bluuebunny/crossref_metadata_2025 huggingface dataset:
Label-free Detection of Influenza Viruses using a Reduced Graphene Oxide-based Electrochemical Immunosensor Integrated with a Microfluidic Platform
Authors: Singh Renu , Hong Seongkyeol , Jang Jaesung
Published: February 2017

Reduced graphene oxide (RGO) has recently gained considerable attention for use in electrochemical biosensing applications due to its outstanding conducting properties and large surface area. This report presents a novel microfluidic chip integrated with an RGO-based electrochemical immunosensor for label-free detection of an influenza virus, H1N1. Three microelectrodes were fabricated on a glass substrate using the photolithographic technique, and the working electrode was functionalized using RGO and monoclonal antibodies specific to the virus. These chips were integrated with polydimethylsiloxane microchannels. Structural and morphological characterizations were performed using X-ray photoelectron spectroscopy and scanning electron microscopy. Electrochemical studies revealed good selectivity and an enhanced detection limit of 0.5 PFU mL−1, where the chronoamperometric current increased linearly with H1N1 virus concentration within the range of 1 to 104 PFU mL−1 (R2 = 0.99). This microfluidic immunosensor can provide a promising platform for effective detection of biomolecules using minute samples.
Polymerase cross-linking spiral reaction (PCLSR) for detection of African swine fever virus (ASFV) in pigs and wild boars
Authors: Woźniakowski Grzegorz , Frączyk Magdalena , Kowalczyk Andrzej , Pomorska-Mól Małgorzata , Niemczuk Krzysztof , Pejsak Zygmunt
Published: February 2017

The study reports the development of a polymerase cross-linking spiral reaction (PCLSR) for the detection of African swine fever virus (ASFV) DNA in blood collected from infected pigs and wild boars. The method uses 3 specifically designed primers. Two outer-spiral primers comprising of 3′ sequences complementary to ASFV p72 gene sequence and 5′end sequences complementary to exogenous gene of black widow alpha-latrotoxin as well as additional ASFV specific cross-linking primer. The method is specific exclusively to ASFV DNA without cross-reactions with cDNA of classical swine fever virus (CSFV), porcine reproductive respiratory syndrome (PRRSV) or porcine epidemic diarrhea virus (PEDV). The sensitivity of this technique reached 7.2 × 102copies perμl−1of plasmid containing p72 gene. The PCLSR was conducted at 65 °C creating cross-linked complex structures. The results of PCLSR were visualized using SYBR Green I dye, gel electrophoresis while the reaction progress was traced using real-time PCR system that resulted in registration of fluorescent curves and melting peaks at 85.3 °C. The developed PCLSR was examined using blood or tissue samples collected from selected 17 ASF cases from infected wild boars and 3 outbreaks in pigs. Further tests have been also conducted using 55 tissue samples from 23 outbreaks and 22 cases. These results showed that PCLSR might be further used for preliminary and cost-effective detection and surveillance of ASFV.
Redox state manipulation of a tris(p-tetrazolylphenyl)amine ligand and its Mn2+ coordination frameworks
Authors: Hua Carol , Ge Jing-Yuan , Tuna Floriana , Collison David , Zuo Jing-Lin , D'Alessandro Deanna M.
Published: February 2017

Two new Mn2+-based metal–organic frameworks containing the tris(p-tetrazolylphenyl)amine (H3TTPA) ligand exhibit multiple redox-accessible states which have been interrogated using in situ solid state spectroelectrochemical methods.
Interstrand DNA covalent binding of two dinuclear Ru(ii) complexes. Influence of the extra ring of the bridging ligand on the DNA interaction and cytotoxic activity
Authors: Lozano Héctor J. , Busto Natalia , Espino Gustavo , Carbayo Arancha , Leal José M. , Platts James A. , García Begoña
Published: February 2017

The quinones naphthazarin and quinizarin intercalate into DNA whereas their p-cymene di-ruthenium(ii) complexes bind covalently via interstrand crosslinking.
Virulence factor activity relationships (VFARs): a bioinformatics perspective
Authors: Waseem Hassan , Williams Maggie R. , Stedtfeld Tiffany , Chai Benli , Stedtfeld Robert D. , Cole James R. , Tiedje James M. , Hashsham Syed A.
Published: February 2017

Virulence factor activity relationships (VFARs) – a concept loosely based on quantitative structure–activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety.
Sugaring-out strategy for counter-current chromatography isolation: podophyllotoxins and flavones from Dysosma versipellis as examples
Authors: Zhang Lihong , Wang Yanyan , Wu Shihua
Published: February 2017

In this work, we introduced a sugaring-out strategy for optimizing two-phase solvent systems for counter-current chromatography by adding some sugars into the selected two-phase solvent system.
Effects of Fe doping on the thermal hysteresis of the La0.5Ca0.5MnO3 system
Authors: Bhaskar Ankam , Huang M.-S. , Liu Chia-Jyi
Published: February 2017

A series of polycrystalline La0.5Ca0.5Mn1−xFexO3 (x = 0.010, 0.025, 0.050, 0.075, 0.100, 0.125, 0.150, 0.175 and 0.200) was synthesized using solid state reaction.
A hybrid polymer/oxide/ionic-liquid solid electrolyte for Na-metal batteries
Authors: Song Shufeng , Kotobuki Masashi , Zheng Feng , Xu Chaohe , Savilov Serguei V. , Hu Ning , Lu Li , Wang Yu , Li Wei Dong Z.
Published: February 2017

The development of solid electrolytes with superior electrical and electrochemical performances for the room-temperature operation of sodium (Na)-based batteries is at the infant stage and still remains a challenge.
Amino acid functionalized ZrO2 nanoparticles decorated reduced graphene oxide based immunosensor
Authors: Gupta Pramod K. , Tiwari Sachchidanand , Khan Zishan H. , Solanki Pratima R.
Published: February 2017

Here, a study is reported on a simple, one-step method for the synthesis of a zirconium dioxide–reduced graphene oxide (ZrO2–RGO) nanocomposite and its functionalization with amino acid to develop an immunosensor for detection of ochratoxin A.
In situ fabrication of Ni nanoparticles on N-doped TiO2 nanowire arrays by nitridation of NiTiO3 for highly sensitive and enzyme-free glucose sensing
Authors: Xu Jiangwen , Xu Na , Zhang Xuming , Gao Biao , Zhang Ben , Peng Xiang , Fu Jijiang , Chu Paul K. , Huo Kaifu
Published: February 2017

A novel strategy for Ni NPs/TiOxNy NWAs by nitridation of NiTiO3 NWAs is designed for highly sensitive and selective non-enzymatic glucose sensing.
Controlled formation of large-area single-crystalline TIPS-pentacene arrays through superhydrophobic micropillar flow-coating
Authors: Xiao Chengyi , Kan Xiaonan , Liu Chunming , Jiang Wei , Zhao Guangyao , Zhao Qiang , Zhang Lei , Hu Wenping , Wang Zhaohui , Jiang Lei
Published: February 2017

Single crystalline arrays with an area of 1 × 2 cm2and high mobilities could be obtained through the superhydrophobic micropillar flow-coating (SMFC) technique.
Ultra-broadband optical amplification at telecommunication wavelengths achieved by bismuth-activated lead iodide perovskites
Authors: Zhou Yang , Yong Zi-Jun , Zhang Wei , Ma Ju-Ping , Sadhanala Aditya , Chen Ya-Meng , Liu Bo-Mei , Zhou Yi , Song Bo , Sun Hong-Tao
Published: February 2017

It is extremely difficult to achieve hybrid halide perovskite semiconductors with luminescence at wavelengths longer than 1.0 μm, because of the inherent limitation of their band gaps.
Luminescent YbVO4 by atomic layer deposition
Authors: Getz Michael , Hansen Per-Anders , Ahmed Mohammed A. K. , Fjellvåg Helmer , Nilsen Ola
Published: February 2017

Thin films of YbVO4 displaying UV to NIR down conversion have been deposited by atomic layer deposition and crystallized through a flux aided process.
A 4,5-quinolimide-based fluorescent sensor for the turn-on detection of Cd2+with live-cell imaging
Authors: Zhang Yu , Guo Xiangfeng , Zheng Mengmeng , Yang Rui , Yang Hongming , Jia Lihua , Yang Mengmeng
Published: February 2017

The first 4,5-quinolimide sensor,BNA, bearing the amide-DPA receptor, was reported for sensing Cd2+with live-cell imaging.
Aggregation-controlled photochromism based on a dithienylethene derivative with aggregation-induced emission
Authors: Chen Shangjun , Li Wenlong , Li Xin , Zhu Wei-Hong
Published: February 2017

An interesting dithienylethene derivative, BTE-EQ, bestows novel aggregation-induced emission (AIE) characteristics and aggregation-controlled photochromism properties, together with density functional theory calculations.
Targeting PAK1
Authors: Semenova Galina , Chernoff Jonathan
Published: February 2017

p21-Activated kinase 1 (PAK1) has attracted much attention as a potential therapeutic target due to its central role in many oncogenic signaling pathways, its frequent dysregulation in cancers and neurological disorders, and its tractability as a target for small-molecule inhibition. To date, several PAK1-targeting compounds have been developed as preclinical agents, including one that has been evaluated in a clinical trial. A series of ATP-competitive inhibitors, allosteric inhibitors and peptide inhibitors with distinct biochemical and pharmacokinetic properties represent useful laboratory tools for studies on the role of PAK1 in biology and in disease contexts, and could lead to promising therapeutic agents. Given the central role of PAK1 in vital signaling pathways, future clinical development of PAK1 inhibitors will require careful investigation of their safety and efficacy.
Stress-induced O-GlcNAcylation: an adaptive process of injured cells
Authors: Martinez Marissa R. , Dias Thiago Braido , Natov Peter S. , Zachara Natasha E.
Published: February 2017

In the 30 years, since the discovery of nucleocytoplasmic glycosylation, O-GlcNAc has been implicated in regulating cellular processes as diverse as protein folding, localization, degradation, activity, post-translational modifications, and interactions. The cell co-ordinates these molecular events, on thousands of cellular proteins, in concert with environmental and physiological cues to fine-tune epigenetics, transcription, translation, signal transduction, cell cycle, and metabolism. The cellular stress response is no exception: diverse forms of injury result in dynamic changes to the O-GlcNAc subproteome that promote survival. In this review, we discuss the biosynthesis of O-GlcNAc, the mechanisms by which O-GlcNAc promotes cytoprotection, and the clinical significance of these data.
Mechanisms of LRRK2-dependent neurodegeneration: role of enzymatic activity and protein aggregation
Authors: Islam Md. Shariful , Moore Darren J.
Published: February 2017

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common cause of familial Parkinson's disease (PD) with autosomal dominant inheritance. Accordingly, LRRK2 has emerged as a promising therapeutic target for disease modification in PD. Since the first discovery of LRRK2 mutations some 12 years ago, LRRK2 has been the subject of intense investigation. It has been established that LRRK2 can function as a protein kinase, with many putative substrates identified, and can also function as a GTPase that may serve in part to regulate kinase activity. Familial mutations influence both of these enzymatic activities, suggesting that they may be important for the development of PD. Many LRRK2 models have been established to understand the pathogenic effects and mechanisms of familial mutations. Here, we provide a focused discussion of the evidence supporting a role for kinase and GTPase activity in mediating the pathogenic effects of familial LRRK2 mutations in different model systems, with an emphasis on rodent models of PD. We also critically discuss the contribution and relevance of protein aggregation, namely of α-synuclein and tau-proteins, which are known to form aggregates in PD brains harboring LRRK2 mutations, to neurodegeneration in LRRK2 rodent models. We aim to provide a clear and unbiased review of some of the key mechanisms that are important for LRRK2-dependent neurodegeneration in PD.
LRRK2: from kinase to GTPase to microtubules and back
Authors: Blanca Ramírez Marian , Lara Ordóñez Antonio Jesús , Fdez Elena , Hilfiker Sabine
Published: February 2017

Mutations in the Leucine-Rich Repeat Kinase 2 (LRRK2) gene are intimately linked to both familial and sporadic Parkinson's disease. LRRK2 is a large protein kinase able to bind and hydrolyse GTP. A wealth of in vitro studies have established that the distinct pathogenic LRRK2 mutants differentially affect those enzymatic activities, either causing an increase in kinase activity without altering GTP binding/GTP hydrolysis, or displaying no change in kinase activity but increased GTP binding/decreased GTP hydrolysis. Importantly, recent studies have shown that all pathogenic LRRK2 mutants display increased kinase activity towards select kinase substrates when analysed in intact cells. To understand those apparently discrepant results, better insight into the cellular role(s) of normal and pathogenic LRRK2 is crucial. Various studies indicate that LRRK2 regulates numerous intracellular vesicular trafficking pathways, but the mechanism(s) by which the distinct pathogenic mutants may equally interfere with such pathways has largely remained elusive. Here, we summarize the known alterations in the catalytic activities of the distinct pathogenic LRRK2 mutants and propose a testable working hypothesis by which the various mutants may affect membrane trafficking events in identical ways by culminating in increased phosphorylation of select substrate proteins known to be crucial for membrane trafficking between specific cellular compartments.
Short-Term Memory and Aphasia: From Theory to Treatment
Authors: Minkina Irene , Rosenberg Samantha , Kalinyak-Fliszar Michelene , Martin Nadine
Published: February 2017

This article reviews existing research on the interactions between verbal short-term memory and language processing impairments in aphasia. Theoretical models of short-term memory are reviewed, starting with a model assuming a separation between short-term memory and language, and progressing to models that view verbal short-term memory as a cognitive requirement of language processing. The review highlights a verbal short-term memory model derived from an interactive activation model of word retrieval. This model holds that verbal short-term memory encompasses the temporary activation of linguistic knowledge (e.g., semantic, lexical, and phonological features) during language production and comprehension tasks. Empirical evidence supporting this model, which views short-term memory in the context of the processes it subserves, is outlined. Studies that use a classic measure of verbal short-term memory (i.e., number of words/digits correctly recalled in immediate serial recall) as well as those that use more intricate measures (e.g., serial position effects in immediate serial recall) are discussed. Treatment research that uses verbal short-term memory tasks in an attempt to improve language processing is then summarized, with a particular focus on word retrieval. A discussion of the limitations of current research and possible future directions concludes the review.
Induction spectrometry using an ultrafast hollow-cored toroidal-coil (HTC) detector
Authors: Arbelo Yunieski , Bleiner Davide
Published: February 2017

Ultrafast photoelectron and photoion spectroscopy (as well as their combination known as “coincidence spectroscopy”) utilizes detectors based on different electron multipliers such as microchannel plates or single-channel electron multipliers. These detectors have a few important limitations such as fast-signal distortion (low pass operation), mutually exclusive positive or negative mode, dead time, and requirement of trigger. A high-pass induction detector, based on a hollow-cored toroidal coil, was developed that overcomes the above-mentioned limitations. The frequency-dispersive response and linearity of different configurations were analyzed. It is shown that the response is enhanced for ultrafast electron signals, dependent on construction parameters, thus offering response flexibility by design. Kinetic energy distributions of pseudospark-induced electron pulses are characterized in order to validate the capabilities in real applications.
A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube
Authors: Liu L. , Patey G. N.
Published: February 2017

Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l−1 and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion “solvation” within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.
Entropy generation in a parallel-plate active magnetic regenerator with insulator layers
Authors: Mugica Guerrero Ibai , Poncet Sébastien , Bouchard Jonathan
Published: February 2017

This paper proposes a feasible solution to diminish conduction losses in active magnetic regenerators. Higher performances of these machines are linked to a lower thermal conductivity of the Magneto-Caloric Material (MCM) in the streamwise direction. The concept presented here involves the insertion of insulator layers along the length of a parallel-plate magnetic regenerator in order to reduce the heat conduction within the MCM. This idea is investigated by means of a 1D numerical model. This model solves not only the energy equations for the fluid and solid domains but also the magnetic circuit that conforms the experimental setup of reference. In conclusion, the addition of insulator layers within the MCM increases the temperature span, cooling load, and coefficient of performance by a combination of lower heat conduction losses and an increment of the global Magneto-Caloric Effect. The generated entropy by solid conduction, fluid convection, and conduction and viscous losses are calculated to help understand the implications of introducing insulator layers in magnetic regenerators. Finally, the optimal number of insulator layers is studied.
Electron motion analysis of a radial-radiated electron beam in a radial-line drift tube with finite magnetic field conducted
Authors: Dang Fangchao , Zhang Xiaoping , Zhong Huihuang
Published: February 2017

Radial-radiated electron beam is widely employed in radial-line structure microwave devices. The quality of the electron beam has a crucial effect on the operating performance of these devices. This paper analyzes theoretically this electron motion in a radial-line drift tube with finite magnetic field conducted. The beam width, spatial period, and fluctuation amplitude are quantitatively analyzed with different beam current parameters. By the particle-in-cell simulation, we examine the theoretical analysis under the condition of a designed realistic coil configuration. It indicates that the derived beam envelope function is capable of predicting the radial-radiated beam trajectory approximately. Meanwhile, it is found that the off-axial z-direction magnetic field, in spite of its greatly slight amplitude, is also one necessary consideration for the propagation characteristic of the radial-radiated electron beam. Furthermore, the presented electron motion analysis may be instructive for the design of the electronic optical system of the radial-line structure microwave devices.
Plant species selection by sheep in semi-natural dry grasslands extensively grazed in the south-western Italian Alps
Authors: Pittarello Marco , Gorlier Alessandra , Lombardi Giampiero , Lonati Michele
Published: February 2017

Sheep can have an important role in the conservation of abandoned and shrub- and tree-encroached, semi-natural dry grasslands because their feeding behaviour is known to affect plant diversity and structure. Nevertheless, little information is available about feeding preferences of sheep at the sward-patch scale and about the effects of stocking density on their selectivity. Consequently, we investigated plant-species selection by sheep managed with a low-intensity grazing, examining the influence of stocking density and plant species abundance by means of vegetation surveys and animal GPS tracking. Sheep grazed a graminoid-dominated, semi-natural dry grassland (Festuco–Brometea) in Piedmont Region, north-west Italy. Plant species, classified into graminoids, suffruticose forbs, and herbaceous forbs, were selected with a different intensity by sheep, which preferred graminoids over suffruticose and herbaceous forbs. Plant species showing a high consumption ratio (CR), i.e. the level of selection of plant species (CR >10%), were mostly graminoids (e.g. Bromus erectus, Koeleria vallesiana and Stipa pennata). Furthermore, Carex species were also noticeably selected, in particular C. humilis, whereas spiny species and those with a rosette or prostrate forms were rarely grazed. The heterogeneity of stocking density over the pasture allowed testing of the relationships between stocking density and CR. For many species, the higher the stocking density, the higher was the CR, regardless of the abundance of dominant neighbouring species. Results suggest that sheep under low-intensity grazing conditions exert a specific plant-species selection in abandoned dry grasslands. By regulating the stocking density through the management of grazing sheep, it may be possible to condition the consumption of certain plant species, with medium–long-term effects on the botanical composition.
Degradation of structure and properties of rail surface layer at long-term operation
Authors: Gromov V. E. , Ivanov Yu. F. , Qin R. S. , Peregudov O. A. , Aksenova K. V. , Semina O. A.
Published: February 2017

The microstructure evolution and properties variation of the surface layer of rail steel after passed 500 and 1000 million tons of gross weight (MTGW) have been investigated. The wear rate increases to 3 and 3.4 times after passed 500 and 1000 MTGW, respectively. The corresponding friction coefficient decreases by 1.4 and 1.1 times. The cementite plates were destroyed and formed the cementite particles of around 10–50nm in size after passed 500 MTGW. The early stage dynamical recrystallisation was observed after passed 1000 MTGW. The mechanisms for these have been suggested. The large number of bend extinction contours is revealed in the surface layer. The internal stress field is evaluated.

This paper is part of a themed issue on Materials in External Fields.
Comparisons of absolute gravimeters (COOMET.M.G-S1)
Authors: Vinnichenko Mr Alexander , Germak Dr Alessandro
Published: February 2017

This report describes the results of the RMO supplementary comparison COOMET.M.G-S1 (also known as bilateral comparison COOMET 634/UA/14). The comparison measurements between the two participants NSC 'IM' (pilot laboratory) and INRIM were started in December 2015 and finished in January 2016.

Participants of comparisons were conducted at their national standards the measurements of the free fall acceleration in gravimetric point laboratory of absolute gravimetry of INRIM named INRiM.2. Absolute measurements of gravimetric acceleration were conducted by ballistic gravimeters.

The agreement between the two participants is good.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
CCQM-K140: carbon stable isotope ratio delta values in honey
Authors: Dunn P J H , Goenaga-Infante H , Goren A C , Şimşek A , Bilsel M , Ogrinc N , Armishaw P , Hai L
Published: February 2017

As there can be small but measureable differences in isotope ratios between different sources of the same element/compound/material, isotope ratio measurements are applied in a number of different fields including archaeology, environmental science, geochemistry, forensic science and ecology. Isotope ratios for the light elements (H, C, N, O and S) are typically reported as δ-values which are isotope ratios expressed relative to an internationally agreed standard (this standard is the zero-point on the scale), although absolute isotope ratios which are traceable to the SI have also been reported. The IAWG has been granted a traceability exception for the use of arbitrary delta scales until SI traceability can be established at the required level of uncertainty but this goal is some years away.

While the CCQM IAWG has previously organised several pilot studies on isotope ratio determination (CCQM-P75: Stable isotope delta values in methionine, 2006; CCQM-P105: Sr isotope ratios in wine, 2008; CCQM-K98: Pb isotope ratios in bronze with additional delta values in CCQM-P134, 2011), it has been a number of years since delta values of light elements have been considered and there has been no key comparison (KC). Therefore, the IAWG has included the need for a KC (CCQM-K140) based on an arbitrary delta scale in its program to support ongoing requirements to demonstrate core capabilities as well as specific claims of measurement capability (CMCs) in this area.

The performance of all five of the CCQM-K140 participants was very good, illustrating their ability to obtain accurate results for carbon isotope ratios, within the calibration range afforded by internationally agreed reference materials (δ13CVPDB-LSVEC between −47.32 % and +535.3 %) with measurement uncertainties of between 0.08 and 0.28 %. This was despite the fact that no two participants used exactly the same approach in terms of instrumentation or data treatment.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Malliavin calculus for non-Gaussian differentiable measures and surface measures in Hilbert spaces
Authors: Da Prato Giuseppe , Lunardi Alessandra , Tubaro Luciano
Published: February 2017

We construct surface measures in a Hilbert space endowed with a probability measure

ν
\nu

. The theory fits for invariant measures of some stochastic partial differential equations such as Burgers and reaction–diffusion equations. Other examples are weighted Gaussian measures and special product measures

ν
\nu

of non-Gaussian measures. In any case we prove integration by parts formulae on sublevel sets of good functions (including spheres and hyperplanes) that involve surface integrals.
Integrative Blood Pressure Response to Upright Tilt Post Renal Denervation
Authors: Howden Erin J. , East Cara , Lawley Justin S. , Stickford Abigail S.L. , Verhees Myrthe , Fu Qi , Levine Benjamin D.
Published: February 2017

BACKGROUND

Whether renal denervation (RDN) in patients with resistant hypertension normalizes blood pressure (BP) regulation in response to routine cardiovascular stimuli such as upright posture is unknown. We conducted an integrative study of BP regulation in patients with resistant hypertension who had received RDN to characterize autonomic circulatory control.

METHODS

Twelve patients (60 ± 9 [SD] years, n = 10 males) who participated in the Symplicity HTN-3 trial were studied and compared to 2 age-matched normotensive (Norm) and hypertensive (unmedicated, HTN) control groups. BP, heart rate (HR), cardiac output (Qc), muscle sympathetic nerve activity (MSNA), and neurohormonal variables were measured supine, and 30° (5 minutes) and 60° (20 minutes) head-up-tilt (HUT). Total peripheral resistance (TPR) was calculated from mean arterial pressure and Qc.

RESULTS

Despite treatment with RDN and 4.8 (range, 3–7) antihypertensive medications, the RDN had significantly higher supine systolic BP compared to Norm and HTN (149 ± 15 vs. 118 ± 6, 108 ± 8 mm Hg, P < 0.001). When supine, RDN had higher HR, TPR, MSNA, plasma norepinephrine, and effective arterial elastance compared to Norm. Plasma norepinephrine, Qc, and HR were also higher in the RDN vs. HTN. During HUT, BP remained higher in the RDN, due to increases in Qc, plasma norepinephrine, and aldosterone.

CONCLUSION

We provide evidence of a possible mechanism by which BP remains elevated post RDN, with the observation of increased Qc and arterial stiffness, as well as plasma norepinephrine and aldosterone levels at approximately 2 years post treatment. These findings may be the consequence of incomplete ablation of sympathetic renal nerves or be related to other factors.
Cognitive Associates of Current and More Intensive Control of Hypertension: Findings From the Hispanic Community Health Study/Study of Latinos
Authors: Lamar Melissa , Wu Donghong , Durazo-Arvizu Ramon A. , Brickman Adam M. , Gonzalez Hector M. , Tarraf Wassim , Daviglus Martha L.
Published: February 2017

BACKGROUND

Hypertension control in Hispanics/Latinos lag behind general US trends by 10–15%. Intensive systolic blood pressure (SBP) management <120 mm Hg may significantly reduce morbidity/mortality risk in adults with hypertension; less is known about cognition. We investigated cross-sectional associations of cognition with observed hypertension control at currently recommended (SBP < 140 mm Hg) and more intensive (SBP < 120 mm Hg) levels using baseline data from the Hispanic Community Health Study/Study of Latinos.

METHODS

From this multicenter cohort study, we focused on 1,735 Hispanic/Latino men and women ages 45–74 years with hypertension and verified antihypertensive use. Verbal fluency, information processing speed, learning, and memory were tested in Spanish or English.

RESULTS

Separate linear regressions revealed that being on 1 vs. >1 antihypertensive medication was not associated with cognition; however, individuals with SBP controlled to currently recommended levels outperformed individuals with uncontrolled SBP on verbal fluency [Beta = 1.44 (0.52), P < 0.01] and information processing speed [Beta = 3.01 (0.89), P < 0.001] in age-adjusted regression analyses; only information processing speed remained significant (P < 0.05) after additional adjustments including acculturation, health insurance, and other cardiovascular disease risk factors. When regrouping individuals based on more intensive SBP control, individuals with levels <120 mm Hg outperformed individuals with higher SBP on verbal fluency regardless of adjustments (P < 0.01). More intensive rather than currently recommended levels of control associated with higher verbal fluency performance regardless of adjustments (P < 0.05).

CONCLUSIONS

Individual cognitive test scores related to distinct SBP management with more intensive management appearing more robust against confounders. While cognitive associations with hypertension in Hispanics/Latinos may be multifactorial, different levels of SBP control should be considered in future prospective intervention studies.
LASER server: ancestry tracing with genotypes or sequence reads
Authors: Taliun Daniel , Chothani Sonia P , Schönherr Sebastian , Forer Lukas , Boehnke Michael , Abecasis Gonçalo R , Wang Chaolong
Published: February 2017

To enable direct comparison of ancestry background in different studies, we developed LASER to estimate individual ancestry by placing either sezquenced or genotyped samples in a common ancestry space, regardless of the sequencing strategy or genotyping array used to characterize each sample. Here we describe the LASER server to facilitate application of the method to a wide range of genetic studies. The server provides genetic ancestry estimation for different geographic regions and user-friendly interactive visualization of the results.

Availability and Implementation

The LASER server is freely accessible at http://laser.sph.umich.edu/

Supplementary information

Supplementary data are available at Bioinformatics online.
Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Authors: Hernandez-Armenta Claudia , Ochoa David , Gonçalves Emanuel , Saez-Rodriguez Julio , Beltrao Pedro
Published: February 2017

Motivation

Phosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.

Results

We used curated phosphoproteomic experiments and a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur to benchmark and compare different kinase activity inference strategies: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model. We also tested weighted variants of the Z-test and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence (in vivo, in vitro or in silico) supporting these influence the predictions.

Conclusions

Most models performed well with the Z-test and the GSEA performing best as determined by the area under the ROC curve (Mean AUC = 0.722). Weighting kinase targets by the kinase target sequence preference improves the results marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions.

Availability and Implementation

The KSEA implementation is available in https://github.com/ evocellnet/ksea. Additional data is available in http://phosfate.com

Supplementary information

Supplementary data are available at Bioinformatics online.
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
Authors: Baele Guy , Lemey Philippe , Rambaut Andrew , Suchard Marc A
Published: February 2017

Motivation

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses.

Results

We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by > 14-fold.

Availability and Implementation

Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference.

Supplementary information

Supplementary data are available at Bioinformatics online.
Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway
Authors: Palaniappan Sucheendra K , Bertaux François , Pichené Matthieu , Fabre Eric , Batt Gregory , Genest Blaise
Published: February 2017

Motivation

Quantitative models are increasingly used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting.

Results

In this paper, we propose to construct abstractions using information theory notions. Entropy is used to discretize the state space and mutual information is used to select a subset of all original variables and their mutual dependencies. We apply our method to an hybrid model of TRAIL-induced apoptosis in HeLa cell. Our abstraction, represented as a Dynamic Bayesian Network (DBN), reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet preserving essential features of cell death time distributions.

Availability and Implementation

This approach is implemented in the tool DBNizer, freely available at http://perso.crans.org/genest/DBNizer.

Supplementary information

Supplementary data are available at Bioinformatics online.
Pln24NT: a web resource for plant 24-nt siRNA producing loci
Authors: Liu Qi , Ding Changjun , Chu Yanguang , Zhang Weixi , Guo Ganggang , Chen Jiafei , Su Xiaohua
Published: February 2017

In plants, 24 nucleotide small interfering RNAs (24-nt siRNAs) account for a large percentage of the total siRNA pool, and they play an important role in guiding plant-specific RNA-directed DNA methylation (RdDM), which transcriptionally silences transposon elements, transgenes, repetitive sequences and some endogenous genes. Several loci in plant genomes produce clusters of 24-nt RNAs, and these loci are receiving increasing attention from the research community. However, at present there is no bioinformatics resource dedicated to 24-nt siRNA loci and their derived 24-nt siRNAs. Thus, in this study, Pln24NT, a freely available web resource, was created to centralize 24-nt siRNA loci and 24-nt siRNA information, including fundamental locus information, expression profiles and annotation of transposon elements, from next-generation sequencing (NGS) data for 10 popular plant species. An intuitive web interface was also developed for convenient searching and browsing, and analytical tools were included to help users flexibly analyze their own siRNA NGS data. Pln24NT will help the plant research community to discover and characterize 24-nt siRNAs, and may prove useful for studying the roles of siRNA in RNA-directed DNA methylation in plants.

Availability and Implementation

http://bioinformatics.caf.ac.cn/Pln24NT.

Supplementary information

Supplementary data are available at Bioinformatics online.
GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification
Authors: Szpiech Zachary A , Blant Alexandra , Pemberton Trevor J
Published: February 2017

Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method (Pemberton et al., 2012) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method.

Availability and Implementation

GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub (https://github.com/szpiech/garlic) under the GNU General Public License version 3.

Supplementary information

Supplementary data are available at Bioinformatics online.
Structural bounds on the dyadic effect
Authors: Cinelli Matteo , Ferraro Giovanna , Iovanella Antonio
Published: February 2017

The dyadic effect is a phenomenon that occurs when the number of links between nodes sharing a common feature is larger than expected if the features are distributed randomly on the network. In this article, we consider the case when nodes are distinguished by a binary characteristic. Under these circumstances, two independent parameters, namely dyadicity and heterophilicity are able to detect the presence of the dyadic effect and to measure how much the considered characteristic affects the network topology. The distribution of nodes characteristics can be investigated within a two-dimensional space that represents the feasible region of the dyadic effect, which is bound by two upper bounds on dyadicity and heterophilicity. Using some network structural arguments, we are able to improve such upper bounds and introduce two new lower bounds, providing a reduction of the feasible region of the dyadic effect as well as constraining dyadicity and heterophilicity within a specific range. Some computational experiences show the bounds effectiveness and their usefulness with regards to different classes of networks.
‘Le Renégat’ d’Albert Camus: de l’insignifiance au terrorisme
Authors: Dalmas Franck
Published: February 2017

La nouvelle ‘Le Renégat, ou, un esprit confus’ reste un texte peu exploré d’Albert Camus malgré de nombreuses exégèses allégoriques. Au tournant du vingt-et-unième siècle, la montée des intégrismes et la prolifération du terrorisme mondial n’ont pourtant guère suscité de regain d’intérêt. C’est notre intention de replacer ce texte ‘étrange’ dans la mouvance hypermoderne de la violence. Les angles d’étude sont multiples et rendent justice à la complexité de la nouvelle. Elle est examinée à la lumière de
L’Homme révolté
, en appréhendant les dérives fondamentalistes et en faisant retour sur la guerre d’Algérie, afin de comparer les mécanismes de la terreur et les pratiques répressives. La responsabilité de l’intellectuel derrière le phénomène terroriste est également invoquée, jusqu’à la lecture contemporaine après les réflexions de Jean Baudrillard sur les attentats du 11 septembre 2001. L’insignifiance des positions présentées par le protagoniste renégat reflète l’engagement idéologique absurde selon Camus.
Effects of pCO2 on photosynthesis and respiration of tropical scleractinian corals and calcified algae
Authors: Comeau S. , Carpenter R. C. , Edmunds P. J.
Published: February 2017

The effects of ocean acidification (OA) on coral reefs have been studied thoroughly with a focus on the response of calcification of corals and calcified algae. However, there are still large gaps in our knowledge of the effects of OA on photosynthesis and respiration of these organisms. Comparisons among species and determination of the functional relationships between pCO2 and either photosynthesis or respiration are difficult using previously published data, because experimental conditions typically vary widely between studies. Here, we tested the response of net photosynthesis, gross photosynthesis, dark respiration, and light-enhanced dark respiration (LEDR) of eight coral taxa and seven calcified alga taxa to six different pCO2 levels (from 280 to 2000 µatm). Organisms were maintained during 7–10 days incubations in identical conditions of light, temperature, and pCO2 to facilitate comparisons among species. Net photosynthesis was not affected by pCO2 in seven of eight corals or any of the algae; gross photosynthesis did not respond to pCO2 in six coral taxa and six algal taxa; dark respiration also was unaffected by pCO2 in six coral and six algae; and LEDR did not respond to pCO2 in any of the tested species. Overall, our results show that pCO2 levels up to 2000 µatm likely will not fertilize photosynthesis or modify respiration rates of most of the main calcifiers on the back reef of Moorea, French Polynesia.
Survival of undersized plaice (Pleuronectes platessa), sole (Solea solea), and dab (Limanda limanda) in North Sea pulse-trawl fisheries
Authors: van der Reijden K. J. , Molenaar P. , Chen C. , Uhlmann S. S. , Goudswaard P. C. , van Marlen B.
Published: February 2017

The European Commission landing obligation, including species-specific “high survival” exemptions, has established a need for accurate discard survival estimates. This study presents the first discard survival estimates on-board Dutch commercial pulse trawlers. During seven, six, and one fishing trip(s), respectively, undersized plaice (Pleuronectes platessa), sole (Solea solea), and dab (Limanda limanda) were collected, assessed for vitality and subsequently monitored up to 21 days. Uncorrected for any potential impacts from predation, tagging, research-related handling, or holding conditions overall survival for plaice (n = 349), sole (n = 226), and dab (n = 187) was assessed as 15% [95% CI: 11–19%], 29% [95% CI: 24–35%], and 16% [95% CI: 10–26%] respectively. Survival was mainly effected by water temperature and factors linked to the fishing vessel. Fish length was not found to affect survival. Catch processing time and haul duration affected plaice survival but not sole. Vitality index, which averages reflex impairment and external damage scores, correlated with survival and may be developed as a proxy for discard survival. Compared to tickler-chain beam trawlers, pulse trawlers showed relatively higher discard survival under fishing conditions pertinent to these studies.