelium was removed. The arteries were co-incubated with TNF-alpha in serum-free Dulbecco's modified Eagle's medium. Real-time reverse transcription-PCR, Western blot and immunohistochemical staining were employed to assess the mRNA/protein expression of ETB2 receptors and activation of NF-kappa B pathway. The results showed that, during organ culture. TNF-alpha concentration-dependently enhanced ET52 receptors expression at both mRNA and protein levels, paralleled with activation of NF-kappa B pathway in VSMC. The up-regulated ETB2 receptor expression and NF-kappa B activation could be effectively suppressed by general transcriptional inhibitor actinomycin D, or either of the selective I kappa B kinase inhibitors wedelolactone and IMD-0354. Conclusively, the activation of intracellular NF-kappa B pathway is responsible for the up-regulation of ETB2 receptors induced by short-term exposure to TNF-alpha. This could partly explain the toxic effects of TNF-alpha on VSMCs that account for cardiovascular diseases. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
33.	Aad, G., et al. (författare) 2012 Tidskriftsartikel (refereegranskat)

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