bluuebunny/crossref_metadata_2025 huggingface dataset:
High In-content InGaN nano-pyramids: Tuning crystal homogeneity by optimized nucleation of GaN seeds
Authors: Bi Zhaoxia , Gustafsson Anders , Lenrick Filip , Lindgren David , Hultin Olof , Wallenberg L. Reine , Ohlsson B. Jonas , Monemar Bo , Samuelson Lars
Published: January 2018

Uniform arrays of submicron hexagonal InGaN pyramids with high morphological and material homogeneity, reaching an indium composition of 20%, are presented in this work. The pyramids were grown by selective area metal-organic vapor phase epitaxy and nucleated from small openings in a SiN mask. The growth selectivity was accurately controlled with diffusion lengths of the gallium and indium species, more than 1 μm on the SiN surface. High material homogeneity of the pyramids was achieved by inserting a precisely formed GaN pyramidal seed prior to InGaN growth, leading to the growth of well-shaped InGaN pyramids delimited by six equivalent 101¯1 facets. Further analysis reveals a variation in the indium composition to be mediated by competing InGaN growth on two types of crystal planes, 101¯1 and (0001). Typically, the InGaN growth on 101¯1 planes is much slower than on the (0001) plane. The formation of the (0001) plane and the growth of InGaN on it were found to be dependent on the morphology of the GaN seeds. We propose growth of InGaN pyramids seeded by 101¯1-faceted GaN pyramids as a mean to avoid InGaN material grown on the otherwise formed (0001) plane, leading to a significant reduction of variations in the indium composition in the InGaN pyramids. The InGaN pyramids in this work can be used as a high-quality template for optoelectronic devices having indium-rich active layers, with a potential of reaching green, yellow, and red emissions for LEDs.
Simulation of FRET dyes allows quantitative comparison against experimental data
Authors: Reinartz Ines , Sinner Claude , Nettels Daniel , Stucki-Buchli Brigitte , Stockmar Florian , Panek Pawel T. , Jacob Christoph R. , Nienhaus Gerd Ulrich , Schuler Benjamin , Schug Alexander
Published: January 2018

Fully understanding biomolecular function requires detailed insight into the systems’ structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.
Interface-induced perpendicular magnetic anisotropy of Co nanoparticles on single-layer h-BN/Pt(111)
Authors: Watanabe Takahiro , Yamada Yoichi , Koide Akihiro , Entani Shiro , Li Songtian , Popov Zakhar I. , Sorokin Pavel B. , Naramoto Hiroshi , Sasaki Masahiro , Amemiya Kenta , Sakai Seiji
Published: January 2018

Ferromagnetism with perpendicular magnetic anisotropy (PMA) was observed at room temperature in cobalt nanoparticles (NPs) grown on hexagonal boron nitride (h-BN) on a Pt(111) surface. It was shown that the Co NPs have planar hexagonal shapes with a mean diameter of ∼20 nm and a mean height of ∼1.6 nm. The depth-resolved analysis of X-ray magnetic circular dichroism at the Co L2,3-edges revealed that in the ferromagnetic Co NPs, the ratio of the orbital magnetic moment to the spin magnetic moment in the out-of-plane direction becomes larger at the Co NP/h-BN interface than the ratio in bulk Co. The B and N K-edge near edge X-ray absorption fine structures showed the orbital hybridization between the π orbitals of h-BN and d orbitals of Co at the interface, as an origin of the orbital magnetic moment enhancement possibly giving rise to PMA in the Co NPs.
Binding branched and linear DNA structures: From isolated clusters to fully bonded gels
Authors: Fernandez-Castanon J. , Bomboi F. , Sciortino F.
Published: January 2018

The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10 °C to 55 °C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel, and as a cluster fluid depending on the selected r.
Directly calculated electrical conductivity of hot dense hydrogen from molecular dynamics simulation beyond Kubo-Greenwood formula
Authors: Ma Qian , Kang Dongdong , Zhao Zengxiu , Dai Jiayu
Published: January 2018

Electrical conductivity of hot dense hydrogen is directly calculated by molecular dynamics simulation with a reduced electron force field method, in which the electrons are represented as Gaussian wave packets with fixed sizes. Here, the temperature is higher than electron Fermi temperature (T>300 eV, ρ=40 g/cc). The present method can avoid the Coulomb catastrophe and give the limit of electrical conductivity based on the Coulomb interaction. We investigate the effect of ion-electron coupled movements, which is lost in the static method such as density functional theory based Kubo-Greenwood framework. It is found that the ionic dynamics, which contributes to the dynamical electrical microfield and electron-ion collisions, will reduce the conductivity significantly compared with the fixed ion configuration calculations.
Effect of the addition of graphite oxide on the morphology of the alumina aerogels
Authors: Ren Lili , He He
Published: January 2018

We have successfully incorporated graphene oxide (GO) into alumina aerogels and found that the morphology of alumina was changed from the original small particle accumulation to the layered accumulation. GO with two-dimensional layered structure was thought acting as a template, and under the influence of it, we obtained the alumina with three-dimensional structure by lamellar stacking finally.
Local strain field engineering on interfacial thermal resistance of graphene nanoribbon
Authors: Xue Yixuan , Chen Yang , Cai Kun , Liu Zi-Yu , Zhang Yingyan , Wei Ning
Published: January 2018

Strain engineering shows distinct advantages in thermal management by tuning thermal resistance in a wide range. Till now, most of the relative studies were concentrated in uniform deformation, wherein the effects of the localized strain field are rarely exploited. Herein, by using non-equilibrium molecular dynamics simulations, we explore the local strain field engineering effects on the interfacial thermal resistance (ITR) of graphene nanoribbons (GNRs). The model of GNRs employed in this work contains extended drag threads, which are used to create a local strain field. Our simulation results show that the ITR has a quasi-linear relationship with the local tensile strain. GNRs are very sensitive to the local strain field in terms of ITR with a maximum enhancement factor of ∼1.5 at the strain of 10%. The ITR is found to depend linearly on the local strain. This phenomenon is thoroughly explained by micro-structure deformation, heat flux scattering, and phonon density of state overlapping. Our findings here offer a simple yet useful tool in modulating the thermal properties of graphene and other two-dimensional materials by using local strain engineering.
Solution-processed single-wall carbon nanotube transistor arrays for wearable display backplanes
Authors: Kang Byeong-Cheol , Ha Tae-Jun
Published: January 2018

In this paper, we demonstrate solution-processed single-wall carbon nanotube thin-film transistor (SWCNT-TFT) arrays with polymeric gate dielectrics on the polymeric substrates for wearable display backplanes, which can be directly attached to the human body. The optimized SWCNT-TFTs without any buffer layer on flexible substrates exhibit a linear field-effect mobility of 1.5cm2/V-s and a threshold voltage of around 0V. The statistical plot of the key device metrics extracted from 35 SWCNT-TFTs which were fabricated in different batches at different times conclusively support that we successfully demonstrated high-performance solution-processed SWCNT-TFT arrays which demand excellent uniformity in the device performance. We also investigate the operational stability of wearable SWCNT-TFT arrays against an applied strain of up to 40%, which is the essential for a harsh degree of strain on human body. We believe that the demonstration of flexible SWCNT-TFT arrays which were fabricated by all solution-process except the deposition of metal electrodes at process temperature below 130oC can open up new routes for wearable display backplanes.
An ecosystem services filter for rangeland restoration
Authors: Brown Joel R. , MacLeod Neil D.
Published: January 2018

Rangeland restoration ecology and practice have profited from an emphasis on research and development that emphasises technical tools for monitoring and altering ecological processes. However, this approach has not been particularly effective in conveying the potential value of restoration projects to both an interested public and funding institutions. Rangelands, by their nature, are extensive in both land area and ecological process, and the ecosystem services derived from them reflects that diversity of resources. Without explicit links to specific ecological process outputs (i.e. commodity production, pollution reduction), it is difficult to capture and convey the values that may be achieved through rangeland restoration efforts. In this paper, we review the intersection of the practice of rangeland restoration ecology and ecosystem service provision as a basis for better evaluating and communicating potential projects. We also suggest that rangeland restoration projects pay more attention to explicitly defining the spatial and temporal extent of projects as a way to enhance communication with land owners, policy-makers and the concerned public.
Using behavioural science to improve Australia’s environmental regulation
Authors: Martin Paul , Hine Donald W.
Published: January 2018

Australia has many environmental regulations intended to alter the behaviour of rural landholders. One key issue relates to managing invasive plants and animals, where effective action requires sustained (and largely voluntary) action and sustained investment. Eliciting high levels of compliance is a difficult problem, because different landholders have widely different attitudes and motivations. What works with one group of people may not work with another, and indeed may be counterproductive.
This study demonstrates the use of contemporary psychological methods to identify groups of landholders who demonstrate different attitudes and behaviours in relation to weed control. It shows that identifiable segments do respond differently to different mixes of regulation, incentives and community action. It suggests that some commonly promoted interventions may actually be counterproductive in encouraging desirable action with some groups.
The study shows that behavioural precision is important in creating effective compliance strategies in weeds management, and it demonstrates some of the methods that may be used to achieve that precision.
Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function
Authors: Rengachari Srinivasan , Groiss Silvia , Devos Juliette M. , Caron Elise , Grandvaux Nathalie , Panne Daniel
Published: January 2018

Significance

Cytokines interact with their receptors and activate JAK–STAT signaling pathways that lead to changes in gene expression. In mammals, there are seven STATs that have arisen due to gene duplication and genetic drift. STATs have similar DNA binding specificity, and how individual STATs have subfunctionalized to regulate very specific cytokine responses in cells is poorly understood. Here we describe X-ray structures that show how one STAT family member, STAT2, specifically pairs with a member of the IRF family of transcription factors, IRF9. Despite overall structural similarity among STAT and IRF family members, surface features in the interacting domains of IRF9 and STAT2 have diverged to enable specific interaction between these family members and to enable the antiviral response.
Aliud pro alio
Authors: Poppi Fabio I. M. , Gattinara Pietro Castelli
Published: January 2018

This article explores how narratives create connections between the micro-context and the macro-context, focusing on the narratives produced by a neo-Nazi group within ‘Blood and Honour’, a neo-Nazi gathering in Italy. The analysis presents a series of thematic narratives that describe how the neo-Nazi members see themselves in daily life, with their private and family sphere and how they aim to impact the political and cultural world. From these narratives, it is possible to understand how the neo-Nazi group sees society and justify the marginal role that they occupy in modern society. From this perspective, narratives operate as symbolic practice of identity creation in which members of the group negotiate new images of themselves and of their political and cultural movement. As we show, the neo-Nazi members aim to obtain legitimation and recognition in order to express a greater symbolic and social power.
Derivational complexity vs. transfer effects
Authors: Hopp Holger , Putnam Michael T. , Vosburg Nora
Published: January 2018

We investigate whether non-targetwh-questions in heritage Low German and L2 English speakers are due primarily to cross-linguistic transfer or the reduction of grammatical complexity in developing grammars as modelled by the Derivational Complexity Hypothesis (DCH,Jakubowicz 2005). Previous research shows that complex (i.e. cross-clausal)wh-dependencies pose more difficulty to child L1 and adult L2 learners than monoclausal dependencies (Jakubowicz & Strik, 2008;Schulz, 2011;Slavkov, 2015). To avoid complex dependencies, learners often use medial constructions where thewh-item surfaces once at the left periphery of the embedded CP and a second time at the left periphery of the matrix clause. Medial-whis ungrammatical in English, though possible in German and its varieties, e.g. the low German Plautdietsch. In this study, we investigate the linguistic behavior of twelve (n = 12) bilingual Plautdietsch-English speakers in Southwestern Kansas, analyzing their production and judgments ofwh-questions in both languages. In production and judgment tasks, we find that, in the L1, only heritage speakers produced medial-wh, while in L2 English, only late L2 learners produced medial-wh. This pattern cannot be due to transfer, since speakers produce medial-whin only one of their languages. Instead, medial-whsurfaces as a mechanism to reduce syntactic complexity in the less dominant language, irrespective of whether it is the L1 or the L2 or whether it was acquired early or late. We argue that the DCH can account for grammatical restructuring in both heritage L1 speakers and late L2 speakers and discuss its potential as a metric of incomplete acquisition and attrition in bilingual syntax.
Building bridges with words: an inferential account of ethical univocity
Authors: Warren Mark Douglas
Published: January 2018

Explaining genuine moral disagreement is a challenge for metaethical theories. For expressivists, this challenge comes from the plausibility of agents making seemingly univocal claims while expressing incongruent conative attitudes. I argue that metaethical inferentialism – a deflationary cousin to expressivism, which locates meaning in the inferential import of our moral assertions rather than the attitudes they express – offers a unique solution to this problem. Because inferentialism doesn’t locate the source of moral disagreements in a clash between attitudes, but instead in conflicts between the inferential import of ethical assertions, the traditional problem for expressivism can be avoided. After considering two forms of inferentialism that lead to revenge versions of the problem, I conclude by recommending that we understand the semantics of moral disagreements pragmatically: the source of univocity does not come from moral or semantic facts waiting to be described, but instead from the needs that ethical and semantic discourses answer – a solution to the problems of what we are to do and how we are to talk about it.
Freedom and the value of games
Authors: Gingerich Jonathan
Published: January 2018

This essay explores the features in virtue of which games are valuable or worthwhile to play. The difficulty view of games holds that the goodness of games lies in their difficulty: by making activities more complex or making them require greater effort, they structure easier activities into more difficult, therefore more worthwhile, activities. I argue that a further source of the value of games is that they provide players with an experience of freedom, which they provide both as paradigmatically unnecessary activities and by offering opportunities for relatively unconstrained choice inside the ‘lusory’ world that players inhabit.
Strain and distortion monitoring during arc welding by 3D digital image correlation
Authors: Chen Jian , Feng Zhili
Published: January 2018

A novel three-dimensional (3D) digital image correlation (DIC) approach using a stereovision system was developed to measure the evolution of strain and distortion near the fusion zone during the gas tungsten arc welding process. Unlike the previously reported two-dimensional (2D) DIC approach using a single camera, the 3D DIC method was immune to the out-of-plane displacement and was capable of measuring 3D deformation. Both 2D and 3D DIC approaches in welding applications were based on the utilisation of the novel high-temperature speckle and the pulsed laser illumination plus bandpass filters. However, the speckle pattern was partially specular reflective causing issues in subset matching in the 3D approach. A new algorithm and experimental procedure was incorporated to solve this problem.
The relationship between form and function throughout the history of excitation–contraction coupling
Authors: Franzini-Armstrong Clara
Published: January 2018

The concept of excitation–contraction coupling is almost as old as Journal of General Physiology. It was understood as early as the 1940s that a series of stereotyped events is responsible for the rapid contraction response of muscle fibers to an initial electrical event at the surface. These early developments, now lost in what seems to be the far past for most young investigators, have provided an endless source of experimental approaches. In this Milestone in Physiology, I describe in detail the experiments and concepts that introduced and established the field of excitation–contraction coupling in skeletal muscle. More recent advances are presented in an abbreviated form, as readers are likely to be familiar with recent work in the field.
Bilateral comparison of 1 V and 10 V standards between the NMISA (South Africa) and the BIPM April to June 2017 (part of the ongoing BIPM key comparison BIPM.EM-K11.a and b)
Authors: Solve S , Chayramy R , Matlejoane A M , Magagula L , Stock M
Published: January 2018

As part of the ongoing BIPM key comparison BIPM.EM-K11.a and b, a comparison of the 1.018 V and 10 V voltage reference standards of the BIPM and the National Metrology Institute of South Africa, NMISA (South Africa), was carried out from April to June 2017. Two BIPM Zener diode-based travelling standards (Fluke 732B), BIPM_A (ZA) and BIPM_B (ZB), were transported by freight to NMISA and back to BIPM. In order to keep the Zeners powered during their transportation phase, a voltage stabilizer developed by BIPM was connected in parallel to the internal battery. It consists of a set of two batteries, electrically protected from surcharge-discharge, easy to recharge and is designed to power two transfer standards for ten consecutive days. At NMISA, the reference standard for DC voltage is a Josephson Voltage Standard. The output EMF (Electromotive Force) of each travelling standard was measured by direct comparison with the primary standard.

At the BIPM, the travelling standards were calibrated, before and after the measurements at NMISA, with the Josephson Voltage Standard. Results of all measurements were corrected for the dependence of the output voltages of the Zener standards on internal temperature and atmospheric pressure.

The final result of the comparison is presented as the difference between the values assigned to DC voltage standards by NMISA, at the level of 1.018 V and 10 V, at NMISA, U
NMISA, and those assigned by the BIPM, at the BIPM, U
BIPM, at the reference dates of the 19th and 18th of May 2017, respectively.

U
NMISA − U
BIPM = + 0.07 μV; u
c = 0.02 μV, at 1.018 V

U
NMISA − U
BIPM = + 0.001 μV; u
c = 0.34 μV, at 10 V

where u
c is the combined standard uncertainty associated with the measured difference, including the uncertainty of the representation of the volt at the BIPM and at NMISA, based on K
J-90, and the uncertainty related to the comparison.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NMISA, June 2017
Authors: Viallon Joële , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Ntsasa Napo G , Tshilongo James , Mphaphuli Gumani E , Norris James E , Hodges Joseph T
Published: January 2018

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

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Economics of Sustainable Development and the Bioeconomy
Authors: Zilberman David , Gordon Ben , Hochman Gal , Wesseler Justus
Published: January 2018

Sustainable development can be attained by policies that are derived by analyses that integrate biophysical considerations into economic models. We show that policies and incentives that correct market failure can attain sustainable development through enhancing conservation, recycling, the use of renewable resources, and development of the bioeconomy, which relies on biological processes and feedstock to produce renewable products. The design of sustainable development policies and analysis of the bioeconomy pose new challenges to applied economists, who are uniquely qualified to integrate economic analysis with biophysical considerations.
Modeling biological problems in computer science: a case study in genome assembly
Authors: Medvedev Paul
Published: January 2018

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded.
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy
Authors: Guo Wei-Feng , Zhang Shao-Wu , Liu Li-Li , Liu Fei , Shi Qian-Qian , Zhang Lei , Tang Ying , Zeng Tao , Chen Luonan
Published: January 2018

Motivation

It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective.

Results

SCS integrates mutation data and expression data into a reference molecular network for each patient to obtain the driver mutation profiles in a personalized-sample manner. This is the first such a computational framework, to bridge the personalized driver mutation discovery problem and the structural network controllability problem. The key idea of SCS is to detect those mutated genes which can achieve the transition from the normal state to the disease state based on each individual omics data from network controllability perspective. We widely validate the driver mutation profiles of our SCS from three aspects: (i) the improved precision for the predicted driver genes in the population compared with other driver-focus methods; (ii) the effectiveness for discovering the personalized driver genes and (iii) the application to the risk assessment through the integration of the driver mutation signature and expression data, respectively, across the five distinct benchmarks from The Cancer Genome Atlas. In conclusion, our SCS makes efficient and robust personalized driver mutation profiles predictions, opening new avenues in personalized medicine and targeted cancer therapy.

Availability and implementation

The MATLAB-package for our SCS is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm.

Supplementary information

Supplementary data are available at Bioinformatics online.
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
Authors: Tchechmedjiev Andon , Abdaoui Amine , Emonet Vincent , Melzi Soumia , Jonnagaddala Jitendra , Jonquet Clement
Published: January 2018

Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014).

Availability and implementation

The Annotator+ has been successfully integrated into the SIFR BioPortal platform—an implementation of NCBO BioPortal for French biomedical terminologies and ontologies—to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject).

Supplementary information

Supplementary data are available at Bioinformatics online.
Hepatobiliary strongyloidiasis presenting as an ampullary lesion on esophagogastroduodenoscopy/endoscopic ultrasound
Authors: Ofori Emmanuel , Ramai Daryl , Khan Alisha , Xiao Philip , Reddy Madhavi , Shahzad Ghulamullah
Published: January 2018

Strongyloidiasis is an intestinal infection caused by the parasitic nematodes of the Strongyloides species, most commonly Strongyloides stercoralis. We report a case of a 66-year-old immigrant male from Haiti who presented with complaints of diarrhea and an unintentional 80-lb weight loss over the past 5 years. Stool examination was positive for strongyloidiasis. Following albendazole therapy, esophagogastroduodenoscopy (EGD) showed a unique ampullary lesion. Histopathology of the ampullary lesion showed reactive epithelium with Strongyloides larva. In addition, endoscopic ultrasound (EUS) detected a large pancreatic cyst. Both these findings were absent on EGD 5 years previously, prior to the onset of his symptoms. This paper documents a rare case of an ampullary lesion and pancreatic cyst secondary to hepatobiliary strongyloidiasis in a non-Human Immunodeficiency Virus (HIV) patient. We review the epidemiology, life cycle, clinical presentation and treatment of strongyloidiasis.
Density-independent and density-dependent factors affecting spatio-temporal dynamics of Atlantic cod (Gadus morhua) distribution in the Gulf of Maine
Authors: Li Zengguang , Ye Zhenjiang , Wan Rong , Tanaka Kisei R , Boenish Robert , Chen Yong
Published: January 2018

Due to strong spatial interplays between intraspecific interactions and environmental forcing, both density-dependent and density-independent processes can affect spatio-temporal dynamics of fish populations in a spatially explicit fashion. To this end, this study investigated the underlying mechanisms of spatio-temporal dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine (GoM). Based on the data from the Northeast Fisheries Science Center (NEFSC) bottom-trawl surveys in spring and fall from 1982 to 2013, empirical cumulative distribution function (ECDF) curves and geographic distribution indices were used to examine the species–environment and abundance–occupancy relationship, respectively. Then, a variable-coefficient generalized additive model was constructed to quantify the simultaneous effects of environmental variables and population size on the spatio-temporal dynamics of cod distribution. Area occupied remained relatively high through the late 1990s, but underwent a pronounced contraction into the western GoM (WGoM) for the reminder of the time-series. The model results suggest that the spatio-temporal dynamics of GoM cod have been driven by complex interactions of density-dependent and density-independent factors over the past three decades. Better knowledge of these dynamics can improve our understanding of the causality of abundance–occupancy and species–environment relationships and help to reduce error estimates for survey-based indices.
Prerupture Intracranial Aneurysm Morphology in Predicting Risk of Rupture: A Matched Case-Control Study
Authors: Skodvin Torbjørn Øygard , Evju Øyvind , Sorteberg Angelika , Isaksen Jørgen Gjernes
Published: January 2018

BACKGROUND

Maximal size and other morphological parameters of intracranial aneurysms (IAs) are used when deciding if an IA should be treated prophylactically. These parameters are derived from postrupture morphology. As time and rupture may alter the aneurysm geometry, possible morphological predictors of a rupture should be established in prerupture aneurysms.

OBJECTIVE

To identify morphological parameters of unruptured IAs associated with later rupture.

METHODS

Nationwide matched case-control study. Twelve IAs that later ruptured were matched 1:2 with 24 control IAs that remained unruptured during a median follow-up time of 4.5 (interquartile range, 3.7-8.2) yr. Morphological parameters were automatically measured on 3-dimensional models constructed from angiograms obtained at time of diagnosis. Cases and controls were matched by aneurysm location and size, patient age and sex, and the PHASES (population, hypertension, age, size of aneurysm, earlier subarachnoid hemorrhage from another aneurysm, and site of aneurysm) score did not differ between the 2 groups.

RESULTS

Only inflow angle was significantly different in cases vs controls in univariate analysis (P = .045), and remained significant in multivariable analysis. Maximal size correlated with size ratio in both cases and controls (P = .015 and <.001, respectively). However, maximal size and inflow angle were correlated in cases but not in controls (P = .004. and .87, respectively).

CONCLUSION

A straighter inflow angle may predispose an aneurysm to changes that further increase risk of rupture. Traditional parameters of aneurysm morphology may be of limited value in predicting IA rupture.
A Novel Single-Nucleotide Polymorphism Loop Mediated Isothermal Amplification Assay for Detection of Artemisinin-Resistant Plasmodium falciparum Malaria
Authors: Mohon Abu Naser , Menard Didier , Alam Mohammad Shafiul , Perera Kevin , Pillai Dylan R
Published: January 2018

Background

Artemisinin-resistant malaria (ARM) remains a significant threat to malaria elimination. In the Greater Mekong subregion, the prevalence of ARM in certain regions has reached greater than 90%. Artemisinin-resistant malaria is clinically identified by delayed parasite clearance and has been associated with mutations in the propeller domain of the kelch 13 gene. C580Y is the most prevalent mutation. The detection of ARM currently relies on labor-intensive and time-consuming methods such as clinical phenotyping or in vitro susceptibility testing.

Methods

We developed a novel single-nucleotide polymorphism loop mediated isothermal amplification (SNP-LAMP) test method for the detection of the C580Y mutation using a novel primer design strategy.

Results

The SNP-LAMP was 90.0% sensitive (95% confidence interval [CI], 66.9–98.3) and 91.9% specific (95% CI, 82.6–96.7) without knowledge of the parasite load and was 100% sensitive (95% CI, 79.9–100) and 97.3% specific (95% CI, 89.7–99.5) when the parasitemia was within the assay dynamic range. Tests with potential application near-to-patient such as SNP-LAMP may be deployed in low- and middle-income and developed countries.

Conclusions

Single-nucleotide polymorphism LAMP can serve as a surveillance tool and guide treatment algorithms for ARM in a clinically relevant time frame, prevent unnecessary use of additional drugs that may drive additional resistance, and avoid longer treatment regimens that cause toxicity for the patient.
The Global Regulatory Protein VelA Is Required for Symbiosis Between the Endophytic FungusEpichloë festucaeandLolium perenne
Authors: Rahnama M. , Johnson R. D. , Voisey C. R. , Simpson W. R. , Fleetwood D. J.
Published: January 2018

Epichloë species fungi form bioprotective endophytic symbioses with many cool-season grasses, including agriculturally important forage grasses. Despite its importance, relatively little is known about the molecular details of the interaction and the regulatory genes involved. The conserved velvet-domain protein VelA (or VeA) is a global regulator of a number of cellular and developmental functions in fungi. In this study, the E. festucae velA gene was functionally characterized in vitro and during interaction with perennial ryegrass. The velA gene is required in E. festucae for resistance to osmotic and cell wall–damaging stresses, repression of conidiation, and normal hyphal morphology during nutrient-limited in-vitro conditions. Expression of velA in E. festucae is light- and nitrogen-dependent and is tissue-specific in mature infected plants. In-planta studies showed that velA is required in E. festucae for a compatible interaction. Inoculating seedlings with mutant ΔvelA induced callose deposition and H2O2production, and a high level of seedling death was observed. In surviving plants infected with ΔvelA mutant fungi, plants were stunted and we observed increased biomass and invasion of vascular bundles. Overall, this work characterizes a key fungal regulatory factor in this increasingly important model symbiotic association.
Assessing Potato Cultivar Sensitivity to Tuber Necrosis Caused by Potato mop-top virus
Authors: Yellareddygari S. K. R. , Whitworth Jonathan L. , Gudmestad Neil C.
Published: January 2018

Potato mop-top virus (PMTV) causes mop top disease in potato. This disease can result in a decline in tuber quality causing economic losses to growers due to the production of necrotic lesions and discolored tissue in infected tubers. Due to the soilborne nature of PMTV, identifying and developing host resistance against the virus is considered the best disease management option. Very little is known about the sensitivity of U.S. potato cultivars to PMTV-induced tuber necrosis. The current study is aimed at investigating the sensitivity of a large number of potato cultivars to PMTV-induced tuber necrosis. Sixty-three cultivars representing all market-types were evaluated in North Dakota over a 2-year period for virus-induced tuber necrosis incidence and severity. PMTV-induced tuber necrosis (P < 0.0001) and severity (P < 0.0001) were significantly different among cultivars. Cultivars were categorized into sensitive, insensitive, and moderately sensitive/insensitive groups based on the virus-tuber induced necrosis data from both years. Based on data from ND trials, six cultivars (Red Endeavor, Viking, Dakota Jewel, Dark Red Norland, Nicolet, and Modoc) were rated as sensitive and 43 were rated as insensitive to PMTV-induced tuber necrosis. Four cultivars, including Bannock Russet, Gemstar Russet, Lelah, and Waneta showed zero PMTV incidence over 2 years. These results will help growers in making individual or coordinated decisions for the management of PMTV-induced tuber necrosis under field and storage conditions.
Molecular Characterization and Expression of PFT, an FHB Resistance Gene at the Fhb1 QTL in Wheat
Authors: He Yi , Zhang Xu , Zhang Yu , Ahmad Dawood , Wu Lei , Jiang Peng , Ma Hongxiang
Published: January 2018

Fusarium head blight (FHB) is a destructive fungal disease in wheat worldwide. Efforts have been carried out to combat this disease, and the pore-forming toxin-like (PFT) gene at the quantitative trait locus (QTL) Fhb1 was isolated and found to confer resistance to FHB in Sumai 3. In this study, we characterized PFT in 348 wheat accessions. Four haplotypes of PFT were identified. The wild haplotype of PFT had higher resistance than other haplotypes and explained 13.8% of phenotypic variation in FHB resistance by association analysis. PFT was highly expressed during early flowering and increased after Fusarium graminearum treatment in Sumai 3. Analysis of the 5′ flanking sequence of PFT predicted that the cis elements of the PFT promoter were related to hormones and biological defense responses. However, PFT existed not only in the FHB-resistant accessions but also in some susceptible accessions. These results suggested that FHB resistance in a diverse range of wheat genotypes is partially conditioned by PFT. The profiling of FHB resistance and the PFT locus in this large collection of wheat germplasm may prove helpful for incorporating FHB resistance into wheat breeding programs, although more work is needed to reveal the exact role of the QTL Fhb1 in conferring resistance to fungal spread.
Parallel Proximal Fixation in Rib-Based Growing Rod System
Authors: Heflin John , Welborn Michelle , Ramirez-Lluch Norman , Iriarte Ivan , El-Hawary Ron , Fedorak Graham T. , Smith John T.
Published: January 2018

Study Design.

Retrospective case control.

Objective.

To report on differences in implant failure rates and complications requiring reoperation in children with early-onset scoliosis (EOS) treated with rib-based distraction utilizing four proximal fixation points in either a parallel or in-line configuration.

Summary of Background Data.

Proximal anchor failure continues to be a significant problem in growth-friendly surgery using rib-based distraction to treat children with EOS. Differences between parallel and in-line proximal anchor constructs have not been previously assessed.

Methods.

A multicenter registry was reviewed to identify children treated for EOS with rib-based distraction between 2011 and 2014 with a minimum of 2 years follow-up after implantation. Patients were divided into those with in-line and parallel proximal rib-cradle configurations, and only those with exactly four fixation points (two per side) were included. Charts were reviewed for demographic, clinical, and radiographic information.

Results.

A total of 56 patients were identified—31 with in-line constructs and 25 with parallel constructs. Follow-up in the in-line group was a mean of 4.06 years versus 3.16 in the parallel group (P = 0.001). Controlling for the different lengths of follow-up in the two groups there was a significantly higher rate of implant failure (P = 0.043) and requirement for nonroutine surgical intervention (P = 0.029) in the in-line group. There was a trend toward increased complications in the in-line group (P = 0.058).

Conclusion.

Failure of proximal fixation is the most common complication in management of EOS with rib-based distraction. This study identifies that when the number of proximal fixation points are matched, parallel constructs result in lower rates of implant failure and need for unplanned reoperation than in-line constructs. Although this study was limited to patients in whom the VEPTR device was employed, these principles are likely applicable to other rib-based distraction devices used to treat EOS.

Level of Evidence: 3
Tidemark Avulsions are a Predominant Form of Endplate Irregularity
Authors: Berg-Johansen Britta , Jain Deeptee , Liebenberg Ellen C. , Fields Aaron J. , Link Thomas M. , O’Neill Conor W. , Lotz Jeffrey C.
Published: January 2018

Study Design.

Descriptive histologic and magnetic resonance imaging study of human cadaveric spines.

Objective.

To identify and characterize common endplate pathologies to form a histologic foundation for an etiology-based classification system.

Summary of Background Data.

Irregularities at the spinal disc-vertebra interface are associated with back pain and intervertebral disc herniation injuries. However, there is currently a lack of consensus regarding terminology for classification. This limits the potential for advancing understanding of back pain mechanisms, and prohibits meaningful comparisons for identifying priorities for prevention and treatment. Prior classification systems largely rely on observations from clinical imaging, which may miss subtle pathologic features.

Methods.

Fifteen cadaveric spines with moderate to severe disc degeneration were obtained and scanned with MRI in the sagittal plane using two-dimensional T1-weighted and T2-weighted fast spin-echo sequences. Eighty-nine lumbar and lower thoracic bone-disc-bone motion segments were extracted, fixed, sectioned, and stained for histologic evaluation. Focal endplate irregularities were identified and categorized based on features that inferred causation. The presence, type, and anatomic location were recorded. A classification system with three major categories of focal endplate irregularities was created.

Results.

Disc-vertebra avulsion and vertebral rim degeneration were more common than subchondral nodes: 50% of irregularities were classified as rim degeneration (75/150), 35% were classified as avulsions (52/150), and 15% were classified as nodes (23/150). Ninety percent of avulsions were subclassified as “tidemark avulsions,” a highly prevalent form of endplate irregularity in which the outer annulus separates from the vertebra at the tidemark. These tidemark avulsions have not been previously described, yet are visible on T2-weighted MRI as high-intensity regions.

Conclusion.

This study provides histologic basis for a system to classify focal endplate irregularities. Included is a previously unidentified but prevalent finding of tidemark avulsions, which are visible with both histology and magnetic resonance imaging. These observations will help clinicians better organize patients into meaningful groups to facilitate diagnosis, treatment, and clinical research.

Level of Evidence: 3
Cochlear Implant Surgery and the Risk of Falls in an Adult Population
Authors: Louza Julia , Klappert Caspar Leon , Ledderose Georg , Gürkov Robert , Krause Eike
Published: January 2018

Objective:

To determine the effect of cochlear implant surgery on the balance and risk of falls in an adult patient population using a mobile posturograph.

Design:

Prospective clinical pilot study.

Setting:

Cochlear implant center at a tertiary referral hospital.

Subjects and Methods:

Twenty adult patients undergoing cochlear implant surgery were tested using a mobile posturograph (VertiGuard). The standard balancing deficit test, or the geriatric standard balancing deficit test protocol (for patients older than 60 yr), was performed both 1 day before and 3 to 5 days after surgery.

Outcome Measures:

The risk of falls (%) was calculated from the body sway both forward-to-backward and side-to-side in degrees per second.

Results:

The mean preoperative risk of falls in the whole study population was 51% (24–max. 86%) and was thus already higher than that in a normal healthy population (norm 0–40%). Comparison of the postoperative risk of falls to the preoperative risk for all 20 patients revealed a mean increased risk of falls of 1.25% after CI surgery. This is not a statistically significant increase. There was also no statistically significant increase when comparing the fall risk calculated using either the standard balancing deficit test protocol or the geriatric standard balancing deficit test protocol alone.

Conclusion:

Postural control in cochlear implant candidates is already decreased before surgery compared with a healthy population. However Comparison of pre- and postoperative body sway measurements did not reveal a significant increase in fall risk as a result of cochlea implant surgery. Therefore in this study population, cochlear implant surgery did not influence balance and risk of falls. Further testing with a larger study population would be necessary to determine the development of falls risk over time after cochlear implant surgery.