bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of DNA lesions using a third base pair for amplification and nanopore sequencing
Authors: Riedl Jan , Ding Yun , Fleming Aaron M. , Burrows Cynthia J. 
Published: November 2015

AbstractDamage to the genome is implicated in the progression of cancer and stress-induced diseases. DNA lesions exist in low levels, and cannot be amplified by standard PCR because they are frequently strong blocks to polymerases. Here, we describe a method for PCR amplification of lesion-containing DNA in which the site and identity could be marked, copied and sequenced. Critical for this method is installation of either the dNaM or d5SICS nucleotides at the lesion site after processing via the base excision repair process. These marker nucleotides constitute an unnatural base pair, allowing large quantities of marked DNA to be made by PCR amplification. Sanger sequencing confirms the potential for this method to locate lesions by marking, amplifying and sequencing a lesion in the KRAS gene. Detection using the α-hemolysin nanopore is also developed to analyse the markers in individual DNA strands with the potential to identify multiple lesions per strand.
Alcohol consumption and the risk of Barrett’s esophagus: a comprehensive meta-analysis
Authors: Ren Lin-Lin , Yan Ting-Ting , Wang Zhen-Hua , Bian Zhao-Lian , Yang Fan , Hong Jie , Chen Hao-Yan , Fang Jing-Yuan 
Published: November 2015

AbstractSeveral studies have been proposed to investigate the association between alcohol consumption and risk of Barrett’s esophagus (BE), but as of yet, no quantitative summary of the literature to clarify the relationship between them. In our study, twenty eligible cohort studies involving 42925 participants were identified. Combined relative risk (RR) ratios for the highest versus lowest alcohol consumption levels were calculated. The alcohol dose-response analysis was performed to investigate the association between the increment consumption of 10 g/d alcohol and the risk of developing BE. Subgroup analyses were used to examine heterogeneity across the studies. A combined RR of 0.98 (0.62–1.34) was found when comparing highest vs. lowest alcohol consumption levels for BE. An inverse association between alcohol and incidence of BE (RR 0.51; 95% CI: 0.055–0.96) was demonstrated in women. Moreover, Asian drinkers had a relative higher risk of BE (RR 1.34; 95% CI: 1.11–1.56) compared with Western drinkers. In conclusion, our results showed that overall alcohol consumption was not associated with increased BE incidence. The limited data available on alcohol consumption supports a tentative inversion of alcohol consumption with BE risk in women, while Asian drinkers tend to have a higher risk of BE.
Nuclear PKM2 contributes to gefitinib resistance via upregulation of STAT3 activation in colorectal cancer
Authors: Li Qiong , Zhang Daoxiang , Chen Xiaoying , He Lei , Li Tianming , Xu Xiaoping , Li Min 
Published: November 2015

AbstractGefitinib (Iressa, ZD-1839), a small molecule tyrosine kinase inhibitor (TKI) of the epidermal growth factor receptor (EGFR) pathway, is currently under investigation in clinical trials for the treatment of colorectal cancer (CRC). However, as known, some patients develop resistance to TKIs and the mechanisms mediating intrinsic resistance to EGFR-TKIs in CRC have not been fully characterized. Resistance to EGFR inhibitors reportedly involves activation of signal transducer and activator of transcription 3 (STAT3) in glioma and lung cancer. Here, we demonstrated that the nuclear pyruvate kinase isoform M2 (PKM2) levels were positively correlated with gefitinib resistance in CRC cells. The overexpression of nuclear PKM2 in HT29 cells decreased the effect of gefitinib therapy, whereas PKM2 knockdown increased gefitinib efficacy. Furthermore, the activation of STAT3 by nuclear PKM2 was associated with gefitinib resistance. Inhibition of STAT3 by Stattic, a STAT3-specific inhibitor, or STAT3-specific siRNA sensitized resistant cells to gefitinib. These results suggest that nuclear PKM2 modulates the sensitivity of CRC cells to gefitinib and indicate that small molecule pharmacological disruption of nuclear PKM2 association with STAT3 is a potential avenue for overcoming EGFR-TKI resistance in CRC patients.
ZFP36L1 promotes monocyte/macrophage differentiation by repressing CDK6
Authors: Chen Ming-Tai , Dong Lei , Zhang Xin-Hua , Yin Xiao-Lin , Ning Hong-Mei , Shen Chao , Su Rui , Li Feng , Song Li , Ma Yan-Ni , Wang Fang , Zhao Hua-Lu , Yu Jia , Zhang Jun-Wu 
Published: November 2015

AbstractRNA binding proteins (RBPs)-mediated post-transcriptional control has been implicated in influencing various aspects of RNA metabolism and playing important roles in mammalian development and pathological diseases. However, the functions of specific RBPs and the molecular mechanisms through which they act in monocyte/macrophage differentiation remain to be determined. In this study, through bioinformatics analysis and experimental validation, we identify that ZFP36L1, a member of ZFP36 zinc finger protein family, exhibits significant decrease in acute myeloid leukemia (AML) patients compared with normal controls and remarkable time-course increase during monocyte/macrophage differentiation of PMA-induced THP-1 and HL-60 cells as well as induction culture of CD34+ hematopoietic stem/progenitor cells (HSPCs). Lentivirus-mediated gain and loss of function assays demonstrate that ZFP36L1 acts as a positive regulator to participate in monocyte/macrophage differentiation. Mechanistic investigation further reveals that ZFP36L1 binds to the CDK6 mRNA 3′untranslated region bearing adenine-uridine rich elements and negatively regulates the expression of CDK6 which is subsequently demonstrated to impede the in vitro monocyte/macrophage differentiation of CD34+ HSPCs. Collectively, our work unravels a ZFP36L1-mediated regulatory circuit through repressing CDK6 expression during monocyte/macrophage differentiation, which may also provide a therapeutic target for AML therapy.
Injecting vascular endothelial growth factor into the temporomandibular joint induces osteoarthritis in mice
Authors: Shen Pei , Jiao ZiXian , Zheng Ji Si , Xu Wei Feng , Zhang Shang Yong , Qin An , Yang Chi 
Published: November 2015

AbstractIt is unclear whether vascular endothelial growth factor (VEGF) can initiate osteoarthritis (OA) in the temporomandibular joint (TMJ). In this study we evaluated the effects of intra-articular injection of exogenous VEGF in the TMJ in mice on the early stage. Forty-eight male Sprague-Dawley mice were equally divided into 3 groups. In the vegf group, the mice received an injection of VEGF solution (50 μL) in the TMJ once a week over a period of 4 weeks. In the sham group, the mice received an injection of saline (50 μL). The control group did not receive any injection. Four mice from each group were sacrificed at 1, 2, 4 and 8 weeks. Gradual prominent cartilage degeneration was observed in the vegf group. Additionally, this group showed higher expressions of metalloproteinase (MMP)-9, MMP-13, receptor activator of nuclear factor-kappa-B ligand (RANKL) and a higher number of apoptotic chondrocytes and VEGF receptor 2 (VEGFR2)-positive chondrocytes. Micro-computed tomography (CT) revealed prominent subchondral bone resorption in the vegf group, with a high number of osteoclasts in the subchondral bone.In vitrostudy demonstrated that VEGF can promote osteoclast differentiation. In conclusion, our study found that VEGF can initiate TMJ OA by destroying cartilage and subchondral bone.
Metallocene Catalytic Insertion Polymerization of 1-Silene to Polycarbosilanes
Authors: Tian Yuelong , Ge Min , Zhang Weigang , Lv Xiaoxu , Yu Shouquan 
Published: November 2015

AbstractMetallocene of zirconium were used as a catalyst for an insertion polymerization of 1-methylsilene directly into pre-ceramic precursor polyzirconocenecarbosilane (PZCS) during dechlorination of dichlorodimethylesilane by sodium, which exhibits high catalytic effectiveness with the maximum conversion ratio of polycarbosilane up to 91%. The average molecular weights of polymers synthesized are less than 1400, all with very narrow polymolecularities. The mechanism of catalytic polymerization was assumed to be similar to a coordination insertion polymerization of 1-olefins by metallocenes. The obtained PZCS show high ceramic yields with formation of composite ceramics of ZrC-SiC, which are novel polymeric precursors of ultra-high temperature ceramic (UHTC) fiber and composite.
Pregnancy diabetes: A comparison of diagnostic protocols based on point-of-care, routine and optimized laboratory conditions
Authors: van den Berg Sjoerd A. A. , de Groot Monique J. M. , Salden Lorenzo P. W. , Draad Patrick J. G. J. , Dijkstra Ineke M. , Lunshof Simone , van Thiel Sjoerd W. , Boonen Kristel J. M. , Thelen Marc H. M. 
Published: November 2015

AbstractIn vitro glycolysis poses a problem during diabetes screening, especially in remote laboratories. Point-of-care analysis (POC) may provide an alternative. We compared POC, routine and STAT analysis and a feasible protocol during glucose tolerance test (GTT) for pregnancy diabetes (GDM) screening. In the routine protocol, heparin tubes were used and turn-around-time (TAT) was unsupervised. In the STAT protocol, tubes were processed immediately. The feasible protocol comprised of citrated tubes with a TAT of 1 hour. Outcome was defined as glucose concentration and clinical diagnosis. Glucose measured by POC was higher compared to routine analysis at t = 0 (0.25 mM) and t = 120 (1.17 mM) resulting in 17% more GDM diagnoses. Compared to STAT analysis, POC glucose was also higher, although less pronounced (0.06 and 0.9 mM at t = 0 and t = 120 minutes, respectively) and misclassification was only 2%. Glucose levels and clinical diagnosis were similar using the feasible protocol and STAT analysis (0.03 mM and −0.07 mM at t = 0 and t = 120, 100% identical diagnoses). POC is an viable alternative for STAT glucose analysis in GDM screening (sensitivity: 100%, specificity: 98%). A feasible protocol (citrated phlebotomy tubes with a TAT of 60 minutes) resulted in 100% identical outcome and provides the best alternative.
Global effects of agriculture on fluvial dissolved organic matter
Authors: Graeber Daniel , Boëchat Iola G. , Encina-Montoya Francisco , Esse Carlos , Gelbrecht Jörg , Goyenola Guillermo , Gücker Björn , Heinz Marlen , Kronvang Brian , Meerhoff Mariana , Nimptsch Jorge , Pusch Martin T. , Silva Ricky C. S. , von Schiller Daniel , Zwirnmann Elke 
Published: November 2015

AbstractAgricultural land covers approximately 40% of Earth’s land surface and affects hydromorphological, biogeochemical and ecological characteristics of fluvial networks. In the northern temperate region, agriculture also strongly affects the amount and molecular composition of dissolved organic matter (DOM), which constitutes the main vector of carbon transport from soils to fluvial networks and to the sea and is involved in a large variety of biogeochemical processes. Here, we provide first evidence about the wider occurrence of agricultural impacts on the concentration and composition of fluvial DOM across climate zones of the northern and southern hemispheres. Both extensive and intensive farming altered fluvial DOM towards a more microbial and less plant-derived composition. Moreover, intensive farming significantly increased dissolved organic nitrogen (DON) concentrations. The DOM composition change and DON concentration increase differed among climate zones and could be related to the intensity of current and historical nitrogen fertilizer use. As a result of agriculture intensification, increased DON concentrations and a more microbial-like DOM composition likely will enhance the reactivity of catchment DOM emissions, thereby fuelling the biogeochemical processing in fluvial networks and resulting in higher ecosystem productivity and CO2 outgassing.
Back‐to‐back F semicircular antenna with frequency and pattern reconfigurability
Authors: Ye Mingying , Gao Peng 
Published: November 2015

A BTBF (back‐to‐back F) semicircular antenna with frequency and pattern reconfigurablity is presented. The reconfigurable antenna consists of a centre‐fed patch encircled by four identical radiation BTBF elements. By controlling four pin diodes, the reconfigurable antenna works in three states, and produces a corporate frequency band of 2.51–2.76 GHz within two states, and a band of 3.01–3.23 GHz. The three states achieve three different patterns. Moreover, the BTBF semicircular antenna is achieved by half‐cutting a BTBF circular antenna. As the circular antenna is highly symmetric, half of this structure basically keeps the original radiation characteristics. This half‐cut method shrinks the original size by half and simplifies the construction. It provides a compact, low‐profile, low‐cost and reconfigurable method for wireless communication application.
GaN nanocolumn arrays with diameter <30 nm prepared by two‐step selective area growth
Authors: Kano T. , Yoshida J. , Miyagawa R. , Mizuno Y. , Oto T. , Kishino K. 
Published: November 2015

A new method of two‐step selective area growth (SAG) by RF‐plasma‐assisted molecular beam epitaxy is developed, enabling the growth of uniform arrays of thin GaN nanocolumns (NCs) with diameters <50 nm. In the SAG, the migration‐enhanced epitaxy mode with an alternating supply of Ga and active nitrogen was employed during the initial growth of NCs on small‐nanohole‐patterned substrates to complete the crystal nucleation in the nanoholes. Once the nucleation occurred, the growth mode to the simultaneous supply of Ga and nitrogen is immediately switched. In the second step, the growth temperature is increased and the nitrogen flow rate to suppress the lateral growth rate is decreased. A high‐density uniform array of very thin NCs in a triangular lattice with a diameter of 26 nm and a lattice constant of 60 nm is demonstrated; the NC density is 3.2 × 1010 cm−2.
Enhancement low‐voltage ride through capability of permanent magnet synchronous generator‐based wind turbines using interval type‐2 fuzzy control
Authors: Yassin Haitham Mahmoud , Hanafy Hanafy Hassan , Hallouda Mohab M. 
Published: November 2015

Increased penetration level of the wind power generation has brought new issues and challenges of power quality. One of these issues is low‐voltage ride through (LVRT). This study proposes an LVRT scheme for the permanent magnet synchronous generator (PMSG) variable speed wind turbine at grid faults. The machine side converter controller is used to control the dc‐link voltage using interval type‐2 fuzzy logic control taking into account the non‐linear relationship between the generator speed and the dc‐link voltage. Under grid faults, there is a power mismatch between the generated active power and the active power delivered to the grid. This excess power is stored in the generator inertia to keep the dc‐link voltage constant. To validate the proposed control strategy, simulation results for 1.5 MW PMSG‐based wind energy conversion system are carried out by MATLAB‐Simulink under symmetrical and asymmetrical faults.
A Systematic Review of Early Results Following Synchronous or Staged Carotid Artery Stenting and Coronary Artery Bypass Grafting
Authors: Zhang Jianbin , Xu Rong , Fan Xueqiang , Ye Zhidong , Liu Peng 
Published: November 2015

Background The optimal management of patients with concomitant coronary artery disease (CAD) and severe carotid artery stenosis remains a controversy. We performed a systematic review of studies comparing early outcomes of synchronous or staged carotid artery stenting (CAS) and coronary artery bypass grafting (CABG) in the treatment of patients with concomitant CAD and severe carotid artery stenosis.
Methods Multiple databases were systematically searched to identify studies of synchronous or staged CAS and CABG in the treatment of concomitant severe carotid and coronary artery disease published from 2005 to 2015. The quality of studies was assessed using the MINORS scale. The demographic data, risk factors, 30-day outcomes, and antiplatelet strategy were extracted.
Results 23 studies were identified with a total of 873 and 459 patients in the staged and synchronous group, respectively. The observed overall death/stroke/MI rate was 8.5% (95% CI: 7.6–9.4%) in staged group and 4.8% (95% CI: 3.8–5.8%) in synchronous group. It seems that the synchronous group has better 30-day outcomes, but these data could not be compared statistically.
Conclusion Our systematic review suggests either synchronous or staged CAS and CABG can be chosen for the treatment of concomitant carotid and coronary artery disease. It seems that the synchronous approach is relatively convenient and the antiplatelet strategy is relatively definite. For these patients, hybrid revascularization by synchronous CAS and CABG might be a feasible and promising therapeutic strategy. Our conclusions and the quality of the existing data suggest that a randomized controlled trial is needed to define the best treatment for patients with concomitant carotid and coronary artery disease.
Atmospheric Ar and Ne returned from mantle depths to the Earth’s surface by forearc recycling
Authors: Baldwin Suzanne L. , Das J. P. 
Published: November 2015

Significance
The abundance of atmospheric noble gases trapped in the deep Earth has been impacted by the extent to which the Earth’s atmosphere is transported into the mantle through subduction processes. However, little is known about the recycling of atmospheric gases in forearcs. We measured Ar and Ne in the world’s youngest exhumed coesite eclogite and found that atmospheric Ar and Ne were trapped in phengite and omphacite during crystallization at mantle depths. This Ar and Ne study is the first study, to our knowledge, to document when atmospheric Ar and Ne were trapped in ultrahigh-pressure metamorphic rocks, and it shows that forearc recycling is a viable mechanism for return of atmospheric Ar and Ne to the Earth’s surface in rocks exhumed from mantle depths.
Intracellular accumulation of trehalose and glycogen in an extreme oligotroph, Rhodococcus erythropolis N9T-4
Authors: Yano Takanori , Funamizu Yuhei , Yoshida Nobuyuki 
Published: November 2015

Abstract
An extreme oligotroph, Rhodococcus erythropolis N9T-4, showed intracellular accumulation of trehalose and glycogen under oligotrophic conditions. No trehalose accumulation was observed in cells grown on the rich medium. Deletion of the polyphosphate kinase genes enhanced the trehalose accumulation and decreases the intracellular glycogen contents, suggesting an oligotrophic relationship between among the metabolic pathways of trehalose, glycogen, and inorganic polyphosphate biosyntheses.
Mediterranean climate future: an insightful look into the Basin’s precipitation response to greenhouse gas forcing
Authors: Kushnir Y 
Published: November 2015

Abstract
In a new investigation of model projections of greenhouse gas warming impact on the Mediterranean, Zappa et al (2015 Environ. Res. Lett.

10 104012) find that the decline in basin-wide precipitation scales linearly with the strength of the 850 hPa zonal wind over North Africa. This result supports previous findings that climate change will affect the Mediterranean primarily through changing the regional atmospheric circulation. The results of this study may guide improvements of climate models to better simulate the impact of greenhouse gas warming in this critical world region.
Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks
Authors: Palma Eduardo , Salinas Lilian , Aracena Julio 
Published: November 2015

Abstract
Motivation: Boolean networks (BNs) are commonly used to model genetic regulatory networks (GRNs). Due to the sensibility of the dynamical behavior to changes in the updating scheme (order in which the nodes of a network update their state values), it is increasingly common to use different updating rules in the modeling of GRNs to better capture an observed biological phenomenon and thus to obtain more realistic models.
In Aracena et al. equivalence classes of deterministic update schedules in BNs, that yield exactly the same dynamical behavior of the network, were defined according to a certain label function on the arcs of the interaction digraph defined for each scheme. Thus, the interaction digraph so labeled (update digraphs) encode the non-equivalent schemes.
Results: We address the problem of enumerating all non-equivalent deterministic update schedules of a given BN. First, we show that it is an intractable problem in general. To solve it, we first construct an algorithm that determines the set of update digraphs of a BN. For that, we use divide and conquer methodology based on the structural characteristics of the interaction digraph. Next, for each update digraph we determine a scheme associated. This algorithm also works in the case where there is a partial knowledge about the relative order of the updating of the states of the nodes. We exhibit some examples of how the algorithm works on some GRNs published in the literature.
Availability and implementation: An executable file of the UpdateLabel algorithm made in Java and the files with the outputs of the algorithms used with the GRNs are available at: www.inf.udec.cl/ ∼lilian/UDE/
Contact: lilisalinas@udec.cl
Supplementary information: Supplementary data are available at Bioinformatics online.
catRAPID signature: identification of ribonucleoproteins and RNA-binding regions
Authors: Livi Carmen Maria , Klus Petr , Delli Ponti Riccardo , Tartaglia Gian Gaetano 
Published: November 2015

Abstract
Motivation: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets.
Availability and implementation: catRAPID signature can be accessed at http://s.tartaglialab.com/new_submission/signature.
Contact: gian.tartaglia@crg.es or gian@tartaglialab.com
Supplementary information: Supplementary data are available at Bioinformatics online.
The discordant method: a novel approach for differential correlation
Authors: Siska Charlotte , Bowler Russell , Kechris Katerina 
Published: November 2015

AbstractMotivation: Current differential correlation methods are designed to determine molecular feature pairs that have the largest magnitude of difference between correlation coefficients. These methods do not easily capture molecular feature pairs that experience no correlation in one group but correlation in another, which may reflect certain types of biological interactions. We have developed a tool, the Discordant method, which categorizes the correlation types for each group to make this possible.Results: We compare the Discordant method to existing approaches using simulations and two biological datasets with different types of –omics data. In contrast to other methods, Discordant identifies phenotype-related features at a similar or higher rate while maintaining reasonable computational tractability and usability.Availability and implementation: R code and sample data are available at https://github.com/siskac/discordant.Contact: katerina.kechris@ucdenver.eduSupplementary information: Supplementary data are available at Bioinformatics online.