bluuebunny/crossref_metadata_2025 huggingface dataset:
A technique for extending by ∼103 the dynamic range of compact proton spectrometers for diagnosing ICF implosions on the National Ignition Facility and OMEGA
Authors: Sio H. , Séguin F. H. , Frenje J. A. , Gatu Johnson M. , Zylstra A. B. , Rinderknecht H. G. , Rosenberg M. J. , Li C. K. , Petrasso R. D.
Published: August 2014

Wedge Range Filter (WRF) proton spectrometers are routinely used on OMEGA and the NIF for diagnosing ρR and ρR asymmetries in direct- and indirect-drive implosions of D3He-, D2-, and DT-gas-filled capsules. By measuring the optical opacity distribution in CR-39 due to proton tracks in high-yield applications, as opposed to counting individual tracks, WRF dynamic range can be extended by 102 for obtaining the spectral shape, and by 103 for mean energy (ρR) measurement, corresponding to proton fluences of 108 and 109 cm−2, respectively. Using this new technique, ρR asymmetries can be measured during both shock and compression burn (proton yield ∼108 and ∼1012, respectively) in 2-shock National Ignition Facility implosions with the standard WRF accuracy of ±∼10 mg/cm2.
Impact ionization in N-polar AlGaN/GaN high electron mobility transistors
Authors: Killat N. , Uren M. J. , Keller S. , Kolluri S. , Mishra U. K. , Kuball M.
Published: August 2014

The existence of impact ionization as one of the open questions for GaN device reliability was studied in N-polar AlGaN/GaN high electron mobility transistors. Electroluminescence (EL) imaging and spectroscopy from underneath the device gate contact revealed the presence of hot electrons in excess of the GaN bandgap energy even at moderate on-state bias conditions, enabling impact ionization with hole currents up to several hundreds of pA/mm. The detection of high energy luminescence from hot electrons demonstrates that EL analysis is a highly sensitive tool to study degradation mechanisms in GaN devices.
Use of ultrasonic array method for positioning multiple partial discharge sources in transformer oil
Authors: Xie Qing , Tao Junhan , Wang Yongqiang , Geng Jianghai , Cheng Shuyi , Lü Fangcheng
Published: August 2014

Fast and accurate positioning of partial discharge (PD) sources in transformer oil is very important for the safe, stable operation of power systems because it allows timely elimination of insulation faults. There is usually more than one PD source once an insulation fault occurs in the transformer oil. This study, which has both theoretical and practical significance, proposes a method of identifying multiple PD sources in the transformer oil. The method combines the two-sided correlation transformation algorithm in the broadband signal focusing and the modified Gerschgorin disk estimator. The method of classification of multiple signals is used to determine the directions of arrival of signals from multiple PD sources. The ultrasonic array positioning method is based on the multi-platform direction finding and the global optimization searching. Both the 4 × 4 square planar ultrasonic sensor array and the ultrasonic array detection platform are built to test the method of identifying and positioning multiple PD sources. The obtained results verify the validity and the engineering practicability of this method.
Optical fiber-based system for continuous measurement of in-bore projectile velocity
Authors: Wang Guohua , Sun Jinglin , Li Qiang
Published: August 2014

This paper reports the design of an optical fiber-based velocity measurement system and its application in measuring the in-bore projectile velocity. The measurement principle of the implemented system is based on Doppler effect and heterodyne detection technique. The analysis of the velocity measurement principle deduces the relationship between the projectile velocity and the instantaneous frequency (IF) of the optical fiber-based system output signal. To extract the IF of the fast-changing signal carrying the velocity information, an IF extraction algorithm based on the continuous wavelet transforms is detailed. Besides, the performance of the algorithm is analyzed by performing corresponding simulation. At last, an in-bore projectile velocity measurement experiment with a sniper rifle having a 720 m/s muzzle velocity is performed to verify the feasibility of the optical fiber-based velocity measurement system. Experiment results show that the measured muzzle velocity is 718.61 m/s, and the relative uncertainty of the measured muzzle velocity is approximately 0.021%.
The Wentzel-Kramers-Brillouin approximation of semiclassical eigenvalues of the Zakharov–Shabat problem
Authors: Kim Yeongjoh , Lee Long , Lyng Gregory
Published: August 2014

The WKB approximation of semiclassical eigenvalues of the non-self-adjoint Zakharov–Shabat problem is a standard element in the theory of the integrable focusing nonlinear Schrödinger equation; this approximation is based on a reformulation of the eigenvalue problem as the eigenvalue problem for a self-adjoint Schrödinger operator with a correction term that depends on the spectral parameter. The approximation results from neglecting the correction term. We perform a numerical experiment which gives new evidence to support the validity of this procedure in the context of the semiclassical limit problem for the focusing nonlinear Schrödinger equation. In particular, our results suggest that the rate of convergence of the approximate eigenvalues to the true ones is of the order of the square of the small parameter. This information is relevant to the task of rigorously incorporating this approximation into the asymptotic analysis of the singular limit for the focusing nonlinear Schrödinger equation.
Self-similar solution for oblique impact of a water column with sharp front on a wall and its zero inner angle steady limit
Authors: Sun S. L. , Wu G. X.
Published: August 2014

The hydrodynamic problem of a three-dimensional (3D) water column impacting on a solid wall is investigated. The focus is on cases of self-similar flow and its related implications in physics. It is demonstrated that limiting process of the self-similar flow can become the steady flow. The problem involves a free surface whose shape is unknown and on which the boundary conditions are nonlinear. It is solved through boundary element method (BEM) with quadrilateral elements within an iterative procedure. The application of the BEM to such a problem has some major challenges. During the process, mesh used in the BEM is regularly regenerated to follow the deformation of the free surface and the data in the old mesh are transferred to the new one. Coordinate rotation technique is used to resolve the difficulties caused by the multi-valued free surface, together with the technique for the thin liquid film over the wall surface. Results are provided for the free surface shapes and pressure distributions for perpendicular and oblique impact cases, including both self-similar flow and its limiting steady flow. Their physics about jet root, the peak pressure and its location, as well as the limiting process to the steady flow are discussed.
Magnetic field effects in singlet-polaron quenching in molecularly doped fluorescence organic light-emitting diodes
Authors: Xu Kai , Ma Dongge
Published: August 2014

The magnetic field effects of electroluminescence (MEL) in 4-[dicyanomethylene]-2-t-butyl-6-(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran(DCJTB) doped tri-(8-hydroxyquinoline)-aluminum (Alq3) based organic light-emitting diodes were investigated. A linear decrease in MEL with the increase of magnetic field was observed at high magnetic field (>20 mT) in this doping devices, which has been attributed to the singlet-polaron quenching effect. It was found that the singlet-polaron quenching is magnetic field dependent. Our results showed that singlet-polaron quenching commonly exists in fluorescence OLEDs and induces the linear decrease in MEL.
An approach to improving transporting velocity in the long-range ultrasonic transportation of micro-particles
Authors: Meng Jianxin , Mei Deqing , Yang Keji , Fan Zongwei
Published: August 2014

In existing ultrasonic transportation methods, the long-range transportation of micro-particles is always realized in step-by-step way. Due to the substantial decrease of the driving force in each step, the transportation is lower-speed and stair-stepping. To improve the transporting velocity, a non-stepping ultrasonic transportation approach is proposed. By quantitatively analyzing the acoustic potential well, an optimal region is defined as the position, where the largest driving force is provided under the condition that the driving force is simultaneously the major component of an acoustic radiation force. To keep the micro-particle trapped in the optimal region during the whole transportation process, an approach of optimizing the phase-shifting velocity and phase-shifting step is adopted. Due to the stable and large driving force, the displacement of the micro-particle is an approximately linear function of time, instead of a stair-stepping function of time as in the existing step-by-step methods. An experimental setup is also developed to validate this approach. Long-range ultrasonic transportations of zirconium beads with high transporting velocity were realized. The experimental results demonstrated that this approach is an effective way to improve transporting velocity in the long-range ultrasonic transportation of micro-particles.
Spectroscopic characterization and imaging of laser- and unipolar arc-induced plasmas
Authors: Aussems Damien U. B. , Nishijima Daisuke , Brandt Christian , Doerner Russell P. , Cardozo Niek J. Lopes
Published: August 2014

Tungsten plasmas induced by unipolar arcs were investigated using optical emission spectroscopy and imaging, and compared with laser-induced tungsten plasmas. The unipolar arcs were initiated in the linear-plasma simulator PISCES-A at UCSD under fusion relevant conditions. The electron temperature and density of the unipolar arc plasmas were in the range 0.5–0.7 eV and 0.7–2.0 × 1020 m−3, respectively, and increased with increasing negative bias voltage, but did not correlate with the surface temperature. In comparison, the electron temperature and density of the laser-induced plasmas were in the range 0.6–1.4 eV and 7 × 1019–1 × 1022 m−3, respectively.
Relating different quantum generalizations of the conditional Rényi entropy
Authors: Tomamichel Marco , Berta Mario , Hayashi Masahito
Published: August 2014

Recently a new quantum generalization of the Rényi divergence and the corresponding conditional Rényi entropies was proposed. Here, we report on a surprising relation between conditional Rényi entropies based on this new generalization and conditional Rényi entropies based on the quantum relative Rényi entropy that was used in previous literature. Our result generalizes the well-known duality relation H(A|B) + H(A|C) = 0 of the conditional von Neumann entropy for tripartite pure states to Rényi entropies of two different kinds. As a direct application, we prove a collection of inequalities that relate different conditional Rényi entropies and derive a new entropic uncertainty relation.
Laser beam induced nanoscale spot through nonlinear “thick” samples: A multi-layer thin lens self-focusing model
Authors: Wei Jingsong , Yan Hui
Published: August 2014

Self-focusing is a well-researched phenomenon. Nanoscale spots can be achieved through self-focusing, which is an alternative method for achieving high-density data storage, high-resolution light imaging, and maskless nanolithography. Several research groups have observed that self-focusing spots can be reduced to nanoscale levels via incident laser power manipulation. Self-focusing spots can be analyzed by solving the nonlinear Schrödinger equation and the finite difference time domain method. However, both procedures are complex and time-consuming. In the present work, a multi-layer thin-lens self-focusing model that considers diffraction effects and changes of refractive index along the radial and film thickness directions is proposed to analyze the self-focusing behavior and traveling process of light beams intuitively. The self-focusing behaviors of As2S3 are simulated, and results show that a nanoscale self-focusing spot with a radius of about 0.12 μm can be formed at the bottom of nonlinear sample when the incident laser power exceeds 4.25 mW. Our findings are basically consistent with experimental reports and provide a good method for analyzing and understanding the self-focusing process. An appropriate application schematic design is also provided.
The surface-plasmon-resonance and band bending effects on the photoluminescence enhancement of Ag-decorated ZnO nanorods
Authors: Su Li , Qin Ni , Xie Wei , Fu Jianhui , Bao Dinghua
Published: August 2014

Doping with noble metal nanoparticles (NPs) is an effective method to tune the photoluminescence (PL) properties of semiconductor materials. The mechanism is widely attributed to the localized surface-plasmon-resonance (SPR) effect of the metal NPs, while the contribution of potential barrier at the interface between metal and semiconductor is less discussed. Taking ZnO nanorods on fused silica substrates as a model system, we present a facile low-temperature fabrication method to derive Ag metal NPs coated ZnO nanorods. Great enhancement of the near-band-edge (NBE) ultraviolet emission of the ZnO nanorods was achieved by the surface decoration with Ag NPs, accompanied with a decrement of deep-level (DL) emission intensity. Since, the Ag NPs are active even at ambient conditions, spontaneous changes in PL properties have been observed with aging time. The influence of oxidation state of Ag on the contacting potential and subsequently on the PL properties of ZnO nanorods were studied by employing a subsequent thermal annealing process. The role of contacting behavior and the varied potential barrier are comprehensively discussed. It was demonstrated that both the SPR effect and band bending effect can enhance the NBE emission and suppress the DL emission. In the Ag-decorated ZnO nanorods, the SPR effect is the main reason for PL enhancement of the metallic silver, while the potential barrier enhancement is the main reason for the oxidized silver.
Effective post-acceleration of ion bunches in foils irradiated by ultra-intense laser pulses
Authors: Andreev A. A. , Nickles P. V. , Platonov K. Yu
Published: August 2014

Two-step laser acceleration of protons with two foils and two laser pulses is modelled and optimized. It is shown that a nearly mono-energetic distribution of proton bunches can be realized by a suitable parameter choice. Two-step acceleration schemes make it possible to obtain both higher efficiency and energy as compared to the acceleration with only one laser pulse of an energy equal to the sum of the energy of the two pulses. With the aid of our analytical model, the optimal distance between the two targets, the delay between the two laser pulses, and the parameters of the laser pulses are determined. Estimates and results of the modelling are proven with 2D PIC simulations of the acceleration of proton bunches moving through the second target.
Voltage and pressure scaling of streamer dynamics in a helium plasma jet with N2 co-flow
Authors: Leiweke Robert J. , Ganguly Biswa N. , Scofield James D.
Published: August 2014

Positive polarity applied voltage and gas pressure dependent scaling of cathode directed streamer propagation properties in helium gas flow guided capillary dielectric barrier discharge have been quantified from streamer velocity, streamer current, and streamer optical diameter measurements. All measurements of the non-stochastic streamer properties have been performed in a variable gas pressure glass cell with N2 co-flow and under self-consistent Poisson electric field dominated conditions to permit data comparison with 2-D streamer dynamics models in air/nitrogen. The streamer optical diameter was found to be nearly independent of both gas pressures, from 170 Torr up to 760 Torr, and also for applied voltages from 6 to 11 kV at 520 Torr. The streamer velocity was found to increase quadratically with increased applied voltage. These observed differences in the 2-D scaling properties of ionization wave sustained cathode directed streamer propagation in helium flow channel with N2 annular co-flow compared to the streamer propagation in air or nitrogen have been shown to be caused by the remnant ionization distribution due to large differences in the dissociative recombination rates of He2+ versus N4+ ions, for this 5 kHz repetition rate applied voltage pulse generated streamers.
Resistivity scaling and electron relaxation times in metallic nanowires
Authors: Moors Kristof , Sorée Bart , Tőkei Zsolt , Magnus Wim
Published: August 2014

We study the resistivity scaling in nanometer-sized metallic wires due to surface roughness and grain-boundaries, currently the main cause of electron scattering in nanoscaled interconnects. The resistivity has been obtained with the Boltzmann transport equation, adopting the relaxation time approximation of the distribution function and the effective mass approximation for the conducting electrons. The relaxation times are calculated exactly, using Fermi's golden rule, resulting in a correct relaxation time for every sub-band state contributing to the transport. In general, the relaxation time strongly depends on the sub-band state, something that remained unclear with the methods of previous work. The resistivity scaling is obtained for different roughness and grain-boundary properties, showing large differences in scaling behavior and relaxation times. Our model clearly indicates that the resistivity is dominated by grain-boundary scattering, easily surpassing the surface roughness contribution by a factor of 10.
Polymer surfaces graphitization by low-energy He+ ions irradiation
Authors: Geworski A. , Lazareva I. , Gieb K. , Koval Y. , Müller P.
Published: August 2014

The electrical and optical properties of surfaces of polyimide and AZ5214e graphitized by low-energy (1 keV) He+ irradiation at different polymer temperatures were investigated. The conductivity of the graphitized layers can be controlled with the irradiation temperature within a broad range and can reach values up to ∼1000 S/cm. We show that the electrical transport in low-conducting samples is governed by thermally activated hopping, while the samples with a high conductivity show a typical semimetallic behavior. The transition from thermally activated to semimetallic conductance governed by the irradiation temperature could also be observed in optical measurements. The semimetallic samples show an unusually high for graphitic materials carrier concentration, which results in a high extinction coefficient in the visible light range. By analyzing the temperature dependence of the conductance of the semimetallic samples, we conclude that the scattering of charge carriers is dominated by Coulomb interactions and can be described by a weak localization model. The transition from a three to two dimensional transport mechanism at low temperatures consistently explains the change in the temperature dependence of the conductance by cooling, observed in experiments.
Electronic phase diagram of epitaxial La1−xSrxFeO3 films
Authors: Xie Y. J. , Scafetta M. D. , Moon E. J. , Krick A. L. , Sichel-Tissot R. J. , May S. J.
Published: August 2014

The electronic phase diagram of epitaxial La1−xSrxFeO3 films is presented. The films were grown on SrTiO3 using molecular beam epitaxy with post-growth annealing to minimize oxygen vacancies. Insulating behavior is observed from x = 0–0.9, with metallic conduction only present for x = 1.0. While the La-rich compounds exhibit polaron conduction over all temperatures measured, the Sr-rich films exhibit an electronic phase transition within the compositional window of x = 0.49–0.9 as revealed by temperature-dependent resistivity measurements. The transition temperatures are found to decrease with increasing Sr content. The constructed phase diagram is discussed in the context of other 3d eg perovskite systems including manganites and cobaltites.
Optimal design of one-dimensional photonic crystal back reflectors for thin-film silicon solar cells
Authors: Chen Peizhuan , Hou Guofu , Zhang Jianjun , Zhang Xiaodan , Zhao Ying
Published: August 2014

For thin-film silicon solar cells (TFSC), a one-dimensional photonic crystal (1D PC) is a good back reflector (BR) because it increases the total internal reflection at the back surface. We used the plane-wave expansion method and the finite difference time domain (FDTD) algorithm to simulate and analyze the photonic bandgap (PBG), the reflection and the absorption properties of a 1D PC and to further explore the optimal 1D PC design for use in hydrogenated amorphous silicon (a-Si:H) solar cells. With identified refractive index contrast and period thickness, we found that the PBG and the reflection of a 1D PC are strongly influenced by the contrast in bilayer thickness. Additionally, light coupled to the top three periods of the 1D PC and was absorbed if one of the bilayers was absorptive. By decreasing the thickness contrast of the absorptive layer relative to the non-absorptive layer, an average reflectivity of 96.7% was achieved for a 1D PC alternatively stacked with a-Si:H and SiO2 in five periods. This reflectivity was superior to a distributed Bragg reflector (DBR) structure with 93.5% and an Ag film with 93.4%. n-i-p a-Si:H solar cells with an optimal 1D PC-based BR offer a higher short-circuit current density than those with a DBR-based BR or an AZO/Ag-based BR. These results provide new design rules for photonic structures in TFSC.
Characterization and reduction of microfabrication-induced decoherence in superconducting quantum circuits
Authors: Quintana C. M. , Megrant A. , Chen Z. , Dunsworth A. , Chiaro B. , Barends R. , Campbell B. , Chen Yu , Hoi I.-C. , Jeffrey E. , Kelly J. , Mutus J. Y. , O'Malley P. J. J. , Neill C. , Roushan P. , Sank D. , Vainsencher A. , Wenner J. , White T. C. , Cleland A. N. , Martinis John M.
Published: August 2014

Many superconducting qubits are highly sensitive to dielectric loss, making the fabrication of coherent quantum circuits challenging. To elucidate this issue, we characterize the interfaces and surfaces of superconducting coplanar waveguide resonators and study the associated microwave loss. We show that contamination induced by traditional qubit lift-off processing is particularly detrimental to quality factors without proper substrate cleaning, while roughness plays at most a small role. Aggressive surface treatment is shown to damage the crystalline substrate and degrade resonator quality. We also introduce methods to characterize and remove ultra-thin resist residue, providing a way to quantify and minimize remnant sources of loss on device surfaces.
Thermal effects and space-charge limited transition in crossed-field devices
Authors: Marini Samuel , Rizzato Felipe B. , Pakter Renato
Published: August 2014

A fully kinetic model for the electron flow in a crossed field device is derived and used to determine the system stationary states. It is found that for low injection temperatures, there is a simultaneous presence of distinct stationary solutions and an abrupt transition between accelerating and space-charge limited regimes. On the other hand, for high injection temperatures, there is only a single stationary solution branch and the change between the regimes becomes continuous. For intermediate temperatures, it is then identified a critical point that separates the abrupt and continuous behaviors. It is also investigated how intrinsic space-charge oscillations may drive stationary states unstable in certain parameter regimes. The results are verified with N-particle self-consistent simulations.
Metallic to hopping conduction transition in Ta2O5−x/TaOy resistive switching device
Authors: Zhang Ye , Deng Ning , Wu Huaqiang , Yu Zhiping , Zhang Jinyu , Qian He
Published: August 2014

In this Letter, a comprehensive analysis of how the metallic behavior transition to hopping was presented by studying the transport mechanisms of low resistance states (LRS) in Ta2O5−x/TaOy resistive switching devices at very low temperatures. Three types of conduction behaviors were reported through temperature-dependent measurements ranging from 5 K to 250 K. Memory cells at low LRS show metallic behavior due to the formation of metallic filament. The temperature dependence of resistance at medium LRS exhibits an interesting phenomenon that a positive temperature coefficient transfers into a negative one at temperature of 20 K. Detailed analysis reveals that this phenomenon is caused by the coexistence of extended and localized states, with metallic conduction at higher temperatures and variable-range hopping at lower temperatures. Carrier transport at high LRS is dominated by electrons hopping conduction with nearest-neighboring hopping conduction changing into variable-range hopping as temperature decreases.
A simple efficient synthesis and biological evaluation of 3-O-ethylascorbic acid
Authors: Tai Akihiro , Aburada Mei , Ito Hideyuki
Published: August 2014

A single-step synthesis of 3-O-ethyl-l-ascorbic acid was performed without the induction of protecting groups. Sodium l-ascorbate reacted with ethyl bromide in DMSO to give 3-O-ethylascorbic acid in a yield of 51.0%. 3-O-Ethylascorbic acid enhanced dibutyryl cyclic AMP-induced neurite outgrowth in PC12 cells.
Maximum Likelihood Estimation of the Standard Commodity Storage Model: Evidence from Sugar Prices
Authors: Cafiero Carlo , Bobenrieth H. Eugenio S.A. , Bobenrieth H. Juan R.A. , Wright Brian D.
Published: August 2014

We present a Maximum Likelihood estimator for the standard commodity storage model with stockouts, based on prices only. While it imposes no additional assumptions on the model, the Maximum Likelihood estimator has small sample properties superior to those of the Pseudo Maximum Likelihood approach. We provide a proof that is crucial for applying our estimator to the model with normal harvests and possibly unbounded prices, thereby eliminating an inconsistency in the empirical storage model literature. Applying our Maximum Likelihood estimator to a series of annual sugar prices from 1921 to 2009 provides new evidence for the empirical relevance of the standard storage model. Our results imply a cutoff price at which discretionary stocks go to zero, which is higher than the price obtained by applying the Pseudo Maximum Likelihood estimator to the same data. The implied frequency of stockouts is lower, and price correlations, skewness, and kurtosis implied by the model closely match those seen in the annual sugar price data. We find the price of sugar to be highly responsive to small changes in consumption. When inventories are not available to buffer the effects of negative supply shocks on consumption, prices must increase sharply to induce the consumption changes needed to clear the market. Our results show why production shocks are not necessarily aligned with price spikes; the same production shock can give rise to very different price responses, depending on whether or not there are sufficient stocks to buffer its impact.
NetComm: a network analysis tool based on communicability
Authors: Campbell Ian M. , James Regis A. , Chen Edward S. , Shaw Chad A.
Published: August 2014

Motivation: Set-based network similarity metrics are increasingly used to productively analyze genome-wide data. Conventional approaches, such as mean shortest path and clique-based metrics, have been useful but are not well suited to all applications. Computational scientists in other disciplines have developed communicability as a complementary metric. Network communicability considers all paths of all lengths between two network members. Given the success of previous network analyses of protein–protein interactions, we applied the concepts of network communicability to this problem. Here we show that our communicability implementation has advantages over traditional approaches. Overall, analyses suggest network communicability has considerable utility in analysis of large-scale biological networks.

Availability and implementation: We provide our method as an R package for use in both human protein–protein interaction network analyses and analyses of arbitrary networks along with a tutorial at http://www.shawlab.org/NetComm/.

Contact:  cashaw@bcm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cordova: Web-based management of genetic variation data
Authors: Ephraim Sean S. , Anand Nikhil , DeLuca Adam P. , Taylor Kyle R. , Kolbe Diana L. , Simpson Allen C. , Azaiez Hela , Sloan Christina M. , Shearer A. Eliot , Hallier Andrea R. , Casavant Thomas L. , Scheetz Todd E. , Smith Richard J. H. , Braun Terry A.
Published: August 2014

Summary: Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician–scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research.

Availability and implementation: Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova.

Contact:  sean.ephraim@gmail.com or terry-braun@uiowa.edu
Barrett Esophagus and Esophageal Cancer
Authors: Iyer Prasad G.
Published: August 2014

Barrett esophagus is an acquired condition characterized by the replacement of the squamous epithelium lining the esophagus by partially intestinalized columnar epithelium. It is thought to be a complication of gastroesophageal reflux and may reflect an adaptive response to reflux of gastric contents into the esophagus. It is the strongest known risk factor for esophageal adenocarcinoma. Barrett esophagus is characterized by proximal displacement of the squamocolumnar junction in the esophagus and has been classified into long-segment Barrett esophagus (visible columnar mucosa in the esophagus of 3 cm or more) and short-segment Barrett esophagus (visible columnar mucosa in the esophagus less than 3 cm in length). Etiology, risk factors, screening and surveillance for esophageal cancer are discussed. Cancer presentation, symptoms, diagnosis, and treatment of the disease are also addressed.
Colorectal Neoplasms
Authors: Kisiel John B.
Published: August 2014

Colorectal cancer is primarily a disease of urban, industrialized societies. In the United States, the lifetime risk for the development of this cancer is approximately 6%. Recent data have suggested that the incidence rates for colorectal cancer may be decreasing gradually in some subgroups of the population. However, the mechanisms underlying these favorable trends have not been defined completely. Several national organizations have endorsed screening and surveillance guidelines, which undoubtedly have contributed to more effective prevention of colorectal cancer.
Liver Disease and Pregnancy
Authors: Eileen Hay J.
Published: August 2014

For diagnostic purposes, it is useful to divide liver diseases in pregnant women into three main categories: 1. Liver diseases occurring coincidentally in a pregnant woman (viral hepatitis is the most common cause of jaundice in pregnant patients). 2. Pregnancy occurring in a woman with chronic liver disease. 3. Liver diseases unique to pregnancy, including hyperemesis gravidarum, intrahepatic cholestasis of pregnancy, preeclampsia, HELLP syndrome, and acute fatty liver of pregnancy. These liver diseases, unique to pregnancy, can be considered liver complications of pregnancy itself, and they have a characteristic timing in relation to the trimesters of pregnancy. Hepatitis E and herpes hepatitis, although not related etiologically to pregnancy, characteristically produce a fulminant and often deadly disease in the third trimester of pregnancy. Recent data suggest that most liver disease in pregnancy is pregnancy-related and incidental and chronic liver diseases are uncommon.
Chronic Pancreatitis
Authors: Chari Suresh T.
Published: August 2014

Chronic pancreatitis is an often painful inflammatory condition of the pancreas characterized by progressive fibrosis that leads to irreversible destruction of exocrine and endocrine tissue, resulting eventually in exocrine and endocrine insufficiency. There is considerable heterogeneity in the manifestation and natural history of the condition. Chronic pancreatitis is classified broadly into chronic calcifying pancreatitis, chronic obstructive pancreatitis, and chronic autoimmune pancreatitis.
Pancreatic Neoplasms
Authors: Pearson Randall K.
Published: August 2014

Almost uniformly, cancer of the pancreas is fatal and is increasingly a health problem. In the United States, the calculated incidence of pancreatic cancer in 2008 was 37,700, with 34,300 deaths due to the disease. The overall survival rate for persons with pancreatic cancer is less than 5%, the lowest 5-year survival rate of any cancer. This partly reflects the low resectability rate. Advanced age is the most common risk factor for pancreatic cancer, and as the population ages, the incidence of pancreatic cancer is predicted to increase. Only 10% to 15% of patients are candidates for curative resection (stage I and stage II disease), and more than 50% have unresectable stage IV disease with distant metastases.
Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1
Authors: Montemayor Eric J. , Katolik Adam , Clark Nathaniel E. , Taylor Alexander B. , Schuermann Jonathan P. , Combs D. Joshua , Johnsson Richard , Holloway Stephen P. , Stevens Scott W. , Damha Masad J. , Hart P. John
Published: August 2014

The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2′,5′-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA. Dbr1 is also involved in the propagation of retrotransposons and retroviruses, although the precise role played by the enzyme in these processes is poorly understood. Here, we report the first structures of Dbr1 alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. The structures, together with functional data on Dbr1 variants, reveal the molecular basis for 2′,5′-phosphodiester recognition and explain why the enzyme lacks activity toward 3′,5′-phosphodiester linkages. The findings illuminate structure/function relationships in a unique enzyme that is central to eukaryotic RNA metabolism and set the stage for the rational design of inhibitors that may represent novel therapeutic agents to treat retroviral infections and neurodegenerative disease.
Clinical Implications of Detectable Baseline Hepatitis C Virus-Genotype 1 NS3/4A-Protease Variants on the Efficacy of Boceprevir Combined With Peginterferon/Ribavirin
Authors: Howe John A. , Long Jianmin , Black Stuart , Chase Robert , McMonagle Patricia , Curry Stephanie , Thompson Seth , DiNubile Mark J. , Howe Anita Y. M.
Published: August 2014

Background.  We analyzed the impact of pretreatment variants conferring boceprevir-resistance on sustained virologic response (SVR) rates achieved with boceprevir plus peginterferon-α/ribavirin (P/R) for hepatitis C virus (HCV)-genotype-1 infection.

Methods.  NS3-protease-polymorphisms emerging coincident with virologic failure on boceprevir/P/R regimens were identified as resistance-associated variants (RAVs). Baseline samples pooled from 6 phase II or phase III clinical trials were analyzed for RAVs by population sequencing. Interferon (IFN)-responsiveness was predefined as >1 log reduction in HCV-RNA level during the initial 4-week lead-in treatment with P/R before boceprevir was added. The effective boceprevir-concentration inhibiting RAV growth by 50% (EC50) was determined using a replicon assay relative to the wild-type referent.

Results.  Sequencing was performed in 2241 of 2353 patients (95.2%) treated with boceprevir. At baseline, RAVs were detected in 178 patients (7.9%), including 153 of 1498 genotype-1a infections (10.2%) and 25 of 742 genotype-1b infections (3.4%) (relative risk, 3.03; 95% confidence interval [CI], [2.01, 4.58]). For IFN-responders, SVR24 (SVR assessed 24 weeks after discontinuation of all study medications) rates were 78% and 76% with or without RAVs detected at baseline, respectively. For the 510 poor IFN-responders, SVR24 rates were 8 of 36 subjects (22.2% [11.7%, 38.1%]) when baseline RAVs were detected vs 174 of 474 subjects (36.7% [32.5%, 41.1%]) when baseline RAVs were not detected (relative likelihood of SVR24 [95% CI], 0.61 [0.32, 1.05]). Sustained virologic response was achieved in 7 of 8 (87.5%) IFN-nonresponders with baseline variants exhibiting ≤2-fold increased EC50 for boceprevir in a replicon assay, whereas only 1 of 15 (7%) IFN-nonresponders with baseline RAVs associated with ≥3-fold increased EC50 achieved SVR.

Conclusions.  Baseline protease-variants appear to negatively impact SVR rates for boceprevir/P/R regimens only when associated with decreased boceprevir susceptibility in vitro after a poor IFN-response during the lead-in period.
The impact of radio-tags on Ruby-throated Hummingbirds (Archilochus colubris)
Authors: Zenzal Theodore J. , Diehl Robert H. , Moore Frank R.
Published: August 2014

Radio telemetry has advanced the field of wildlife biology, especially with the miniaturization of radio-tags. However, the major limitation faced with radio-tagging birds is the size of the animal to which a radio-tag can be attached. We tested how miniature radio-tags affected flight performance and behavior of Ruby-throated Hummingbirds (Archilochus colubris), possibly the smallest bird species to be fitted with radio-tags. Using eyelash adhesive, we fitted hatch year individuals (n=20 males and 15 females) with faux radio-tags of three sizes varying in mass and antenna length (220mg-12.7cm, 240mg-12.7cm, and 220mg-6.35cm), then filmed the birds in a field aviary to quantify activity budgets. We also estimated flight range using flight simulation models. When the three radio-tag packages were pooled for analysis, the presence of a radio-tag significantly decreased both flight time (-8%) and modeled flight range (-23%) when compared to control birds. However, a multiple comparison analysis between the different packages revealed that there was a significant difference in flight time when the larger radio-tag package (240mg) was attached and no significant difference in flight time when the lighter radio-tag packages (220mg) were attached. Our results are similar to other studies which analyzed the flight time or flight range of birds wearing radio-tags. Therefore, currently available light weight radio-tags (≤220mg) may be a new option to aid in the study of hummingbird biology. Future study should focus upon the additional drag created by the radio-tag and the effects of the lightest radio-tag packages on free ranging birds. These studies would provide additional information to determine the feasibility on the use of radio-tags to study hummingbird biology.
Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells
Authors: Luyten Annouck , Zang Chongzhi , Liu X. Shirley , Shivdasani Ramesh A.
Published: August 2014

Tissues may adopt diverse strategies to establish specific transcriptional programs in daughter lineages. In intestinal crypts, enhancers for genes expressed in both major cell types appear broadly permissive in stem and specified progenitor cells. In blood, another self-renewing tissue, it is unclear when chromatin becomes permissive for transcription of genes expressed in distinct terminal lineages. Using chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) to profile activating histone marks, we studied enhancer dynamics in primary mouse blood stem, progenitor, and specified cells. Stem and multipotent progenitor cells show scant H3K4me2 marking at enhancers bound by specific transcription factors in their committed progeny. Rather, enhancers are modulated dynamically and serially, with substantial loss and gain of H3K4me2, at each cellular transition. Quantitative analysis of these dynamics accurately modeled hematopoiesis according to Waddington’s notion of epigenotypes. Delineation of enhancers in terminal blood lineages coincides with cell specification, and enhancers active in single lineages show well-positioned H3K4me2- and H3K27ac-marked nucleosomes and DNaseI hypersensitivity in other cell types, revealing limited lineage fidelity. These findings demonstrate that enhancer chronology in blood cells differs markedly from that in intestinal crypts. Chromatin dynamics in hematopoiesis provide a useful foundation to consider classical observations such as cellular reprogramming and multilineage locus priming.
The FACT complex interacts with the E3 ubiquitin ligase Psh1 to prevent ectopic localization of CENP-A
Authors: Deyter Gary M.R. , Biggins Sue
Published: August 2014

Centromere identity and its epigenetic maintenance require the incorporation of a histone H3 variant called CENP-A at centromeres. CENP-A mislocalization to ectopic sites may disrupt chromatin-based processes and chromosome segregation, so it is important to uncover the mechanisms by which this variant is exclusively localized to centromeres. Here, we identify a role for the conserved chromatin-modifying complex FACT (facilitates chromatin transcription/transactions) in preventing budding yeast CENP-ACse4 mislocalization to euchromatin by mediating its proteolysis. The Spt16 subunit of the FACT complex binds to Psh1 (Pob3/Spt16/histone), an E3 ubiquitin ligase that targets CENP-ACse4 for degradation. The interaction between Psh1 and Spt16 is critical for both CENP-ACse4 ubiquitylation and its exclusion from euchromatin. We found that Psh1 cannot efficiently ubiquitylate CENP-ACse4 nucleosomes in vitro, suggesting that additional factors must facilitate CENP-ACse4 removal from chromatin in vivo. Consistent with this, a Psh1 mutant that cannot associate with FACT has a reduced interaction with CENP-ACse4 in vivo. Together, our data identify a previously unknown mechanism to maintain centromere identity and genomic stability through the FACT-mediated degradation of ectopically localized CENP-ACse4.
Small intestinal stem cell identity is maintained with functional Paneth cells in heterotopically grafted epithelium onto the colon
Authors: Fukuda Masayoshi , Mizutani Tomohiro , Mochizuki Wakana , Matsumoto Taichi , Nozaki Kengo , Sakamaki Yuriko , Ichinose Shizuko , Okada Yukinori , Tanaka Toshihiro , Watanabe Mamoru , Nakamura Tetsuya
Published: August 2014

To develop stem cell therapy for small intestinal (SI) diseases, it is essential to determine whether SI stem cells in culture retain their tissue regeneration capabilities. By using a heterotopic transplantation approach, we show that cultured murine SI epithelial organoids are able to reconstitute self-renewing epithelia in the colon. When stably integrated, the SI-derived grafts show many features unique only to the SI but distinct from the colonic epithelium. Our study provides evidence that cultured adult SI stem cells could be a source for cell therapy of intestinal diseases, maintaining their identity along the gastrointestinal tract through an epithelium-intrinsic mechanism.
How substrate specificity is imposed on a histone demethylase—lessons from KDM2A
Authors: Tsai Chi-Lin , Shi Yang , Tainer John A.
Published: August 2014

Histone lysine methylation and demethylation regulate histone methylation dynamics, which impacts chromatin structure and function. To read and erase the methylated histone residues, lysine demethylases must specifically recognize the histone sequences and methylated sites and discriminate the degree of these methylations. In this issue of Genes & Development, Cheng and colleagues (pp. 1758–1771) determine a crystal structure of histone lysine demethylase KDM2A that specifically targets lower degrees of H3K36 methylation. The results reveal the structural basis for H3K36 substrate specificity and suggest mechanisms of Lys36 demethylation. This KDM2A–H3K36 complex structure, coupled with functional studies, provides needed insight into the process and regulation of histone demethylation.
Crystal structure of {2-[({2-[(2-aminoethyl)amino]ethyl}imino)methyl]phenolato}aquacopper(II) bromide
Authors: Plyuta Nataliya I. , Rusanova Julia A. , Petrusenko Svitlana R. , Omelchenko Irina V.
Published: August 2014

In the mononuclear copper(II) title complex, [Cu(C11H16N3O)(H2O)]Br, the CuIIatom is coordinated by one O and three N atoms of the Schiff base ligand that forms together with one water molecule a slightly distorted [CuN3O2] square-pyramidal polyhedron. The deviation of the CuIIatom from the mean equatorial plane is 0.182 (2) Å. The equatorial plane is nearly coplanar to the aromatic ring of the ligand [angle between planes = 10.4 (1)°], and the water molecule is situated in the apical site. All coordinating atoms (except the imine nitrogen) and the bromide ion contribute to the formation of the N—H...Br, O—H...Br and O—H...O hydrogen bonds, which link molecules into chains along [01-1].
Crystal structure ofN-[3-(2-chlorobenzoyl)-5-ethylthiophen-2-yl]-2-[(E)-(2-hydroxybenzylidene)amino]acetamide
Authors: Kaur Manpreet , Jasinski Jerry P. , Kavitha Channappa N. , Yathirajan Hemmige S. , Byrappa K.
Published: August 2014

In the title compound, C22H19ClN2O3S, the dihedral angle between the mean planes of the thiophene ring and the chlorophenyl and hydroxyphenyl rings are 70.1 (1) and 40.2 (4)°, respectively. The benzene rings are twisted with respect to each other by 88.9 (3)°. The imine bond lies in anEconformation. Intramolecular O—H...N and N—H...O hydrogen bonds each generateS(6) ring motifs. In the crystal, weak C—H...O interactions link the molecules, forming chains along thecaxis and zigzag chains along thebaxis, generating sheets lying parallel to (100).
Crystal structure of 1-benzoyl-3-(4-fluorophenyl)thiourea
Authors: Jassas Rabab Sharaf , Asiri Abdullah M. , Arshad Muhammad Nadeem , Zayed Mohie E. M. , Mustafa Ghulam
Published: August 2014

The title compound, C14H11FN2OS, contains two molecules (AandB) in the asymmetric unit, with different conformations. In moleculeA, the dihedral angles between the central thiourea grouping and the phenyl and fluorobenzene rings are 28.77 (8) and 41.82 (8)°, respectively, and the dihedral angle between the ring planes is 70.02 (9)°. Equivalent data for moleculeBare 8.46 (8), 47.78 (8) and 52.99 (9)°, respectively. Both molecules feature an intramolecular N—H...O hydrogen bond, which closes anS(6) ring. In the crystal,A+Bdimers linked by pairs of N—H...S hydrogen bonds generateR22(8) loops.
Crystal structure of (2,4-di-tert-butyl-6-{[(6,6′-dimethyl-2′-oxido-1,1′-biphenyl-2-yl)imino]methyl}phenolato-κ3O,N,O′)bis(propan-2-olato-κO)titanium(IV)
Authors: Chen Liang , Wang Huiran , Deng Xuebin
Published: August 2014

In the mononuclear TiIVtitle complex, [Ti(C29H33NO2)(C3H6O)2], the TiNO4coordination polyhedron comprises an N-atom and two O-atom donors from the dianionic Schiff base ligand and two O-atom donors from monodentate isopropoxide anions. The stereochemistry is distorted trigonal–bipyramidal with the N-donor in an elongated axial site [Ti—N = 2.2540 (17) Å], the O-donors having normal Ti—O bond lengths [1.7937 (14) Å (axial)–1.8690 (14) Å]. In the crystal, C—H...π interactions link molecules into centrosymmetric dimers.