ALBERT

Description: Ag 9 (SiO 4 ) 2 NO 3 was prepared by a reactive flux method. The structures, morphologies, and light absorption properties were investigated. Owing to the polar crystal structure, an internal electric field can be formed inside the material, which can facilitate the photogenerated charge separation during the photocatalytic process. Based on both the wide light absorption spectra and high charge separation efficiency originated from the polarized internal electric field, Ag 9 (SiO 4 ) 2 NO 3 exhibit higher efficiency over Ag 3 PO 4 during the degradation of organic dyes under visible light irradiation, which is expected to be a potential material for solar energy harvest and conversion.

Description: We obtained photovoltaic response in pristine multilayer WSe 2 by sandwiching WSe 2 between top and bottom metals. In this structure, the work-function difference between the top metal and WSe 2 plays a critical role in generating built-in potentials and photovoltaic responses. Our devices with Zn as top metal exhibit photo-conversion efficiencies up to 6.7% under 532 nm illumination and external quantum efficiencies in the range of 40%–83% for visible light. This work provides a method for generating photovoltaic responses in layered semiconductors without detrimental doping or exquisite heterostructures, and also advances the physics for modulating the band structures of such emerging semiconductors.

Description: We use cyclotron resonance THz-spectroscopy in pulsed magnetic fields up to 63 T to measure the electron effective mass in Si-doped GaAsN semiconductor alloys with nitrogen content up to 0.2%. This technique directly probes the transport properties of the N-modified conduction band, particularly the electron effective mass, which has been discussed controversially in the experimental and theoretical literature. We report a slight increase of the electron effective mass and nonparabolicity with N-content for different photon energies in agreement with the two-level band anticrossing model calculations. Furthermore, we show a pronounced electron mobility drop with increasing N-content.

Description: Blending the conjugated polymer poly(3-hexylthiophene) (P3HT) with the insulating electret polystyrene (PS), we show that the threshold voltage V t of organic field-effect transistors (OFETs) can be easily and reversely tuned by applying a gate bias stress at 130 °C. It is proposed that this phenomenon is caused by thermally activated charge injection from P3HT into PS matrix, and that this charge is immobilized within the PS matrix after cooling down to room temperature. Therefore, room-temperature hysteresis-free FETs with desired V t can be easily achieved. The approach is applied to reversely tune the OFET mode of operation from accumulation to depletion, and to build inverters.

Description: Reflective surfaces are one of the key elements of solar plants to concentrate energy in the receivers of solar thermal electricity plants. Polymeric substrates are being considered as an alternative to the widely used glass mirrors due to their intrinsic and processing advantages, but optimizing both the reflectance and the physical stability of polymeric mirrors still poses technological difficulties. In this work, polymeric surfaces have been functionalized with ceramic thin-films by atomic layer deposition. The characterization and optimization of the parameters involved in the process resulted in surfaces with a reflection index of 97%, turning polymers into a real alternative to glass substrates. The solution we present here can be easily applied in further technological areas where seemingly incompatible combinations of polymeric substrates and ceramic coatings occur.

Description: Understanding the coupling of different modal frequencies and their tuning mechanisms has become essential to design multi-frequency MEMS devices. In this work, we fabricate a MEMS beam with fixed boundaries separated from two side electrodes and a bottom electrode. Subsequently, we perform experiments to obtain the frequency variation of in-plane and out-of-plane mechanical modes of the microbeam with respect to both DC bias and laser heating. We show that the frequencies of the two modes coincide at a certain DC bias, which in turn can also be varied due to temperature. Subsequently, we develop a theoretical model to predict the variation of the two modes and their coupling due to a variable gap between the microbeam and electrodes, initial tension, and fringing field coefficients. Finally, we discuss the influence of frequency tuning parameters in arrays of 3, 33, and 40 microbeams, respectively. It is also found that the frequency bandwidth of a microbeam array can be increased to as high as 25 kHz for a 40 microbeam array with a DC bias of 80 V.

Description: Atomic-scale knowledge and control of oxidation of GaSb(100), which is a potential interface for energy-efficient transistors, are still incomplete, largely due to an amorphous structure of GaSb(100) oxides. We elucidate these issues with scanning-tunneling microscopy and spectroscopy. The unveiled oxidation-induced building blocks cause defect states above Fermi level around the conduction-band edge. By interconnecting the results to previous photoemission findings, we suggest that the oxidation starts with substituting second-layer Sb sites by oxygen. Adding small amount of indium on GaSb(100), resulting in a (4 × 2)-In reconstruction, before oxidation produces a previously unreported, crystalline oxidized layer of (1 × 3)-O free of gap states.

Description: A scanning transmission electron microscope equipped with a backscattered and secondary electron detector is shown capable to image graphene and hexagonal boron nitride monolayers. Secondary electron contrasts of the two lightest monolayer materials are clearly distinguished from the vacuum level. A signal difference between these two materials is attributed to electronic structure differences, which will influence the escape probabilities of the secondary electrons. Our results show that the secondary electron signal can be used to distinguish between the electronic structures of materials with atomic layer sensitivity, enhancing its applicability as a complementary signal in the analytical microscope.

Description: Refractive index sensing plays a key role in various environmental and biological sensing applications. Here, a method is presented for measuring the absolute refractive index dispersion of liquids using an array of photonic crystal resonant reflectors of varying periods. It is shown that by covering the array with a sample liquid and measuring the resonance wavelength associated with transverse electric polarized quasi guided modes as a function of period, the refractive index dispersion of the liquid can be accurately obtained using an analytical expression. This method is compact, can perform measurements at arbitrary number of wavelengths, and requires only a minute sample volume. The ability to sense a material's dispersion profile offers an added dimension of information that may be of benefit to optofluidic lab-on-a-chip applications.

Description: Brillouin microscopy is an emerging technique to yield high spatial resolution mechanical images in a non-contact manner. The main challenge in Brillouin spectroscopy is given by the detection and the localisation of the Brillouin peaks, in particular, when a high amount of elastic light is collected. We demonstrate a purely interferometric method to suppress the parasitic light which overwhelms the Brillouin spectrum using destructive interference in a Michelson interferometer. A suppression ratio of 35 dB is readily achieved. Both double and single stage virtually imaged phased array spectrometers are tested showing that the Brillouin peaks can still be measured when the intensity of the elastic light is higher by 53 dB, hence, enabling 3D mechanical imaging of thin biological systems such as cells.

Description: Background: Host genetic variability has been implicated in chemotherapy-induced peripheral neuropathy (CIPN). A dose-limiting toxicity for chemotherapy agents, CIPN is also a debilitating condition that may progress to chronic neuropathic pain. We utilized a bioinformatics approach, which captures the complexity of intracellular and intercellular interactions, to identify genes for CIPN. Methods: Using genes pooled from the literature as a starting point, we used Ingenuity Pathway Analysis (IPA) to generate gene networks for CIPN. Results: We performed IPA core analysis for genes associated with platinum-, taxane- and platinum-taxane–induced neuropathy. We found that IL6, TNF, CXCL8, IL1B and ERK1/2 were the top genes in terms of the number of connections in platinum-induced neuropathy and TP53, MYC, PARP1, P38 MAPK and TNF for combined taxane-platinum–induced neuropathy. Conclusion: Neurotoxicity is common in cancer patients treated with platinum compounds and anti-microtubule agents and CIPN is one of the debilitating sequela. The bioinformatic approach helped identify genes associated with CIPN in cancer patients.

Description: Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (α/β) 8 TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T m of 44 °C and a Gibbs free energy of unfolding (ΔG°) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C m of 1.6 M and a ΔG° of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Description: Background: Tumorigenesis is an evolutionary process by which tumor cells acquire mutations through successive diversification and differentiation. There is much interest in reconstructing this process of evolution due to its relevance to identifying drivers of mutation and predicting future prognosis and drug response. Efforts are challenged by high tumor heterogeneity, though, both within and among patients. In prior work, we showed that this heterogeneity could be turned into an advantage by computationally reconstructing models of cell populations mixed to different degrees in distinct tumors. Such mixed membership model approaches, however, are still limited in their ability to dissect more than a few well-conserved cell populations across a tumor data set. Results: We present a method to improve on current mixed membership model approaches by better accounting for conserved progression pathways between subsets of cancers, which imply a structure to the data that has not previously been exploited. We extend our prior methods, which use an interpretation of the mixture problem as that of reconstructing simple geometric objects called simplices, to instead search for structured unions of simplices called simplicial complexes that one would expect to emerge from mixture processes describing branches along an evolutionary tree. We further improve on the prior work with a novel objective function to better identify mixtures corresponding to parsimonious evolutionary tree models. We demonstrate that this approach improves on our ability to accurately resolve mixtures on simulated data sets and demonstrate its practical applicability on a large RNASeq tumor data set. Conclusions: Better exploiting the expected geometric structure for mixed membership models produced from common evolutionary trees allows us to quickly and accurately reconstruct models of cell populations sampled from those trees. In the process, we hope to develop a better understanding of tumor evolution as well as other biological problems that involve interpreting genomic data gathered from heterogeneous populations of cells.

Description: Background: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Description: Background: Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information. Results: We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported. Conclusion: IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/.

Description: Background: For faithful chromosome segregation during cell division, correct attachments must be established between sister chromosomes and microtubules from opposite spindle poles through kinetochores (chromosome bi-orientation). Incorrect attachments of kinetochore microtubules (kMTs) lead to chromosome mis-segregation and aneuploidy, which is often associated with developmental abnormalities such as Down syndrome and diseases including cancer. The interaction between kinetochores and microtubules is highly dynamic with frequent attachments and detachments. However, it remains unclear how chromosome bi-orientation is achieved with such accuracy in such a dynamic process. Results: To gain new insight into this essential process, we have developed a simple mathematical model of kinetochore–microtubule interactions during cell division in general, i.e. both mitosis and meiosis. Firstly, the model reveals that the balance between attachment and detachment probabilities of kMTs is crucial for correct chromosome bi-orientation. With the right balance, incorrect attachments are resolved spontaneously into correct bi-oriented conformations while an imbalance leads to persistent errors. In addition, the model explains why errors are more commonly found in the first meiotic division (meiosis I) than in mitosis and how a faulty conformation can evade the spindle assembly checkpoint, which may lead to a chromosome loss. Conclusions: The proposed model, despite its simplicity, helps us understand one of the primary causes of chromosomal instability—aberrant kinetochore–microtubule interactions. The model reveals that chromosome bi-orientation is a probabilistic self-organisation, rather than a sophisticated process of error detection and correction.

Description: Background: Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. It is highly prevalent and is characterized by symptoms including odor, discharge and irritation. No single microbe has been found to cause BV. In this paper we use random forests and logistic regression classifiers to model the relationship between the microbial community and BV. We use subsets of the microbial community features in order to determine which features are important to the classification models. Results: We find that models generated using logistic regression and random forests perform nearly identically and identify largely similar important features. Only a few features are necessary to obtain high BV classification accuracy. Additionally, there appears to be substantial redundancy between the microbial community features. Conclusions: These results are in contrast to a previous study in which the important features identified by the classifiers were dissimilar. This difference appears to be the result of using different feature importance measures. It is not clear whether machine learning classifiers are capturing patterns different from simple correlations.

Description: In earlier works, we used spheres of various sizes as impedance probes in demonstrating a method of determining plasma potential, φ p , when the probe radius is much larger than the Debye length, λ D . The basis of the method in those works [Walker et al ., Phys. Plasmas 13 , 032108 (2006); ibid . 15 , 123506 (2008); ibid . 17 , 113503 (2010)] relies on applying a small amplitude signal of fixed frequency to a probe in a plasma and, through network analyzer-based measurements, determining the complex reflection coefficient, Γ , for varying probe bias, V b . The frequency range of the applied signal is restricted to avoid sheath resonant effects and ion contributions such that ω pi  ≪ ω ≪ ω pe , where ω pi is the ion plasma frequency and ω pe is the electron plasma frequency. For a given frequency and applied bias, both Re( Z ac ) and Im( Z ac ) are available from Γ . When Re( Z ac ) is plotted versus V b , a minimum predicted by theory occurs at φ p [Walker et al ., Phys. Plasmas 17 , 113503 (2010)]. In addition, Im (Z ac ) appears at, or very near, a maximum at φ p . As n e decreases and the sheath expands, the minimum becomes harder to discern. The purpose of this work is to demonstrate that when using network analyzer-based measurements, Γ itself and Im (Z ac ) and their derivatives are useful as accompanying indicators to Re( Z ac ) in these difficult cases. We note the difficulties encountered by the most commonly used plasma diagnostic, the Langmuir probe. Spherical probe data is mainly used in this work, although we present limited data for a cylinder and a disk. To demonstrate the effect of lowered density as a function of probe geometry, we compare the cylinder and disk using only the indicator Re( Z ac ).

Description: The classical gravitational instability of a layer of denser fluid overlying a layer of less dense fluid, commonly known as the Rayleigh-Taylor instability, has been studied for well over a hundred years. In this article, we present the results of numerical simulations of a variant of this instability in which a plug of dense fluid is released from rest in a thin channel between two flat, vertical walls, causing a downward acceleration of the entire fluid column and formation of boundary layers near the walls. The plug of dense fluid undergoes distinctly different evolution near the walls and in the fluid interior. The instability in the interior, which we label the “hammerhead” instability based on its shape, is robust over a range of physical parameters, but disappears below a threshold Schmidt number. Fluid near the wall is slowed, and thin tendrils that link the near wall fluid to the main body of the fluid plug form, and in some cases undergo their own instability. We characterize the fully three-dimensionalized state, finding that while bulk measures of kinetic energy three-dimensionalization do not discriminate between low and high Schmidt number cases, the geometric distributions of the dynamical parameters Q and R from the turbulence literature are profoundly different in the high Schmidt number case. Finally, we consider the role of shear in situations in which the two plates are not exactly vertical, demonstrating that shear diminishes the importance of three-dimensionalization, while the hammerhead instability remains relevant.

Description: Flow past two cylinders of different diameters in close proximity is simulated numerically for a constant diameter ratio of 0.45, a gap ratio of 0.0625, and a Reynolds number of 1000 (defined using the diameter of the main cylinder). The effect of the position angle α of the small cylinder relative to the large one on force coefficients and wake flow patterns are studied. Depending on the position angle α of the small cylinder, four wake flow modes are identified: the upstream interference mode for α = 0°, 22.5°, and 45°, the intermittent attached gap flow mode for α = 67.5° and 90°, the attached gap flow mode for α = 112.5° and 135°, and the wake interference mode for α = 157.5° and 180°. The RMS lift coefficients of both cylinders are reduced significantly compared with that of a single cylinder, regardless of the position angle of the small cylinder. Although the variation trends of the mean drag and lift coefficients with the position angle of the small cylinder obtained from the two-dimensional (2D) and three-dimensional (3D) simulations are similar, the 2D simulations overestimate the mean drag coefficient, the RMS drag and lift coefficients compared with those obtained from the 3D simulations.

Description: Farley-Buneman modes are an example of the collisional instability, which is thought to be the dominant mechanism for the irregularities in low ionosphere region. Despite high collisionality due to electron-neutral and ion-neutral collisions, the kinetic effects associated with finite temperature are important for determination of the mode frequencies and growth rate. This is especially important for ion component that is largely unmagnetized due to low ion cyclotron frequency. The ion thermal effects are strongly pronounced for shorter wavelengths and are crucial for the growth rate cut-off at high wavenumbers. We develop an extended fluid model for ion dynamics to incorporate the effects of ion thermal motion. The model is based on the extended MHD model that includes the evolution equations for higher order moments such as ion viscosity and ion heat flux. We also develop the generalized Chapman-Enskog closure model that provides exact linear closures based on the linearized kinetic equation. The results of these models are compared and tested against the linear kinetic model. The dispersion of Farley-Buneman modes and growth rate behavior are investigated in the short wavelength region.

Description: Background: Bacterial populations communicate through the cell density-dependent mechanism of quorum sensing (QS). Vibrio harveyi, one of the best studied model organisms for QS, was used to explore effects of the synthetic cannabinoid HU-210 on QS and different QS-regulated physiological processes in bacteria. Results: Analysis of QS-regulated bioluminescence in wild-type and mutant strains of V. harveyi revealed that HU-210 affects the autoinducer-2 (AI-2) pathway, one of three known QS cascades of V. harveyi. Furthermore, QS-mediated biofilm formation and swimming motility in the mutant strain BB152 (AI-1 − , AI-2 + ) were significantly reduced in the presence of HU-210. HU-210 inhibited QS-mediated virulence factor production without any inhibitory effect on bacterial growth. It also alters the expression of several genes, which are regulated by QS, specifically downregulating the genes of the AI-2 QS cascade. Conclusion: First evidence is being provided for interference of bacterial signal-transduction systems by a synthetic cannabinoid. The effect of HU-210 was specific to the AI-2 cascade in V. harveyi. AI-2 is known as a "universal autoinducer" and interference with its activity opens a broad spectrum of applications for synthetic cannabinoids in future research as a potential anti-QS agent.

Description: Ultrafast energy relaxation process in Bi 2 Te 3 thin films is studied using a collinear two color pump-probe technique. The coherent optical phonon is enhanced and destroyed by changing the separation times of double pump pulses. The non-oscillatory component of the reflectivity trace after the second pump pulse shows a distinct difference with and without the presence of coherent optical phonons, thus providing a direct evidence of the effect of optical phonon on the hot carrier relaxation process. The deduced characteristic times are systematically smaller when coherent optical phonons are involved in the energy transfer process. Comparatively, the conventional relaxation process is relatively slow, which is explained by the screening effect of the incoherent optical phonon. This work suggests that the energy relaxation can be manipulated through the excitation of coherent optical phonons.

Description: Using first-principles calculations, we show that the conduction and valence band energies and their deformation potentials exhibit a non-negligible compositional bowing in strained ternary semiconductor alloys such as InGaAs. The electronic structure of these compounds has been calculated within the framework of local density approximation and hybrid functional approach for large cubic supercells and special quasi-random structures, which represent two kinds of model structures for random alloys. We find that the predicted bowing effect for the band energy deformation potentials is rather insensitive to the choice of the functional and alloy structural model. The direction of bowing is determined by In cations that give a stronger contribution to the formation of the In x Ga 1− x As valence band states with x ≳ 0.5, compared to Ga cations.

Description: Background: Several studies described the phytochemical constituents of plants in relation with the free radical scavenging property and inhibition of lipid peroxidation. This study investigated the in vitro antioxidant property, and the protective effects of ethanolic and aqueous ethanol extract of the leaves and barks of Afrostyrax lepidophyllus (Huaceae) against ion mediated oxidative damages. Methods: Four extracts (ethanol and aqueous-ethanol) from the leaves and barks of A. lepidophyllus were used in this study. The total phenols content, the antiradical and antioxidant properties were determined using standard colorimetric methods. Results: The plant extracts had a significant scavenging potential on the 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl (OH), nitrite oxide (NO) and 2,2-azinobis (3-ethylbenzthiazoline)-6-sulfonic acid (ABTS) radicals with the IC 50 varied between 47 and 200 µg/mL depending on the part of plant and the type of extract. The ethanol extract of A. lepidophyllus bark (GEE) showed the highest polyphenolic (35.33 ± 0.29) and flavonoid (12.00 ± 0.14) content. All the tested extracts demonstrated a high protective potential with the increased of superoxide dismutase, catalase and peroxidase activities. Conclusion: Afrostyrax lepidophyllus extracts exhibited higher antioxidant potential and significant protective potential on liver enzymes.

Description: Background: The internalization of Aspergillus fumigatus into alveolar epithelial cells (AECs) is tightly controlled by host cellular actin dynamics, which require close modulation of the ADF (actin depolymerizing factor)/cofilin family. However, the role of cofilin in A. fumigatus internalization into AECs remains unclear. Results: Here, we demonstrated that germinated A. fumigatus conidia were able to induce phosphorylation of cofilin in A549 cells during the early stage of internalization. The modulation of cofilin activity by overexpression, knockdown, or mutation of the cofilin gene in A549 cells decreased the efficacy of A. fumigatus internalization. Reducing the phosphorylation status of cofilin with BMS-5 (LIM kinase inhibitor) or overexpression of the slingshot phosphatases also impeded A. fumigatus internalization. Both the C. botulimun C3 transferase (a specific RhoA inhibitor) and Y27632 (a specific ROCK inhibitor) reduced the internalization of A. fumigatus and the level of phosphorylated cofilin. β-1,3-glucan (the major component of the conidial cell wall) and its host cell receptor dectin-1 did not seem to be associated with cofilin phosphorylation during A. fumigatus infection. Conclusion: These results indicated that cofilin might be involved in the modulation of A. fumigatus internalization into type II alveolar epithelial cells through the RhoA-ROCK-LIM kinase pathway.

Description: Background: With the introduction and implementation of a variety of government programs and policies to encourage adoption of electronic medical records (EMRs), EMRs are being increasingly adopted in North America. We sought to evaluate the completeness of a variety of EMR fields to determine if family physicians were comprehensively using their EMRs and the suitability of use of the data for secondary purposes in Ontario, Canada. Methods: We examined EMR data from a convenience sample of family physicians distributed throughout Ontario within the Electronic Medical Record Administrative data Linked Database (EMRALD) as extracted in the summer of 2012. We identified all physicians with at least one year of EMR use. Measures were developed and rates of physician documentation of clinical encounters, electronic prescriptions, laboratory tests, blood pressure and weight, referrals, consultation letters, and all fields in the cumulative patient profile were calculated as a function of physician and patient time since starting on the EMR. Results: Of the 167 physicians with at least one year of EMR use, we identified 186,237 patients. Overall, the fields with the highest level of completeness were for visit documentations and prescriptions (〉70 %). Improvements were observed with increasing trends of completeness overtime for almost all EMR fields according to increasing physician time on EMR. Assessment of the influence of patient time on EMR demonstrated an increasing likelihood of the population of EMR fields overtime, with the largest improvements occurring between the first and second years. Conclusions: All of the data fields examined appear to be reasonably complete within the first year of adoption with the biggest increase occurring the first to second year. Using all of the basic functions of the EMR appears to be occurring in the current environment of EMR adoption in Ontario. Thus the data appears to be suitable for secondary use.

Description: Background: Recognising the limitations of a paper-based approach to documenting vital sign observations and responding to national clinical guidelines, we have explored the use of an electronic solution that could improve the quality and safety of patient care. We have developed a system for recording vital sign observations at the bedside, automatically calculating an Early Warning Score, and saving data such that it is accessible to all relevant clinicians within a hospital trust. We have studied current clinical practice of using paper observation charts, and attempted to streamline the process. We describe our user-focussed design process, and present the key design decisions prior to describing the system in greater detail. Results: The system has been deployed in three pilot clinical areas over a period of 9 months. During this time, vital sign observations were recorded electronically using our system. Analysis of the number of observations recorded (21,316 observations) and the number of active users (111 users) confirmed that the system is being used for routine clinical observations. Feedback from clinical end-users was collected to assess user acceptance of the system. This resulted in a System Usability Scale score of 77.8, indicating high user acceptability. Conclusions: Our system has been successfully piloted, and is in the process of full implementation throughout adult inpatient clinical areas in the Oxford University Hospitals. Whilst our results demonstrate qualitative acceptance of the system, its quantitative effect on clinical care is yet to be evaluated.

Description: ObjectivesExcess adiposity (obesity and excess gestational weight gain, GWG) during pregnancy (EADP) increases risk for gestational diabetes, preeclampsia, and child and maternal obesity. Personal GWG goals predict total GWG. Some estimates suggest only 30% of pregnant women have personal GWG goals that are congruent with Institute of Medicine GWG recommendations. The primary purpose of this study was to determine the extent to which perceived pre-pregnancy weight status, healthcare provider advice, knowledge of EADP risks, and value for healthy GWG predicted knowledge of GWG recommendations. The secondary purpose was to determine sources of GWG information among pregnant women. Methods: Pregnant women with a confirmed singleton pregnancy completed a one-time survey in obstetric clinic waiting rooms. Logistic regression analysis was used. Results: 246 predominantly African American, low income, overweight/obese women completed surveys. Average age was 25 (SD 5.3) and gestation age ranged from 7 to 40 weeks. Knowledge of pre-pregnancy weight status was the only unique predictor of GWG recommendation knowledge (B = .642, p = .03). The top three sources of GWG information were physicians, internet, and books. The least frequently reported sources of GWG information were other healthcare providers, community programs, and television. Conclusion: In low income diverse overweight/obese pregnant women, accurate pre-pregnancy weight status perception was the only significant unique predictor of knowledge of GWG recommendations. Physicians were the preferred source of GWG information. Clinicians should have frequent, ongoing conversations about weight status with women before, during, and after pregnancy.

Description: Background: In Morocco, families play a major role in caring for elderly cancer patients. Methods: We conducted a prospective descriptive study, in the National Institute of Oncology in Morocco. The study aimed to include family members who are caregivers for patients aged ≥70 years old.FindingsAfter obtaining IRB approval, a total of 150 caregivers responded to the questionnaire. Mean age was 44.7 years. The majority were females (59.3%), living in urban areas (66.7%), and educated (62.7%).Offspring (sons or daughters) represented 56.7, 54% lived with their relatives in the same house. Most of the participants were married and have familial responsibilities. In relatives, anxiety was found in 79.3%, it was related to fear of losing the patient in 57% and resulted in the use of anxiolytics in 10%. Guilt feeling towards patients regarding neglecting their early symptoms was reported in 38%. Depression and anxiety were more frequent among female relatives and among those of urban origin. Obsession of dying from cancer was present in about 30% and fear of contagion was more common among those from rural areas and illiterate. Economic resources were exceeded in 78.7 and 56% have used banking credits, and sale of properties. Work lay-off was recorded in 54%. Relatives participated in treatment making decisions in 86% of patients. Conclusion: Even there was a great impact on elderly cancerous patients relatives, the benefits of caregiving was observed in 80%. More studies have to be conducted, especially in developing countries where the lack of resources majors the impact on family caregivers.

Description: Background: Leptospirosis and dengue are endemic in countries with subtropical or tropical climates and have epidemic potential. The incidence of both these diseases peaks during monsoons and both diseases present with similar clinical manifestations making differentiation of leptospirosis from dengue difficult. It is important to distinguish leptospirosis from dengue as early antibiotic therapy in leptospirosis leads to a favourable outcome, while dengue has no specific treatment, yet early recognition is vital for close monitoring and careful fluid management. Despite the high prevalence of both these infections, co-infection of leptospirosis and dengue has not been reported previously in Sri Lanka. We present the first case of co-infection with leptospirosis and dengue in a Sri Lankan male.Case presentationA 52 year old previously healthy Sri Lankan male was admitted to our facility with a history of fever for 4 days associated with headache, generalized myalgia, reduced urine output. On examination, he was rational, hypotensive, tacycardic, tacypneic and he did not have clinical evidence of fluid leakage or pneumonitis. His serology showed high titre of dengue IgG and IgM and rising titre of leptospirosis antibody. His course of illness was complicated with septic shock, acute renal failure, acute respiratory distress syndrome and disseminated intravascular coagulation and he succumbed to his illness on the eighth day of admission. Conclusion: In areas where both leptospirosis and dengue are endemic, both infections should be include in the differential diagnosis when evaluating patients with acute febrile illness and should consider the possibility of co-infection. Leptospirosis, being a condition having definitive antibiotic therapy, should always be ruled out even if the patient is positive for dengue serology in regions endemic to both these diseases as early initiation of antibiotic therapy can reduce mortality significantly.

Description: Magnetic, dielectric, and ac conductivity as well as room temperature structural and Raman studies are performed on double perovskite Dy 2 NiMnO 6 . The crystal structure of the compound adopts monoclinic P2 1 /n space group, where alternate Mn and Ni distorted octahedral are arranged in anti-phase a − a − b + order in Glazer notation. Magnetization studies show two magnetic transitions around 100 K and 20 K which are related to the ordering of transition and rare earth cations moment, respectively. Temperature dependent dielectric permittivity shows Havriliak-Negami type thermally activated dielectric relaxation. The ac conductivity at different temperature is found to follow Jonscher power law behavior. Time-temperature scaling of the conductivity spectra reveals that the charge transport dynamics is independent of temperature. Intriguingly, an anomaly in the dielectric constant is observed close to the order of Dy moment which indicates intrinsic magnetoelectric coupling. The hybridization between Dy and Ni/Mn is suggested to be correlated with the magnetoelectric coupling.

Description: The stable configurations and electronic and magnetic properties of nonmetal atoms (H, N, P, O, S, F, and Cl) adsorbed ReS 2 monolayers have been investigated by first-principles calculations. It is found that H, O, S, F, and Cl prefer to occupy the peak sites of S atoms, while both N and P atoms favor the valley sites of S atoms. The ReS 2 sheet exhibits a good adsorption capability to nonmetal atoms. The reconstruction of the surface is pronounced in N- and P-adsorbed ReS 2 monolayers. In H-adsorbed case, the Fermi level is pulled into the conduction band, which results in the semiconductor-metal transition. The same magnetic moment of 1 μ B is found in the N-, P-, F-, and Cl-adsorbed ReS 2 monolayers, while the mechanisms of forming magnetic moment for N (P)- and F (Cl)-adsorbed cases are different. In addition, the spatial extensions of spin density in P-, F-, and Cl-adsorbed cases are larger than that in N-adsorbed case, which is more suitable to achieve long-range magnetic coupling interaction at low defect concentrations. Our results provide insight for achieving metal-free magnetism and a tunable band gap for various electronic and spintronic devices based on ReS 2 .

Description: Three different chemical solutions are used to remove the possible contamination on GaN surface, while Ga 2 O 3 is still found at the surface. After thermal annealing at 710 °C in the ultrahigh vacuum (UHV) chamber and activated with Cs/O, all the GaN samples are successfully activated to the effective negative electron affinity (NEA) photocathodes. Among all samples, the GaN sample with the highest content of Ga 2 O 3 after chemical cleaning obtains the highest quantum efficiency. By analyzing the property of Ga 2 O 3 , the surface processing results, and electron affinity variations during Cs and Cs/O 2 deposition on GaN of other groups, it is suggested that before the adsorption of Cs, Ga 2 O 3 is not completely removed from GaN surface in our samples, which will combine with Cs and lead to a large decrease in electron affinity. Furthermore, the effective NEA is formed for GaN photocathode, along with the surface downward band bending. Based on this assumption, a new dipole model Ga 2 O 3 -Cs is suggested, and the experimental effects are explained and discussed.

Description: The phase transitions and ferroelectricity of LiNbO 3 and LiTaO 3 have been investigated theoretically from first principles. The phonon analyses and the molecular dynamics simulations revealed that the ferroelectric phase transition is not conventional displacive type but order-disorder type with strong correlation between cation displacements. According to the evaluated potential energy surfaces around the paraelectric structures, the large difference in ferroelectricity between the two oxides results from the little difference in short-range interionic interaction between Nb-O and Ta-O. As the results of the crystal orbital overlap population analyses, the different short-range interaction originates from the difference in covalency between Nb4 d -O2 p and Ta5 d -O2 p orbitals, particularly d xz - p x / d yz - p y orbitals ( π orbitals), from the electronic point of view.

Description: The reported values of bandgap of rutile GeO 2 calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO 2 using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O- p and Ge-( s and p ) orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.

Description: Carrier-type control of spin-glass (cluster spin-glass) is studied in order to engineer basic magnetic semiconductor elements using the memory functions of spin-glass. A key of carrier-polarity control in magnetite is the valence engineering between Fe(II) and Fe(III) that is achieved by Ti(IV) substitution. Single phases of (001)-oriented Fe 3− x Ti x O 4 thin films have been obtained on spinel MgAl 2 O 4 substrates by pulsed laser deposition. Thermoelectric power measurements reveal that Ti-rich films ( x  = 0.8) show p -type conduction, while Ti-poor films ( x  = 0.6–0.75) show n -type conduction. The systematic Fe(III) reduction to Fe(II) followed by Ti(IV) substitution in the octahedral sublattice is confirmed by the X-ray absorption spectra. All of the Fe 3− x Ti x O 4 films ( x  = 0.6–0.8) exhibit ferrimagnetism above room temperature. Next, the spin-glass behaviors of Ti-rich Fe 2.2 Ti 0.8 O 4 film are studied, since this magnetically diluted system is expected to exhibit the spin-glass behaviors. The DC magnetization and AC susceptibility measurements for the Ti-rich Fe 2.2 Ti 0.8 O 4 film reveal the presence of the spin glass phase. Thermal- and magnetic-field-history memory effects are observed and are attributed to the long time-decay nature of remanent magnetization. The detailed analysis of the time-dependent thermoremanent magnetization reveals the presence of the cluster spin glass state.

Description: We study the pair complexation of a single, highly charged polyelectrolyte (PE) chain (of 25 or 50 monomers) with like-charged patchy protein models (CPPMs) by means of implicit-solvent, explicit-salt Langevin dynamics computer simulations. Our previously introduced set of CPPMs embraces well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size with mono- and multipole moments comparable to those of globular proteins with similar size. We observe large binding affinities between the CPPM and the like-charged PE in the tens of the thermal energy, k B T , that are favored by decreasing salt concentration and increasing charge of the patch(es). Our systematic analysis shows a clear correlation between the distance-resolved potentials of mean force, the number of ions released from the PE, and CPPM orientation effects. In particular, we find a novel two-site binding behavior for PEs in the case of two-patched CPPMs, where intermediate metastable complex structures are formed. In order to describe the salt-dependence of the binding affinity for mainly dipolar (one-patched) CPPMs, we introduce a combined counterion-release/Debye-Hückel model that quantitatively captures the essential physics of electrostatic complexation in our systems.

Description: We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Description: A high-speed impedance measurement system was developed, which enables the measurement of various characteristics of CW and pulsed plasmas with time resolution of less than a microsecond. For this system, a voltage and current sensor is implemented in a printed circuit board to sense the radio frequency signals. A digital board, which has a high-speed analog to digital converter and a field-programmable gate-array, is used to calculate the impedance of the signal. The final output of impedance is measured and stored with a maximum speed of 3 Msps. This sensor system was tested in a pulsed-plasma by applying it to the point between the matching box and the plasma chamber. The experimental equipment was constructed connecting the matching box, a 13.56 MHz generator, a 2 MHz generator that produced pulsed power, and a pulse-signal generator. From the temporal behavior of the measured impedance, we were able to determine the time intervals of transient states, especially of the initial active state. This information can be used to set the pulse frequency and duty for plasma processing.

Description: The type of the Electron String Ion Sources (ESIS) is considered to be the appropriate one to produce pulsed C 4+ and C 6+ ion beams for cancer therapy accelerators. In fact, the new test ESIS Krion-6T already now provides more than 10 10 C 4+ ions per pulse and about 5 × 10 9 C 6+ ions per pulse. Such ion sources could be suitable to apply at synchrotrons. It has also been found that Krion-6T can provide more than 10 11 C 6+ ions per second at the 100 Hz repetition rate, and the repetition rate can be increased at the same or larger ion output per second. This makes ESIS applicable at cyclotrons as well. ESIS can be also a suitable type of ion source to produce the 11 C radioactive ion beams. A specialized cryogenic cell was experimentally tested at the Krion-2M ESIS for pulse injection of gaseous species into the electron string. It has been shown in experiments with stable methane that the total conversion efficiency of methane molecules to C 4+ ions reached 5%÷10%. For cancer therapy with simultaneous irradiation and precise dose control (positron emission tomography) by means of 11 C, transporting to the tumor with the primary accelerated 11 C 4+ beam, this efficiency is preliminarily considered to be large enough to produce the 11 C 4+ beam from radioactive methane and to inject this beam into synchrotrons.

Description: Magnetically tunable microwave bandpass filter structure have been designed and prepared by filling the ferrite rods into the metallic slits. The electromagnetic wave cannot propagate through the metallic slits. By filling the ferrite rods into the metallic slits, an enhanced optical transmission is obtained, which can be ascribed to the ferromagnetic resonance of the ferrite rods. Both the experimental and the simulated results show the center frequency and bandwidth of the passband can be tuned by the applied magnetic field, which exhibits a magnetically tunable behavior. This approach opens a way for designing tunable microwave bandpass filters.

Description: Background: Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction between Shine-Dalgarno (SD) sequence and its complementary sequence in the 16S rRNA is important in initiation, some genes lacking an SD ribosome binding site (RBS) are still well expressed. The objective of this study is to examine the pattern of distribution and diversity of RBS in fully sequenced bacterial genomes. The following three hypotheses were tested: SD motifs are prevalent in bacterial genomes; all previously identified SD motifs are uniformly distributed across prokaryotes; and genes with specific cluster of orthologous gene (COG) functions differ in their use of SD motifs. Results: Data for 2,458 bacterial genomes, previously generated by Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm) and currently available at the National Center for Biotechnology Information (NCBI), were analyzed. Of the total genes examined, ~77.0 % use an SD RBS, while ~23.0 % have no RBS. Majority of the genes with the most common SD motifs are distributed in a manner that is representative of their abundance for each COG functional category, while motifs 13 (5′-GGA-3′/5′-GAG-3′/5′-AGG-3′) and 27 (5′-AGGAGG-3′) appear to be predominantly used by genes for information storage and processing, and translation and ribosome biogenesis, respectively. Conclusion: These findings suggest that an SD sequence is not obligatory for translation initiation; instead, other signals, such as the RBS spacer, may have an overarching influence on translation of mRNAs. Subsequent analyses of the 5′ secondary structure of these mRNAs may provide further insight into the translation initiation mechanism.

Description: Background: Retention of sister centromere cohesion during meiosis I and its dissolution at meiosis II is necessary for balanced chromosome segregation and reduction of chromosome number. PATRONUS1 (PANS1) has recently been proposed to regulate centromere cohesion in Arabidopsis after meiosis I, during interkinesis. pans1 mutants lose centromere cohesion prematurely during interkinesis and segregate randomly at meiosis II. PANS1 protein interacts with components of the Anaphase Promoting Complex/Cyclosome (APC/C). Results: We show here that PANS1 protein is found mainly in prophase I of meiosis, with its level declining late in prophase I during diplotene. PANS1 also shows expression in dividing tissues. We demonstrate that, in addition to the previously reported premature loss of centromere cohesion during interkinesis, pans1 mutants show partially penetrant defects in centromere cohesion during meiosis I. We also determine that pans1 shows synthetic lethality at the level of the sporophyte, with Omission of Second Division 1 (osd1), which encodes a known inhibitor of the APC/C that is required for cell cycle progression during mitosis, as well as meiosis I and II. Conclusions: Our results show that PANS1 is expressed mainly in meiosis I where it has an important function and together with previous studies indicate that PANS1 and OSD1 are part of a network linking centromere cohesion and cell cycle progression through control of APC/C activity.

Description: Background: Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis. Results: We identified GIRAFFE2.1, a major QTL explaining ~18 % of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth. Conclusions: In combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod information to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation.

Description: Background: In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. Results: We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring

Description: In electrolyte solutions, an electric potential difference, called the Ionic Vibration Potential (IVP), related to the ionic vibration intensity, is generated by the application of an acoustic wave. Several theories based on a mechanical framework have been proposed over the years to predict the IVP for high ionic strengths, in the case where interactions between ions have to be accounted for. In this paper, it is demonstrated that most of these theories are not consistent with Onsager’s reciprocal relations. A new expression for the IVP will be presented that does fulfill the Onsager’s reciprocal relations. We obtained this expression by deriving general expressions of the corrective forces describing non-ideal effects in electrolyte solutions.

Description: In the framework of irreversible thermodynamics, we show that the sedimentation current in electrolyte solutions is mathematically equivalent to the low frequency limit of the ionic vibration current, appearing in the presence of an acoustic wave. This non-trivial result is obtained thanks to a careful choice of the reference frame used to express the mass fluxes in the context of electroacoustics. Coupled transport phenomena in electrolyte solutions can also be investigated in a mechanical framework, with a set of Newtonian equations for the dynamics of charged solutes. Both in the context of sedimentation and of electroacoustics, we show that the results obtained in the mechanical framework, in the ideal case (i.e., without interactions between ions), do satisfy the Onsager’s reciprocal relations. We also derive the general relation between corrective forces accounting for ionic interactions which must be fulfilled so that the Onsager’s reciprocal relations are verified. Finally, we show that no additional diffusion term needs to be taken into account in the flux of solutes (far from the walls), even if local concentration gradients exist, contrarily to what was done previously in the literature.

Description: Polyacenes in their armchair geometry (phenacenes) have recently been found to possess appealing electronic and optical properties with higher chemical stability and comparatively larger band gap as compared to linear polyacenes. They also behave as high-temperature superconductors upon alkali metal doping. Moreover, the optical properties of crystalline picene can be finely tuned by applying external pressure. We investigated the variation of optical gap as a function of altering the interplanar distances between parallel cofacial phenacene dimers. We employed both time-dependent density functional theory and density matrix renormalization group (DMRG) technique to investigate the lowest singlet excitations in phenacene dimer. Our study showed that the lowest singlet excitation in these systems evolved as a function of interplanar separation. The optical excitation energy gap decreases as a function of inverse interplanar separation of the phenacene dimer. The distant dependent variation of optical absorption at the dimer level may be comparable with experimental observation in picene crystal under pressure. DMRG study also demonstrates that besides picene, electronic properties of higher phenacenes can also be tunable by altering interplanar separation.

Description: A combined experimental and theoretical study is presented of fluctuations observed by field ion microscopy in the catalytic reaction of water production on a rhodium tip. A stochastic approach is developed to provide a comprehensive understanding of the different phenomena observed in the experiment, including burst noise manifesting itself in a bistability regime, noisy oscillations, and nanopatterns with a cross-like oxidized zone separating the surface into four quadrants centered on the {111} facets. The study is based on a stochastic model numerically simulating the processes of adsorption, desorption, reaction, and transport. The surface diffusion of hydrogen is described as a percolation process dominated by large clusters corresponding to the four quadrants. The model reproduces the observed phenomena in the ranges of temperature, pressures, and electric field of the experiment.

Description: A Gaussian- Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian- Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H 2 , O 2 , and N 2 , and the multi-atom system benzene. Together, it is shown that the Gaussian- Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.

Description: The hierarchical equations of motion (HEOM) method has recently emerged as an effective approach to simulate linear and nonlinear spectroscopic signals of molecular aggregates in the intermediate coupling regime. However, its application to large systems is still limited when there are a large number of molecules in the molecular aggregate. In this work, we propose a time domain two-particle approximation (TPA) in combination with the HEOM method to calculate the absorption and circular dichroism line shapes of molecular aggregates. The new method is shown to reduce the number of auxiliary density operators (ADOs) significantly for large systems, and a further truncation of the two-bath-set excited terms based on geometric considerations can lead to a linear increase of the number of ADOs with the system size. The validity of the HEOM-TPA method is first tested on one-dimensional model systems. The new method is then applied to calculate the absorption and circular dichroism line shapes of the Photosystem I core complex, as well as the population evolution of the Fenna-Matthews-Olson complex to demonstrate its effectiveness.

Description: We consider a system consisting of two interacting qubits that are individually coupled to separate heat baths at different temperatures. The quantum effects in heat transport are investigated in a numerically rigorous manner with a hierarchial equations of motion (HEOM) approach for non-perturbative and non-Markovian system-bath coupling cases under non-equilibrium steady-state conditions. For a weak interqubit interaction, the total system is regarded as two individually thermostatted systems, whereas for a strong interqubit interaction, the two-qubit system is regarded as a single system coupled to two baths. The roles of quantum coherence (or entanglement) between the two qubits (q-q coherence) and between the qubit and bath (q-b coherence) are studied through the heat current calculated for various strengths of the system-bath coupling and interqubit coupling for high and low temperatures. The same current is also studied using the time convolutionless (TCL) Redfield equation and using an expression derived from the Fermi golden rule (FGR). We find that the HEOM results exhibit turnover behavior of the heat current as a function of the system-bath coupling strength for all values of the interqubit coupling strength, while the results obtained with the TCL and FGR approaches do not exhibit such behavior, because they do not possess the capability of treating the q-b and q-q coherences. The maximum current is obtained in the case that the q-q coherence and q-b coherence are balanced in such a manner that coherence of the entire heat transport process is realized. We also find that the heat current does not follow Fourier’s law when the temperature difference is very large, due to the non-perturbative system-bath interactions.

Description: Recent progress in electronic and electromagnetic topological insulators has led to the demonstration of one way propagation of electron and photon edge states and the possibility of immunity to backscattering by edge defects. Unfortunately, such topologically protected propagation of waves in the bulk of a material has not been observed. We show, in the case of sound/elastic waves, that bulk waves with unidirectional backscattering-immune topological states can be observed in a time-dependent elastic superlattice. The superlattice is realized via spatial and temporal modulation of the stiffness of an elastic material. Bulk elastic waves in this superlattice are supported by a manifold in momentum space with the topology of a single twist Möbius strip. Our results demonstrate the possibility of attaining one way transport and immunity to scattering of bulk elastic waves.

Description: Amorphous silicon enables the fabrication of very high-efficiency crystalline-silicon-based solar cells due to its combination of excellent passivation of the crystalline silicon surface and permeability to electrical charges. Yet, amongst other limitations, the passivation it provides degrades upon high-temperature processes, limiting possible post-deposition fabrication possibilities (e.g., forcing the use of low-temperature silver pastes). We investigate the potential use of intrinsic amorphous silicon carbide passivating layers to sidestep this issue. The passivation obtained using device-relevant stacks of intrinsic amorphous silicon carbide with various carbon contents and doped amorphous silicon are evaluated, and their stability upon annealing assessed, amorphous silicon carbide being shown to surpass amorphous silicon for temperatures above 300 °C. We demonstrate open-circuit voltage values over 700 mV for complete cells, and an improved temperature stability for the open-circuit voltage. Transport of electrons and holes across the hetero-interface is studied with complete cells having amorphous silicon carbide either on the hole-extracting side or on the electron-extracting side, and a better transport of holes than of electrons is shown. Also, due to slightly improved transparency, complete solar cells using an amorphous silicon carbide passivation layer on the hole-collecting side are demonstrated to show slightly better performances even prior to annealing than obtained with a standard amorphous silicon layer.

Description: The crack initiation and growth mechanisms in an 2D graphene lattice structure are studied based on molecular dynamics simulations. Crack growth in an initial edge crack model in the arm-chair and the zig-zag lattice configurations of graphene are considered. Influence of the time steps on the post yielding behaviour of graphene is studied. Based on the results, a time step of 0.1 fs is recommended for consistent and accurate simulation of crack propagation. Effect of temperature on the crack propagation in graphene is also studied, considering adiabatic and isothermal conditions. Total energy and stress fields are analyzed. A systematic study of the bond stretching and bond reorientation phenomena is performed, which shows that the crack propagates after significant bond elongation and rotation in graphene. Variation of the crack speed with the change in crack length is estimated.

Description: Transfer-free graphene synthesis was performed on sapphire substrates by using the catalyst metal agglomeration technique, and the graphene film quality was compared to that synthesized on sputtered SiO 2 /Si substrates. Raman scattering measurements indicated that the graphene film on sapphire has better structural qualities than that on sputtered SiO 2 /Si substrates. The cross-sectional transmission microscopic study also revealed that the film flatness was drastically improved by using sapphire substrates instead of sputtered SiO 2 /Si substrates. These quality improvements seemed to be due the chemical and thermal stabilities of sapphire. Top-gate field-effect transistors were fabricated using the graphene films on sapphire, and it was confirmed that their drain current can be modulated with applied gate voltages. The maximum field-effect mobilities were estimated to be 720 cm 2 /V s for electrons and 880 cm 2 /V s for holes, respectively.

Description: A series of Si-doped AlN-rich AlGaN layers with low resistivities was characterized by a combination of nanoscale imaging techniques. Utilizing the capability of scanning electron microscopy to reliably investigate the same sample area with different techniques, it was possible to determine the effect of doping concentration, defect distribution, and morphology on the luminescence properties of these layers. Cathodoluminescence shows that the dominant defect luminescence depends on the Si-doping concentration. For lower doped samples, the most intense peak was centered between 3.36 eV and 3.39 eV, while an additional, stronger peak appears at 3 eV for the highest doped sample. These peaks were attributed to the (V III -O N ) 2− complex and the V III 3 − vacancy, respectively. Multimode imaging using cathodoluminescence, secondary electrons, electron channeling contrast, and atomic force microscopy demonstrates that the luminescence intensity of these peaks is not homogeneously distributed but shows a strong dependence on the topography and on the distribution of screw dislocations.

Description: A wide variety of physical systems respond to changing external conditions through discrete impulsive events called jerks, typically leading to collective “crackling noise” behaviour. Statistical distributions of jerky events often exhibit a universal scale-invariant power law, regardless of the specific mechanisms that are responsible for crackling noise processes and microstructural features that affect them. Here, we analyse uniaxial compression loading curves of two different physical systems that exhibit jerky behaviour: a martensitic NiMnGa single crystal and a stack of corrugated fiberboards. The jerky response is attributed to a non-uniform twin boundary motion along the NiMnGa crystal and to a local buckling of individual fiberboard layers. In both cases, our analysis reveals that different variables exhibit different statistical distributions. While the velocity of temporal processes within jerky events exhibits scale invariant distribution, the irreversible displacements induced throughout complete events are distributed around a characteristic value. In the case of NiMnGa, the displacement of a twin boundary is directly related to the length-scale of the internal magneto-mechanical microstructure. Similarly, the displacement of the fiberboard stack corresponds to the thickness of individual board layers. These observations reveal the effect of the internal microstructure on crackling noise systems and demonstrate an analysis approach for uncovering the details of the jerk mechanism.

Description: Background: The historical orogenesis and associated climatic changes of mountain areas have been suggested to partly account for the occurrence of high levels of biodiversity and endemism. However, their effects on dispersal, differentiation and evolution of many groups of plants are still unknown. In this study, we examined the detailed diversification history of Primula sect. Armerina, and used biogeographic analysis and macro-evolutionary modeling to investigate a series of different questions concerning the evolution of the geographical and ecological distribution of the species in this section. Results: We sequenced five chloroplast and one nuclear genes for species of Primula sect. Armerina. Neither chloroplast nor nuclear trees support the monophyly of the section. The major incongruences between the two trees occur among closely related species and may be explained by hybridization. Our dating analyses based on the chloroplast dataset suggest that this section began to diverge from its relatives around 3.55 million years ago, largely coinciding with the last major uplift of the Qinghai-Tibet Plateau (QTP). Biogeographic analysis supports the origin of the section in the Himalayan Mountains and dispersal from the Himalayas to Northeastern QTP, Western QTP and Hengduan Mountains. Furthermore, evolutionary models of ecological niches show that the two P. fasciculata clades have significantly different climatic niche optima and rates of niche evolution, indicating niche evolution under climatic changes and further providing evidence for explaining their biogeographic patterns. Conclusion: Our results support the hypothesis that geologic and climatic events play important roles in driving biological diversification of organisms in the QTP area. The Pliocene uplift of the QTP and following climatic changes most likely promoted both the inter- and intraspecific divergence of Primula sect. Armerina. This study also illustrates how niche evolution under climatic changes influences biogeographic patterns.

Description: Background: Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that putatively encodes a vacuolar aluminum-activated malate transporter1 (ALMT1)-like protein is a strong candidate gene. We hypothesize that fruit acidity is governed by a gene network in which Ma1 is key member. The goal of this study is to identify the gene network and the potential mechanisms through which the network operates. Results: Guided by Ma1, we analyzed the transcriptomes of mature fruit of contrasting acidity from six apple accessions of genotype Ma_ (MaMa or Mama) and four of mama using RNA-seq and identified 1301 fruit acidity associated genes, among which 18 were most significant acidity genes (MSAGs). Network inferring using weighted gene co-expression network analysis (WGCNA) revealed five co-expression gene network modules of significant (P 

Description: Background: Squaliform sharks represent approximately 27 % of extant shark diversity, comprising more than 130 species with a predominantly deep-dwelling lifestyle. Many Squaliform species are highly specialized, including some that are bioluminescent, a character that is reported exclusively from Squaliform sharks within Chondrichthyes. The interfamiliar relationships within the order are still not satisfactorily resolved. Herein we estimate the phylogenetic interrelationships of a generic level sampling of “squaloid” sharks and closely related taxa using aligned sequences derived from a targeted gene capture approach. The resulting phylogenetic estimate is further used to evaluate the age of first occurrence of bioluminescence in Squaliformes. Results: Our dataset comprised 172 putative ortholog exon sequences. Phylogenetic estimates result in a fully resolved tree supporting a monophyletic lineage of Squaliformes excluding Echinorhinus. Non-luminous Squalidae are inferred to be the sister to a clade comprising all remaining Squaliform families. Our results suggest that the origin of photophores is coincident with an elevated diversification rate and the splitting of families Dalatiidae, Etmopteridae, Oxynotidae and Somniosidae at the transition of the Lower to the Upper Cretaceous. The presence of luminous organs was confirmed for the Sleeper shark genus Zameus. These results indicate that bioluminescence in sharks is not restricted solely to the families Etmopteridae and Dalatiidae as previously believed. Conclusions: The sister-clade to non-luminous Squalidae comprises five families. The presence of photophores is reported for extant members of three out of these five families based on results of this study, i.e. Lantern sharks (Etmopteridae), Kitefin sharks (Dalatiidae) and Sleeper sharks (Somniosidae). Our results suggest that the origin of luminous organs arose during the rapid diversification event that gave rise to the extant Squaliform families. These inferences are consistent with the idea of diversification of Squaliform sharks being associated with the emergence of new deep-sea habitats in the Lower Cretaceous, which may have been facilitated by the evolution of bioluminescence.

Description: We performed density functional theory (DFT) calculations for a bi-layered heterostructure combining a graphene layer with a MoS 2 layer with and without intercalated Li atoms. Our calculations demonstrate the importance of the van der Waals (vdW) interaction, which is crucial for forming stable bonding between the layers. Our DFT calculation correctly reproduces the linear dispersion, or Dirac cone, feature at the Fermi energy for the isolated graphene monolayer and the band gap for the MoS 2 monolayer. For the combined graphene/MoS 2 bi-layer, we observe interesting electronic structure and density of states (DOS) characteristics near the Fermi energy, showing both the gap like features of the MoS 2 layer and in-gap states with linear dispersion contributed mostly by the graphene layer. Our calculated total DOS in this vdW heterostructure reveals that the graphene layer significantly contributes to pinning the Fermi energy at the center of the band gap of MoS 2 . We also find that intercalating Li ions in between the layers of the graphene/MoS 2 heterostructure enhances the binding energy through orbital hybridizations between cations (Li adatoms) and anions (graphene and MoS 2 monolayers). Moreover, we calculate the dielectric function of the Li intercalated graphene/MoS 2 heterostructure, the imaginary component of which can be directly compared with experimental measurements of optical conductivity in order to validate our theoretical prediction. We observe sharp features in the imaginary component of the dielectric function, which shows the presence of a Drude peak in the optical conductivity, and therefore metallicity in the lithiated graphene/MoS 2 heterostructure.

Description: Carrier injection from Au electrodes to organic thin-film active layers can be greatly improved for both electrons and holes by nano-structural surface control of organic semiconducting thin films using long-chain aliphatic molecules on a SiO 2 gate insulator. In this paper, we demonstrate a stark contrast for a 2,5-bis(4-biphenylyl)bithiophene (BP2T) active semiconducting layer grown on a modified SiO 2 dielectric gate insulator between two different modifications of tetratetracontane and poly(methyl methacrylate) thin films. Important evidence that the field effect transistor (FET) characteristics are independent of electrode metals with different work functions is given by the observation of a conversion of the metal-semiconductor contact from the Schottky limit to the Bardeen limit. An air-stable light emitting FET with an Au electrode is demonstrated.

Description: Femtosecond optical pump-probe spectroscopy is used to reveal the influence of charge and magnetic order on polaron dynamics and coherent acoustic phonon oscillations in single crystals of charge-ordered, ferrimagnetic LuFe 2 O 4 . We experimentally observed the influence of magnetic order on polaron dynamics. We also observed a correlation between charge order and the amplitude of the acoustic phonon oscillations, due to photoinduced changes in the lattice constant that originate from the photoexcited electrons. This provides insight into the general behavior of coherent acoustic phonon oscillations in charge-ordered materials.

Description: In this work, we explore the hardening mechanisms in WB 4 -based solid solutions upon addition of Ta, Mn, and Cr using in situ radial X-ray diffraction techniques under non-hydrostatic pressure. By examining the lattice-supported differential strain, we provide insights into the mechanism for hardness increase in binary solid solutions at low dopant concentrations. Speculations on the combined effects of electronic structure and atomic size in ternary WB 4 solid solutions containing Ta with Mn or Cr are also included to understand the extremely high hardness of these materials.

Description: Background: Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. Results: Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties’ region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time. Conclusions: In conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.

Description: Background: The study evaluated genetic progress of a breeding program for common carp undergoing four generations of selection for increased harvest body weight from 2004 to 2014. The pedigree included 17,351 individual fish which were offspring of 342 sires and 352 dams. Genetic parameters for body weight at about two years of age and survival rate during grow-out period were also estimated using the residual maximum likelihood method applied to a two-trait linear mixed model. Direct response in body weight and correlated changes in survival were measured as the differences in: i) estimated breeding values (EBVs) between the two lines; and ii) EBVs of the selection line between successive generations. Results: Direct gain in body weight ranged from 0.20 to 0.90 genetic standard deviation units and averaged 7 % of the base population per generation (two years per generation). Correlated changes in survival were negligible, indicating that the selection program for high growth did not have any adverse effect on this trait in the present population. The heritability for body weight was moderate (0.17, s.e. 0.05), whereas the estimate for survival was low (0.05–0.17) but significantly different from zero across linear mixed and threshold generalised statistical models. Our results predict that body weight or/and other growth related traits will continue to respond to selection and that there is potential to improve survival through direct genetic means. Correlated improvement in survival to selection for increased body weight was hardly achieved, as the genetic correlation between the two traits was not different from zero. Conclusions: It is concluded that selection for increased harvest body weight resulted in significant improvement in growth performance of the present population of common carp Cyprinus carpio.

Description: Background: Spine surgery is one of the most difficult areas in which to achieve a good clinical outcome and pain medication is often used for a long period of time after surgery. The purpose of this study was to investigate whether pain medication use after spine surgery has been assessed previously with respect to clinical outcome. Methods: A systematic review of PubMed/MEDLINE databases was conducted from Jan 1st 2000 to Dec 31st 2009 using the search key words, “spine surgery” and “clinical outcome.” All publications reporting clinical outcomes were examined and analyzed for outcome measures and data with respect to pain medication use after spine surgery. Results: In total 990 articles met the inclusion criteria. Among them, 56 articles (5.7%) described definitive pain medication use after spine surgery; 98 articles (9.9%) used clinical outcome measures that incorporate pain medication assessment, although only one such study included a definitive description of pain medication use. Conclusions: Pain medication use after spine surgery was assessed in 15.5% of articles published during the last decade. The use of pain medication following spine surgery can affect clinical outcome and, therefore, needs to be taken into consideration for clinical assessment. In future studies, a detailed description of pain medication use and/or clinical outcome measures that incorporate pain medication assessment are advocated when reporting clinical outcomes after spine surgery so that it can be better assessed.

Description: Background: Matrix-metalloproteinases 9 (MMP-9) belongs to the class of matrix metalloproteinases whose main function is to degrade and remodel the extracellular matrix (ECM). MMP-9 has been shown to be an integral part of many diseases where modulation of the ECM is a key step such as cancer, osteoporosis and fibrosis. MMP-9 is secreted as a latent pro-enzyme that requires activation in the extracellular space. Therefore, identifying physiological and molecular contexts, which can activate MMP-9 is important. Results: Acidification of osteoclast-conditioned media to pH 5 resulted in a fragment with a size corresponding to active MMP-9. Also, treatment of recombinant proMMP-9 with recombinant cathepsin K (CTSK) at pH 5 yielded a fragment that corresponded to the molecular weight of active MMP-9, and showed MMP-9 activity. This activation was abrogated in the presence of CTSK inhibitor indicating that CTSK was responsible for the activation of pro-MMP-9. Knocking down CTSK in MDA-MB-231 cells also diminished MMP-9 activity compared to wild type control. Conclusions: Here we provide the first evidence that CTSK can cleave and activate MMP-9 in acidic environments such as seen in tumors and during bone resorption. This finding provides a key link between CTSK expression in tumors and bone and ECM remodeling, through MMP-9 activation. This novel mechanism to activate MMP-9 through extracellular physiological changes elucidated in this study reveals a protease-signaling network involving CTSK and MMP-9 and provides the impetus to explore ECM proteases as physiological markers and pharmacological targets.

Description: Background: Several epidemiologic studies indicate that maternal gestational weight gain (GWG) influences health outcomes in offspring. Any underlying mechanisms have, however, not been established. A recent study of 88 children based on the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort examined the methylation levels at 1,505 Cytosine-Guanine methylation (CpG) loci and found several to be significantly associated with maternal weight gain between weeks 0 and 18 of gestation. Since these results could not be replicated we wanted to examine associations between 0 and 18 week GWG and genome-wide methylation levels using the Infinium HumanMethylation450 BeadChip (450K) platform on a larger sample size, i.e. 729 newborns sampled from the Norwegian Mother and Child Cohort Study (MoBa). Results: We found no CpG loci associated with 0–18 week GWG after adjusting for the set of covariates used in the ALSPAC study (i.e. child’s sex and maternal age) and for multiple testing (q 〉 0.9, both 1,505 and 473,731 tests). Hence, none of the CpG loci linked with the genes found significantly associated with 0–18 week GWG in the ALSPAC study were significant in our study. Conclusions: The inconsistency in the results with the ALSPAC study with regards to the 0–18 week GWG model may arise for several reasons: sampling from different populations, dissimilar methylome coverage, sample size and/or false positive findings.

Description: Background: High disease burden and scarcity of healthcare resources present complex ethical dilemmas for nurses working in developing countries. We assessed nurses’ knowledge in ethics and their perceptions about Continuous Nurses’ Ethics Education (CNEE) for in-service nurses. Methods: Using an anonymous, pre-tested self-administered questionnaire, we assessed nurses’ knowledge in basic ethics concepts at three regional hospitals in Uganda. Adequate knowledge was measured by a score ≥50% in the knowledge assessment test. Nurses’ perceptions on CNEE were assessed using a six-point Likert scale. Results: Of 114 nurses, 91% were female; with mean age 44.7 (SD 10) years. Half were diploma, 47 (41%) certificates, 6 (5%) bachelors’ degrees and one masters’ level training. Overall, 18 (16%) scored ≥50% in the ethics knowledge test. Nurses with diploma or higher level of nursing training were less likely to fail the ethics knowledge than certificate-level nurses (OR 0.14, 95% CI: 0.02–0.7). Only 45% had ever attended at least one CNEE session and up to 93% agreed that CNEE is required to improve nurses’ ethics knowledge and practice. Conclusions: Nurses exhibited low knowledge in ethics and positive attitudes towards CNEE. We recommend structured CNEE programs to address basic concepts in nursing ethics and their application in clinical practice.

Description: Background: Pentalogy of Cantrell is a rare syndrome, first described by Cantrell and co-workers in 1958. The syndrome is characterized by the presence of five major congenital defects involving the diaphragm, abdominal wall, the diaphragmatic pericardium, lower sternum and various congenital intra-cardiac abnormalities. The syndrome has never been reported in Tanzania, although may have been reported from other African countries. Survival rate of the complete form of pentalogy of Cantrell is as low as 20%, but recent studies have reported normal growth achieved by 6 years of age where corrective surgeries were done; showing that surgical repair early in life is essential for survival.Case presentationThe African baby residing in Tanzania was referred from a district hospital on the second day of life. She was noted to have a huge omphalocele and ectopia cordis covered by a thin membrane, with bowels visible through the membrane and the cardiac impulse visible just below the epigastrium. Despite the physical anomaly, she appeared to saturate well in room air and had stable vitals. Her chest X-ray revealed the absence of the lower segments of the sternum and echocardiography showed multiple intra-cardiac defects. Based on these findings, the diagnosis of pentalogy of Cantrell was reached. On her fifth day of life, the neonate was noted to have signs of cardiac failure characterized by easy fatigability and restlessness during feeding. Cardiac failure treatment was initiated and she was discharged on parents’ request on the second week of life. Due to inadequate facilities to undertake this complex corrective surgery, arrangements were being made to refer her abroad. In the meantime, her growth and development was satisfactory until the age of 9 months, when she ran out of the medications and succumbed to death. Her parents could no longer afford transport cost to attend the monthly clinic visits, where the infant was getting free medication refill. Conclusions: The case reported here highlights that in resource limited settings; poor outcome in infants with complex congenital anomalies is a function of multiple factors. However, we believe that surgery would have averted mortality in this 9-month-old female infant. We hope to be able to manage these cases better in future following the recent establishment of cardiac surgery facilities at Muhimbili National Hospital.

Description: Semiconductor fabrication often requires the deposition of hydrogenated silicon nitride (SiN x H y ) film using SiH 4 /NH 3 /N 2 /He capacitively coupled plasma (CCP) discharge. As analysis of the discharge geometry is essential to understanding CCP deposition, the effect of electrode spacing on the two-dimensional distributions of electrons, ions, and metastable and radical molecules was analyzed numerically using a fluid model. The simulation shows that the spatial variations in the ionization rates near the sheath become more obvious as the electrode spacing increases. In addition, as molecule-molecule gas-phase reactions are significantly affected by the local residence time, large electrode spacings are associated with significant volumetric losses for positive ions. Consequently, an increase of the electrode spacing leads axial density profiles of ions to change from bell shaped to double humped. However, NH 4 + persistently maintains a bell-shaped axial density profile regardless of the degree of electrode spacing. We set the mole fraction of NH 3 to only 1% of the total flow at the inlet, but NH 4 + is the most abundant positive ion at the large electrode spacings. As the gas flow can transport the radicals around the space between the electrodes, we found that radical density distribution shifts toward the grounded electrode. The shift becomes pronounced as the electrode spacing increases. Finally, to validate our model, we compared the calculated deposition rate profile with the experimental data obtained along the wafer radius. According to our numerical results, the SiN x H y deposition rate decreases by approximately 16% when the electrode spacing increases from 9 to 20 mm.

Description: We have evaluated tunnel barriers formed in multi-walled carbon nanotubes (MWNTs) by an Ar atom beam irradiation method and applied the technique to fabricate coupled double quantum dots. The two-terminal resistance of the individual MWNTs was increased owing to local damage caused by the Ar beam irradiation. The temperature dependence of the current through a single barrier suggested two different contributions to its Arrhenius plot, i.e., formed by direct tunneling through the barrier and by thermal activation over the barrier. The height of the formed barriers was estimated. The fabrication technique was used to produce coupled double quantum dots with serially formed triple barriers on a MWNT. The current measured at 1.5 K as a function of two side-gate voltages resulted in a honeycomb-like charge stability diagram, which confirmed the formation of the double dots. The characteristic parameters of the double quantum dots were calculated, and the feasibility of the technique is discussed.

Description: Previous studies on magnetic flux expulsion as a function of cooldown procedures for elliptical superconducting radio frequency (SRF) niobium cavities showed that when the cavity beam axis is placed parallel to the helium cooling flow and sufficiently large thermal gradients are achieved, all magnetic flux could be expelled and very low residual resistance could be achieved. In this paper, we investigate flux trapping for the case of resonators positioned perpendicularly to the helium cooling flow, which is more representative of how SRF cavities are cooled in accelerators and for different directions of the applied magnetic field surrounding the resonator. We show that different field components have a different impact on the surface resistance, and several parameters have to be considered to fully understand the flux dynamics. A newly discovered phenomenon of concentration of flux lines at the cavity top leading to temperature rise at the cavity equator is presented.

Description: Detailed magnetically tunable ac electrical properties of x La 0.7 Sr 0.3 MnO 3 (LSMO)–(1 − x) ErMnO 3 (EMO) (x = 0.1, 0.3, and 0.5) multiferroic nanocomposites have been studied at 300 K in presence of varying magnetic field (H appl ), applied both in parallel and perpendicular configuration with respect to the measuring electric field. AC electrical properties have exhibited significant variation with H appl for all composites, whereas for parallel configuration of H appl such effect is very feeble for x = 0.3 composite. We have attributed this anisotropic behavior to the demagnetization effect in the sample. In contrast, for x = 0.1 and 0.5 composites, no such anisotropy effect is experimentally evidenced. Impedance and real part of impedance have been found to decrease with H appl at low frequency ( f ) region. We attribute this observation to the depinning of the magnetic domain walls from the grain boundaries pinning centers and thereby enhancing the spin dependent transport in the composite. For x = 0.3 composite, Nyquist plots have been fitted considering dominant contributions of LSMO and EMO grain boundaries and the interface region between them. However, for x = 0.1 composite, it corresponds to EMO grain boundaries and grain boundary interface region. The relaxation frequency ( f R ) is observed to shift at higher/lower f region in perpendicular/parallel configuration of H appl for x = 0.3 composite. This opposite variation of f R s with H appl for perpendicular and parallel configurations has been attributed to two competing factors of H appl induced enhancement of inductive part and H appl enhanced spin dependent transport causing fast relaxation processes in the sample. For x = 0.1 composite, in both configurations of H appl , f R s is shifting towards high f region, which has been discussed in terms of dominant role of spin dependent transport.

Description: A new high quality potential energy surface is calculated at a coupled-cluster single double triple level with an aug-cc-pV5Z basis set for the HCS + –He system. This potential energy surface is used in low energy quantum scattering calculations to provide a set of (de)-excitation cross sections and rate coefficients among the first 20 rotational levels of HCS + by He in the range of temperature from 5 K to 100 K. The paper discusses the impact of the new ab initio potential energy surface on the cross sections at low energy and provides a comparison with the HCO + –He system. The HCS + –He rate coefficients for the strongest transitions differ by factors of up to 2.5 from previous rate coefficients; thus, analysis of astrophysical spectra should be reconsidered with the new rate coefficients.

Description: A weak, paradoxically narrow resonance feature (shortly, the r -line) near the O 2 fundamental frequency in the collision-induced absorption spectrum of oxygen dissolved in liquid argon and liquid nitrogen ( T = 89 K) is resolved for the first time. An accurate band shape fitting routine to separate the r -line from the by-far more intense diffuse background and to study its behavior versus the oxygen mole fraction x which ranged from 0.03 up to 0.23 has been elaborated. At small x (≲0.07), the r -line intensity was found to scale as x 2 leaving no doubt that it is due to the solute-solute (O 2 –O 2 ) interactions. In line with our results on the p H 2 –LNe cryosystem [Herrebout, Phys. Rev. Lett. 101 , 093001 (2008)], the Lorentzian r -line shape and its extraordinary sharpness (half width at half height ≈ 1 cm −1 ) are indicative of the motional narrowing of the relative solute-solute translational spectrum. As x is further raised, ternary solute-solute interactions impede the r -line growth in the O 2 –LAr spectrum because of the cancellation effect [J. Van Kranendonk, Physica 23 , 825 (1957)]. Theoretical arguments are given that multiple interactions between the solutes should finally destroy the solute-solute induced r -line when the mixed solution approaches the limit of the pure liquid ( x = 1). Interestingly, the nonbinary effects are too weak to appreciably affect the quadratic r -line scaling in the O 2 –LN 2 cryosystem which persists up to x = 0.23. It is emphasized that studies of the resonant features in the collision-induced spectra of binary cryosolutions open up unique opportunities to spectroscopically trace the microscopic-scale diffusion.

Description: Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O ( N 6 ) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O ( N 5 ) computational cost.

Description: A first sharp diffraction peak (FSDP) is observed in the X-ray total structure factor of a molten mixture of RbCl-AgCl, while both pure melts of RbCl and AgCl do not exhibit FSDP individually. Molecular dynamics simulations were performed to investigate the origin of the FSDP with the polarizable ion model (PIM). Coexistence of covalent Ag–Cl and ionic Rb–Cl bonds leads the system to evolve intermediate range ordering, which is simulated by introducing the induced polarization in different ways between Ag–Cl with fully polarizable treatment based on Vashishta-Raman potential and Rb–Cl with suppression over-polarization in the nearest neighbor contribution based on Born-Meyer potential. The partial structure factors for both the Ag–Ag and Rb–Rb correlations, S AgAg ( Q ) and S RbRb ( Q ), show a positive contribution to the FSDP, while S AgRb ( Q ) for the Ag–Rb correlation exhibits a negative contribution, indicating that Ag and Rb ions are distributed in an alternating manner within the intermediate-range length scale. The origin of the intermediate-range chemical ordering of cations can be ascribed to the preferred direction of the dipole moments of anions in the PIM.

Description: The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N -body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.

Description: Despite the fundamental importance of electron density in density functional theory, perturbations are still usually dealt with using Hartree-Fock-like orbital equations known as coupled-perturbed Kohn-Sham (CPKS). As an alternative, we develop a perturbation theory that solves for the perturbed density directly, removing the need for CPKS. This replaces CPKS with a true Hohenberg-Kohn density perturbation theory. In CPKS, the perturbed density is found in the basis of products of occupied and virtual orbitals, which becomes ever more over-complete as the size of the orbital basis set increases. In our method, the perturbation to the density is expanded in terms of a series of density basis functions and found directly. It is possible to solve for the density in such a way that it makes the total energy stationary even if the density basis is incomplete.

Description: We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

Description: The characteristic properties of graphene make it useful in an assortment of applications. One particular application—the use of graphene in biosensors—requires a thorough understanding of graphene-peptide interactions. In this study, the binding of glycine (G) capped amino acid residues (termed GXG tripeptides) to trilayer graphene surfaces in aqueous solution was examined and compared to results previously obtained for peptide binding to single-layer free-standing graphene [A. N. Camden, S. A. Barr, and R. J. Berry, J. Phys. Chem. B 117 , 10691–10697 (2013)]. In order to understand the interactions between the peptides and the surface, binding enthalpy and free energy values were calculated for each GXG system, where X cycled through the typical 20 amino acids. When the GXG tripeptides were bound to the surface, distinct conformations were observed, each with a different binding enthalpy. Analysis of the binding energy showed the binding of peptides to trilayer graphene was dominated by van der Waals interactions, unlike the free-standing graphene systems, where the binding was predominantly electrostatic in nature. These results demonstrate the utility of computational materials science in the mechanistic explanation of surface-biomolecule interactions which could be applied to a wide range of systems.

Description: A class of real spectral triples that are similar in structure to a Riemannian manifold but have a finite-dimensional Hilbert space is defined and investigated, determining a general form for the Dirac operator. Examples include fuzzy spaces defined as real spectral triples. Fuzzy 2-spheres are investigated in detail, and it is shown that the fuzzy analogues correspond to two spinor fields on the commutative sphere. In some cases, it is necessary to add a mass mixing matrix to the commutative Dirac operator to get a precise agreement for the eigenvalues.

Description: Scanning nano-focused X-ray diffraction and high-angle annular dark-field scanning transmission electron microscopy are used to investigate the crystal structure of ramp-edge junctions between superconducting electron-doped Nd 1.85 Ce 0.15 CuO 4 and superconducting hole-doped La 1.85 Sr 0.15 CuO 4 thin films, the latter being the top layer. On the ramp, a new growth mode of La 1.85 Sr 0.15 CuO 4 with a 3.3° tilt of the c -axis is found. We explain the tilt by developing a strain accommodation model that relies on facet matching, dictated by the ramp angle, indicating that a coherent domain boundary is formed at the interface. The possible implications of this growth mode for the creation of artificial domains in morphotropic materials are discussed.

Description: We propose a tunable metasurface consisting of an array of graphene ribbons on a silver mirror with a SiO 2 gap layer to control reflected wavefront at terahertz frequencies. The graphene ribbons exhibit localized plasmon resonances depending on their Fermi levels to introduce abrupt phase shifts along the metasurface. With interference of the Fabry-Perot resonances in the SiO 2 layer, phase shift through the system is largely accumulated, covering the 0-to-2π range for full control of the wavefront. Numerical simulations prove that wide-angle beam steering up to 53° with a high reflection efficiency of 60% is achieved at 5 THz within a switching time shorter than 0.6 ps.

Description: We introduce a transparent diode that shows both high rectifying ratio and low leakage current at process temperature below 250 °C. This device is clearly distinguished from all previous transparent diodes in that the rectifying behavior results from the junction between a semiconductor (amorphous indium-gallium-zinc oxide (a-IGZO)) and insulator (SiN x ). We systematically study the properties of each junction within the device structure and demonstrate that the a-IGZO/SiN x junction is the source of the outstanding rectification. The electrical characteristics of this transparent diode are: 2.8 A/cm 2 on-current density measured at −7 V; lower than 7.3 × 10 −9 A/cm 2 off-current density; 2.53 ideality factor; and high rectifying ratio of 10 8 –10 9 . Furthermore, the diode structure has a transmittance of over 80% across the visible light range. The operating principle of the indium-tin oxide (ITO)/a-IGZO/SiN x /ITO device was examined with an aid of the energy band diagram and we propose a preliminary model for the rectifying behavior. Finally, we suggest further directions for research on this transparent diode.

Description: Relaxation mechanisms in polyaniline (PANI)/Reduced Graphene Oxide (RGO) nanocomposites are investigated using broad band dielectric spectroscopy. The multilayered nanostructural features of the composites and the intimate interactions between PANI and RGO are evidenced by field emission scanning electron microscopy, transmission electron microscopy, and Raman spectroscopy. Increasing the RGO fraction in the composites results in a relaxation process observed at a frequency of ca. 5 kHz. This mechanism is associated with an electrical charge trapping phenomenon occurring at the PANI/RGO interfaces. The dielectric relaxation processes are interpreted according to the Sillars approach and the results are consistent with the presence of conducting prolate spheroids (RGO) embedded into a polymeric matrix (PANI). Dielectric permittivity data are analyzed within the framework of the Kohlrausch-William-Watts model, evidencing a Debye-like relaxation process.

Description: The lattice strain and domain switching behavior of x BiScO 3 –(1- x )PbTiO 3 ( x  = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral x BiScO 3 –(1- x )PbTiO 3 ( x  = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic.

Description: We present a comparative study of high frequency dynamics and low frequency noise in elliptical magnetic tunnel junctions with lateral dimensions under 100 nm presenting current-switching phenomena. The analysis of the high frequency oscillation modes with respect to the current reveals the onset of a steady-state precession regime for negative bias currents above J = 10 7 A / cm 2 , when the magnetic field is applied along the easy axis of magnetization. By the study of low frequency noise for the same samples, we demonstrate the direct link between changes in the oscillation modes with the applied current and the normalised low frequency (1/f) noise as a function of the bias current. These findings prove that low frequency noise studies could be a simple and powerful technique to investigate spin-torque based magnetization dynamics.

Description: Copper is a harmful metal impurity that significantly impacts the performance of silicon-based devices if present in active regions. In this contribution, we propose a fast method consisting of simultaneous illumination and annealing for the detection of copper contamination in p-type silicon. Our results show that, within minutes, such method is capable of producing a significant reduction of the minority carrier lifetime. A spatial distribution map of copper contamination can then be obtained through the lifetime values measured before and after degradation. In order to separate the effect of the light-activated copper defects from the other metastable complexes in low resistivity Cz-silicon, we carried out a dark anneal at 200 °C, which is known to fully recover the boron-oxygen defect. Similar to the boron-oxygen behavior, we show that the dark anneal also recovers the copper defects. However, the recovery is only partial and it can be used to identify the possible presence of copper contamination.

Description: Normal-incidence Ge-on-Si photodiodes with 300 nm thick intrinsic Ge absorber layer and black silicon light-trapping are fabricated and analyzed with regard to their responsivity. Compared to a standard Ge-on-Si photodiode without black silicon, the black silicon device exhibits a 3-times increased responsivity of 0.34 A/W at 1550 nm. By that, the problematic bandwidth-responsivity trade-off in ultrafast Ge-on-Si detectors can be widely overcome. The black silicon light-trapping structure can be applied to the device rear during back-end processing.

Description: An integrated approach to thermal modulation of relative phase between two optical vortices with opposite chirality has been demonstrated on a silicon-on-insulator substrate. The device consists of a silicon-integrated optical vortex emitter and a phase controlled 3 dB coupler. The relative phase between two optical vortices can be actively modulated on chip by applying a voltage on the integrated heater. The phase shift is shown to be linearly proportional to applied electrical power, and the rotation angle of the interference pattern is observed to be inversely proportional to topological charge. This scheme can be used in lab-on-chip, communications and sensing applications. It can be intentionally implemented with other modulation elements to achieve more complicated applications.

Description: Tailored optical output, such as color purity and efficient optical intensity, are critical considerations for displays, particularly in mobile applications. To this end, we demonstrate a replica molded photonic crystal structure with embedded quantum dots. Electrohydrodynamic jet printing is used to control the position of the quantum dots within the device structure. This results in significantly less waste of the quantum dot material than application through drop-casting or spin coating. In addition, the targeted placement of the quantum dots minimizes any emission outside of the resonant enhancement field, which enables an 8× output enhancement and highly polarized emission from the photonic crystal structure.

Description: This paper investigates the effects of particle shape and Stokes number on the behaviour of non-spherical particles in turbulent channel flow. Although there are a number of studies concerning spherical particles in turbulent flows, most important applications occurring in process, energy, and pharmaceutical industries deal with non-spherical particles. The computation employs a unique and novel four-way coupling with the Lagrangian point-particle approach. The fluid phase at low Reynolds number ( Re τ = 150) is modelled by direct numerical simulation, while particles are tracked individually. Inter-particle and particle-wall collisions are also taken into account. To explore the effects of particles on the flow turbulence, the statistics of the fluid flow such as the fluid velocity, the terms in the turbulence kinetic energy equation, the slip velocity between the two phases and velocity correlations are analysed considering ellipsoidal particles with different inertia and aspect ratio. The results of the simulations show that the turbulence is considerably attenuated, even in the very dilute regime. The reduction of the turbulence intensity is predominant near the turbulence kinetic energy peak in the near wall region, where particles preferentially accumulate. Moreover, the elongated shape of ellipsoids strengthens the turbulence attenuation. In simulations with ellipsoidal particles, the fluid-particle interactions strongly depend on the orientation of the ellipsoids. In the near wall region, ellipsoids tend to align predominantly within the streamwise ( x ) and wall-normal ( y ) planes and perpendicular to the span-wise direction, whereas no preferential orientation in the central region of the channel is observed. Important conclusions from this work include the effective viscosity of the flow is not affected, the direct dissipation by the particles is negligible, and the primary mechanism by which the particles affect the flow is by altering the turbulence structure around the turbulence kinetic energy peak.

Description: Alternative acceleration technologies are currently under development for cost-effective, robust, compact, and efficient solutions. One such technology is plasma wakefield acceleration, driven by either a charged particle or laser beam. However, the potential issues must be studied in detail. In this paper, the emittance evolution of a witness beam through elastic scattering from gaseous media and under transverse focusing wakefields is studied.

Description: The potential of a laser-ablation plasma was controlled stably up to +2 kV by using external ring electrodes. A stable electron sheath was formed between the plasma and the external electrodes by placing the ring electrodes away from the boundary of the drifting plasma. The plasma kept the potential for a few μ s regardless of the flux change of the ablation plasma. We also found that the plasma potential changed with the expansion angle of the plasma from the target. By changing the distance between the plasma boundary and the external electrodes, we succeeded in controlling the potential of laser-ablation plasma.