bluuebunny/crossref_metadata_2025 huggingface dataset:
Trauma during Pregnancy: A Population‐based Analysis of Maternal Outcome
Authors: Cheng Han‐Tsung , Wang Yu‐Chun , Lo Hung‐Chieh , Su Li‐Ting , Lin Chiu‐Hsiu , Sung Fung‐Chang , Hsieh Chi‐Hsun
Published: September 2012

Background

Serious injury during pregnancy is known to cause adverse maternal outcomes. However, the significance of minor injuries in adverse maternal outcomes requires clarification because most injuries sustained during pregnancy are minor ones.

Methods

Two population‐based databases (inpatient and ambulatory care) were used to identify pregnant women who had severe (required hospitalization) or minor injuries (required ambulatory care only) prenatally. ICD‐9‐CM coding was used to categorize the types of prenatal injury and complications during delivery. The patient demographics, types and timing of the injuries, and their association with adverse maternal outcomes were compared among the uninjured, those with minor injury, and those with severe injury. Odds ratios were calculated to estimate the risks of having adverse outcomes in injured pregnant women compared with those who are uninjured.

Results

The severely injured women tended to be younger (<20 years old), lived in less urbanized regions, and had lower income levels than those who were uninjured or had minor injury. Motor vehicle crash was the most common mechanism of injury. While minor injuries were associated with preterm labor [odds ratio (OR) = 1.25], a severe injury was strongly associated with increased risks of preterm labor, placental abruption, uterine rupture, and maternal death, especially during the third trimester (OR = 2.71, 6.12, 7.79, and 20.15, respectively). Injuries away from the trunk could also lead to adverse maternal outcomes.

Conclusions

Trauma during pregnancy, whether minor or severe, is associated with unfavorable maternal outcomes. Injuries considered minor for the general population are not minor for pregnant women. Therefore, these patients should be monitored carefully.
Improving Surgical Care in Mongolia: A Model for Sustainable Development
Authors: Price Raymond , Sergelen Orgoi , Unursaikhan Chadraabal
Published: September 2012

The W. C. Swanson Family Foundation selected Mongolia to help improve access to affordable quality surgical and medical care in 2000. Over the last 12 years of partnering with the Health Sciences University of Mongolia, three major concepts have been identified that have promoted sustainable progress in expanding and improving surgical care throughout the healthcare system—including urban and rural areas. Understanding and targeting the needs identified by the Mongolian surgical community has cultivated a critical working environment that has had a profound effect on expanding surgical care in Mongolia. Integrating modern surgical care training with basic emergency and essential surgical and medical initiatives created a trusting foundation providing many unforeseen educational opportunities. Lastly, the educational model introduced, including long‐term capacity‐building programs, has helped enable the local Mongolian surgeons, nurses, biotechnicians, administrators, and educators to continue pioneering independent efforts to further expand modern surgical care in Mongolia.
Oleic Acid Attenuates trans‐10,cis‐12 Conjugated Linoleic Acid‐Mediated Inflammatory Gene Expression in Human Adipocytes
Authors: Reardon Meaghan , Gobern Semone , Martinez Kristina , Shen Wan , Reid Tanya , McIntosh Michael
Published: September 2012

The weight loss supplement conjugated linoleic acid (CLA) consists of an equal mixture of trans‐10,cis‐12 (10,12) and cis‐9,trans‐11 (9,11) isomers. However, high levels of mixed CLA isomers, or the 10,12 isomer, causes chronic inflammation, lipodystrophy, or insulin resistance. We previously demonstrated that 10,12 CLA decreases de novo lipid synthesis along with the abundance and activity of stearoyl‐CoA desaturase (SCD)‐1, a δ‐9 desaturase essential for the synthesis of monounsaturated fatty acids (MUFA). Thus, we hypothesized that the 10,12 CLA‐mediated decrease in SCD‐1, with the subsequent decrease in MUFA, was responsible for the observed effects. To test this hypothesis, 10,12 CLA‐treated human adipocytes were supplemented with oleic acid for 12 h to 7 days, and inflammatory gene expression, insulin‐stimulated glucose uptake, and lipid content were measured. Oleic acid reduced inflammatory gene expression in a dose‐dependent manner, and restored the lipid content of 10,12 CLA‐treated adipocytes without improving insulin‐stimulated glucose uptake. In contrast, supplementation with stearic acid, a substrate for SCD‐1, or 9,11 CLA did not prevent inflammatory gene expression by 10,12 CLA. Notably, 10,12 CLA impacted the expression of several G‐protein coupled receptors that was attenuated by oleic acid. Collectively, these data show that oleic acid attenuates 10,12 CLA‐induced inflammatory gene expression and lipid content, possibly by alleviating cell stress caused by the inhibition of MUFA needed for phospholipid and neutral lipid synthesis.
Cenancestor, the Last Universal Common Ancestor
Authors: Delaye Luis , Becerra Arturo
Published: September 2012

Darwin suggested that all life on Earth could be phylogenetically related. Modern biology has confirmed Darwin’s extraordinary insight; the existence of a universal genetic code is just one of many evidences of our common ancestry. Based on the three domain phylogeny proposed by Woese and Fox in the early 1970s that all living beings can be classified on one of three main cellular lineages (Archaea, Bacteria, and Eukarya), it is possible to reconstruct some of the characteristics of the Last Universal Common Ancestor or cenancestor. Comparative genomics of organisms from the three domains has shown that the cenancestor was not a direct descendant of the prebiotic soup nor a primitive cellular entity where the genotype and the phenotype had an imprecise relationship (i.e., a progenote), rather it was an organism similar in complexity to extant cells. Due to the process of horizontal gene transfer and secondary gene losses, several questions regarding the nature of the cenancestor remain unsolved. However, attempts to infer its nature have led to the identification of a set of universally conserved genes. The research on the nature of the last universal common ancestor promises to shed light on fundamental aspects of living beings.
Transitional cell carcinoma of the bladder with parotid metastasis: a case report
Authors: Kitchen M , Pugh A , Wharton Ip , Bhatt Ri
Published: September 2012

Transitional cell carcinoma (TCC) of the bladder is the most common urothelial malignancy. Sites of metastatic spread are usually predictable; typically the pelvic and para-aortic lymphatics, followed by extra-vesical tissues, i.e. liver, lung, bone and adrenal glands. There is currently little literature describing metastatic spread to the head and neck region, and none to the authors’ knowledge, of spread to the parotid salivary glands. This report describes a rare case of parotid metastasis of bladder TCC in a 75-year-old Caucasian woman.
Evaluation of a novel training package among frontline maternal, newborn, and child health workers in South Sudan
Authors: Nelson Brett D. , Ahn Roy , Fehling Maya , Eckardt Melody J. , Conn Kathryn L. , El‐Bashir Alaa , Tiernan Margaret , Purcell Genevieve , Burke Thomas F.
Published: September 2012

Objective

To develop, implement, and evaluate an evidence‐based Maternal, Newborn, and Child Survival (MNCS) package for frontline health workers (FHWs) in South Sudan.

Methods

A multimodal needs assessment was conducted to develop a best‐evidence package comprised of targeted training, pictorial checklists, and reusable equipment and commodities. Implementation utilized a training‐of‐trainers model. Program effectiveness was assessed through knowledge assessments, objective structured clinical examinations (OSCEs), focus groups, and questionnaires.

Results

A total of 72 trainers and 708 FHWs were trained in 7 South Sudan states. Trainer knowledge assessments improved significantly: from 62.7% to 92.0% (P < 0.001). Mean FHW scores on maternal OSCEs were 21.1% pre‐training, 83.4% post‐training, and 61.5% 2–3 months after training (P < 0.001). Corresponding mean newborn OSCE scores were 41.6%, 89.8%, and 45.7% (P < 0.001). Questionnaires revealed high levels of use, satisfaction, and confidence. FHWs reported an average of 3.0 referrals (range, 0–20) to healthcare facilities during the 2–3 months following training, and 78.3% of FHWs were more likely to refer patients. Seven focus groups showed high satisfaction with trainings, commodities, and checklists, with few barriers.

Conclusion

The MNCS package has led to improved FHW knowledge, skills, and referral. A novel package of training, checklists, and equipment can be successfully implemented in resource‐limited settings and enhance links between community‐based providers and healthcare facilities.
Physicochemical prerequisites for the formation of primary orebody zoning at copper-nickel sulfide deposits (by the example of the systemsFe–Ni–SandCu–Fe–S)
Authors: Kosyakov V.I. , Sinyakova E.F.
Published: September 2012

The zoning of massive orebodies at Cu–Ni sulfide deposits such as Noril’sk and Sudbury is commonly explained by fractional crystallization of magmatic sulfide melt. On the theoretical description of fractionation of its components, the results of mineralogical studies of orebodies are usually interpreted using the Rayleigh equation or its modification. But this equation is not applicable to describe crystallization of multicomponent melt and cocrystallization of several phases. In this work we present strict equations describing the distribution of components in a directly crystallized sample. We analyzed the influence of phase reactions on the successive formation of phases during crystallization and on the formation of primary zoning in the sample. This approach permits one to compute the component distribution curves and the crystallization paths by the quantitative phase diagram model. An experimental study of fractionation in the systems Fe–Ni–S and Cu–Fe–S was carried out. They can be regarded as systems modeling the formation of Ni- or Cu-rich sulfide ores. Such studies also yield qualitative and quantitative information about the phase diagrams of geochemical systems. We demonstrated that directed crystallization can be applied to determine the equations of phase reactions and the dependence of partition coefficients on the melt composition and to construct the paths of crystallization and evolution of the tie-line position during one-phase and cotectic crystallization. By the example of the system Fe–Ni–S, all possible types of sample zoning after fractional crystallization are shown. The main regularities of fractionation have been formulated, which are also applicable to multicomponent systems, e.g., Cu–Fe–Ni–S, which is widely used on the modeling of formation of zonal Cu–Ni sulfide ores.
Geodynamic nature of the Baikal Rift Zone and its sedimentary filling in the Cretaceous–Cenozoic: the effect of the far-range impact of the Mongolo-Okhotsk and Indo-Eurasian collisions
Authors: Buslov M.M.
Published: September 2012

The problem of the Late Meso-Cenozoic tectonics and geodynamics of the southern framing of the Siberian Platform is discussed. This area abounds in Late Meso-Cenozoic structures composed of sedimentary deposits. Analysis of voluminous geologo-stratigraphic, geophysical, and geochronological (track dating) data showed that these structures, including the Baikal Rift Zone, resulted from the far-range impact of two collisions related to the prolonged convergence of the North China and Indian continents with Eurasia, which took place in the Late Jurassic–Paleocene and Cenozoic, respectively. The synchronous occurrence of two great tectonic events led to the formation of a complex structure and a sedimentary basin, which are of different geodynamic nature and cannot be united into the same sequence of Late Cretaceous–Cenozoic formation of the Baikal Rift Zone. The Baikal system of shears and conjugate rifts formed in the Pliocene–Quaternary as a result of the far-range impact of the Indo-Eurasian collision. The latter led to the accumulation of the upper layered undeformed seismostratigraphic complex in all three Baikal basins. The sediments in Central Baikal are up to 3 km thick, and in the Selenga River valley they reach 5–6 km in thickness. The active intracontinental rift structures are characterized by zonal sedimentation. The middle layered deformed seismostratigraphic complex 1–1.5 km thick is recognized in all three Baikal basins and is similar to the Upper Oligocene–Lower Pliocene sediments of lacustrine-littoral, deltaic, and lacustrine facies widespread throughout the Baikal and Altai–Sayan regions and in Mongolia, where they formed in the environments of large lake systems. As a result of the deformations caused by the Indo-Eurasian collision, the Upper Oligocene–Lower Pliocene sediments were involved in the Pliocene–Quaternary ramp and unilateral-ramp structures in intermontane basins of the Altai–Sayan region and in Mongolia. The lower seismically transparent seismostratigraphic complex occurs only in South Baikal and Central Baikal. It is 1 km thick in the east and up to 45 km thick in the west. The complex is a fragment of the Late Cretaceous–Paleogene lacustrine-river sediments of the large fore-Baikal piedmont basin, which formed at the final stage of evolution of the vast Mongolo-Okhotsk orogen.
The Sphinx Crest in the Ribchester Hoard
Authors: Breeze David J , Edwards† B J N
Published: September 2012

A review of the account of the discovery of the Ribchester hoard in 1796 leads to the conclusion that the figure forming a crest was a sphinx but that it was unlikely to have been attached to the helmet in the hoard. The hoard is therefore likely to have been composed of material for reuse.
Priority, Preference and Value
Authors: O'NEILL MARTIN
Published: September 2012

This article seeks to defend prioritarianism against a pair of challenges from Michael Otsuka and Alex Voorhoeve. Otsuka and Voorhoeve first argue that prioritarianism makes implausible recommendations in one-person cases under conditions of risk, as it fails to allow that it is reasonable to act to maximize expected utility, rather than expected weighted benefits, in such cases. I show that, in response, prioritarians can either reject Otsuka and Voorhoeve's claim, by means of appealing to a distinction between personal and impersonal value, or alternatively they can harmlessly accommodate it, by means of appealing to the status of prioritarianism as a view about the moral value of outcomes, rather than as an account of all-things-considered reasonable action. Otsuka and Voorhoeve secondly claim that prioritarianism fails to explain a divergence in our considered moral judgement between one-person and many-person cases. I show that the prioritarian has two alternative, and independently plausible, lines of response to this charge, one more concessive and the other more unyielding. Hence, neither of Otsuka and Voorhoeve's challenges need seriously trouble the prioritarian.
FLEXIBILITY OF WAGES AND MACROECONOMIC INSTABILITY IN AN AGENT-BASED COMPUTATIONAL MODEL WITH ENDOGENOUS MONEY
Authors: Seppecher Pascal
Published: September 2012

We present a model of a dynamic and complex economy in which the creation and the destruction of money result from interactions between multiple and heterogeneous agents. In the baseline scenario, we observe the stabilization of the income distribution between wages and profits. We then alter the model by increasing the flexibility of wages. This change leads to the formation of a deflationary spiral. Aggregate activity decreases and unemployment increases. The macroeconomic stability of the model is affected and eventually a systemic crisis arises. Finally, we show that the introduction of a minimum wage would have made it possible to boost the aggregate demand and to avoid this crisis.
Charge transfer excited state energies by perturbative delta self consistent field method
Authors: Baruah Tunna , Olguin Marco , Zope Rajendra R.
Published: September 2012

We use our recently outlined perturbative approach to compute the lowest charge transfer excitation energies for a set of tetracynoehylene (TCNE)-hydrocarbon complexes, C2H4-C2F4, NH3-F2, pentacene-C60, and tetraphenyl porphyrin-C60 complexes. Results show that the method can provide a reliable description of charge transfer excitation energies, which are comparable to that obtained by time-dependent density functional theory using specially optimized range-corrected functionals. As the calculation cost of excited state is comparable to the ground state and the calculation of each excited state is independent of others, the method can be easily used to describe the charge transfer excited states of large donor-acceptor complexes containing 200 or more atoms.
Charge transfer excitations in cofacial fullerene-porphyrin complexes
Authors: Zope Rajendra R. , Olguin Marco , Baruah Tunna
Published: September 2012

Porphyrin and fullerene donor-acceptor complexes have been extensively studied for their photo-induced charge transfer characteristics. We present the electronic structure of ground states and a few charge transfer excited states of four cofacial porphyrin-fullerene molecular constructs studied using density functional theory at the all-electron level using large polarized basis sets. The donors are base and Zn-tetraphenyl porphyrins and the acceptor molecules are C60 and C70. The complexes reported here are non-bonded with a face-to-face distance between the porphyrin and the fullerene of 2.7 to 3.0 Å. The energies of the low lying excited states including charge transfer states calculated using our recent excited state method are in good agreement with available experimental values. We find that replacing C60 by C70 in a given dyad may increase the lowest charge transfer excitation energy by about 0.27 eV. Variation of donor in these complexes has marginal effect on the lowest charge transfer excitation energy. The interfacial dipole moments and lowest charge transfer states are studied as a function of face-to-face distance.
Separated shear layer transition over an airfoil at a low Reynolds number
Authors: Boutilier Michael S. H. , Yarusevych Serhiy
Published: September 2012

Shear layer development over a NACA 0018 airfoil at a chord Reynolds number of 100 000 was investigated using a combination of flow visualization, velocity field mapping, surface pressure fluctuation measurements, and stability analysis. The results provide a detailed description of shear layer transition on an airfoil at low Reynolds numbers. An extensive comparison of measured surface pressure and velocity fluctuations demonstrated that time-resolved surface pressure sensor arrays can be used to identify the presence of flow separation, estimate the extent of the separated flow region, and measure disturbance growth rate spectra in significantly less time than is required by conventional techniques. Surface pressure sensor measurements of disturbance growth rate, wave number, and convection speed are found to compare well with predictions of linear stability theory, supporting the claim that convection speeds measured in separation bubbles over low Reynolds number airfoils are associated with wave packets of growing disturbances propagating through the shear layer. Through a comparison of measured convection speeds in this investigation and prior low Reynolds number airfoil experiments, it is shown that disturbance convection speeds of between 30% and 50% of the edge velocity are typical for this type of flow, consistent with phase speed estimates from previous analytical studies on transitional separation bubbles. Modal RMS velocity profiles were measured and found to be reasonably predicted by stability theory. The results suggest that, even for the relatively thick NACA 0018 airfoil profile, disturbance development over the majority of the laminar separated shear layer is primarily governed by a linear inviscid mechanism.
Multibody local approximation: Application to conformational entropy calculations on biomolecules
Authors: Suárez Ernesto , Suárez Dimas
Published: September 2012

Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.
Resonance Raman and vibronic absorption spectra with Duschinsky rotation from a time-dependent perspective: Application to β-carotene
Authors: Banerjee Shiladitya , Kröner Dominik , Saalfrank Peter
Published: September 2012

The time-dependent approach to electronic spectroscopy, as popularized by Heller and co-workers in the 1980s, is applied here in conjunction with linear-response, time-dependent density functional theory to study vibronic absorption and resonance Raman spectra of β-carotene, with and without a solvent. Two-state models, the harmonic and the Condon approximations are used in order to do so. A new code has been developed which includes excited state displacements, vibrational frequency shifts, and Duschinsky rotation, i.e., mode mixing, for both non-adiabatic spectroscopies. It is shown that Duschinsky rotation has a pronounced effect on the resonance Raman spectra of β-carotene. In particular, it can explain a recently found anomalous behaviour of the so-called ν1 peak in resonance Raman spectra [N. Tschirner, M. Schenderlein, K. Brose, E. Schlodder, M. A. Mroginski, C. Thomsen, and P. Hildebrandt, Phys. Chem. Chem. Phys. 11, 11471 (2009)]10.1039/b917341b, which shifts with the change in excitation wavelength.
Understanding of nonlinear optical properties of CS2 from a microscopic viewpoint
Authors: Li Weiqi , Tian Wei Quan , Sun Xiudong
Published: September 2012

This study is to improve understanding of nonlinear optics through investigating the microstructures of carbon disulfide (CS2) liquid, an important nonlinear optical material. First principles methods are employed in this work to investigate the structure, vibrational spectra, and the 2nd hyperpolarizabilites of CS2 clusters up to tetramers. Three types of molecular arrangements of clusters with different sizes are identified. The cluster conformations are prone to inter-converting under external disturbance due to the weak interactions among molecules. The correlation between the nonlinear optical properties and the conformation of CS2 clusters are studied in detail in this work.
Electronic band structure and optical phonons of BaSnO3 and Ba0.97La0.03SnO3 single crystals: Theory and experiment
Authors: Stanislavchuk T. N. , Sirenko A. A. , Litvinchuk A. P. , Luo X. , Cheong S.-W.
Published: September 2012

Optical properties of insulating BaSnO3 (BSO) and conducting Ba0.97La0.03SnO3 (BLSO) single crystals were studied at room temperature in a wide spectral range between 0.01 and 5.9 eV by means of spectroscopic ellipsometry. The far-infrared spectra of the optical phonons in BSO and BLSO were complemented by polarized Raman scattering measurements in BSO. The electronic band structure and the optical response (dielectric function) were calculated using density functional theory, which allowed for the interpretation of the main spectroscopic features such as optical phonons and electronic interband transitions. To reconcile the observed experimental spectra with the theory, a departure from the ideal perovskite structure on the local scale was proposed for BSO.
A study of beam position diagnostics using beam-excited dipole modes in third harmonic superconducting accelerating cavities at a free-electron laser
Authors: Zhang Pei , Baboi Nicoleta , Jones Roger M. , Shinton Ian R. R. , Flisgen Thomas , Glock Hans-Walter
Published: September 2012

We investigate the feasibility of beam position diagnostics using higher order mode (HOM) signals excited by an electron beam in the third harmonic 3.9 GHz superconducting accelerating cavities at FLASH. After careful theoretical and experimental assessment of the HOM spectrum, three modal choices have been narrowed down to fulfill different diagnostics requirements. These are localized dipole beam-pipe modes, trapped cavity modes from the fifth dipole band, and propagating modes from the first two dipole bands. These modes are treated with various data analysis techniques: modal identification, direct linear regression (DLR), and singular value decomposition (SVD). Promising options for beam diagnostics are found from all three modal choices. This constitutes the first prediction, subsequently confirmed by experiments, of trapped HOMs in third harmonic cavities, and also the first direct comparison of DLR and SVD in the analysis of HOM-based beam diagnostics.
Target normal sheath acceleration sheath fields for arbitrary electron energy distribution
Authors: Schmitz Holger
Published: September 2012

Relativistic electrons, generated by ultraintense laser pulses, travel through the target and form a space charge sheath at the rear surface which can be used to accelerate ions to high energies. If the laser pulse duration is comparable or shorter than the time needed for the electrons to travel through the target, the electrons will not have the chance to form an equilibrium distribution but must be described by a non-equilibrium distribution. We present a kinetic theory of the rear sheath for arbitrary electron distribution function f(E), where E is the electron energy, and evaluate it for different shapes of f(E). We find that the far field is mainly determined by the high energy tail of the distribution, a steep decay of f(E) for high energies results in a small electric field and vice versa. The model is extended to account for electrons escaping the sheath region thereby allowing a finite potential drop over the sheath. The consequences of the model for the acceleration of ions are discussed.
Collisionless kinetic regimes for quasi-stationary axisymmetric accretion disc plasmas
Authors: Cremaschini C. , Tessarotto M.
Published: September 2012

This paper is concerned with the kinetic treatment of quasi-stationary axisymmetric collisionless accretion disc plasmas. The conditions of validity of the kinetic description for non-relativistic magnetized and gravitationally bound plasmas of this type are discussed. A classification of the possible collisionless plasma regimes which can arise in these systems is proposed, which can apply to accretion discs around both stellar-mass compact objects and galactic-center black holes. Two different classifications are determined, which are referred to, respectively, as energy-based and magnetic field-based classifications. Different regimes are pointed out for each plasma species, depending both on the relative magnitudes of kinetic and potential energies and the magnitude of the magnetic field. It is shown that in all cases, there can be quasi-stationary Maxwellian-like solutions of the Vlasov equation. The perturbative approach outlined here permits unique analytical determination of the functional form for the distribution function consistent, in each kinetic regime, with the explicit inclusion of finite Larmor radius-diamagnetic and/or energy-correction effects.
Communication: Thermal rectification in liquids by manipulating the solid-liquid interface
Authors: Murad Sohail , Puri Ishwar K.
Published: September 2012

Thermal rectification, the origin of which lies in modifying the thermal resistance in a nonlinear manner, could significantly improve the thermal management of a wide range of nano-devices (both electronic and thermoelectric), thereby improving their efficiencies. Since rectification requires a material to be inhomogeneous, it has been typically associated with solids. However, the structure of solids is relatively difficult to manipulate, which makes the tuning of thermal rectification devices challenging. Since liquids are more amenable to tuning, this could open up new applications for thermal rectification. We use molecular dynamics simulations to demonstrate thermal rectification using liquid water. This is accomplished by creating an inhomogeneous water phase, either by changing the morphology of the surface in contact with the liquid or by imposing an arbitrary external force, which in practice could be through an electric or magnetic field. Our system consists of a bulk fluid that is confined in a reservoir that is bounded by two walls, one hot and the other cold. The interfacial (Kapitza) thermal resistance at the solid-fluid interface and the density gradient of the bulk fluid both influence the magnitude of the thermal rectification. However, we find that the role of the interfacial resistance is more prominent than the application of an external force on the bulk fluid.
Study on the mechanical behavior of tilt bicrystal graphene by molecular dynamics simulations: Bulk verse nanoribbons
Authors: Cao Ajing , Qu Jianmin
Published: September 2012

Recent experimental studies have shown that multi-grains are ubiquitously present in graphene grown with chemical vapor deposition method technique. The potential application of the unique two-dimensional material in future nanotechnology demands full understandings of their structure and properties. Using molecular dynamics simulations, we study the mechanical response of various bicrystal graphene consisting of symmetric tilt boundary subject to uniaxial tensile loading. Both bulk graphene and graphene nanoribbons (GNRs) are studied. We revealed that nano-crack initiated at grain boundaries (GBs) leads to brittle failure with no plasticity at room temperature. The mechanism that crack nucleated at the intersection of GB and free surface followed by fast advance of crack, preventing plasticity that involves dislocation slip or GB sliding that is seen in metals. Cleavage along GBs is observed to be dominant fracture behavior in the studied GNRs. Furthermore, the ultimate tensile strength decreases with increasing vacancy concentration, illustrating that the lowered strength of GB interface is primarily due to not well-bonded atoms, shedding light to the structure-properties relationship. Finally, local strain and atomic-level stress have been shown to be able to characterize the onset of crack nucleation and thereby good quantities for predicting the resulting ultimate tensile strength.
Note: A microfluidic chip setup for capillarity-assisted particle assembly
Authors: Klein M. J. K. , Kuemin C. , Tamulevicius T. , Manning M. , Wolf H.
Published: September 2012

We developed a microfluidic chip setup for capillarity-assisted particle assembly (CAPA). A capillary bridge is formed between the aperture of a silicon chip and the assembly template. The bridge is fed with particle suspension through a microfluidic channel on the chip top side. With this setup, we can control the particle assembly location and tune the suspension composition during particle assembly. In this note, we describe the chip setup, the CAPA process using the microfluidic chip, and results of complex particle assemblies, such as composite particle arrays and particle gradients, that could not be obtained using a conventional CAPA setup.
Electron profile stiffness and critical gradient studies
Authors: DeBoo J. C. , Petty C. C. , White A. E. , Burrell K. H. , Doyle E. J. , Hillesheim J. C. , Holland C. , McKee G. R. , Rhodes T. L. , Schmitz L. , Smith S. P. , Wang G. , Zeng L.
Published: September 2012

Electron profile stiffness was studied in DIII-D L-mode discharges by systematically varying the heat flux in a narrow region with electron cyclotron heating and measuring the local change produced in ∇Te. Electron stiffness was found to slowly increase with toroidal rotation velocity. A critical inverse temperature gradient scale length 1/LC ∼ 3 m−1 was identified at ρ=0.6 and found to be independent of rotation. Both the heat pulse diffusivity and the power balance diffusivity, the latter determined by integrating the measured dependence of the heat pulse diffusivity on –∇Te, were fit reasonably well by a model containing a critical inverse temperature gradient scale length and varying linearly with 1/LT above the threshold.
Romney, Obama surrogates spell out candidates’ energy policies
Authors: Kramer David
Published: September 2012

Presidential candidates differ sharply on government involvement in energy R&D and climate change. But both favor more nuclear power and fracking.
Ultrafast spectroscopy of quantum materials
Authors: Orenstein Joseph
Published: September 2012

Subpicosecond laser pulses can selectively excite modes of strongly correlated electron systems and controllably push materials from one ordered phase to another.
Prospective memory and ageing paradox with event-based tasks: A study of young, young-old, and old-old participants
Authors: Kvavilashvili Lia , Cockburn Janet , Kornbrot Diana E.
Published: September 2012

Research on ageing and prospective memory—remembering to do something in the future—has resulted in paradoxical findings, whereby older adults are often impaired in the laboratory but perform significantly better than younger adults in naturalistic settings. Nevertheless, there are very few studies that have examined prospective memory both in and outside the laboratory using the same sample of young and old participants. Moreover, most naturalistic studies have used time-based tasks, and it is unclear whether the prospective memory and ageing paradox extends to event-based tasks. In this study, 72 young (18–30 years), 79 young-old (61–70 years), and 72 old-old (71–80 years) participants completed several event-based tasks in and outside the laboratory. Results showed that the ageing paradox does exist for event-based tasks but manifests itself differently from that in time-based tasks. Thus, younger adults outperformed old-old participants in two laboratory event-based tasks, but there were no age effects for a naturalistic task completed at home (remembering to write the date and time in the upper left corner of a questionnaire). The young and old-old also did not differ in remembering to retrieve a wristwatch from a pocket at the end of the laboratory session. This indicates that the paradox may be due to differences in ongoing task demands in the lab and everyday life, rather than the location per se. The findings call for a concentrated effort towards a theory of cognitive ageing that identifies the variables that do, or do not, account for this paradox.
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
Authors: Plagnol Vincent , Curtis James , Epstein Michael , Mok Kin Y. , Stebbings Emma , Grigoriadou Sofia , Wood Nicholas W. , Hambleton Sophie , Burns Siobhan O. , Thrasher Adrian J. , Kumararatne Dinakantha , Doffinger Rainer , Nejentsev Sergey
Published: September 2012

Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.

Results: Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized reference set in order to maximize the power to detect CNVs. As a result, ExomeDepth is effective across a wider range of exome datasets than the previously existing tools, even for small (e.g. one to two exons) and heterozygous deletions. We used this new approach to analyse exome data from 24 patients with primary immunodeficiencies. Depending on data quality and the exact target region, we find between 170 and 250 exonic CNV calls per sample. Our analysis identified two novel causative deletions in the genes GATA2 and DOCK8.

Availability: The code used in this analysis has been implemented into an R package called ExomeDepth and is available at the Comprehensive R Archive Network (CRAN).

Contact: v.plagnol@ucl.ac.uk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Antisense transcription is coupled to nucleosome occupancy in sense promoters
Authors: Dai Zhiming , Dai Xianhua
Published: September 2012

Motivation: Genome-wide pervasive transcription is widespread in eukaryotes, revealing an extensive array of antisense transcription that involves hundreds of previously unknown non-coding RNAs. Individual cases have shown that antisense transcription influences sense transcription, however, genome-wide mechanisms of how antisense transcription regulates sense transcription remain to be elucidated.

Results: Here, we performed a systematic analysis of sense–antisense transcription and nucleosome occupancy in yeast. We found that antisense transcription is associated with nucleosome occupancy in sense promoters. Using RNA polymerase II inactivation data as a reasonable approximation to antisense transcription inactivation data, we further showed that antisense transcripts increase nucleosome occupancy in sense promoter regions they overlap, and reduce nucleosome occupancy in sense promoter regions around their transcription termination sites. These results reveal the previously unappreciated roles of antisense transcription in directing nucleosome occupancy in sense promoters. Our findings will have implications in understanding regulatory functions of antisense transcription.

Contact:  zhimdai@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Statistical challenges associated with detecting copy number variations with next-generation sequencing
Authors: Teo Shu Mei , Pawitan Yudi , Ku Chee Seng , Chia Kee Seng , Salim Agus
Published: September 2012

Motivation: Analysing next-generation sequencing (NGS) data for copy number variations (CNVs) detection is a relatively new and challenging field, with no accepted standard protocols or quality control measures so far. There are by now several algorithms developed for each of the four broad methods for CNV detection using NGS, namely the depth of coverage (DOC), read-pair, split-read and assembly-based methods. However, because of the complexity of the genome and the short read lengths from NGS technology, there are still many challenges associated with the analysis of NGS data for CNVs, no matter which method or algorithm is used.

Results: In this review, we describe and discuss areas of potential biases in CNV detection for each of the four methods. In particular, we focus on issues pertaining to (i) mappability, (ii) GC-content bias, (iii) quality control measures of reads and (iv) difficulty in identifying duplications. To gain insights to some of the issues discussed, we also download real data from the 1000 Genomes Project and analyse its DOC data. We show examples of how reads in repeated regions can affect CNV detection, demonstrate current GC-correction algorithms, investigate sensitivity of DOC algorithm before and after quality control of reads and discuss reasons for which duplications are harder to detect than deletions.

Contact: g0801862@nus.edu.sg or agus_salim@nuhs.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mechanical stretch via transforming growth factor‐β1 activates microRNA208a to regulate endoglin expression in cultured rat cardiac myoblasts
Authors: Shyu Kou‐Gi , Wang Bao‐Wei , Wu Gong‐Jhe , Lin Chiu‐Mei , Chang Hang
Published: September 2012

Aims

MicroRNAs (miRNAs) play a role in cardiac remodelling. MiR208a is essential for the expression of the genes involved in cardiac hypertrophy and fibrosis. The mechanism of regulation of miR208a involved in cardiac hypertrophy by mechanical stress is still unclear. We sought to investigate the mechanism of regulation of miR208a and the target gene of miR208a in cardiac cells by mechanical stretch.

Methods and results

Rat H9c2 cells (cardiac myoblasts) grown on a flexible membrane base were stretched via vacuum to 20% of maximum elongation at 60 cycles/min. Mechanical stretch significantly enhanced miR208a expression after 4 h of stretch. Exogenous addition of transforming growth factor‐β1 (TGF‐β1) increased miR208a expression, and pre‐treatment with TGF‐β1 antibody attenuated the miR208a expression induced by stretch. Mechanical stretch significantly increased endoglin and collagen I expression for 6–24 h. Exogenous addition of TGF‐β1 and overexpression of miR208a up‐regulated endoglin and collagen I expression, while antagomir208a and Smad3/4 inhibitor attenuated endoglin and collagen I expression induced by stretch. Mechanical stretch and TGF‐β1 increased Smad3/4–DNA binding activity and miR208a promoter activity, and TGF‐β1 antibody and Smad3/4 inhibitor decreased the Smad3/4–DNA binding activity and miR208a promoter activity induced by stretch.

Conclusion

Cyclic mechanical stretch enhances miR208a expression in cultured rat cardiac myoblasts. The stretch‐induced miR208a is mediated by TGF‐β1. Mir208a activates endoglin expression and may result in cardiac fibrosis.
Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa
Authors: Zhang Jian , Wang Zi-Ting , Yu Hui-Min , Ma Yuchao
Published: September 2012

A bacterial strain, designated D75T, was isolated from the rhizosphere soil of Catalpa speciosa. Phylogenetic analysis based on the complete 16S rRNA gene sequence revealed that strain D75T was a member of the genus

Paenibacillus

. High levels of 16S rRNA gene sequence similarity were found between strain D75T and

Paenibacillus glycanilyticus

DS-1T (99.2 %),

Paenibacillus xinjiangensis

B538T (97.5 %) and

Paenibacillus castaneae

Ch-32T (97.2 %). The chemotaxonomic properties of strain D75T were consistent with those of the genus

Paenibacillus

: the cell-wall peptidoglycan type was based on meso-diaminopimelic acid (A1γ), the predominant menaquinone was MK-7, and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. However, levels of DNA–DNA relatedness between strain D75T and

P. glycanilyticus

NBRC 16618T,

P. xinjiangensis

DSM 16970T and

P. castaneae

DSM 19417T were 35, 20 and 18 %, respectively. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic data and DNA–DNA relatedness values, strain D75T is considered to represent a novel species of the genus

Paenibacillus

, for which the name Paenibacillus
catalpae sp. nov. is proposed. The type strain is D75T ( = DSM 24714T = CGMCC 1.10784T).
Friedmanniella flava sp. nov., a soil actinomycete
Authors: Zhang Xuefang , Zhang Jianli , Zhang Yabo , Xin Yuhua , He Hongju
Published: September 2012

A novel actinomycete, strain W6T, was isolated from a soil sample of Yunnan Province, China. The bacterium was aerobic, non-motile, non-spore-forming and Gram-stain-positive. Genetic, phenotypic and chemical properties of the isolate were studied. 16S rRNA gene sequence data suggested that the novel isolate belonged to the genus

Friedmanniella

and shared 98.6 % sequence similarity with

Friedmanniella antarctica

DSM 11053T and

Friedmanniella okinawensis

DSM 21744T, the most closely related species. The cell-wall peptidoglycan contained ll-diaminopimelic acid, and mycolic acids were absent. The main menaquinone was MK-9(H4) and the predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The phospholipid profile contained phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content of strain W6T was 72 mol%. Strain W6T showed 30.0 % and 28.5 % DNA–DNA relatedness, respectively, to

F. antarctica

DSM 11053T and

F. okinawensis

DSM 21744T. The combined genotypic and phenotypic data showed that strain W6T should be assigned to the genus

Friedmanniella

as a representative of a novel species, for which the name Friedmanniella flava sp. nov. is proposed. The type strain is W6T ( = CGMCC 4.6856T = JCM 17701T).
Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees
Authors: Degefu Tulu , Wolde-meskel Endalkachew , Liu Binbin , Cleenwerck Ilse , Willems Anne , Frostegård Åsa
Published: September 2012

A total of 18 strains, representing members of the genus

Mesorhizobium

, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours

Mesorhizobium plurifarium

,

Mesorhizobium amorphae

,

Mesorhizobium septentrionale

and

Mesorhizobium huakuii

was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus

Mesorhizobium

. The DNA–DNA relatedness between the representative strains of genospecies I–III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39aT ( = LMG 26966T = HAMBI 3295T), AC99bT ( = LMG 26968T = HAMBI 3301T) and AC98cT ( = LMG 26967T = HAMBI 3306T) are proposed as type strains for the respective novel species.