bluuebunny/crossref_metadata_2025 huggingface dataset:
Description of poly(ethylenepropylene) confined in nanopores by a modified Rouse model
Authors: Muthmann Matthias , Krutyeva Margarita , Willner Lutz , Allgaier Jürgen , Richter Dieter , Zorn Reiner , Ohl Michael , Rebbin Vivian , Lindner Peter
Published: February 2017

A recent model for unentangled polymer chains in confinement [M. Dolgushev and M. Krutyeva, Macromol. Theory Simul. 21, 565 (2012)] is scrutinized by small-angle neutron scattering (SANS) with respect to its static prediction, the single-chain structure factor. We find a remarkable agreement although the model simplifies the effect of the confinement to a harmonic potential. The effective confinement size from fits of SANS data with the model agrees well with the actual pore size. Starting from this result we discuss the possibility of an experiment on the dynamic structure factor predicted by the model. It turns out that such an experiment would need a large ratio polymer dimension/pore size which is difficult but not impossible to achieve.
Kinematics in a slowly drying porous medium: Reconciliation of pore network simulations and continuum modeling
Authors: Attari Moghaddam Alireza , Kharaghani Abdolreza , Tsotsas Evangelos , Prat Marc
Published: February 2017

We study the velocity field in the liquid phase during the drying of a porous medium in the capillarity-dominated regime with evaporation from the top surface. A simple mass balance in the continuum framework leads to a linear variation of the filtration velocity across the sample. By contrast, the instantaneous slice-averaged velocity field determined from pore network simulations leads to step velocity profiles. The vertical velocity profile is almost constant near the evaporative top surface and zero close to the bottom of the sample. The relative extent of the two regions with constant velocity is dictated by the position of the most unstable meniscus. It is shown that the continuum and pore network results can be reconciled by averaging the velocity field obtained from the pore network simulations over time. This opens up interesting prospects regarding the transport of dissolved species during drying. Also, the study reveals the existence of an edge effect, which is not taken into account in the classical continuum models of drying.
Anomalous angular dispersion in lithium niobate one-dimensional waveguide array in the near-infrared wavelength range
Authors: Apetrei Alin Marian , Rambu Alicia Petronela , Minot Christophe , Moison Jean-Marie , Belabas Nadia , Tascu Sorin
Published: February 2017

Knowing the dispersion properties of a device is important in many applications (e.g., wavelength separation). For an isolated waveguide, besides the material dispersion, one must consider the waveguide influence as well, through waveguide dispersion and mode dispersion. For a waveguide array, one must consider the influence of evanescent coupling between adjacent waveguides as well. We investigate by the Finite Element Method the angular dispersion of a LiNbO3 waveguide array using two techniques. The first one assumes the Coupled Mode Theory in a 2-waveguide system. The other one uses the actual diffraction curve determined in a 7-waveguide system. In both approaches, we find that by decreasing the array period, one passes from normal angular dispersion by an achromatic point to anomalous angular dispersion. We then illustrate the wavelength separation by the waveguide array by doing Runge-Kutta light propagation simulations. As all the values of parameters are technologically feasible, this opens new possibilities for optical data processing, such as WDM and dispersion compensation.
Emergent propagation modes of ferromagnetic swimmers in constrained geometries
Authors: Bryan M. T. , Shelley S. R. , Parish M. J. , Petrov P. G. , Winlove C. P. , Gilbert A. D. , Ogrin F. Y.
Published: February 2017

Magnetic microswimmers, composed of hard and soft ferromagnets connected by an elastic spring, are modelled under low Reynolds number conditions in the presence of geometrical boundaries. Approaching a surface, the magneto-elastic swimmer's velocity increases and its trajectory bends parallel to the surface contour. Further confinement to form a planar channel generates new propagation modes as the channel width narrows, altering the magneto-elastic swimmer's speed, orientation, and direction of travel. Our results demonstrate that constricted geometric environments, such as occuring in microfluidic channels or blood vessels, may influence the functionality of magneto-elastic microswimmers for applications such as drug delivery.
Biodiesel synthesis from Brassica napus seed oil using statistical optimization approach
Authors: Anwar Faiza , Rashid Umer , Ashraf Sobia , Al-Resayes Saud Ibrahim , Mehmood Muhammad Aamer , Nehdi Imededdine Arbi , Ibrahim Muhammad , Hanif Muhammad Asif
Published: February 2017

In this study, response surface methodology (RSM) based on a central composite rotatable design was applied to establish the optimum conditions for the methanolysis of Brassica napus (B. napus) seed oil. Four process variables were evaluated at two levels (24 experimental design): the methanol/oil molar ratio (3:1–12:1), the catalyst concentration in relation to oil mass (0.25–1.25 wt. % KOH), the reaction temperature (25–65 °C), and the alcoholysis reaction time (20–120 min). The use of RSM resulted in a quadratic polynomial equation obtained by multiple regression analysis to predict transesterification. The results have shown that the methanol-oil-molar ratio and reaction time significantly affect the biodiesel yield. The highest biodiesel yield (95.7%) was obtained with the 8:1 methanol/oil ratio and 0.97% catalyst concentration at 55 °C reaction temperature for 70 min reaction time. A linear relationship was noted between the observed and predicted values. The characteristics of biodiesel produced in the present study as revealed by gas chromatography analyses confirmed the existence of four major fatty acid methyl esters (FAME) (oleic-, linoleic-, linolenic-, and palmitic-acids). The fuel properties of B. napus oil methyl esters, i.e., cetane number, kinematic viscosity, oxidative stability, cloud point, pour point, cold filter plugging point, flash point, ash and sulfur-contents, acid value, copper strip corrosion, density, and higher heating value, were determined, which were within the limit of biodiesel standards such as ASTM D6751 and EN 14214.
Langmuir oscillations in a nonthermal nonextensive electron-positron plasma
Authors: El-Taibany W. F. , Zedan N. A.
Published: February 2017

The high-frequency Langmuir-type oscillations in a pure pair plasma are studied using Vlasov-Poisson's equations in the presence of hybrid nonthermal nonextensive distributed species. The characteristics of the Langmuir oscillations, Landau damping, and growing unstable modes in a nonthermal nonextensive electron-positron (EP) plasma are remarkably modified. It is found that the phase velocity of the Langmuir waves increases by decreasing (increasing) the value of nonextensive (nonthermal) parameter, q (α). In particular, depending on the degree of nonthermality and nonextensivity, both damping and growing oscillations are predicted in the proposed EP plasma. It is seen that the Langmuir waves suffer from Landau damping in two different q regions. Furthermore, the mechanism that leads to unstable modes is established in the context of the nonthermal nonextensive formalism, yet the damping mechanism is the same developed by Landau. The present study is useful in the regions where such mixed distributions in space or laboratory plasmas exist.
Inversely-designed printed microwave ablation antenna for controlled temperature profile synthesis
Authors: Sharma Shashwat , Sarris Costas D.
Published: February 2017

Microwave ablation (MWA) is based on localized heating of biological tissues, enabled by an electric field. Antennas for ablation are commonly designed in a forward approach to generate a temperature profile specific to the design. The concept of an inversely-designed MWA antenna, consisting of printed dipoles, is presented herein. This design can be configured to synthesize a desired target temperature profile by controlling and optimizing its current distribution, as demonstrated by simulations. This concept provides the functionality of a phased array on the tip of an interstitial device.
Electrically tunable diffraction efficiency from gratings in Al-doped ZnO
Authors: George David , Li Li , Lowell David , Ding Jun , Cui Jingbiao , Zhang Hualiang , Philipose Usha , Lin Yuankun
Published: February 2017

Transparent conducting aluminum-doped zinc oxide (AZO) can be used as part of an active plasmonic device due to its electrically tunable permittivity, which is accomplished by changing the carrier concentration with electrical biasing. In this letter, we report a continuous electrical tuning of diffraction efficiency from AZO gratings in the visible range (specifically 532 nm) when the AZO is under bias voltages between −1 V and −3.5 V. The carrier concentration in AZO under negative bias has been measured and simulated. The diffraction efficiency changes have been explained by the carrier concentration variation and induced complex refractive index change at the Al2O3 and AZO interface. The reported results can lead toward the application of post-fabrication tuning of optoelectronic devices using AZO.
Exchange-coupled hard magnetic Fe-Co/CoPt nanocomposite films fabricated by electro-infiltration
Authors: Wen Xiao , Andrew Jennifer S. , Arnold David P.
Published: February 2017

This paper introduces a potentially scalable electro-infiltration process to produce exchange-coupled hard magnetic nanocomposite thin films. Fe-Co/CoPt nanocomposite films are fabricated by deposition of CoFe2O4 nanoparticles onto Si substrate, followed by electroplating of CoPt. Samples are subsequently annealed under H2 to reduce the CoFe2O4 to magnetically soft Fe-Co and also induce L10 ordering in the CoPt. Resultant films exhibit 0.97 T saturation magnetization, 0.70 T remanent magnetization, 127 kA/m coercivity and 21.8 kJ/m3 maximum energy density. First order reversal curve (FORC) analysis and δM plot are used to prove the exchange coupling between soft and hard magnetic phases.
Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis
Authors: Shimizu Takayuki , Shen Jiangchuan , Fang Mingxu , Zhang Yixiang , Hori Koichi , Trinidad Jonathan C. , Bauer Carl E. , Giedroc David P. , Masuda Shinji
Published: February 2017

Significance

Hydrogen sulfide is a universal bioactive molecule that functions in both prokaryotes and eukaryotes. However, little is known about intra- and extracellular sulfide-sensing mechanisms. Here we show that the sulfide-regulated repressor SqrR from a purple bacterium forms an intramolecular tetrasulfide bond in response to sulfide stress in vivo and organic persulfides in vitro, revealing the importance of this cysteine modification for sulfide sensing in cells. These findings provide new insights into bacterial sulfide homeostasis and its potential applications in synthetic biology. Given that purple bacteria retain characteristics of ancestral photosynthesis and photosynthetic electron transfer, the functional characterization of SqrR also provides new information on plausible mechanisms that regulated electron flow early in the evolution of photosynthesis.
Brownian motion of solitons in a Bose–Einstein condensate
Authors: Aycock Lauren M. , Hurst Hilary M. , Efimkin Dmitry K. , Genkina Dina , Lu Hsin-I , Galitski Victor M. , Spielman I. B.
Published: February 2017

Significance

Solitons, spatially localized, mobile excitations resulting from an interplay between nonlinearity and dispersion, are ubiquitous in physical systems from water channels and oceans to optical fibers and Bose–Einstein condensates (BECs). From our pulse throbbing at our wrists to rapidly moving tsunamis, solitons appear naturally at a wide range of scales. In nonlinear optical fibers, solitons can travel long distances with applications for communication technology and potential for use in quantum switches and logic. Understanding how random processes contribute to the decay and the diffusion of solitons is essential to advancing these technologies.
Engineered holocytochrome
c
synthases that biosynthesize new cytochromes
c
Authors: Mendez Deanna L. , Babbitt Shalon E. , King Jeremy D. , D’Alessandro John , Watson Michael B. , Blankenship Robert E. , Mirica Liviu M. , Kranz Robert G.
Published: February 2017

Significance

Specific mutations in human holocytochrome
c
synthase (HCCS) confer enhanced biosynthesis of cyt
c
, including cyt
c
variants never before produced. These include a bis-Met and single thioether cyt
c
. We designate these as HCCS “release mutants” because evidence indicates they are mechanistically affected in step 4 of biosynthesis, release of cyt
c
from the HCCS/cyt
c
complex. Characteristics of cyt
c
WT (His/Met), cyt
c
H19M (bis-Met), cyt
c
M81H (bis-His), and cyt
c
M81A (His/OH
−
) indicate proper folding and that the engineered ligands are present. This panel of variants spans a redox gradient of more than 400 mV, which will be useful for studying various redox-dependent cellular processes and other physical properties.
Extending enzyme molecular recognition with an expanded amino acid alphabet
Authors: Windle Claire L. , Simmons Katie J. , Ault James R. , Trinh Chi H. , Nelson Adam , Pearson Arwen R. , Berry Alan
Published: February 2017

Significance

The remarkable power of enzymes as catalysts is derived from the precise spatial positioning of amino acids as a result of a polypeptide folding into its native, active fold. Protein engineers have a wide arsenal of tools available to alter the properties of enzymes but, until recently, have been limited to replacement of amino acids with one of the other naturally occurring proteogenic amino acids. Here we describe a protein engineering approach to introduce a noncanonical amino acid that results in altered substrate specificity of an aldolase to produce a novel activity that cannot be achieved by simple substitution with any of the canonical amino acids.
Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion
Authors: Ahmadzadeh Hossein , Webster Marie R. , Behera Reeti , Jimenez Valencia Angela M. , Wirtz Denis , Weeraratna Ashani T. , Shenoy Vivek B.
Published: February 2017

Significance

The mechanical cross talk between intracellular and extracellular forces can promote the invasive potential of tumor cells in tumors. Using a quantitative model, we elucidate the two-way feedback loop between stress-dependent cell contractility and matrix fiber realignment and strain stiffening, which enables the cells to polarize and enhance their contractility to break free from the tumor and invade into the matrix. Our model predicts that intermediate matrix stiffness is optimal for invasion, and we find a positive correlation between cell elongation and alignment of fibers in the matrix. Importantly, our model can be used to explain how morphological and structural changes in the tumor microenvironment, such as elevated rigidity and fiber alignment prior to cell invasion, are prognostic of the malignant phenotype.
Spontaneous activity in the piriform cortex extends the dynamic range of cortical odor coding
Authors: Tantirigama Malinda L. S. , Huang Helena H.-Y. , Bekkers John M.
Published: February 2017

Significance

Sensory neurons are often spontaneously active even in the absence of the relevant stimuli, raising the question, Is this background activity a bug or a feature of neural circuits? Using in vivo calcium imaging in mice, we show that neurons in the primary olfactory (piriform) cortex are spontaneously active when the animal is breathing unodorized air and this activity is entirely driven by spontaneous firing in the upstream olfactory bulb. When the animal smells an odor, some piriform neurons fire more strongly, and others have their spontaneous activity suppressed. By allowing two-way changes in firing, spontaneous background activity serves as a mechanism to extend the range of odor coding.
AgRP to Kiss1 neuron signaling links nutritional state and fertility
Authors: Padilla Stephanie L. , Qiu Jian , Nestor Casey C , Zhang Chunguang , Smith Arik W. , Whiddon Benjamin B. , Rønnekleiv Oline K. , Kelly Martin J. , Palmiter Richard D.
Published: February 2017

Significance

Women suffering from malnutrition and athletes with low body fat become infertile as a result of low gonadotropin secretion. Gonadotropin release is determined by a neural endocrine circuit; however, the metabolic cues that are responsible for attenuating this axis during starvation remain unclear. Here, we find that starvation-activated agouti-related peptide (AgRP) neurons can inhibit the reproductive neuroendocrine circuit. Furthermore, artificial activation of genetically defined AgRP neurons is sufficient to delay estrous cycle length and parturition in female mice. This work demonstrates a mechanism by which AgRP neurons can relay metabolic information to the fertility axis during starvation.
Mental and Physical Healthcare Utilization Among Young Prisoners: A Longitudinal Study
Authors: Gonçalves Leonel Cunha , Dirkzwager Anja J. E. , Rossegger Astrid , Gonçalves Rui Abrunhosa , Martins Carla , Endrass Jérôme
Published: February 2017

The present longitudinal study describes changes in and covariates of healthcare utilization in 75 young males (aged 17– 22 years) during their first year in a Portuguese prison. The prisoners were assessed 1, 3, 6, and 12 months after their arrival in custody. Multilevel negative binomial regression analyses were conducted to examine the effect of time in prison as well as several clinical, socio-demographic, and criminological characteristics on: (a) treatment for mental health problems and (b) treatment for physical health problems. Although healthcare utilization for mental health issues remained stable over 12 months of imprisonment, visits for physical health problems were highest during the first month and then declined significantly. Patterns of healthcare utilization were associated with time spent in prison, mental health symptoms, Portuguese nationality, older age at the onset of imprisonment, criminal history, and severe disciplinary infractions. Strikingly, prisoners who initially reported more mental health symptoms upon arrival to the prison facility received less mental health services for the first six months of imprisonment. The limitations of this study and its implications for correctional research and practice are discussed.
Ontology of Fake: Discerning the Philippine Elite
Authors: Reyes Angela
Published: February 2017

Hilary Putnam (1975) proposes that a “natural kind” term relies on a division of linguistic labor in which experts discern what is or is not a member of a kind. Centering on a Philippine-elite social kind term, this essay examines how self-appointed experts develop and share “scientific” instruments, or tests, that discern whether someone is a “real” or “fake” elite. These tests report about signs of realness and fakeness by assigning “gentle” and “rough” qualities to speech and body of differentiated social types. This essay demonstrates that such qualia are central to shaping ontologies of social types; that the discerning subject, who speaks from an elevated social position as reflexive expert, is critical to this process; and that the discerner shares expertise by developing tests that rest on different ontologies of emblem. The essay argues that discerning Philippine elite types and their aspiring subtypes and countertypes presupposes an overarching ontology of fake that already renders real elites as fakes.
Final report on APMP supplementary comparison of industrial platinum resistance thermometer for range -50 °C to 400 °C. (APMP.T-S6)
Authors: Ali Nurulaini Md , Othman Hafidzah , Ho Mong-Kim , Yang Inseok , Gabi Victor , Zhang Zhe , Sheng Ying , Hu Jing , Zhang Jintao , Tsai Shu-Fei , Liao Su-Chuion , Alam Md Shafiqul , Norranim Uthai , Yaokulbodee Charuayrat , Liedberg Hans , Ahmed Mohamed Gamal , Harba Naser , Flaifel Mustafa Fuad , Suherlan  , Achmadi Aditya , Haoyuan Kho , Yan Fan , Kwee Neoh Boon , Binh Pham Thanh , Ragay Monalisa
Published: February 2017

The National Metrology Laboratory, Malaysia (NML-SIRIM) had coordinated the Supplementary Comparison of Industrial Platinum Resistance Thermometer (IPRT) started from July 2009 until April 2011 together with the National Measurement Institute of Australia (NMIA) and Korea Research Institute of Standards and Science (KRISS). This comparison was opened to all APMP members and 16 participants had taken part in order to consolidate or improve their calibration and measurement capabilities (CMCs). Three units of artefacts 100-ohm IPRT belonging to NML-SIRIM, NMIA and KRISS were used and three loops of measurement were run in parallel to shorten the circulation time. The stability of artefacts was monitored with initial and final ice point measurement by each laboratory. The participants need to perform measurement at temperature points (0,-50,-30, 0, 100, 200, 300, 400,0) °C. All submitted data were compiled and adjusted at nominal temperature and by using the linkage from NMIA and KRISS as reference value for all three loops , the temperature deviation from participants from different loops can be compared. The approach of Birge Ratio for final exclusion comprised all the excluded results from the analysis of each loop and the measurement performance for each participant were summarized by the En number value.

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 CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NIST, July 2015
Authors: Viallon Joële , Moussay Philippe , Wielgosz Robert , Hodges Joe , Norris James E
Published: February 2017

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the National Institute of Standards and Technology (NIST) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range of 0 nmol/mol to 500 nmol/mol.

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).
Convexity of the 𝐾-energy on the space of Kähler metrics and uniqueness of extremal metrics
Authors: Berman Robert , Berndtsson Bo
Published: February 2017

We establish the convexity of Mabuchi’s

K
K

-energy functional along weak geodesics in the space of Kähler potentials on a compact Kähler manifold, thus confirming a conjecture of Chen, and give some applications in Kähler geometry, including a proof of the uniqueness of constant scalar curvature metrics (or more generally extremal metrics) modulo automorphisms. The key ingredient is a new local positivity property of weak solutions to the homogeneous Monge-Ampère equation on a product domain, whose proof uses plurisubharmonic variation of Bergman kernels.
Energy stability and error estimates of exponential time differencing schemes for the epitaxial growth model without slope selection
Authors: Ju Lili , Li Xiao , Qiao Zhonghua , Zhang Hui
Published: February 2017

In this paper, we propose a class of exponential time differencing (ETD) schemes for solving the epitaxial growth model without slope selection. A linear convex splitting is first applied to the energy functional of the model, and then Fourier collocation and ETD-based multistep approximations are used respectively for spatial discretization and time integration of the corresponding gradient flow equation. Energy stabilities and error estimates of the first and second order ETD schemes are rigorously established in the fully discrete sense. We also numerically demonstrate the accuracy of the proposed schemes and simulate the coarsening dynamics with small diffusion coefficients. The results show the logarithm law for the energy decay and the power laws for growth of the surface roughness and the mound width, which are consistent with the existing theories in the literature.
Minimal surfaces in finite volume noncompact hyperbolic 3-manifolds
Authors: Collin Pascal , Hauswirth Laurent , Mazet Laurent , Rosenberg Harold
Published: February 2017

We prove there exists a compact embedded minimal surface in a complete finite volume hyperbolic

3
3

-manifold

N

\mathcal {N}

. We also obtain a least area, incompressible, properly embedded, finite topology,

2
2

-sided surface. We prove a properly embedded minimal surface of bounded curvature has finite topology. This determines its asymptotic behavior. Some rigidity theorems are obtained.
Topology of two-row Springer fibers for the even orthogonal and symplectic group
Authors: Wilbert Arik
Published: February 2017

We define an explicit topological model for every two-row Springer fiber associated with the even orthogonal group and prove that the respective topological model is homeomorphic to its corresponding Springer fiber. This confirms a conjecture by Ehrig and Stroppel concerning the topology of the equal-row Springer fiber for the even orthogonal group. Moreover, we show that every two-row Springer fiber for the symplectic group is homeomorphic (even isomorphic as an algebraic variety) to a connected component of a certain two-row Springer fiber for the even orthogonal group.
Frobenius reciprocity and the Haagerup tensor product
Authors: Crisp Tyrone
Published: February 2017

In the context of operator-space modules over

C
∗

C^*

-algebras, we give a complete characterisation of those

C
∗

C^*

-correspondences whose associated Haagerup tensor product functors admit left adjoints. The characterisation, which builds on previous joint work with N. Higson, exhibits a close connection between the notions of adjoint operators and adjoint functors. As an application, we prove a Frobenius reciprocity theorem for representations of locally compact groups on operator spaces: the functor of unitary induction for a closed subgroup

H
H

of a locally compact group

G
G

admits a left adjoint in this setting if and only if

H
H

is cocompact in

G
G

. The adjoint functor is given by the Haagerup tensor product with the operator-theoretic adjoint of Rieffel’s induction bimodule.
Diagnostic Testing Approaches for Activated Protein C Resistance and Factor V Leiden
Authors: Perez Botero Juliana , Majerus Julie A. , Strege Ann K. , Johnson Ryan D. , Chen Dong , Pruthi Rajiv K.
Published: February 2017

Objectives

To analyze the economic impact of testing for activated protein C resistance (APC-R) due to factor V Leiden (FVL) mutation with APC-R with reflexive FVL genotyping (algorithmic approach) or genotyping alone.

Methods

OptumLabs Data Warehouse (OLDW) data were used to assess testing approaches. Insurance claims for APC-R and FVL in 2013 were compared with the Mayo Clinic database. Centers for Medicare & Medicaid Services diagnostic fee schedules were used to assign costs.

Results

Of 19.3 million OLDW-covered individuals, 74,242 (0.385%) received 75,608 tests: APC-R, 2,265 (2.9%); FVL genotyping, 70,619 (90.1%); and both APC-R and FVL, 2,724 (7.0%). In total, 1,317 tests were performed at Mayo Clinic: APC-R with reflex FVL (1,256; 95.4%) and FVL alone (61; 4.6%). Costs per evaluated individual and per total population (person/year) in OLDW and algorithmic approach were $83.77 vs $36.38 and $0.32 vs $0.14, respectively.

Conclusions

The cost-optimized algorithmic approach reduces health care costs.
Resequencing Study Identifies Rare Renin–Angiotensin–Aldosterone System Variants Associated With Blood Pressure Salt-Sensitivity: The GenSalt Study
Authors: Kelly Tanika N. , Li Changwei , Hixson James E. , Gu Dongfeng , Rao Dabeeru C. , Huang Jianfeng , Rice Treva K. , Chen Jichun , Cao Jie , Li Jianxin , Anderson Christopher E. , He Jiang
Published: February 2017

BACKGROUND

The role of rare variants in blood pressure (BP) salt-sensitivity is unknown. We conducted a resequencing study of the renin–angiotensin–aldosterone system (RAAS) to identify rare variants associated with BP salt-sensitivity among participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study.

METHODS

The GenSalt study was conducted among 1,906 participants who underwent a 7-day low-sodium (51.3 mmol sodium/day) followed by a 7-day high-sodium feeding study (307.8 mmol sodium/day). The 300 most salt-sensitive and 300 most salt-resistant GenSalt participants were selected for the resequencing study. Seven RAAS genes were resequenced using capillary-based sequencing methods. Rare variants were tested for association with BP salt-sensitivity using traditional burden tests. Single-marker analyses were employed to test associations of low-frequency and common variants.

RESULTS

Aggregate rare variant analysis revealed an association of the RAAS pathway with BP salt-sensitivity. Carriers of rare RAAS variants had a 1.55-fold [95% confidence interval (CI): 1.15, 2.10] higher odds of salt-sensitivity compared to noncarriers (P = 0.004), a finding which was significant after Bonferroni correction. A nominal association of the APLN gene with salt-sensitivity was also identified, with rare APLN variants conferring a 2.22-fold (95% CI: 1.05, 6.58) higher odds of salt-sensitivity (P = 0.03). Single-marker analyses did not identify variant-BP salt-sensitivity associations after Bonferroni adjustment. A nominal association of a low-frequency, missense RENBP variant was identified. Each minor allele of rs78377269 conferred a 2.21-fold (95% CI: 1.10, 4.42) increased odds of salt-sensitivity (P = 0.03).

CONCLUSIONS

This study presents of the first evidence of a contribution of rare RAAS variants to BP salt-sensitivity.

Clinical Trial RegistryTrial Number: NCT00721721
Changes associated with Ebola virus adaptation to novel species
Authors: Pappalardo Morena , Reddin Ian G , Cantoni Diego , Rossman Jeremy S , Michaelis Martin , Wass Mark N
Published: February 2017

Motivation

Ebola viruses are not pathogenic but can be adapted to replicate and cause disease in rodents. Here, we used a structural bioinformatics approach to analyze the mutations associated with Ebola virus adaptation to rodents to elucidate the determinants of host-specific Ebola virus pathogenicity.

Results

We identified 33 different mutations associated with Ebola virus adaptation to rodents in the proteins GP, NP, L, VP24 and VP35. Only VP24, GP and NP were consistently found mutated in rodent-adapted Ebola virus strains. Fewer than five mutations in these genes seem to be required for the adaptation of Ebola viruses to a new species. The role of mutations in GP and NP is not clear. However, three VP24 mutations located in the protein interface with karyopherin α5 may enable VP24 to inhibit karyopherins and subsequently the host interferon response. Three further VP24 mutations change hydrogen bonding or cause conformational changes. Hence, there is evidence that few mutations including crucial mutations in VP24 enable Ebola virus adaptation to new hosts. Since Reston virus, the only non-human pathogenic Ebolavirus species circulates in pigs in Asia, this raises concerns that few mutations may result in novel human pathogenic Ebolaviruses.

Supplementary information

Supplementary data are available at Bioinformatics online.
nala: text mining natural language mutation mentions
Authors: Cejuela Juan Miguel , Bojchevski Aleksandar , Uhlig Carsten , Bekmukhametov Rustem , Kumar Karn Sanjeev , Mahmuti Shpend , Baghudana Ashish , Dubey Ankit , Satagopam Venkata P , Rost Burkhard
Published: February 2017

Motivation

The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. ‘E6V’), leaving relevant mentions natural language (NL) largely untapped (e.g. ‘glutamic acid was substituted by valine at residue 6’).

Results

We introduced three new corpora suggesting named-entity recognition (NER) to be more challenging than anticipated: 28–77% of all articles contained mentions only available in NL. Our new method nala captured NL and ST by combining conditional random fields with word embedding features learned unsupervised from the entire PubMed. In our hands, nala substantially outperformed the state-of-the-art. For instance, we compared all unique mentions in new discoveries correctly detected by any of three methods (SETH, tmVar, or nala). Neither SETH nor tmVar discovered anything missed by nala, while nala uniquely tagged 33% mentions. For NL mentions the corresponding value shot up to 100% nala-only.

Availability and Implementation

Source code, API and corpora freely available at: http://tagtog.net/-corpora/IDP4+.

Supplementary information

Supplementary data are available at Bioinformatics online.
MapReduce for accurate error correction of next-generation sequencing data
Authors: Zhao Liang , Chen Qingfeng , Li Wencui , Jiang Peng , Wong Limsoon , Li Jinyan
Published: February 2017

Motivation

Next-generation sequencing platforms have produced huge amounts of sequence data. This is revolutionizing every aspect of genetic and genomic research. However, these sequence datasets contain quite a number of machine-induced errors—e.g. errors due to substitution can be as high as 2.5%. Existing error-correction methods are still far from perfect. In fact, more errors are sometimes introduced than correct corrections, especially by the prevalent k-mer based methods. The existing methods have also made limited exploitation of on-demand cloud computing.

Results

We introduce an error-correction method named MEC, which uses a two-layered MapReduce technique to achieve high correction performance. In the first layer, all the input sequences are mapped to groups to identify candidate erroneous bases in parallel. In the second layer, the erroneous bases at the same position are linked together from all the groups for making statistically reliable corrections. Experiments on real and simulated datasets show that our method outperforms existing methods remarkably. Its per-position error rate is consistently the lowest, and the correction gain is always the highest.

Availability and Implementation

The source code is available at bioinformatics.gxu.edu.cn/ngs/mec.

Supplementary information

Supplementary data are available at Bioinformatics online.
An approach to infer putative disease-specific mechanisms using neighboring gene networks
Authors: Ansari Sahar , Donato Michele , Saberian Nafiseh , Draghici Sorin
Published: February 2017

Motivation

The ultimate goal of any experiment is to understand the biological phenomena underlying the condition investigated. This process often results in genes network through which a certain biological mechanism is explained. Such networks have been proven to be extremely useful, for the prediction of mechanisms of action of drugs or the responses of an organism to a specific impact (e.g. a disease, a treatment, etc.). Here, we introduce an approach able to build a network that captures the putative mechanisms at play in the given condition, by using datasets from multiple experiments studying the same phenotype. This method takes advantage of known interactions extracted from multiple sources such as protein–protein interactions and curated biological pathways. Based on such prior knowledge, we overcome the drawbacks of snap-shot data by considering the possible effects of each gene on its neighbors.

Results

We show the effectiveness of this approach in three different case studies and validate the results in two ways considering the identified genes and interactions between them. We compare our findings with the results of two widely-used methods in the same category as well as the classical approach of selecting differentially expressed (DE) genes in an investigated condition. The results show that ‘neighbor-net’ analysis is able to report biological mechanisms that are significantly relevant to the given diseases in all the three case studies, and performs better compared to all reference methods using both validation approaches.

Availability and Implementation

The proposed method is implemented as in R and will be available an a Bioconductor package.

Supplementary information

Supplementary data are available at Bioinformatics online.
Efficient inference for genetic association studies with multiple outcomes
Authors: Ruffieux Helene , Davison Anthony C. , Hager Jorg , Irincheeva Irina
Published: February 2017

Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single clinical outcome on many genetic variants one by one, but there is an increasing demand for joint analysis of many molecular outcomes and genetic variants in order to unravel functional interactions. Unfortunately, most existing approaches to joint modeling are either too simplistic to be powerful or are impracticable for computational reasons. Inspired by Richardson and others (2010, Bayesian Statistics 9), we consider a sparse multivariate regression model that allows simultaneous selection of predictors and associated responses. As Markov chain Monte Carlo (MCMC) inference on such models can be prohibitively slow when the number of genetic variants exceeds a few thousand, we propose a variational inference approach which produces posterior information very close to that of MCMC inference, at a much reduced computational cost. Extensive numerical experiments show that our approach outperforms popular variable selection methods and tailored Bayesian procedures, dealing within hours with problems involving hundreds of thousands of genetic variants and tens to hundreds of clinical or molecular outcomes.
‘Après la guerre’: John Redmond, the Irish Volunteers and Armed Constitutionalism, 1913–1915
Authors: McConnel James
Published: February 2017

The received narrative of the Ulster crisis relegates John Redmond to the role of bystander as parliamentary politics were sidelined by paramilitarism. Only the First World War, in this account, arrested the advance of armed force in Irish politics. This article seeks to disrupt this narrative by demonstrating that Redmondites were not untouched by the militarist turn which Ireland experienced in these years. Instead, home rulers developed an armed strategy of their own in response to the advent of militant extra-parliamentary politics. Having taken over the Irish Volunteers in spring 1914, Redmondites began to arm their supporters in defence of self-government. Separatists were scornful of these efforts, and it is true that Redmondites initially saw this activity primarily in political terms. But the outbreak of war persuaded Redmond that the eventual return of loyalist soldiers to Ireland at the end of the conflict could be decisive if the Ulster crisis resumed. Believing that nationalists needed to plan for this contingency, Ireland’s prime minister-in-waiting resolved to use the war to build a home rule army. Initially, pro-war nationalists hoped that this could be achieved through the Volunteers becoming a government-sponsored home guard, but War Office opposition forced Redmond to the conclusion that only British military service could ensure a sufficient force to secure the future of self-government. Though this strategy of armed constitutionalism had unravelled by Easter 1916, that it was attempted suggests that late Redmondism should not be conceived of only in terms of Redmond’s public rhetoric of orange and green reconciliation through common battlefield sacrifice.
Charles II, Lucy Walter, and the Stuart Courts in Exile
Authors: Greenspan Nicole
Published: February 2017

This article examines the challenges to maintaining royal authority during periods of exile by focusing on the relationship between Charles II and Lucy Walter, who became the king’s mistress and the mother of his firstborn child James, the future Duke of Monmouth. As a king in exile, Charles was without recourse to the machinery and institutions of government. While Charles and his agents often found it difficult to secure the obedience of his subjects and of other members of the royal family, Lucy Walter proved to be particularly troublesome in this regard. Lucy’s actions highlight at once the resourcefulness, relative freedom, and precarious position of exiles. As an unwed mother and former mistress, she lacked financial stability and spent the last decade of her short life in search of support from various quarters. The relationship between Charles II and Lucy Walter therefore sheds important light on central aspects of the experience of exile, the extent of royal authority, and the limitations and opportunities encountered by king and exiles alike.
Utilization and in-hospital complications of cardiac resynchronization therapy: trends in the United States from 2003 to 2013
Authors: Hosseini Seyed Mohammadreza , Moazzami Kasra , Rozen Guy , Vaid Jeena , Saleh Ahmed , Kevin Heist E. , Vangel Mark , Ruskin Jeremy N.
Published: February 2017

Aims

Cardiac resynchronization therapy (CRT) device implantation has been shown to reduce morbidity and mortality in selected patients with heart failure. We sought to investigate the utilization and in-hospital complications of cardiac resynchronization therapy defibrillator (CRT-D) and pacemaker (CRT-P) implantations in the United States from 2003 to 2013.

Methods and results

Patients receiving CRT-D or CRT-P were identified in the National Inpatient Sample database (NIS), using the International Classification of Diseases-Ninth Revision-Clinical Modification procedure codes. Annual implantation rates, patient demographics, co-morbidities, in-hospital complications, and length of stay were analysed. From 2003 to 2013, an estimated total of 439 010 (95% CI: 406 723–471 296) inpatient CRT implantations were performed in the U.S. The median age of patients was 72 and 71% were male. Overall, 6.1% had at least one complication. During the study period, comorbidity index and overall complication rate increased (P = 0.002 and P = 0.01, respectively). Mortality and length of stay showed no significant trend. Predictors of complications included: age 65 and older, female sex (OR: 1.19; 95% CI: 1.12–1.27), Deyo–Charlson Comorbidity Index, and elective admission (OR: 0.61; 95% CI: 0.57–0.66).

Conclusion

From 2003 to 2013, the severity of comorbid conditions increased and a rising trend was observed in the rate of periprocedural complications among patients undergoing CRT in the United States. In-hospital mortality and length of stay showed no uniform trend.
Location and source characteristics of the 2016 January 6 North Korean nuclear test constrained by InSAR
Authors: Wei Meng
Published: February 2017

The interferometric synthetic aperture radar (InSAR) data from the Japan Aerospace Exploration Agency ALOS-2 satellite show possible deformation associated with the 2016 January 6 North Korean nuclear test whereas the European Space Agency Sentinel-1A data are decorrelated. This is the first time that deformation related to a nuclear test has been measured since 1992. Here, I present two interpretations of the observed deformation: First, the deformation can be explained by a triggered landslide on the western slope of Mt Mantap, with a displacement of up to 10 cm across a patch of 1 km2. Second, the observation may be from uplift created by the nuclear explosion. In the second interpretation, the location, depth and cavity size can be estimated from a topography-corrected homogenous half-space model (Mogi). The preferred location of the 2016 January 6 event is 41.2993°N 129.0715°E, with an uncertainty of 100 m. The estimated depth is 420–700 m and the cavity radius is 23–27 m. Based on empirical data and the assumption of granite as the host rock, the yield is estimated to be 11.6–24.4 kilotons of TNT, which is consistent with previous results based on seismic data. With these two interpretations, I demonstrate that InSAR data provide an independent tool to locate and estimate source characteristics of nuclear tests in North Korea. The ambiguity of interpretation is mainly due to the limited InSAR data acquisition. Future frequent data collection by current and upcoming InSAR satellites will allow full use of InSAR for nuclear monitoring and characterization in North Korea and around the world.
Realizing the promise of The Partnership for Maternal, Newborn and Child Health
Authors: Fassil Hareya , Borrazzo John , Greene Richard , Jacobs Troy , Norton Maureen , Stanton Mary Ellen , Kuo Nana Taona , Rogers K , Pearson Luwei , Chaiban Ted , Banerjee Anshu , Kuruvilla Shyama , Seaone Marta , Starrs Ann , McCallon Betsy , Germann Stefan , Mohan Anshu , Bustreo Flavia , Fogstad Helga , Mishra C K
Published: February 2017

Reflecting on Storeng and Béhague (“Lives in the balance”: the politics of integration in the Partnership for Maternal, Newborn and Child Health. Health Policy and Planning Storeng and Béhague (2016).) historical ethnography of the Partnership for Maternal, Newborn and Child Health (PMNCH), this commentary provides a more current account of PMNCH’s trajectory since its inception in 2005. It highlights PMNCH’s distinct characteristics and how it is positioned to play an instrumental role in the current global health landscape.
Reassessment of the life cycle of the pteropod Limacina helicina from a high resolution interannual time series in the temperate North Pacific
Authors: Wang Kang , Hunt Brian P. V. , Liang Cui , Pauly Daniel , Pakhomov Evgeny A.
Published: February 2017

Limacina helicina is the dominant pelagic gastropod mollusc species in temperate and polar ecosystems, where it contributes significantly to food webs and vertical flux. Currently, considerable uncertainty exists in the interpretation of L. helicina’s life cycle, hindering our understanding of its potential responses to environmental change. Here, we present size-frequency data on L. helicina collected from three consecutive years (2008–2010) in a North Pacific temperate fjord. Two methods of length-frequency analysis were used to infer the growth of L. helicina, i.e. linking successive means extracted from finite-mixture distributions, and using the ELEFAN software to fit seasonally oscillating versions of the von Bertalanffy growth equation to the available length-frequency data. Against a background of continuous low level spawning between spring and autumn, both approaches identified two sets of major cohorts, i.e. (i) spring cohorts (G1) spawned in March/April by (ii) overwintering cohorts (G). G overwintered with minimal to low growth, before undergoing rapid growth the following spring and completing the cycle by spawning the G1 generation and disappearing from the population by May/June. Our findings are discussed in the context of L. helicina response to climate change.