bluuebunny/crossref_metadata_2025 huggingface dataset:
High sensitivity and high Q-factor nanoslotted parallel quadrabeam photonic crystal cavity for real-time and label-free sensing
Authors: Yang Daquan , Kita Shota , Liang Feng , Wang Cheng , Tian Huiping , Ji Yuefeng , Lončar Marko , Quan Qimin
Published: August 2014

We experimentally demonstrate a label-free sensor based on nanoslotted parallel quadrabeam photonic crystal cavity (NPQC). The NPQC possesses both high sensitivity and high Q-factor. We achieved sensitivity (S) of 451 nm/refractive index unit and Q-factor >7000 in water at telecom wavelength range, featuring a sensor figure of merit >2000, an order of magnitude improvement over the previous photonic crystal sensors. In addition, we measured the streptavidin-biotin binding affinity and detected 10 ag/mL concentrated streptavidin in the phosphate buffered saline solution.
Theoretical predictions of properties and volatility of chlorides and oxychlorides of group-4 elements. II. Adsorption of tetrachlorides and oxydichlorides of Zr, Hf, and Rf on neutral and modified surfaces
Authors: Pershina V. , Borschevsky A. , Iliaš M. , Türler A.
Published: August 2014

With the aim to interpret results of gas-phase chromatography experiments on volatility of group-4 tetrachlorides and oxychlorides including those of Rf, adsorption enthalpies of these species on neutral, and modified quartz surfaces were estimated on the basis of relativistic, two-component Density Functional Theory calculations of MCl4, MOCl2, MCl6−, and MOCl42 with the use of adsorption models. Several mechanisms of adsorption were considered. In the case of physisorption of MCl4, the trend in the adsorption energy in the group should be Zr > Hf > Rf, so that the volatility should change in the opposite direction. The latter trend complies with the one in the sublimation enthalpies, ΔHsub, of the Zr and Hf tetrachlorides, i.e., Zr < Hf. On the basis of a correlation between these quantities, ΔHsub(RfCl4) was predicted as 104.2 kJ/mol. The energy of physisorption of MOCl2 on quartz should increase in the group, Zr < Hf < Rf, as defined by increasing dipole moments of these molecules along the series. In the case of adsorption of MCl4 on quartz by chemical forces, formation of the MOCl2 or MOCl42− complexes on the surface can take place, so that the sequence in the adsorption energy should be Zr > Hf > Rf, as defined by the complex formation energies. In the case of adsorption of MCl4 on a chlorinated quartz surface, formation of the MCl62− surface complexes can occur, so that the trend in the adsorption strength should be Zr ≤ Hf < Rf. All the predicted sequences, showing a smooth change of the adsorption energy in the group, are in disagreement with the reversed trend Zr ≈ Rf < Hf, observed in the “one-atom-at-a-time” gas-phase chromatography experiments. Thus, currently no theoretical explanation can be found for the experimental observations.
Density functional theory study of CO-induced segregation in gold-based alloys
Authors: Sansa Myriam , Dhouib Adnene , Guesmi Hazar
Published: August 2014

This paper reports a systematic study of the effect of CO gas on the chemical composition at the surface of gold-based alloys. Using DFT periodic calculations in presence of adsorbed CO the segregation behavior of group 9-10-11 transition metals (Ag, Cu, Pt, Pd, Ni, Ir, Rh, Co) substituted in semi-infinite gold surfaces is investigated. Although, CO is found to be more strongly adsorbed on (100) than on the (111) surface, the segregation of M impurities is found to be more pronounced on the (111) surface. The results reveal two competitive effects: the effect of M on CO and the effect of CO on M. Thus, on one hand, if M exists on the (100) gold facet, CO would be strongly adsorbed on it. But if M is initially located in the bulk, it would segregate to the (111) facet instead of the (100) in order to bind to CO.
Characterizing velocity fluctuations in partially resolved turbulence simulations
Authors: Reyes Dasia A. , Cooper Jacob M. , Girimaji Sharath S.
Published: August 2014

Many current turbulence model simulations follow the accuracy-on-demand paradigm to partially resolve the flow field for achieving optimal compromise between accuracy and computational effort. In many such approaches, the sub-grid viscosity is modeled using kinetic energy and dissipation of unresolved scales. It is of scientific value and practical utility to characterize the resolved velocity fluctuations of such flow fields to: (i) establish if the computed fields exhibit the self-similarity and scaling properties consistent with physical turbulence and (ii) demonstrate if the flow field tends to the limit of fully-resolved turbulence in a prescribed and controlled manner. Toward this end, we begin by characterizing partially-resolved flow computations as direct numerical simulations of non-Newtonian fluids. This paradigm permits the extension of the Kolmogorov and finite Reynolds number scaling to the computed fields. The statistical behavior of the intermediate and smallest computed scales is then postulated as a function of the degree of resolution. Then it is demonstrated that the flow field in partially-averaged Navier-Stokes simulations behaves in accordance with the adapted Kolmogorov hypotheses in isotropic turbulence computations. Further, the statistics of sub-Kolmogorov fluctuations are demonstrated to be self-similar over a range of resolutions.
Measurement of axial injection displacement with trim coil current unbalance
Authors: Covo Michel Kireeff
Published: August 2014

The Dee probe used for measuring internal radial beam intensity shows large losses inside the radius of 20 cm of the 88 in. cyclotron. The current of the top and bottom innermost trim coil 1 is unbalanced to study effects of the axial injection displacement. A beam profile monitor images the ion beam bunches, turn by turn. The experimental bunch center of mass position is compared with calculations of the magnetic mirror effect displacement and shows good agreement.
Analogues of Lusztig's higher order relations for the q-Onsager algebra
Authors: Baseilhac P. , Vu T. T.
Published: August 2014

Let A, A* be the generators of the q-Onsager algebra. Analogues of Lusztig's r−th higher order relations are proposed. In a first part, based on the properties of tridiagonal pairs of q-Racah type which satisfy the defining relations of the q-Onsager algebra, higher order relations are derived for r generic. The coefficients entering in the relations are determined from a two-variable polynomial generating function. In a second part, it is conjectured that A, A* satisfy the higher order relations previously obtained. The conjecture is proven for r = 2, 3. For r generic, using an inductive argument recursive formulae for the coefficients are derived. The conjecture is checked for several values of r ≥ 4. Consequences for coideal subalgebras and integrable systems with boundaries at q a root of unity are pointed out.
Charge transport across organic heterostructure: Role of interfacial density of states
Authors: Tripathi Durgesh C. , Mohapatra Y. N.
Published: August 2014

The mechanism of carrier transport across organic-organic hetero-interfaces is crucial for organic devices. For purposes of this study, we choose two hole transport materials 4, 4′, 4″-tris(N-3-methylphenyl-N-phenyl-amino) triphenyl-amine (m-MTDATA) and N, N′-diphenyl-N, N′-bis(1-naphthyl) (1, 1′-biphenyl)-4, 4′diamine. We demonstrate that transport across such interfaces can be controlled by introducing a thin undoped layer, which is chosen to be 10–30 nm of m-MTDATA layer in this particular case. By correlating the low frequency capacitance-voltage and temperature dependence of current density-voltage (J-V) characteristics, we show that the occupation of local density of states (LDOS) on both sides controls the transport at the hetero-interface and that it can be modified by the introduction of interlayer. The thickness of the undoped interlayer effectively acts as a control on carrier concentration at the interface leading to the modification of the effective energy offset, and overlap of the LDOS. The slope of the J-V characteristics in the exponential regime has a temperature dependent term and a purely voltage dependent term. The temperature dependence of J-V characteristics is explained by including field dependence of mobility and tunneling across LDOS. We trace the origin of the offset at the hetero-interface and estimate its values for the different cases consistent with the proposed model of thermally assisted tunneling at the interface.
Fast electromigration crack in nanoscale aluminum film
Authors: Emelyanov O. A. , Ivanov I. O.
Published: August 2014

The current-induced breakage of 20 nm thin aluminum layers deposited onto capacitor grade polypropylene (PP) films is experimentally studied. Biexponential current pulses of different amplitude (10–15 A) and duration (0.1–1 μs) were applied to the samples. Breakage occurred after fast development of electromigrating ∼200 nm-wide cracks with initial propagation velocity of ∼1 m/s under a high current density of ∼1012 A/m2. The cracks stopped when their lengths reached 250–450 μm. This behavior is explained by the balance of electromigration and stress-induced atomic fluxes.
Reduction in the interface-states density of metal-oxide-semiconductor field-effect transistors fabricated on high-index Si (114) surfaces by using an external magnetic field
Authors: Molina J. , De La Hidalga J. , Gutierrez E.
Published: August 2014

After fabrication of Metal-Oxide-Semiconductor Field-Effect Transistor (MOSFET) devices on high-index silicon (114) surfaces, their threshold voltage (Vth) and interface-states density (Dit) characteristics were measured under the influence of an externally applied magnetic field of B = 6 μT at room temperature. The electron flow of the MOSFET's channel presents high anisotropy on Si (114), and this effect is enhanced by using an external magnetic field B, applied parallel to the Si (114) surface but perpendicular to the electron flow direction. This special configuration results in the channel electrons experiencing a Lorentzian force which pushes the electrons closer to the Si (114)-SiO2 interface and therefore to the special morphology of the Si (114) surface. Interestingly, Dit evaluation of n-type MOSFETs fabricated on Si (114) surfaces shows that the Si (114)-SiO2 interface is of high quality so that Dit as low as ∼1010 cm−2·eV−1 are obtained for MOSFETs with channels aligned at specific orientations. Additionally, using both a small positive Vds ≤ 100 mV and B = 6 μT, the former Dit is reduced by 35% in MOSFETs whose channels are aligned parallel to row-like nanostructures formed atop Si (114) surfaces (channels having a 90° rotation), whereas Dit is increased by 25% in MOSFETs whose channels are aligned perpendicular to these nanostructures (channels having a 0° rotation). From these results, the special morphology of a high-index Si (114) plane having nanochannels on its surface opens the possibility to reduce the electron-trapping characteristics of MOSFET devices having deep-submicron features and operating at very high frequencies.
Experimental and numerical investigations of the phase-shift effect in capacitively coupled discharges
Authors: Gao Fei , Zhang Yu-Ru , Zhao Shu-Xia , Wang You-Nian
Published: August 2014

The phase-shift effect has been investigated by a Langmuir probe and a fluid model in Ar capacitively coupled plasmas at 50 mTorr. In the discharge, two sources with the same frequency, i.e., 27.12 MHz, are applied on the top and bottom electrodes simultaneously, and the phase shift between them varies from 0 to π. It is found that the electron density has an off-axis peak near the radial edge when the phase difference is equal to 0 due to the electrostatic edge effect, and the best radial uniformity is observed at a phase difference equal to π. Furthermore, when the voltage increases, the best radial uniformity is obtained at lower phase shift values. Moreover, the electron energy probability function has a bi-temperature structure at all the selected phase differences at r = 1–15 cm. The evolution of the plasma characteristics with the phase difference implies that the best radial uniformity can be obtained, by balancing the electrostatic edge effect and the phase shift effect.
Reduced model prediction of electron temperature profiles in microtearing-dominated National Spherical Torus eXperiment plasmas
Authors: Kaye S. M. , Guttenfelder W. , Bell R. E. , Gerhardt S. P. , LeBlanc B. P. , Maingi R.
Published: August 2014

A representative H-mode discharge from the National Spherical Torus eXperiment is studied in detail to utilize it as a basis for a time-evolving prediction of the electron temperature profile using an appropriate reduced transport model. The time evolution of characteristic plasma variables such as βe, νe∗, the MHD α parameter, and the gradient scale lengths of Te, Ti, and ne were examined as a prelude to performing linear gyrokinetic calculations to determine the fastest growing micro instability at various times and locations throughout the discharge. The inferences from the parameter evolutions and the linear stability calculations were consistent. Early in the discharge, when βe and νe∗ were relatively low, ballooning parity modes were dominant. As time progressed and both βe and νe∗ increased, microtearing became the dominant low-kθ mode, especially in the outer half of the plasma. There are instances in time and radius, however, where other modes, at higher-kθ, may, in addition to microtearing, be important for driving electron transport. Given these results, the Rebut-Lallia-Watkins (RLW) electron thermal diffusivity model, which is based on microtearing-induced transport, was used to predict the time-evolving electron temperature across most of the profile. The results indicate that RLW does a good job of predicting Te for times and locations where microtearing was determined to be important, but not as well when microtearing was predicted to be stable or subdominant.
Simulating x-ray Thomson scattering signals from high-density, millimetre-scale plasmas at the National Ignition Facility
Authors: Chapman D. A. , Kraus D. , Kritcher A. L. , Bachmann B. , Collins G. W. , Falcone R. W. , Gaffney J. A. , Gericke D. O. , Glenzer S. H. , Guymer T. M. , Hawreliak J. A. , Landen O. L. , Le Pape S. , Ma T. , Neumayer P. , Nilsen J. , Pak A. , Redmer R. , Swift D. C. , Vorberger J. , Döppner T.
Published: August 2014

We have developed a model for analysing x-ray Thomson scattering data from high-density, millimetre-scale inhomogeneous plasmas created during ultra-high pressure implosions at the National Ignition Facility in a spherically convergent geometry. The density weighting of the scattered signal and attenuation of the incident and scattered x-rays throughout the target are included using radial profiles of the density, opacity, ionization state, and temperature provided by radiation-hydrodynamics simulations. These simulations show that the scattered signal is strongly weighted toward the bulk of the shocked plasma and the Fermi degenerate material near the ablation front. We show that the scattered signal provides a good representation of the temperature of this highly nonuniform bulk plasma and can be determined to an accuracy of ca. 15% using typical data analysis techniques with simple 0D calculations. On the other hand, the mean ionization of the carbon in the bulk is underestimated. We suggest that this discrepancy is due to the convolution of scattering profiles from different regions of the target. Subsequently, we discuss modifications to the current platform to minimise the impact of inhomogeneities, as well as opacity, and also to enable probing of conditions more strongly weighted toward the compressed core.
Influence of finite geometrical asymmetry of the electrodes in capacitively coupled radio frequency plasma
Authors: Bora B. , Soto L.
Published: August 2014

Capacitively coupled radio frequency (CCRF) plasmas are widely studied in last decades due to the versatile applicability of energetic ions, chemically active species, radicals, and also energetic neutral species in many material processing fields including microelectronics, aerospace, and biology. A dc self-bias is known to generate naturally in geometrically asymmetric CCRF plasma because of the difference in electrode sizes known as geometrical asymmetry of the electrodes in order to compensate electron and ion flux to each electrode within one rf period. The plasma series resonance effect is also come into play due to the geometrical asymmetry and excited several harmonics of the fundamental in low pressure CCRF plasma. In this work, a 13.56 MHz CCRF plasma is studied on the based on the nonlinear global model of asymmetric CCRF discharge to understand the influences of finite geometrical asymmetry of the electrodes in terms of generation of dc self-bias and plasma heating. The nonlinear global model on asymmetric discharge has been modified by considering the sheath at the grounded electrode to taking account the finite geometrical asymmetry of the electrodes. The ion density inside both the sheaths has been taken into account by incorporating the steady-state fluid equations for ions considering that the applied rf frequency is higher than the typical ion plasma frequency. Details results on the influences of geometrical asymmetry on the generation of dc self-bias and plasma heating are discussed.
Resistance switching in epitaxial SrCoOx thin films
Authors: Tambunan Octolia T. , Parwanta Kadek J. , Acharya Susant K. , Lee Bo Wha , Jung Chang Uk , Kim Yeon Soo , Park Bae Ho , Jeong Huiseong , Park Ji-Yong , Cho Myung Rae , Park Yun Daniel , Choi Woo Seok , Kim Dong-Wook , Jin Hyunwoo , Lee Suyoun , Song Seul Ji , Kang Sung-Jin , Kim Miyoung , Hwang Cheol Seong
Published: August 2014

We observed bipolar switching behavior from an epitaxial strontium cobaltite film grown on a SrTiO3 (001) substrate. The crystal structure of strontium cobaltite has been known to undergo topotactic phase transformation between two distinct phases: insulating brownmillerite (SrCoO2.5) and conducting perovskite (SrCoO3−δ) depending on the oxygen content. The current–voltage characteristics of the strontium cobaltite film showed that it could have a reversible insulator-to-metal transition triggered by electrical bias voltage. We propose that the resistance switching in the SrCoOx thin film could be related to the topotactic phase transformation and the peculiar structure of SrCoO2.5.
Citrus diseases with global ramifications including citrus canker and huanglongbing.
Authors: Gottwald T. R. , Graham J. H.
Published: August 2014

Although there are a number of diseases that plague citrus production worldwide, two bacterial diseases are particularly problematic. Both are of Asian origin and currently cause severe economic damage: Asiatic citrus canker (ACC) and citrus huanglongbing (HLB). Although ACC has been found in the Western Hemisphere since the early 1900s, HLB was only discovered in 2004. ACC causes foliar, fruit and twig lesions that reduce marketability, can result in significant crop loss, and restrict international trade with areas where the disease has not yet been introduced or become endemic. While ACC has been the impetus for eradication programmes in several countries, only those conducted to combat limited outbreaks have been successful. The costs for 'living with ACC' in Florida including additional bactericidal sprays and quarantine inspections for fresh fruit range from 10 to 20% depending on cultivar susceptibility and market destination of the fruit. By comparison citrus HLB, the most severe of all known citrus diseases has increased production costs by 50-60%. The disease is vectored by the Asian citrus psyllid and was first recognized in India about 150 years ago. HLB has spread throughout most of the citrus producing areas of the world with the exception of the Mediterranean. Worldwide, nowhere that HLB exists, is it under adequate control. Extensive research is underway especially in the newly infected Western hemisphere countries in an attempt to discover and deploy effective control measures for HLB. The presence of these diseases poses an imminent threat of economic survival for affected citrus industries.
Identification of crypto- and neochlorogenic lactones as potent xanthine oxidase inhibitors in roasted coffee beans
Authors: Honda Sari , Miura Yukari , Masuda Akiko , Masuda Toshiya
Published: August 2014

Xanthine oxidase (XO) inhibitory activity has been found in boiling water extracts from roasted coffee beans. Therefore, assay-guided purification of the extracts was performed using size-exclusion column chromatography, and subsequently with reversed phase HPLC to afford lactone derivatives of chlorogenic acids. Among the tested lactones, crypto- and neochlorogenic lactones showed potent XO inhibitory activities compared with three major chlorogenic acids found in coffee beans. These XO inhibitory lactones may ameliorate gout and hyperuricemia in humans who drink coffee.
Gastric Neoplasms and Gastroenteric and Pancreatic Neuroendocrine Tumors
Authors: Larson Mark V.
Published: August 2014

Gastric neoplasms are an important contributor to cancer-related mortality. Of the various neoplasms that can affect the stomach, adenocarcinoma is the most common and accounts for up to 95% of all gastric neoplasms. Less common are gastric lymphomas, gastrointestinal stromal tumors, neuroendocrine tumors, and metastatic disease involving the stomach. This chapter considers the epidemiology, pathogenesis, clinical manifestation, diagnostic evaluation, treatment, and prognosis of these neoplastic diseases.
Inflammatory Bowel Disease:
Authors: Pardi Darrell S.
Published: August 2014

Many therapies are available for patients with inflammatory bowel disease (IBD). Medical therapies include aminosalicylate drugs such as sulfasalazine, olsalazine, balsalazide, and various formulations of mesalamine; antibiotics; corticosteroids; immunosuppressive medications such as azathioprine, 6-mercaptopurine (6-MP), methotrexate, and cyclosporine; and biotechnology medications such as anti–tumor necrosis factor (TNF) agents and newer agents with different mechanisms of action. This chapter reviews these various treatments and their positions in the treatment algorithms for Crohn disease and ulcerative colitis. Many surgical therapies also are used in patients with IBD, although a detailed review of these options is beyond the scope of this chapter.
Approach to the Patient With Abnormal Liver Test Results and Acute Liver Failure
Authors: Poterucha John J.
Published: August 2014

This chapter includes the following topics: 1. General discussion of commonly used liver tests. 2. Differential diagnosis and discussion of diseases characterized by an increase in hepatocellular enzyme levels. 3. Differential diagnosis and discussion of diseases characterized by an increase in cholestatic enzyme levels. 4. Evaluation of patients who have jaundice. 5. Diagnostic algorithms for evaluating patients who have abnormal liver tests. 6. Management of patients who have acute liver failure.
Vascular Diseases of the Liver
Authors: Sanchez William , Kamath Patrick S.
Published: August 2014

Vascular diseases of the liver can be divided into disorders of hepatic inflow (ie, diseases of the portal venous and hepatic arterial inflow) and disorders of hepatic venous outflow.

For a better understanding of the vascular diseases of the liver, a concise review of the vascular anatomy of the liver is important. This chapter reviews the anatomy of the splanchnic circulation, acute and chronic mesenteric venous thrombosis; hepatic artery thrombosis, aneurysm, and fistulas; ischemic hepatitis; hereditary hemorrhagic telangiectasia; veno-occlusive disease, and Budd-Chiari syndrome.
Ascites, Hepatorenal Syndrome, and Encephalopathy
Authors: Hay J. Eileen
Published: August 2014

The portal hypertension and hepatic synthetic dysfunction of cirrhosis cause three main complications as liver disease progresses: variceal bleeding, ascites, and hepatic encephalopathy. Ascites is the most common major complication of cirrhosis and occurs in about 50% of patients with compensated cirrhosis in 10 years. The development of ascites denotes the transition from compensated to decompensated cirrhosis. Hepatic encephalopathy is a debilitating complication of cirrhosis for which therapies are still very limited and nonspecific. Furthermore, no weight is given for this complication in the MELD system for organ allocation, resulting in considerable morbidity for patients and a burden for families and the health care system. In chronic liver disease, noxious substances, presumed nitrogenous compounds from protein breakdown, are ineffectively detoxified or bypassed (or both) by the diseased liver and affect the brain, causing a neuropsychiatric syndrome called hepatic encephalopathy.
Epilepsy in the end of life phase of brain tumor patients: a systematic review
Authors: Koekkoek Johan A.F. , Dirven Linda , Reijneveld Jaap C. , Postma Tjeerd J. , Grant Robin , Pace Andrea , Oberndorfer Stefan , Heimans Jan J. , Taphoorn Martin J.B.
Published: August 2014

Epileptic seizures are common in patients with primary or secondary malignant brain tumor. However, current knowledge on the occurrence of seizures during the end of life (EOL) phase of brain tumor patients is limited. Because symptom management with preservation of quality of life is of major importance for patients with a malignant brain tumor, particularly in the EOL, it is necessary to gain a deeper understanding of seizures and their management during this phase. We performed a systematic review of literature related to epilepsy in the EOL phase of brain tumor patients, based on the electronic resources PubMed, Embase, and Cinahl. The search yielded 442 unique records, of which 11 articles were eligible for further analysis after applying predefined inclusion criteria. Seizures occur relatively frequently in the EOL phase, particularly in patients with high-grade glioma. However, seizure management is often hampered by swallowing difficulties and impaired consciousness. Treatment decisions are largely dependent on expert opinion because a standardized approach for treating seizures in the terminal stage of brain tumor patients is still lacking.
How cultural transmission facilitates a long juvenile learning period
Authors: Baldini Ryan
Published: August 2014

The evolution of the long, slow human life history is a major challenge to evolutionary biologists. A compelling theory states that our late age at maturity allows us to acquire the many skills needed to survive in the economically intensive human foraging niche. Cultural transmission may be a crucial part of this process, by exposing learners to a wealth of information and skills that they would otherwise not likely discover. I use mathematical models to show that whether cultural transmission allows a later age at maturity depends on the details of selection and population regulation. In particular, cultural transmission appears to readily allow a later age at maturity under density-dependent fertility, but may not under density-dependent mortality or density-independent population growth. I close with a discussion of possibilities for future theoretical and empirical research.
Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing
Authors: Berlin Konstantin , Koren Sergey , Chin Chen-Shan , Drake James , Landolin Jane M. , Phillippy Adam M.
Published: August 2014

We report reference-gradede novoassemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. Here we introduce the MinHash Alignment Process (MHAP) for efficient overlapping of noisy, long reads using probabilistic, locality-sensitive hashing. Together with Celera Assembler, MHAP was used to reconstruct the genomes ofEscherichia coli,Saccharomyces cerevisiae,Arabidopsis thaliana,Drosophila melanogaster, and human from high-coverage SMRT sequencing. The resulting assemblies include fully resolved chromosome arms and close persistent gaps in these important reference genomes, including heterochromatic and telomeric transition sequences. ForD. melanogaster, MHAP achieved a 600-fold speedup relative to prior methods and a cloud computing cost of a few hundred dollars. These results demonstrate that single-molecule sequencing alone can produce near-complete eukaryotic genomes at modest cost.
Estimating strength of polygenic selection with principal components analysis of spatial genetic variation
Authors: Piffer Davide
Published: August 2014

Principal components analysis on allele frequencies for 14 and 50 populations (from 1K Genomes and ALFRED databases) produced a factor accounting for over half of the variance, which indicates selection pressure on intelligence or genotypic IQ. Very high correlations between this factor and phenotypic IQ, educational achievement were observed (r>0.9 and r>0.8), also after partialling out GDP and the Human Development Index. Regression analysis was used to estimate a genotypic (predicted) IQ also for populations with missing data for phenotypic IQ. Socio-economic indicators (GDP and Human Development Index) failed to predict residuals, not providing evidence for the effects of environmental factors on intelligence. Another analysis revealed that the relationship between IQ and the genotypic factor was not mediated by race, implying that it exists at a finer resolution, a finding which in turn suggests selective pressures postdating sub-continental population splits.

Genotypic height and IQ were inversely correlated but this correlation was mostly mediated by race. In at least two cases (Native Americans vs East Asians and Africans vs Papuans) genetic distance inferred from evolutionarily neutral genetic markers contrasts markedly with the resemblance observed for IQ and height increasing alleles.

A principal component analysis on a random sample of 20 SNPs revealed two factors representing genetic relatedness due to migrations. However, the correlation between IQ and the intelligence PC was not mediated by them. In fact, the intelligence PC emerged as an even stronger predictor of IQ after entering the “migratory” PCs in a regression, indicating that it represents selection pressure instead of migrational effects.

Finally, some observations on the high IQ of Mongoloid people are made which lend support to the “cold winters theory” on the evolution of intelligence.
CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma
Authors: Huang Chun-Hao , Lujambio Amaia , Zuber Johannes , Tschaharganeh Darjus F. , Doran Michael G. , Evans Michael J. , Kitzing Thomas , Zhu Nan , de Stanchina Elisa , Sawyers Charles L. , Armstrong Scott A. , Lewis Jason S. , Sherr Charles J. , Lowe Scott W.
Published: August 2014

One-year survival rates for newly diagnosed hepatocellular carcinoma (HCC) are <50%, and unresectable HCC carries a dismal prognosis owing to its aggressiveness and the undruggable nature of its main genetic drivers. By screening a custom library of shRNAs directed toward known drug targets in a genetically defined Myc-driven HCC model, we identified cyclin-dependent kinase 9 (Cdk9) as required for disease maintenance. Pharmacological or shRNA-mediated CDK9 inhibition led to robust anti-tumor effects that correlated with MYC expression levels and depended on the role that both CDK9 and MYC exert in transcription elongation. Our results establish CDK9 inhibition as a therapeutic strategy for MYC-overexpressing liver tumors and highlight the relevance of transcription elongation in the addiction of cancer cells to MYC.
MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures
Authors: Kumar Prasun , Kailasam Senthilkumar , Chakraborty Shaunak , Bansal Manju
Published: August 2014

Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity.MolBridgeis an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation–π, π–π and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server withJmolandJMEincorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.
The lipid cubic phase orin mesomethod for crystallizing proteins. Bushings for better manual dispensing
Authors: Caffrey Martin , Eifert Robert , Li Dianfan , Howe Nicole
Published: August 2014

The lipid cubic phase orin mesomethod can be used to set up crystallization trials of soluble and membrane proteins. The cubic phase is noted for being a sticky and viscous mesophase. Dispensing the protein-laden mesophase by hand into wells on crystallization plates has been facilitated by the use of an inexpensive repeat dispenser. However, the assembled dispensing device is prone to damage. Specifically, the delicate plunger used to dispense the viscous mesophase by positive displacement can be bent and scarred when the locking nut that fixes the plunger to the ratchet-driven dispensing mechanism is inadvertently overtightened. A defective plunger can render the device useless as a dispensing tool. More importantly, it can lead to catastrophic loss of valuable protein and lipid due to leakage when the dispensing syringe is being recharged with fresh mesophase. This note describes two types of bushings designed to protect the plunger from mechanical damage, which provide facile and reliable dispenser performance. One is a split bushing in brass and is a highly durable solution. The other is a small sleeve made from readily available plastic tubing. While it lacks durability, the plastic sleeve is simple yet highly effective, and can be replaced as the need arises.
Peak broadening anisotropy in deformed face-centred cubic and hexagonal close-packed alloys
Authors: Simm T. H. , Withers P. J. , Quinta da Fonseca J.
Published: August 2014

The broadening of diffraction peaks representing different families of grain orientations has been measured for a number of deformed metals: austenitic stainless steel 316, nickel 200 and the titanium alloy Ti-6Al-4V. These measurements have been compared with predictions that explain differences in broadening in terms of the contrast factor of dislocationsviatwo different approaches. This was done in order to understand the effect the contrast factor has on the results of diffraction peak profile analysis methods and the cause of broadening anisotropy. An approach that considers all grains and orientations to behave similarly was found to be unsuccessful in explaining the large variations of broadening in different peaks. These variations can be explained, and errors reduced, by adopting an approach that uses a polycrystal plasticity model. However, if the plasticity based approach is used to solely calculate changes in the contrast factor, it only partly explains changes in broadening. Instead, factors such as variations in the dislocation density and crystallite size in different orientations, the number of dislocations that are mobile, and the number of edge and screw dislocations need consideration. The way to incorporate these additional factors is difficult, but their contribution to broadening anisotropy can be as important as that of the contrast factor.
Minimal benefit of earlier‐than‐recommended repeat colonoscopy among US Medicare enrollees following a negative colonoscopy
Authors: Yang Y.‐X. , French B. , Localio A. R. , Brensinger C. M. , Lewis J. D.
Published: August 2014

Background

A large proportion of US Medicare beneficiaries undergo earlier‐than‐recommended follow‐up colonoscopies after negative screening colonoscopy. Such practice entails substantial cost and added risk.

Aims

To compare the risk of colorectal cancer (CRC) associated with varying follow‐up colonoscopy intervals following a negative colonoscopy, and to determine whether the potential benefit of a shorter colonoscopy follow‐up interval would differ by gender.

Methods

We conducted a weighted cohort study using the Surveillance, Epidemiology and End Results‐Medicare linked database (1991–2006) among 932 370 Medicare enrollees who are representative of the entire US elderly population. We compared the cumulative incidence of CRC among patients who underwent follow‐up colonoscopies at different intervals following a negative colonoscopy. The primary outcome was incident CRC.

Results

The eligible study cohort (n = 480 864) included 106 924 patients who underwent ≥1 colonoscopy. Men were more likely to require polypectomy during their initial colonoscopy than women. Compared to the recommended 9–10 year follow‐up colonoscopy interval, an interval of 5–6 years was associated with the largest CRC cumulative risk reduction [i.e. 0.17% (95% CI: 0.009–0.32%)]. The magnitude of risk reduction associated with shorter colonoscopy follow‐up intervals was not significantly different between men and women.

Conclusions

Among elderly individuals who undergo a negative colonoscopy, the magnitude of reduction in the cumulative CRC risk afforded by earlier‐than‐recommended follow‐up colonoscopy is quite small, and probably cannot justify the risk and cost of increased colonoscopy frequency. In addition, there are insufficient differences between men and women to warrant gender‐specific recommendations.
Preoperative C‐reactive protein and operative blood loss predict poor prognosis in patients with gastric cancer after laparoscopy‐assisted gastrectomy
Authors: Ishino Yoshito , Saigusa Susumu , Ohi Masaki , Yasuda Hiromi , Tanaka Koji , Toiyama Yuji , Mohri Yasuhiko , Kusunoki Masato
Published: August 2014

Introduction

The aim of this study was to clarify the factors associated with postoperative complications and prognoses following laparoscopy‐assisted gastrectomy for gastric cancer.

Methods

A total of 214 patients who underwent laparoscopy‐assisted gastrectomy for gastric cancer were enrolled in this retrospective study. Factors that were potentially associated with postoperative complications and prognosis were assessed using the following clinical and perioperative parameters: the Estimation of Physiologic Ability and Surgical Stress scoring system, the Prognostic Nutritional Index, and the Clavien–Dindo classification.

Results

Postoperative complications developed in 18.7% of patients. Blood loss ≥ 1% of body weight was significantly correlated with anastomotic leakage (P = 0.0108). Severe complications, based on the Clavien–Dindo classification, were more frequent in patients with proximal or total gastrectomies (P = 0.0324). A preoperative C‐reactive protein level > 0.5 mg/dL, blood loss > 1% of body weight, age ≥ 70 years at the time of operation, and an Estimation of Physiologic Ability and Surgical Stress score ≥ 0.2 were significantly correlated with poor prognosis. Multivariate analysis revealed that two of these factors, preoperative C‐reactive protein level ≥ 0.5 mg/dL and operative blood loss ≥ 1% of body weight, were independent prognostic factors (P = 0.0376 and P = 0.0112, respectively). The Prognostic Nutritional Index had no significant correlation with prognosis or the occurrence of postoperative complications.

Conclusion

Operative blood loss ≥ 1% of body weight and type of resection were associated with an increased frequency of postoperative complications, while preoperative C‐reactive protein levels and operative blood loss may be prognostic predictors for gastric cancer patients following laparoscopy‐assisted gastrectomy.
Identification of differential selection traces in two Polish cattle breeds
Authors: Gurgul Artur , Pawlina Klaudia , Frys‐Żurek Monika , Bugno‐Poniewierska Monika
Published: August 2014

Genetic improvement of animals based on artificial selection is leading to changes in the frequency of genes related to desirable production traits. The changes are reflected by the neutral, intergenic single nucleotide polymorphims (SNPs) being in long‐range linkage disequilibrium with functional polymorphisms. Genome‐wide SNP analysis tools designed for cattle, allow for scanning divergences in allelic frequencies between distinct breeds and thus for identification of genomic regions which were divergently selected in breeds' histories. In this study, by using Bovine SNP50 assay, we attempted to identify genomic regions showing the highest differences in allele frequencies between two distinct cattle breeds – preserved, unselected Polish Red breed and highly selected Holstein cattle. Our study revealed 19 genomic regions encompassing 55 protein‐coding genes and numerous quantitative trait loci which potentially may underlie some of the phenotypic traits distinguishing the breeds.
A critical evaluation of the contribution of trust to effective Technology Enhanced Learning in the workplace: A literature review
Authors: Short Heather
Published: August 2014

This paper offers a critical review of the literature that explores the building and development of trust in workplace learning, particularly in a virtual context and its implications for Technology Enhanced Learning (TEL) in business. Trust is increasingly recognised as important in both business and education, and is the focus of increasing attention in relation to the virtual environment. TEL offers a range of potential benefits, but adoption levels remain low. However, there are indications that trust may be a significant factor in both low workplace participation in TEL and its effectiveness as a learning medium. Although savings in both money and time are the main perceived advantages of TEL, this review highlights the positive role of face‐to‐face contact in increasing TEL take‐up and effectiveness, even though this diminishes cost savings. This paper highlights the scant level of research into TEL, particularly in work situations, and the extent to which trust has been overlooked in this context. In the light of this gap in knowledge, further investigations are suggested to contribute to understanding the issues affecting TEL in the workplace.
Pedogenic and biogenic alkaline‐extracted silicon distributions along a temperate land‐use gradient
Authors: Barão L. , Clymans W. , Vandevenne F. , Meire P. , Conley D. J. , Struyf E.
Published: August 2014

The primary source of dissolved silicon (Si: DSi) is the weathering of silicate minerals. In recent years, it has been shown that Si cycling through vegetation creates a more soluble Si pool in the soil, as amorphous Si (ASi) deposits in plants (phytoliths) are returned to the soil through litter. Amorphous Si accumulation in soils depends on a number of factors, including land use. In addition to the biogenic ASi fraction, soils contain other non‐biogenic amorphous and sorbed Si fractions that could contribute significantly to DSi export to rivers, but hitherto these Si fractions have been difficult to separate from each other with traditionally applied extraction methods. The objective of this paper is to understand better how land use affects the distribution of the different extractable Si fractions. We re‐analysed samples from the land‐use gradient studied previously by Clymans et al. () with a continuous Si and aluminium (Al) extraction technique. Different extractable Si fractions of biogenic or pedogenic origin were successfully separated on the basis of their dissolution in alkaline solutions (Na2CO3 and NaOH) and Si:Al ratios. We show that forests store almost all alkaline extractable Si (AlkExSi) in the pedogenic fraction while the importance of phytoliths increases with human disturbance to become the dominant fraction in the AlkExSi pool at the arable site. The pedogenic AlkExSi pool is also more reactive than the phytolith‐bound Si. Conversely, pastures and croplands tend to preserve phytoliths in the soil, which are less reactive, decreasing the potential of DSi export relative to forested ecosystems.
Factors responsible for incomplete linkage to care after HIV diagnosis: preliminary results from the Test and Keep in Care (TAK) project
Authors: Ankiersztejn‐Bartczak M , Firląg‐Burkacka E , Czeszko‐Paprocka H , Kubicka J , Cybula A , Horban A , Kowalska JD
Published: August 2014

Objectives

Linkage to care after HIV diagnosis remains underinvestigated in Europe, yet delays in linkage to care are an important obstacle to controlling the HIV epidemic. The Test and Keep in Care (TAK) project aims to determine the prevalence of HIV‐positive persons who are lost or late to care and factors associated with this.

Methods

Data from community‐based voluntary counselling and testing that occurred in 2010–2011 were linked with data from HIV clinics using unique test numbers. Persons not registered in HIV clinics were considered lost to care (LTC). For statistical analysis, nonparametric tests were used for comparison, and a multivariable logistic regression model was developed that included all variables with P < 0.1 from the univariable models.

Results

A total of 110 persons were diagnosed as HIV‐positive: 91% lived in central Poland, 5% were female and 71% were men who have sex with men (MSM). Forty‐seven (42%) persons were LTC, seven of whom did not collect their enzyme‐linked immunosorbent assay (ELISA) test result. Of those who registered, 75% registered within 1 month from HIV diagnosis, and 54% were late presenters. LTC individuals were more likely to have heterosexual or bisexual orientation, to have > 20 sexual partners, to not be in a relationship with an HIV‐positive partner, to not use condoms, and to be taking their first HIV test. In a logistic regression model, after adjusting for these factors, using condoms in a stable relationship decreased the odds of LTC by 72% (odds ratio 0.28; confidence interval 0.11−0.67).

Conclusions

Integration into care after HIV diagnosis requires improvement. Our results suggest that broadening awareness and counselling about sexual risks may have a positive impact.