bluuebunny/crossref_metadata_2025 huggingface dataset:
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

RNA 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

It 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

Metallocene 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

In 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

Agricultural 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.
Biomarker detection technologies and future directions
Authors: Nimse Satish Balasaheb , Sonawane Mukesh Digambar , Song Keum-Soo , Kim Taisun
Published: November 2015

Advancement in technologies which can provide highly selective and sensitive multiplex detection of biomarkers is inevitable for accurate disease prognosis, diagnosis, and treatment follow-up.
Synthesis of urea in cometary model ices and implications for Comet 67P/Churyumov–Gerasimenko
Authors: Förstel M. , Maksyutenko P. , Jones B. M. , Sun B.-J. , Chang A. H. H. , Kaiser R. I.
Published: November 2015

Formamide and urea, two building blocks of life, form easily in astrophysical ices made of very simple, inorganic materials.
Fast lithium-ionic conduction in a new complex hydride–sulphide crystalline phase
Authors: Unemoto Atsushi , Wu Hui , Udovic Terrence J. , Matsuo Motoaki , Ikeshoji Tamio , Orimo Shin-ichi
Published: November 2015

A new fast-lithium-ion-conducting crystalline phase formed from complex hydride and sulphide components was developed for all-solid-state batteries.
Amyloid-β adopts a conserved, partially folded structure upon binding to zwitterionic lipid bilayers prior to amyloid formation
Authors: Korshavn Kyle J. , Bhunia Anirban , Lim Mi Hee , Ramamoorthy Ayyalusamy
Published: November 2015

Aggregation at the neuronal cell membrane's lipid bilayer surface is implicated in amyloid-β (Aβ) toxicity associated with Alzheimer's disease; however, structural and mechanistic insights into the process remain scarce.
Theoretical tools to distinguish O-ylides from O-ylidic complexes in carbene–solvent interactions
Authors: Gómez Sara , Restrepo Albeiro , Hadad C. Z.
Published: November 2015

Orbital interactions and bond indices are among the theoretical tools suitable to distinguishO-ylides fromO-ylidic carbene–solvent complexes.
Magnetic properties of C–N planar structures: d0 ferromagnetism and half-metallicity
Authors: Brito W. H. , da Silva-Araújo Joice , Chacham H.
Published: November 2015

We investigate, from first principles calculations, the magnetic properties of planar carbon nitride structures with the lowest formation energies within twenty eight distinct stoichiometries and porosities.
Variable electronic properties of lateral phosphorene–graphene heterostructures
Authors: Tian Xiaoqing , Liu Lin , Du Yu , Gu Juan , Xu Jian-bin , Yakobson Boris I.
Published: November 2015

Phosphorene and graphene have a tiny lattice mismatch along the armchair direction, which can result in an atomically sharp in-plane interface.
Particle size distribution and perchlorate levels in settled dust from urban roads, parks, and roofs in Chengdu, China
Authors: Li Yiwen , Shen Yang , Pi Lu , Hu Wenli , Chen Mengqin , Luo Yan , Li Zhi , Su Shijun , Ding Sanglan , Gan Zhiwei
Published: November 2015

A total of 27 settled dust samples were collected from urban roads, parks, and roofs in Chengdu, China to investigate particle size distribution and perchlorate levels in different size fractions.
In-vitro evaluation of layered double hydroxide–Fe3O4 magnetic nanohybrids for thermo-chemotherapy
Authors: Komarala EswaraVara Prasadarao , Nigam Saumya , Aslam Mohammed , Bahadur Dhirendra
Published: November 2015

Combining layered double hydroxides with Fe3O4 nanoparticles resulted in the desired “cut-off switch” for threshold temperature towards magnetic hyperthermia.
CO2 capture in the presence of water vapour in MIL-53(Al)
Authors: Sánchez-Serratos Mayra , Bayliss Peter A. , Peralta Ricardo A. , González-Zamora Eduardo , Lima Enrique , Ibarra Ilich A.
Published: November 2015

By kinetic uptake experiments, MIL-53(Al) shows under anhydrous conditions at 30 °C a CO2 capture of 3.5 wt%. When this material is exposed to water vapour (20% RH and 30 °C), there is a considerable 1.5-fold increase in the CO2 capture up to 5.2 wt%.
Electrostatics of DNA nucleotide–carbon nanotube hybrids evaluated from QM:MM simulations
Authors: Chehel Amirani Morteza , Tang Tian
Published: November 2015

Electric potential generated by a DNA nucleotide near a carbon nanotube is shown by QM:MM simulations to depend on the types of nucleotide and nanotube.
Antisense precision polymer micelles require less poly(ethylenimine) for efficient gene knockdown
Authors: Fakhoury Johans J. , Edwardson Thomas G. , Conway Justin W. , Trinh Tuan , Khan Farhad , Barłóg Maciej , Bazzi Hassan S. , Sleiman Hanadi F.
Published: November 2015

Therapeutic nucleic acid polymer conjugates are powerful molecules for shutting down protein expression.
Charge generation and morphology in P3HT : PCBM nanoparticles prepared by mini-emulsion and reprecipitation methods
Authors: Schwarz Kyra N. , Farley Sam B. , Smith Trevor A. , Ghiggino Kenneth P.
Published: November 2015

P3HT : PCBM nanoparticles exhibit charge generation and nanomorphology similar to unannealed and annealed blend films, depending on the preparation method.
Low ensemble disorder in quantum well tube nanowires
Authors: Davies Christopher L. , Parkinson Patrick , Jiang Nian , Boland Jessica L. , Conesa-Boj Sonia , Tan H. Hoe , Jagadish Chennupati , Herz Laura M. , Johnston Michael B.
Published: November 2015

Single core–multishell nanowires with a radial quantum well are probed by micro-photoluminescence spectroscopy revealing low disorder in both the core and quantum well.
Calcined ZnAl- and Fe3O4/ZnAl–layered double hydroxides for efficient removal of Cr(vi) from aqueous solution
Authors: Yan Liang-guo , Yang Kun , Shan Ran-ran , Yu Hai-qin , Du Bin
Published: November 2015

Calcined ZnAl- and Fe3O4/ZnAl–layered double hydroxides (ZnAl–CLDH and Fe3O4/ZnAl–CLDH) were used as adsorbents to evaluate the uptake properties for Cr(vi) removal from aqueous solution by batch equilibrium experiments.
Synthesis of silver nanoparticles in a microfluidic coaxial flow reactor
Authors: Baber Razwan , Mazzei Luca , Thanh Nguyen T. K. , Gavriilidis Asterios
Published: November 2015

The coaxial flow reactor allows tuning of size and dispersity of silver nanoparticles because of its unique mass transfer characteristics.
Continuous supercritical route for quantum-confined GaN nanoparticles
Authors: Giroire B. , Marre S. , Garcia A. , Cardinal T. , Aymonier C.
Published: November 2015

GaN quantum dots (QDs) are prepared in a one-step continuous process using anhydrous solvents at supercritical conditions (and temperatures below 450 °C) in short residence times, typically less than 25 s.
Boronic acid–DMAPO cooperative catalysis for dehydrative condensation between carboxylic acids and amines
Authors: Ishihara Kazuaki , Lu Yanhui
Published: November 2015

Arylboronic acid and DMAPO cooperatively catalyse the dehydrative condensation reaction between carboxylic acids and amines to give the corresponding amides under azeotropic reflux conditions. This cooperative use is much more effective than their individual use as catalysts.
Thermodynamics and structure of macromolecules from flat-histogram Monte Carlo simulations
Authors: Janke Wolfhard , Paul Wolfgang
Published: November 2015

Over the last decade flat-histogram Monte Carlo simulations, especially multi-canonical and Wang–Landau simulations, have emerged as a strong tool to study the statistical mechanics of polymer chains.
Ultra-light 3D nanofibre-nets binary structured nylon 6–polyacrylonitrile membranes for efficient filtration of fine particulate matter
Authors: Wang Na , Yang Yinjing , Al-Deyab Salem S. , El-Newehy Mohamed , Yu Jianyong , Ding Bin
Published: November 2015

A novel ultra-light nylon 6–polyacrylonitrile nanofibre-nets binary (N6–PAN NNB) structured membrane is produced for effective air filtration to remove particulate matter.
Conversion of amorphous polymer networks to covalent organic frameworks under ionothermal conditions: a facile synthesis route for covalent triazine frameworks
Authors: Kuecken Sophie , Schmidt Johannes , Zhi Linjie , Thomas Arne
Published: November 2015

Covalent triazine frameworks (CTFs) are prepared from amorphous, non-porous polymer networks using a facile and scalable procedure.
Exploring the local electronic structure and geometric arrangement of ALD Zn(O,S) buffer layers using X-ray absorption spectroscopy
Authors: Dadlani Anup L. , Trejo Orlando , Acharya Shinjita , Torgersen Jan , Petousis Ioannis , Nordlund Dennis , Sarangi Ritimukta , Schindler Peter , Prinz Fritz B.
Published: November 2015

This work explains the bowing effect of the band gap as a result of the changing S concentration in Zn(O,S).
Meeting the Cultural, Therapeutic, and Individual Needs of the Lesbian, Gay, Bisexual or Transgendered Patient
Authors: Voyzey George A.
Published: November 2015

As our population ages, providers will encounter the lesbian, gay, bisexual, and transgender (LGBT) patient possessing varying individual degrees of cultural identity and psycho-social acceptance. In addition to adjusting to the debilitating disease or injury, the patient's spouse/domestic partner, adult children, friend(s), and/or parents can play critical roles in his, her, or hir successful rehabilitation and acute and long-term care. This article documents current trends, resources, and research with the aging LGBT population. In addition, this article identifies the multiple contexts and barriers confronting the LGBT patient and LGBT care provider's quality of life. This article offers care practices designed to the experiences, expectations, and needs of older LGBT patients, including HIV-associated dementia, its stages, and its symptoms as it relates to cognitive, motor, and behavioral domains.
Robust non‐unitary joint block diagonalisation for non‐square mixture
Authors: Yuan Xiao‐Guang , Zhang Wei‐Tao , Guo Jiao
Published: November 2015

The non‐unitary joint block diagonalisation (JBD) of a set of given matrices in non‐square mixing situation is addressed. To eliminate the degenerate solutions, the JBD problem is reformulated as a multicriteria optimisation model. The resulting algorithm is numerically robust for non‐square mixing matrix estimation. Moreover, it outperforms the existing JBD algorithms in terms of convergence rate and stability, which has been verified by simulation results.
DCM operation analysis of KY converter
Authors: Zeng Wen‐Liang , Lam Chi‐Seng , Zheng Wen‐Ming , Sin Sai‐Weng , Dai Ning‐Yi , Wong Man‐Chung , U Seng‐Pan , Martins Rui Paulo
Published: November 2015

A KY converter has the characteristics of non‐pulsating output current, low‐output voltage ripple and no right‐half plane zero in continuous conduction mode which can overcome the drawbacks of the conventional boost and buck–boost converters. However, when the KY converter is implemented into an integrated circuit, its discontinuous conduction mode (DCM) operation cannot be avoided due to a small‐inductor value. The boundary for the DCM operation region, DCM dc voltage and small‐signal transfer functions are proposed, which fill the gap of the DCM operation theory for the KY converter. Simulation results, using MATLAB and Cadence, are provided to verify the deduced DCM operation theory of the KY converter. The DCM closed‐loop controller design can be achievable in future.
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.
Wideband common noise suppression filter based on coupled microstrip lines and edge‐coupled coplanar waveguides
Authors: Oh Sangyeol , Jeong Jichai , Lee Jaehoon
Published: November 2015

A common noise suppression filter in a differential pair using the coupled microstrip line (CML) to edge‐coupled coplanar waveguide (ECCPW) transition is proposed. The filter consists of CMLs, ECCPWs, and shorting via holes that connect the CMLs and ECCPWs, and provides wideband common noise signal suppression using an even‐mode impedance mismatching technique between the CMLs and ECCPWs and wideband differential signal propagation for high‐speed circuit systems. A bandgap effect is realised in even mode, based on the CML to ECCPW transition without a multilayer. This method was verified using the three‐dimensional full‐wave high‐frequency structure simulator and experimental measurements.
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.
Study of ablation and implosion stages in wire arrays using coupled ultraviolet and X-ray probing diagnostics
Authors: Anderson A. A. , Ivanov V. V. , Astanovitskiy A. L. , Papp D. , Wiewior P. P. , Chalyy O.
Published: November 2015

Star and cylindrical wire arrays were studied using laser probing and X-ray radiography at the 1-MA Zebra pulse power generator at the University of Nevada, Reno. The Leopard laser provided backlighting, producing a laser plasma from a Si target which emitted an X-ray probing pulse at the wavelength of 6.65 Å. A spherically bent quartz crystal imaged the backlit wires onto X-ray film. Laser probing diagnostics at the wavelength of 266 nm included a 3-channel polarimeter for Faraday rotation diagnostic and two-frame laser interferometry with two shearing interferometers to study the evolution of the plasma electron density at the ablation and implosion stages. Dynamics of the plasma density profile in Al wire arrays at the ablation stage were directly studied with interferometry, and expansion of wire cores was measured with X-ray radiography. The magnetic field in the imploding plasma was measured with the Faraday rotation diagnostic, and current was reconstructed.
Unraveling the success and failure of mode coupling theory from consideration of entropy
Authors: Nandi Manoj Kumar , Banerjee Atreyee , Sengupta Shiladitya , Sastry Srikanth , Bhattacharyya Sarika Maitra
Published: November 2015

We analyze the dynamics of model supercooled liquids in a temperature regime where predictions of mode coupling theory (MCT) are known to be valid qualitatively. In this regime, the Adam-Gibbs (AG) relation, based on an activation picture of dynamics, also describes the dynamics satisfactorily, and we explore the mutual consistency and interrelation of these descriptions. Although entropy and dynamics are related via phenomenological theories, the connection between MCT and entropy has not been argued for. In this work, we explore this connection and provide a microscopic derivation of the phenomenological Rosenfeld theory. At low temperatures, the overlap between the MCT power law regime and AG relation implies that the AG relation predicts an avoided divergence at Tc, the origin of which can be related to the vanishing of pair configurational entropy, which we find occurring at the same temperature. We also show that the residual multiparticle entropy plays an important role in describing the relaxation time.
A three-dimensional numerical modelling of the PHOENIX-SPES charge breeder based on the Langevin formalism
Authors: Galatà A. , Mascali D. , Neri L. , Torrisi G. , Celona L.
Published: November 2015

A Charge Breeder (CB) is a crucial device of an ISOL facility, allowing post-acceleration of radioactive ions: it accepts an incoming 1+ beam, then multiplying its charge with a highly charged q+ beam as an output. The overall performances of the facility (intensity and attainable final energy) critically depend on the charge breeder optimization. Experimental results collected along the years confirm that the breeding process is still not fully understood and room for improvements still exists: a new numerical approach has been therefore developed and applied to the description of a 85Rb1+ beam capture by the plasma of the 14.5 GHz PHOENIX ECR-based CB, installed at the Laboratoire de Physique Subatomique et de Cosmologie (LPSC), and adopted for the Selective Production of Exotic Species project under construction at Laboratori Nazionali di Legnaro. The results of the numerical simulations, obtained implementing a plasma-target model of increasing accuracy and different values for the plasma potential, will be described along the paper: results very well agree with the theoretical predictions and with the experimental results obtained on the LPSC test bench.
The importance of electrothermal terms in Ohm's law for magnetized spherical implosions
Authors: Davies J. R. , Betti R. , Chang P.-Y. , Fiksel G.
Published: November 2015

The magnetohydrodynamics (MHD) of magnetic-field compression in laser-driven spherical targets is considered. Magnetic-field evolution is cast in terms of an effective fluid velocity, a convective term resulting from resistivity gradients, a resistive diffusion term, and a source term. Effective velocity is the sum of fluid velocity, drift velocity, and heat-flux velocity, given by electron heat flux divided by electron enthalpy density, which has two components: the perpendicular or Nernst velocity and the cross-field velocity. The Nernst velocity compresses the magnetic field as the heat front moves into gas. The cross-field velocity leads to dynamo generation of an azimuthal magnetic field. It is proposed that the heat-flux velocity should be flux limited using a “Nernst” flux limiter independent of the thermal flux limiter but should not exceed it. The addition of the MHD routines to the 1D, Lagrangian hydrocode LILAC and the Eulerian version of the 2D hydrocode DRACO is described, and the codes are used to model a magnetized spherical compression on the OMEGA laser. Thermal flux limiting at a shock front is found to cause unphysical electron temperature gradients that lead to large, unphysical magnetic fields caused by the resistivity gradient, so thermal flux limiting in the gas is removed. The Nernst term reduces the benefits of magnetization in inertial fusion. A Nernst flux limiter ≤0.12 is required in the gas in order to agree with measured neutron yield and increases in the neutron-averaged ion temperature caused by magnetization. This corresponds to preventing the Nernst velocity from exceeding the shock velocity, which prevents significant decoupling of the magnetic field and gas compression.
A note on convective heat transfer of an MHD Jeffrey fluid over a stretching sheet
Authors: Ahmed Jawad , Shahzad Azeem , Khan Masood , Ali Ramzan
Published: November 2015

This article focuses on the exact solution regarding convective heat transfer of a magnetohydrodynamic (MHD) Jeffrey fluid over a stretching sheet. The effects of joule and viscous dissipation, internal heat source/sink and thermal radiation on the heat transfer characteristics are taken in account in the presence of a transverse magnetic field for two types of boundary heating process namely prescribed power law surface temperature (PST) and prescribed heat flux (PHF). Similarity transformations are used to reduce the governing non-linear momentum and thermal boundary layer equations into a set of ordinary differential equations. The exact solutions of the reduced ordinary differential equations are developed in the form of confluent hypergeometric function. The influence of the pertinent parameters on the temperature profile is examined. In addition the results for the wall temperature gradient are also discussed in detail.
Finding the needle in the haystack: comparing sampling methods for detecting an endangered freshwater fish
Authors: Lintermans Mark
Published: November 2015

Accurately detecting the presence or absence of threatened species is vital for threatened species management, and the detection power of individual sampling methods can vary significantly between species and life stages. The present study compares the detection power of six sampling methods in sampling the endangered Macquarie perch in riverine habitats in south-eastern Australia. In an initial survey in 1998 and 1999, fyke nets captured Macquarie perch at 100% of sites where the species was detected; gill-nets captured the species at 86%; with no other method having >50% detection efficiency. Most Macquarie perch were captured by fyke nets (90% in 1998 and 94% in 1999), followed by gill-nets (7 and 2%). A monitoring program at one of the survey sites over 7 years returned similar results with fyke nets detecting the species in all years. Fyke nets captured primarily young-of-year (YOY) individuals, whereas gill-nets captured adults and subadults. Boat electrofishing returned a high level of false negatives for Macquarie perch. Future sampling for this species should employ fyke and gill-nets to adequately characterise population structure (adults, juveniles, YOY), minimise false negatives and detect the occurrence of successful breeding the previous year.
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.
Screening for tumor suppressors: Loss of ephrin receptor A2 cooperates with oncogenic
KRas
in promoting lung adenocarcinoma
Authors: Yeddula Narayana , Xia Yifeng , Ke Eugene , Beumer Joep , Verma Inder M.
Published: November 2015

Significance

A large number of genetic alterations have been found in the cancer genome of lung adenocarcinoma. However, they need experimental validation to determine their tumorigenic potential, as well as the therapeutic utility of individual alterations. Here, we provide an shRNA-mediated screen to validate a large set of genes for their tumor suppressor efficacy in vivo in a mouse lung adenocarcinoma model. We identified several tumor suppressors, including ephrin receptor A2 (
EphA2
) loss of which promotes adenocarcinoma in the context of oncogenic mutant
KRas
mutation.
EphA2
loss promotes cell proliferation by activating ERK MAP kinase signaling and hedgehog signaling pathways, leading to tumorigenesis. Identification of these pathways provides important therapeutic targets for lung adenocarcinoma.
“A very big thank you to…”
Authors: Rojas-Lizana Isolda
Published: November 2015

Letters to the Editor (LTEs) in the local press are a relatively formalised everyday genre in which readers’ opinions appear in a publication. In this article 20 Chilean and 20 Australian LTEs which contained the macro communicative intention of ‘thanking’ were analysed and compared with regard to the structural moves and Politeness Strategies (PS) they presented. The results show that addressers in both cultures follow a highly schematic way of constructing their Letters of Gratitude. This is evident not only in the sharing of most of their obligatory moves but also in that some of these moves present similar lexico-syntactic compositions to establish their limits. With regard to PS, the Chilean group showed the exclusive presence of strategies that acknowledged the role of the editor as a letter mediator directly. This suggests that the similarities found are genre-defining aspects. Conversely, the differences are connected to the cultural context of publication. The results also suggest that expressing gratitude in the written form may functionally differ from the way it is expressed orally. This type of contrastive study helps to identify both the genre- and culture specific aspects of discourse, which deepen our understanding of cultural, everyday manifestations and their realization in different settings.
Intracellular accumulation of trehalose and glycogen in an extreme oligotroph, Rhodococcus erythropolis N9T-4
Authors: Yano Takanori , Funamizu Yuhei , Yoshida Nobuyuki
Published: November 2015

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

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

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

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

Motivation: 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.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
PHYLUCE is a software package for the analysis of conserved genomic loci
Authors: Faircloth Brant C.
Published: November 2015

Summary: Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (<5 Ma to > 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.

Availability and Implementation: PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from https://www.github.com/faircloth-lab/phyluce/. PHYLUCE is also available as a package (https://binstar.org/faircloth-lab/phyluce) for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from http://phyluce.readthedocs.org/en/latest/ and test data are available from doi: 10.6084/m9.figshare.1284521.

Contact:  brant@faircloth-lab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exact quantification of cellular robustness in genome-scale metabolic networks
Authors: Gerstl Matthias P. , Klamt Steffen , Jungreuthmayer Christian , Zanghellini Jürgen
Published: November 2015

Motivation: Robustness, the ability of biological networks to uphold their functionality in spite of perturbations, is a key characteristic of all living systems. Although several theoretical approaches have been developed to formalize robustness, it still eludes an exact quantification. Here, we present a rigorous and quantitative approach for the structural robustness of metabolic networks by measuring their ability to tolerate random reaction (or gene) knockouts.

Results: In analogy to reliability theory, based on an explicit consideration of all possible knockout sets, we exactly quantify the probability of failure for a given network function (e.g. growth). This measure can be computed if the network’s minimal cut sets (MSCs) are known. We show that even in genome-scale metabolic networks the probability of (network) failure can be reliably estimated from MSCs with lowest cardinalities. We demonstrate the applicability of our theory by analyzing the structural robustness of multiple Enterobacteriaceae and Blattibacteriaceae and show a dramatically low structural robustness for the latter. We find that structural robustness develops from the ability to proliferate in multiple growth environments consistent with experimentally found knowledge.

Conclusion: The probability of (network) failure provides thus a reliable and easily computable measure of structural robustness and redundancy in (genome-scale) metabolic networks.

Availability and implementation: Source code is available under the GNU General Public License at https://github.com/mpgerstl/networkRobustnessToolbox.

Contact:  juergen.zanghellini@boku.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data
Authors: Xu Zheng , Zhang Guosheng , Jin Fulai , Chen Mengjie , Furey Terrence S. , Sullivan Patrick F. , Qin Zhaohui , Hu Ming , Li Yun
Published: November 2015

Motivation: Advances in chromosome conformation capture and next-generation sequencing technologies are enabling genome-wide investigation of dynamic chromatin interactions. For example, Hi-C experiments generate genome-wide contact frequencies between pairs of loci by sequencing DNA segments ligated from loci in close spatial proximity. One essential task in such studies is peak calling, that is, detecting non-random interactions between loci from the two-dimensional contact frequency matrix. Successful fulfillment of this task has many important implications including identifying long-range interactions that assist interpreting a sizable fraction of the results from genome-wide association studies. The task – distinguishing biologically meaningful chromatin interactions from massive numbers of random interactions – poses great challenges both statistically and computationally. Model-based methods to address this challenge are still lacking. In particular, no statistical model exists that takes the underlying dependency structure into consideration.

Results: In this paper, we propose a hidden Markov random field (HMRF) based Bayesian method to rigorously model interaction probabilities in the two-dimensional space based on the contact frequency matrix. By borrowing information from neighboring loci pairs, our method demonstrates superior reproducibility and statistical power in both simulation studies and real data analysis.

Availability and implementation: The Source codes can be downloaded at: http://www.unc.edu/∼yunmli/HMRFBayesHiC.

Contact:  ming.hu@nyumc.org or yunli@med.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.