bluuebunny/crossref_metadata_2025 huggingface dataset:
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
Authors: Vonk Freek J. , Casewell Nicholas R. , Henkel Christiaan V. , Heimberg Alysha M. , Jansen Hans J. , McCleary Ryan J. R. , Kerkkamp Harald M. E. , Vos Rutger A. , Guerreiro Isabel , Calvete Juan J. , Wüster Wolfgang , Woods Anthony E. , Logan Jessica M. , Harrison Robert A. , Castoe Todd A. , de Koning A. P. Jason , Pollock David D. , Yandell Mark , Calderon Diego , Renjifo Camila , Currier Rachel B. , Salgado David , Pla Davinia , Sanz Libia , Hyder Asad S. , Ribeiro José M. C. , Arntzen Jan W. , van den Thillart Guido E. E. J. M. , Boetzer Marten , Pirovano Walter , Dirks Ron P. , Spaink Herman P. , Duboule Denis , McGlinn Edwina , Kini R. Manjunatha , Richardson Michael K.
Published: December 2013

Significance

Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms. After co-option, toxin genes important for prey capture have massively expanded by gene duplication and evolved under positive selection, resulting in protein neofunctionalization. This diverse and dramatic venom-related genomic response seemingly occurs in response to a coevolutionary arms race between venomous snakes and their prey.
Diversity and abundance of phosphonate biosynthetic genes in nature
Authors: Yu Xiaomin , Doroghazi James R. , Janga Sarath C. , Zhang Jun Kai , Circello Benjamin , Griffin Benjamin M. , Labeda David P. , Metcalf William W.
Published: December 2013

Significance

Phosphonic acids are organophosphorus molecules containing direct carbon–phosphorus bonds that are often perceived as biological rarities. The data presented here show that the ability to synthesize diverse phosphonates is both widespread and relatively common among microbes. These findings are consistent with recent evidence suggesting that phosphonates are important intermediates in the global phosphorus cycle. Moreover, they support the idea that these molecules play a significant role in the biology of producing organisms, including a mechanism to sequester scarce phosphorus resources and to compete via chemical warfare using toxic phosphonate mimics of common metabolic intermediates.
Dexras1 mediates glucocorticoid-associated adipogenesis and diet-induced obesity
Authors: Cha Jiyoung Y. , Kim Hyo Jung , Yu Jung Hwan , Xu Jing , Kim Daham , Paul Bindu D. , Choi Hyeonjin , Kim Seyun , Lee Yoo Jeong , Ho Gary P. , Rao Feng , Snyder Solomon H. , Kim Jae-woo
Published: December 2013

Significance

Glucocorticoids are well known to play a major role in obesity, but underlying mechanisms have been obscure. We demonstrate that the small G protein Dexras1, first identified based on its dramatic induction by glucocorticoids, mediates adipogenic differentiation of preadipocytes, as well as diet-induced obesity in intact rodents. Thus, the adipogenesis of preadipocytes is abolished by
Dexras1
deletion and selectively induced by Dexras1 expression. Relevance to intact animals is evident from our experiments wherein diet-induced obesity is prevented in mice with knockout of Dexras1. Thus, pharmacotherapy involving Dexras1 may afford a promising approach to the therapy of obesity.
Gata2 is required for HSC generation and survival
Authors: de Pater Emma , Kaimakis Polynikis , Vink Chris S. , Yokomizo Tomomasa , Yamada-Inagawa Tomoko , van der Linden Reinier , Kartalaei Parham Solaimani , Camper Sally A. , Speck Nancy , Dzierzak Elaine
Published: December 2013

Knowledge of the key transcription factors that drive hematopoietic stem cell (HSC) generation is of particular importance for current hematopoietic regenerative approaches and reprogramming strategies. Whereas GATA2 has long been implicated as a hematopoietic transcription factor and its dysregulated expression is associated with human immunodeficiency syndromes and vascular integrity, it is as yet unknown how GATA2 functions in the generation of HSCs. HSCs are generated from endothelial cells of the major embryonic vasculature (aorta, vitelline, and umbilical arteries) and are found in intra-aortic hematopoietic clusters. In this study, we find that GATA2 function is essential for the generation of HSCs during the stage of endothelial-to-hematopoietic cell transition. Specific deletion of Gata2 in Vec (Vascular Endothelial Cadherin)-expressing endothelial cells results in a deficiency of long-term repopulating HSCs and intra-aortic cluster cells. By specific deletion of Gata2 in Vav-expressing hematopoietic cells (after HSC generation), we further show that GATA2 is essential for HSC survival. This is in contrast to the known activity of the RUNX1 transcription factor, which functions only in the generation of HSCs, and highlights the unique requirement for GATA2 function in HSCs throughout all developmental stages.
Fingerprinting protein structures effectively and efficiently
Authors: Cui Xuefeng , Li Shuai Cheng , He Lin , Li Ming
Published: December 2013

Motivation: One common task in structural biology is to assess the similarities and differences among protein structures. A variety of structure alignment algorithms and programs has been designed and implemented for this purpose. A major drawback with existing structure alignment programs is that they require a large amount of computational time, rendering them infeasible for pairwise alignments on large collections of structures. To overcome this drawback, a fragment alphabet learned from known structures has been introduced. The method, however, considers local similarity only, and therefore occasionally assigns high scores to structures that are similar only in local fragments.

Method: We propose a novel approach that eliminates false positives, through the comparison of both local and remote similarity, with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group of the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently.

Results: We tested our method on the high-quality protein structure subset of SCOP30 containing 3297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the Receiver-Operating Characteristic curve, archived by ContactLib, is as high as 0.960. This is a significant improvement compared with 0.747, the best result achieved by FragBag. We also demonstrated that incorporating remote contact information is critical to consistently retrieve accurate neighbor protein structures for all- query protein structures.

Availability and implementation: https://cs.uwaterloo.ca/∼xfcui/contactlib/.

Contact: shuaicli@cityu.edu.hk or mli@uwaterloo.ca
AISAIC: a software suite for accurate identification of significant aberrations in cancers
Authors: Zhang Bai , Hou Xuchu , Yuan Xiguo , Shih Ie-Ming , Zhang Zhen , Clarke Robert , Wang Roger R. , Fu Yi , Madhavan Subha , Wang Yue , Yu Guoqiang
Published: December 2013

Summary: Accurate identification of significant aberrations in cancers (AISAIC) is a systematic effort to discover potential cancer-driving genes such as oncogenes and tumor suppressors. Two major confounding factors against this goal are the normal cell contamination and random background aberrations in tumor samples. We describe a Java AISAIC package that provides comprehensive analytic functions and graphic user interface for integrating two statistically principled in silico approaches to address the aforementioned challenges in DNA copy number analyses. In addition, the package provides a command-line interface for users with scripting and programming needs to incorporate or extend AISAIC to their customized analysis pipelines. This open-source multiplatform software offers several attractive features: (i) it implements a user friendly complete pipeline from processing raw data to reporting analytic results; (ii) it detects deletion types directly from copy number signals using a Bayes hypothesis test; (iii) it estimates the fraction of normal contamination for each sample; (iv) it produces unbiased null distribution of random background alterations by iterative aberration-exclusive permutations; and (v) it identifies significant consensus regions and the percentage of homozygous/hemizygous deletions across multiple samples. AISAIC also provides users with a parallel computing option to leverage ubiquitous multicore machines.

Availability and implementation: AISAIC is available as a Java application, with a user’s guide and source code, at https://code.google.com/p/aisaic/.

Contact: yug@vt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction
Authors: Dümcke Sebastian , Bräuer Johannes , Anchang Benedict , Spang Rainer , Beerenwinkel Niko , Tresch Achim
Published: December 2013

Motivation: For biological pathways, it is common to measure a gene expression time series after various knockdowns of genes that are putatively involved in the process of interest. These interventional time-resolved data are most suitable for the elucidation of dynamic causal relationships in signaling networks. Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network.

Results: In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks. In particular, we solve the problem of exact likelihood computation in Boolean networks with probabilistic exponential time delays. Simulations demonstrate the high accuracy of our approach. We apply our method to data of Ivanova et al. (2006), where RNA interference knockdown experiments were used to build a network of the key regulatory genes governing mouse stem cell maintenance and differentiation. In contrast to previous analyses of that data set, our method can identify feedback loops and provides new insights into the interplay of some master regulators in embryonic stem cell development.

Availability and implementation: The algorithm is implemented in the statistical language R. Code and documentation are available at Bioinformatics online.

Contact:  duemcke@mpipz.mpg.de or tresch@mpipz.mpg.de

Supplementary information: Supplementary Materials are available at Bioinfomatics online.
Poly(A) RNA and Paip2 act as allosteric regulators of poly(A)-binding protein
Authors: Lee Seung Hwan , Oh Jungsic , Park Jonghyun , Paek Ki Young , Rho Sangchul , Jang Sung Key , Lee Jong–Bong
Published: December 2013

When bound to the 3′ poly(A) tail of mRNA, poly(A)-binding protein (PABP) modulates mRNA translation and stability through its association with various proteins. By visualizing individual PABP molecules in real time, we found that PABP, containing four RNA recognition motifs (RRMs), adopts a conformation on poly(A) binding in which RRM1 is in proximity to RRM4. This conformational change is due to the bending of the region between RRM2 and RRM3. PABP-interacting protein 2 actively disrupts the bent structure of PABP to the extended structure, resulting in the inhibition of PABP-poly(A) binding. These results suggest that the changes in the configuration of PABP induced by interactions with various effector molecules, such as poly(A) and PABP-interacting protein 2, play pivotal roles in its function.
ARF induction in response to DNA strand breaks is regulated by PARP1
Authors: Orlando Giulia , Khoronenkova Svetlana V. , Dianova Irina I. , Parsons Jason L. , Dianov Grigory L.
Published: December 2013

The ARF tumour suppressor protein, the gene of which is frequently mutated in many human cancers, plays an important role in the cellular stress response by orchestrating up-regulation of p53 protein and consequently promoting cell-cycle delay. Although p53 protein function has been clearly linked to the cellular DNA damage response, the role of ARF protein in this process is unclear. Here, we report that arf gene transcription is induced by DNA strand breaks (SBs) and that ARF protein accumulates in response to persistent DNA damage. We discovered that poly(ADP-ribose) synthesis catalysed by PARP1 at the sites of unrepaired SBs activates ARF transcription through a protein signalling cascade, including the NAD+-dependent deacetylase SIRT1 and the transcription factor E2F1. Our data suggest that poly(ADP-ribose) synthesis at the sites of SBs initiates DNA damage signal transduction by reducing the cellular concentration of NAD+, thus down-regulating SIRT1 activity and consequently activating E2F1-dependent ARF transcription. Our findings suggest a vital role for ARF in DNA damage signalling, and furthermore explain the critical requirement for ARF inactivation in cancer cells, which are frequently deficient in DNA repair and accumulate DNA damage.
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling
Authors: Zhang Xiaojun , Dantas Machado Ana Carolina , Ding Yuan , Chen Yongheng , Lu Yan , Duan Yankun , Tham Kenneth W. , Chen Lin , Rohs Remo , Qin Peter Z.
Published: December 2013

The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein–DNA interactions.
The output of the tRNA modification pathways controlled by theEscherichia coliMnmEG and MnmC enzymes depends on the growth conditions and the tRNA species
Authors: Moukadiri Ismaïl , Garzón M.-José , Björk Glenn R. , Armengod M.-Eugenia
Published: December 2013

In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In and , however, cmnm5 appears as the final modification, whereas in the remaining tRNAs, the MnmEG products are converted into 5-methylaminomethyl (mnm5) through the two-domain, bi-functional enzyme MnmC. MnmC(o) transforms cmnm5 into nm5, whereas MnmC(m) converts nm5 into mnm5, thus producing an atypical network of modification pathways. We investigate the activities and tRNA specificity of MnmEG and the MnmC domains, the ability of tRNAs to follow the ammonium or glycine pathway and the effect of mnmC mutations on growth. We demonstrate that the two MnmC domains function independently of each other and that and are substrates for MnmC(m), but not MnmC(o). Synthesis of mnm5s2U by MnmEG-MnmC in vivo avoids build-up of intermediates in . We also show that MnmEG can modify all the tRNAs via the ammonium pathway. Strikingly, the net output of the MnmEG pathways in vivo depends on growth conditions and tRNA species. Loss of any MnmC activity has a biological cost under specific conditions.
Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin
Authors: Lan Li , Nakajima Satoshi , Wei Leizhen , Sun Luxi , Hsieh Ching-Lung , Sobol Robert W. , Bruchez Marcel , Van Houten Bennett , Yasui Akira , Levine Arthur S.
Published: December 2013

Reactive oxygen species (ROS)-induced DNA damage is repaired by the base excision repair pathway. However, the effect of chromatin structure on BER protein recruitment to DNA damage sites in living cells is poorly understood. To address this problem, we developed a method to specifically produce ROS-induced DNA damage by fusing KillerRed (KR), a light-stimulated ROS-inducer, to a tet-repressor (tetR-KR) or a transcription activator (TA-KR). TetR-KR or TA-KR, bound to a TRE cassette (∼90 kb) integrated at a defined genomic locus in U2OS cells, was used to induce ROS damage in hetero- or euchromatin, respectively. We found that DNA glycosylases were efficiently recruited to DNA damage in heterochromatin, as well as in euchromatin. PARP1 was recruited to DNA damage within condensed chromatin more efficiently than in active chromatin. In contrast, recruitment of FEN1 was highly enriched at sites of DNA damage within active chromatin in a PCNA- and transcription activation-dependent manner. These results indicate that oxidative DNA damage is differentially processed within hetero or euchromatin.
Long-term depression: a cell biological view
Authors: Sheng Morgan , Ertürk Ali
Published: December 2013

Recent studies of the molecular mechanisms of long-term depression (LTD) suggest a crucial role for the signalling pathways of apoptosis (programmed cell death) in the weakening and elimination of synapses and dendritic spines. With this backdrop, we suggest that LTD can be considered as the electrophysiological aspect of a larger cell biological programme of synapse involution, which uses localized apoptotic mechanisms to sculpt synapses and circuits without causing cell death.
Microtubule-associated protein tau is essential for long-term depression in the hippocampus
Authors: Kimura Tetsuya , Whitcomb Daniel J. , Jo Jihoon , Regan Philip , Piers Thomas , Heo Seonghoo , Brown Christopher , Hashikawa Tsutomu , Murayama Miyuki , Seok Heon , Sotiropoulos Ioannis , Kim Eunjoon , Collingridge Graham L. , Takashima Akihiko , Cho Kwangwook
Published: December 2013

The microtubule-associated protein tau is a principal component of neurofibrillary tangles, and has been identified as a key molecule in Alzheimer's disease and other tauopathies. However, it is unknown how a protein that is primarily located in axons is involved in a disease that is believed to have a synaptic origin. To investigate a possible synaptic function of tau, we studied synaptic plasticity in the hippocampus and found a selective deficit in long-term depression (LTD) in tau knockout mice
in vivo
and
in vitro
, an effect that was replicated by RNAi knockdown of tau
in vitro
. We found that the induction of LTD is associated with the glycogen synthase kinase-3-mediated phosphorylation of tau. These observations demonstrate that tau has a critical physiological function in LTD.
Impact of e-business on perceived supply chain risks
Authors: Caldwell Nigel , Harland Christine , Powell Philip , Zheng Jurong
Published: December 2013

Purpose

– The purpose of this paper is to understand the risks managers and individual supply chains perceive from e-business.

Design/methodology/approach

– This research takes a long-term, staged view of the risks managers and individual supply chains perceive from e-business. By taking a two-stage approach, investigating four supply chains at a three year interval, the research considers perceived risks from e-business and the extent to which these risks obtained.

Findings

– E-business has the potential to deliver substantial benefits, but it also involves new and different risks. This research finds that small firms (SMEs) adopted a “watching brief” rather than implemented e-business. Between the two studies it emerges that e-business can support rather than detract from inter-organisational relationships. Global forces are in evidence in terms of low cost competition, but low cost competitors are not e-enabled.

Research limitations/implications

– Limitations, pragmatism and opportunism in the sampling is acknowledged. For example, the work and concepts that led to the expectation of e-business dominating and decimating industrial supply chains may have been based in chains more open to external forces than the ones examined here. Further research is required that identifies the minimum critical mass necessary to retain national manufacturing capacity at a chain or sector level, and empirical work is needed on the suggested link between supply chain stability and certainty of payment. The cases here are based on four UK supply chains, so various chain forms are likely to have been excluded.

Originality/value

– This research, by taking a staged approach and going back to the same chain and reviewing perceived risks, identifies how the build up of numerous – but small – events, for example factory closures, can aggregate over time to be just as significant as high profile, headline-worthy risks. Methods that produce a snapshot such as a one-off survey may be inadequate for fully exploring an area such as risk. Especially if the risks are hard to assess and are biased toward high profile events – catastrophic risks rather than accumulations of smaller, less noticeable risks.
The role of owner/manager in adoption of electronic commerce in small businesses
Authors: Ghobakhloo Morteza , Tang Sai Hong
Published: December 2013

Purpose

– Based on theories from the innovation diffusion literature, the purpose of this paper is to develop an integrated model of electronic commerce (EC) adoption in small businesses (SBs) of developing countries. The research model specifies variables at managerial level as the primary determinants to EC adoption in SBs.

Design/methodology/approach

– A questionnaire-based field survey was conducted to collect data from 268 owner/managers of SBs in Iran. The data were analysed using factorial analysis. Subsequently, six hypotheses were derived and tested by hierarchical multiple regression and logistic regression analysis.

Findings

– Perceived benefits, perceived compatibility, perceived risks, perceived costs, and innovativeness were found to be the significant determinants of decision to adopt EC. Likewise, discussion on discriminators between adopters and non-adopters of different EC applications has been provided.

Research limitations/implications

– Cross-sectional data of this research tends to have certain limitations when it comes to explaining the direction of causality of the relationships between the variables. The study focuses only on the manufacturing SBs of Iran.

Practical implications

– The research findings have important implications for practising managers, information systems experts, and policy-makers. Governments should follow specific policies to facilitate institutionalisation of EC in SBs. Similarly, EC vendors and technology providers should collaborate with SBs to enhance the compatibility of different EC applications with specific characteristics of these businesses.

Originality/value

– To the best of the authors' knowledge, this paper is perhaps one of the first that examines the adoption of EC by SBs in a developing country context, using a research model which tests the effects of owner/managers' attributes on adoption of simple and advanced EC applications.
Measurement of the difference in intraocular pressure between the sitting and lying body positions in healthy subjects: direct comparison of the Icare Pro with the Goldmann applanation tonometer, Pneumatonometer and Tonopen XL
Authors: Barkana Yaniv , Gutfreund Shay
Published: December 2013

Background

Change in intraocular pressure is known to occur with body posture. Previously, markedly different estimations of this change were reported. The Icare Pro (Icare; Tiolat Oy, Helsinki, Finland) is designed to measure intraocular pressure with the subject supine. We compared the measurement of postural change in intraocular pressure obtained with this and 3 other tonometers: Goldmann applanation tonometer (CSO, Firenze, Italy), Pneumatonometer (Model 30, Reichert, Depew, NY, USA) and the Tonopen XL (Reichert).

Design

Prospective comparative study.

Participants

Twenty‐one healthy subjects.

Methods

Intraocular pressure was measured in random order with four tonometers, first sitting then after 10 min of lying.

Main Outcome Measures

Average postural intraocular pressure change (mmHg) and the 95% limits of agreement for measuring postural intraocular pressure change between tonometers.

Results

Average postural intraocular pressure change (lying minus sitting, mmHg) was measured highest with the Goldmann applanation tonometer (4.1 ± 2.6) and Pneumatonometer (3.9 ± 2.1), significantly lower with the Tonopen (0.9 ± 1.7) and was negative with the Icare (−0.9 ± 3.3). The 95% limits of agreement for measuring postural intraocular pressure change between Goldmann applanation tonometer and Icare, Pneumatonometer and Tonopen were −3.2–13.3, −6.4–6.9 and −2.8–9.4 mmHg, respectively.

Conclusions

Postural change in intraocular pressure was measured similarly, on average, with Goldmann applanation tonometer and Pneumatonometer, and much lower with Tonopen and Icare Pro. There was poor interdevice agreement in measuring this parameter. We observed high intersubject variability, suggesting the clinical importance of this measurement in the diagnosis and management of glaucoma.
Effect of HLA‐DP and IL28B gene polymorphisms on response to interferon treatment in hepatitis B e‐antigen seropositive chronic hepatitis B patients
Authors: Cheng Lin , Sun Xiaowen , Tan Shun , Tan Wenting , Dan Yunjie , Zhou Yi , Mao Qing , Deng Guohong
Published: December 2013

Aim

The reason why the majority of chronic hepatitis B (CHB) patients do not respond to conventional interferon (IFN)‐α or pegylated interferon (PEG IFN) treatment has not been formally demonstrated. The aim of this study was to investigate the association between single nucleotide polymorphisms (SNPs) and response to IFN‐α or PEG IFN therapy in Chinese patients with CHB.

Methods

Four SNPs among the HLA‐DPA1, HLA‐DPB1 (rs3077 and rs9277535) and IL28B (rs12979860 and rs8099917) regions were genotyped using the MGB‐TaqMan SNP genotyping assay in 144 hepatitis B e‐antigen (HBeAg) seropositive CHB patients who had received 6–12 months IFN‐α or PEG IFN treatment. Patients were classified as responders who achieved any of the four targets: (i) the loss of HBeAg; (ii) anti‐HBe seroconversion; (iii) suppression of hepatitis B virus (HBV) DNA level to below 3 log of baseline; and (iv) alanine aminotransferase normalization.

Results

By multivariate analysis at 6 months of therapy and 6 months post‐therapy, the results showed that rs3077‐GG genotype was independently associated with higher HBeAg loss rate and anti‐HBe seroconversion rate, and rs9277535‐GG genotype was independently associated with decline of HBV DNA level. However, we did not observe the significant association between SNP near IL28B and the response to IFN‐α or PEG IFN treatment.

Conclusion

This study suggested that HLA‐DPA1 and HLA‐DPB1 variants were significantly associated with HBeAg loss, anti‐HBe seroconversion and HBV DNA level suppression in HBeAg seropositive CHB patients who received IFN‐α or PEG IFN treatment.
Detection and Molecular Characterization of a 16SrII‐A* Phytoplasma in Grapefruit (Citrus paradisi) with Huanglongbing‐like Symptoms in China
Authors: Lou Binghai , Bai Xianjin , Bai Yang , Deng Chongling , RoyChowdhury Moytri , Chen Chuanwu , Song Yaqin
Published: December 2013

In the year 2010, in a survey in Guangxi Province, China, to detect and characterize phytoplasmas in a huanglongbing (HLB)‐infected grapefruit (Citrus paradisi) orchard, 87 leaf samples with symptoms of blotchy mottle were collected from symptomatic grapefruit trees, and 320 leaf samples from symptomless trees adjacent to the symptomatic trees. Nested polymerase chain reaction (PCR) using universal phytoplasma primer set P1/P7 followed by primer set fU5/rU3 identified 7 (8.0%) positive samples from symptomatic samples but none from symptomless samples. Of the 87 symptomatic samples, 77 (88.5%) were positive for ‘Candidatus Liberibacter asiaticus’ and 5 for both phytoplasma and ‘Ca. L. asiaticus’. Sequence analysis indicated that seven 881‐bp amplicons, amplified by nested phytoplasma primer sets P1/P7 and fU5/rU3, shared 100.0% sequence identity with each other. Genome walking was then performed based on the 881 bp known sequences, and 5111 bp of upstream and downstream sequences were obtained. The total 5992 bp sequences contained a complete rRNA operon, composed of a 16S rRNA gene, a tRNAIle gene, a 23S rRNA gene and a 5S rRNA gene followed by eight tRNA genes. Phylogenetic analysis and virtual restriction fragment length polymorphism analysis confirmed the phytoplasma was a variant (16SrII‐A*) of phytoplasma subgroup 16SrII‐A. As phytoplasmas were only detected in blotchy‐mottle leaves, the 16SrII‐A* phytoplasma identified was related to HLB‐like symptoms.
Assessing benthic health under multiple human pressures in Bohai Bay (China), using density and biomass in calculating AMBI and M‐AMBI
Authors: Cai Wenqian , Borja Ángel , Liu Lusan , Meng Wei , Muxika Iñigo , Rodríguez José Germán
Published: December 2013

In recent decades, China has undergone an impressive development, which has produced increasing human pressures including coastal degradation. Bohai Bay, located in the west of the Bohai Sea (north of China), has been affected by various human pressures, including waste water discharges, land reclamation and oil exploitation. To monitor the effects of these pressures on this ecosystem, benthic macroinvertebrates and environmental variables (dissolved oxygen, nutrients, metals, etc.) were sampled in 2009 and 2011. To assess the ecological status of the benthic communities, the AZTI Marine Biotic Index (AMBI) and multivariate‐AMBI (M‐AMBI) were used, including both density and biomass in the calculation. This is the first research in which M‐AMBI based on biomass (M‐bAMBI) is applied. Both methods showed that the nearshore areas, especially close to the Haihe and Jiyun estuaries, were affected by human pressures, with a clear gradient of decreasing impacts offshore. The ecological status as assessed using density and biomass was quite similar. Significant relationships were also found between both methods and environmental variables. The use of AMBI and M‐AMBI, based upon density and biomass, in assessing the ecological status of water bodies in China seems to be promising.
Bubble Coalescence and Moving Contact Line Evaporation During Flow Boiling in a Single Minichannel
Authors: Freystein Martin , Stephan Peter , Kirse Christoph
Published: December 2013

Cooling systems incorporating flow boiling in mini- and microchannels achieve very high thermal performance. In this study a comprehensive measurement technique is used for the investigation of flow boiling in a single rectangular minichannel. This technique allows the measurement of local surface heat flux and temperature with a very high spatial and temporal resolution in combination with a synchronized flow regime observation [1]. This way, an insight into the basic phenomena is possible and will contribute to the fundamental understanding of the process. The experimental results show different phenomena such as an alternating area of high heat transfer between bubble front and end for elongated bubbles and the coalescence of bubbles in the flow. These observed phenomenon are comparable to experimental and numerical results of pool boiling.
Development of Organic Electroluminescent Sensor for Pressure/Oxygen Measurement
Authors: Matsuda Yu , Ueno Kaori , Yamaguchi Hiroki , Egami Yasuhiro , Niimi Tomohide
Published: December 2013

Pressure-sensitive paints (PSP) and pressure-sensitive molecular film (PSMF) are drawing much attention, since the techniques enable us to measure pressure/oxygen concentration distribution with high spatial resolution. A measurement system of PSP/PSMF is generally composed of a sensor layer (PSP/PSMF itself), an illumination light source, a photo-detector, and optics such as optical filters and mirrors. Since dye molecules in a sensor layer are photo-excited by an illumination light, the measurement system needs optical windows to transmit UV light for the illumination light and needs an optical filter to eliminate the illumination light, which also reduces the luminescence detected by a photo-detector. We have proposed a novel concept of a pressure sensor called electroluminescent pressure/oxygen sensor (ELPS/ELOS) based on oxygen quenching of electroluminescence without an external illumination light source. The sensor was fabricated as an organic light-emitting device (OLED) with phosphorescent dyes whose phosphorescence can be quenched by oxygen molecules, and with a polymer electrode which permeates oxygen molecules. The pressure sensitivity of the fabricated ELPS sample was equivalent to that of the sensor excited by an illumination light source. Moreover, the pressure sensitivity of the sensor is comparable to that of conventional PSP.
Characterization and Modeling of Micro Swimmers With Helical Tails and Cylindrical Heads Inside Circular Channels
Authors: Acemoglu Alperen , Temel F. Zeynep , Yesilyurt Serhat
Published: December 2013

Micro swimming robots offer many advantages in biomedical applications, such as delivering potent drugs to specific locations in targeted tissues and organs with limited side effects, conducting surgical operations with minimal damage to healthy tissues, treatment of clogged arteries, and collecting biological samples for diagnostic purposes. Reliable navigation techniques for micro swimmers need to be developed to improve the localization of robots inside the human body in future biomedical applications. In order to estimate the dynamic trajectory of magnetically propelled micro swimmers in channels, that mimic blood vessels and other conduits, fluid-micro robot interaction and the effect of the channel wall must be understood well. In this study, swimming of one-link robots with helical tails is modeled with Stokes equations and solved numerically with the finite element method. Forces acting on the robot are set to zero to enforce the force-free swimming and obtain forward, lateral and angular velocities that satisfy the constraints. Effects of the number of helical waves, wave amplitude, relative size of the cylindrical head of micro swimmer and the radial position on angular and linear velocity vectors of micro swimmer are presented.
Experimental Investigation on Thermal Performance of Gas-to-Gas Micro Heat Exchanger With Three Flow Arrangements
Authors: Yang Yahui , Brandner Juergen J. , Morini Gian Luca
Published: December 2013

In this paper a double-layered microchannel gas-to-gas heat exchanger has been designed and experimentally investigated. The micro heat exchanger (micro HEX) core is based on 133 parallel microchannels machined into polished PEEK plate for both hot side and cold side. Each microchannel is 200 μm high, 200 μm wide and 39.8 mm long. The microchannel layers have been designed in order to be able to test the effect on the thermal performances of the micro heat exchanger of partition foils made in different materials and of various thicknesses. In addition, the device allows to test the layers under three different flow arrangements, namely, countercurrent flow, cocurrent flow and cross flow. Customized pressure and temperature sensors are integrated into the microHEX to enable in-situ measurements. Experimental tests have been performed for various mass flow rates of hot and cold currents. The experimental results are compared with the predictions of the classical theory for conventionally sized heat exchangers. The influence of flow arrangements and wall axial conduction on the thermal performance of the micro heat exchanger are analyzed by considering both the theory and the experimental results.
Thermal Performance of Oscillating Heat Pipes With Nanofluid: A Theoretical Study
Authors: Seyf Hamid Reza , Kim Sejung , Zhang Yuwen
Published: December 2013

This numerical study is performed to investigate heat transfer performance and effect of nanofluids on U-shaped oscillating heat pipes. Pure water is employed as the base fluid while Al2O3 with two different particle sizes i.e., 47nm and 38.4 nm is used as nanoparticle. The results show that nanofluid has significant effect on heat transfer enhancement of the system and with increasing volume fraction and decreasing particles diameter the enhancement intensifies.
Numerical Analysis of Two-Phase Flow in Sintered Copper Wick by Lattice Boltzmann Method
Authors: Yamaguchi Tomohiko , Wang Qian , Yan Yuying
Published: December 2013

Thermal management is one of the significant issues in improving the performance of new electric or hybrid vehicles. Since heat pipes can conduct a large heat flux per unit mass, this device is expected to be a key technology in making progress in the energy efficiency of automobiles. The structure of the wick affects the performance and operating conditions of the heat pipe. A wick made of sintered metal powder is used as a sort of the material for the heat pipe because it is easy to control the thickness and the porosity [1]. Though the sintered wick shows high performance and usability, it is difficult to know the physical phenomena of a two-phase flow in the wick because of the complexity of its fabric. The eventual aims of our study are to elucidate the mass and heat transfer in a porous wick and to optimise the structure of the wick for heat pipes. The numerical simulations of the fluid flow in porous media by means of the Lattice Boltzmann Method (LBM) have been reported from the 1990’s because the LBM is a promising numerical method for fluid dynamics and suitable for complex boundary structures such as porous media[2].
Susceptibility to Acute Rheumatic Fever Based on Differential Expression of Genes Involved in Cytotoxicity, Chemotaxis, and Apoptosis
Authors: Bryant Penelope A. , Smyth Gordon K. , Gooding Travis , Oshlack Alicia , Harrington Zinta , Currie Bart , Carapetis Jonathan R. , Robins-Browne Roy , Curtis Nigel
Published: December 2013

It is unknown why only some individuals are susceptible to acute rheumatic fever (ARF). We investigated whether there are differences in the immune response, detectable by gene expression, between individuals who are susceptible to ARF and those who are not. Peripheral blood mononuclear cells (PBMCs) from 15 ARF-susceptible and 10 nonsusceptible (control) adults were stimulated with rheumatogenic (Rh+) group A streptococci (GAS) or nonrheumatogenic (Rh−) GAS. RNA from stimulated PBMCs from each subject was cohybridized with RNA from unstimulated PBMCs on oligonucleotide arrays to compare gene expression. Thirty-four genes were significantly differentially expressed between ARF-susceptible and control groups after stimulation with Rh+ GAS. A total of 982 genes were differentially expressed between Rh+ GAS- and Rh− GAS-stimulated samples from ARF-susceptible individuals. Thirteen genes were differentially expressed in the same direction (predominantly decreased) between the two study groups and between the two stimulation conditions, giving a strong indication of their involvement. Seven of these were immune response genes involved in cytotoxicity, chemotaxis, and apoptosis. There was variability in the degree of expression change between individuals. The high proportion of differentially expressed apoptotic and immune response genes supports the current model of autoimmune and cytokine dysregulation in ARF. This study also raises the possibility that a “failed” immune response, involving decreased expression of cytotoxic and apoptotic genes, contributes to the immunopathogenesis of ARF.
Center of mass energy for charged particles in regular black holes
Authors: Sharif M. , Haider Nida
Published: December 2013

This paper is devoted to study the acceleration and collision of charged particles in a general regular space–time. Using angular momentum, energy, and components of four-velocity, we explore the effect of charged particles on the center of mass energy. It is found that the collision energy of charged particles (independent of both singularity as well as horizon) is greater than that of uncharged particles. This depends not only on the mass to charge ratio of the black hole but also on the charge of the particle. Finally, we evaluate the collision energy of charged particles for a regular black hole, a particular example.
CONSTRUCTION OF THE MULTI-WAVELETS ON SOME SMOOTH PLANE CURVES VIA LENGTH-PRESERVING PROJECTION
Authors: WANG BAOQIN , WANG GANG , ZHOU XIAOHUI
Published: December 2013

Based on the theory of the discrete multi-wavelets in the space L2(R), the theory of the discrete multi-wavelets in the space L2(C) is presented properly in this paper, where C denotes a smooth plane curve. Firstly, the length-preserving projection is constructed, and by the length-preserving projection, the multiplicity multi-resolution analysis in the space L2(C) is defined properly and we define the dilation operator and translation operator in the space L2(C). Then, the two-scale refinement equations of multi-scaling function and multi-wavelet in the space L2(C) is deduced by using length-preserving mapping, the orthogonality is discussed, and the decomposition and reconstruction algorithm is computed. Finally, the example is given.
Effect of excess PbO on the microstructures and electric field induced strain of Pb0.97La0.02(Zr0.63Sn0.26Ti0.11)O3 antiferroelectric ceramics
Authors: Zhang Q. F. , Xiao Z. , Wang X. C. , Yang T. Q. , Wang J. F. , Chen S. C. , Yao X.
Published: December 2013

Microstructures and electrical properties of ( Pb 0.97 La 0.02)( Zr 0.63 Sn 0.26 Ti 0.11) O 3 (PLZST) antiferroelectric (AFE) ceramics with different PbO content were investigated in this study. X-ray diffraction analysis showed that with the increase of PbO amount, the stability of AFE phase reduced due to the decrease of lead vacancies. Besides, it was observed that the sintering properties could be improved by adding a small amount of PbO . Further, the electric field induced polarization and strain first increased, and then decreased with increasing PbO addition and they showed good frequency stability at low frequency. The maximum strain of 0.65% was obtained in the specimens with 8 mol% PbO content at the frequency 1 Hz. Both a high strain level and relatively good frequency stability in this composition can make a potential candidate for actuators applications over a wide-frequency working range.
Probabilistic Source Separation for Robust Fetal Electrocardiography
Authors: Vullings Rik , Mischi Massimo
Published: December 2013

Blind source separation (BSS) techniques are widely used to extract signals of interest from a mixture with other signals, such as extracting fetal electrocardiogram (ECG) signals from noninvasive recordings on the maternal abdomen. These BSS techniques, however, typically lack possibilities to incorporate any prior knowledge on the mixing of the source signals. Particularly for fetal ECG signals, knowledge on the mixing is available based on the origin and propagation properties of these signals. In this paper, a novel source separation method is developed that combines the strengths and accuracy of BSS techniques with the robustness of an underlying physiological model of the fetal ECG. The method is developed within a probabilistic framework and yields an iterative convergence of the separation matrix towards a maximum a posteriori estimation, where in each iteration the latest estimate of the separation matrix is corrected towards a tradeoff between the BSS technique and the physiological model. The method is evaluated by comparing its performance with that of FastICA on both simulated and real multichannel fetal ECG recordings, demonstrating that the developed method outperforms FastICA in extracting the fetal ECG source signals.
On Higher Dimensional Kaluza-Klein Theories
Authors: Bejancu Aurel
Published: December 2013

We present a new method for the study of general higher dimensional Kaluza-Klein theories. Our new approach is based on the Riemannian adapted connection and on a theory of adapted tensor fields in the ambient space. We obtain, in a covariant form, the fully general 4D equations of motion in a (4 +n)D general gauge Kaluza-Klein space. This enables us to classify the geodesics of the (4 +n)D space and to show that the induced motions in the 4D space bring more information than motions from both the 4D general relativity and the 4D Lorentz force equations. Finally, we note that all the previous studies on higher dimensional Kaluza-Klein theories are particular cases of the general case considered in the present paper.
Benidipine Protects Kidney through Inhibiting ROCK1 Activity and Reducing the Epithelium-Mesenchymal Transdifferentiation in Type 1 Diabetic Rats
Authors: Wu Ganlin , Xu Meirong , Xu Kui , Hu Yilan
Published: December 2013

We investigated the protective effect of benidipine, by testing the changes of the activity of Rho kinase and transdifferentiation of renal tubular epithelium cellsin vivo. Wistar rats were randomly divided into two groups: normal (N) and diabetes. STZ were used to make the rats type 1 diabetic and were randomly assigned as diabetes without treatment (D), diabetes treated with benidipine (B), and diabetes treated with fasudil (F) and treated for 3 months. Immunohistochemistry and western blotting were for protein expressions of ROCK1,α-SMA, and E-cadherin and real-time PCR for the mRNA quantification of ROCK1. Compared with N group, D group had significant proliferation of glomerular mesangial matrix, increased cell number, thickened basement membrane, widely infiltrated by inflammatory cells and fibrosis in the renal interstitial, and dilated tubular. Those presentations in F and B groups were milder. Compared with N group, D group showed elevated MYPT1 phosphorylation, increased expression of ROCK1,α-SMA protein, and ROCK1 mRNA and decreased expression of E-cadherin protein. B group showed attenuated MYPT1 phosphorylation, decreased ROCK1,α-SMA protein, and ROCK1 mRNA expression and increased expression of E-cadherin protein. In conclusion, benidipine reduces the epithelium-mesenchymal transdifferentiation and renal interstitial fibrosis in diabetic kidney by inhibiting ROCK1 activity.