bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel approach to describe chemical environments in high-dimensional neural network potentials
Authors: Kocer Emir , Mason Jeremy K. , Erturk Hakan
Published: April 2019

A central concern of molecular dynamics simulations is the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system and have generally been calculated using either predefined analytical formulas (classical) or quantum mechanical simulations (ab initio). The former can accurately reproduce only a selection of material properties, whereas the latter is restricted to short simulation times and small systems. Machine learning potentials have recently emerged as a third approach to model atomic interactions, and are purported to offer the accuracy of ab initio simulations with the speed of classical potentials. However, the performance of machine learning potentials depends crucially on the description of a local atomic environment. A set of invariant, orthogonal, and differentiable descriptors for an atomic environment is proposed, implemented in a neural network potential for solid-state silicon, and tested in molecular dynamics simulations. Neural networks using the proposed descriptors are found to outperform ones using the Behler–Parinello and smooth overlap of atomic position descriptors in the literature.
Magneto-resistance in pristine and irradiated TaAs2
Authors: Harimohan V. , Bharathi A. , Rajaraman R. , Magudapathy P. , David C. , Sundar C. S.
Published: April 2019

Here we report the single crystal synthesis, characterization and the systematic study of the magneto-transport and magnetization measurements up to a magnetic field of 14 T and down to 3 K from room temperature in the semimetal TaAs2. By experiments on magneto-transport in pristine and irradiated samples, it is inferred that the turn on temperature behavior in the resistivity measurements is better analyzed based on Kohler’s rule, rather than as arising due to a metal insulator transition. The absence of negative longitudinal magneto-resistance in TaAs2 has been confirmed by careful measurements on both pristine and irradiated samples. The low energy ion irradiation altered the surface states that were reflected in the suppression of de Haas van Alphen oscillations. Hall analysis reaffirmed the role of multiple carriers, electrons and holes, in the magneto-transport of this class of materials.
Theoretical study of acoustic radiation force and torque on a pair of polymer cylindrical particles in two Airy beams fields
Authors: Wang Haibin , Gao Sha , Qiao Yupei , Liu Jiehui , Liu Xiaozhou
Published: April 2019

In this work, we describe the acoustic radiation force (ARF) and torque acting on a pair of cylindrical particles induced by two Airy beams. The finite series expansion method and the addition theorem of the cylindrical Bessel function are used to analyze the acoustic scattered field by a pair of cylindrical particles in an effective incident acoustic field. The mathematical expressions for the ARF and the torque functions in multiple acoustic scattering by a pair of cylindrical particles are obtained. The influences of the phase difference, the beam distance, and the beam amplitude on the ARFs and torques are taken into consideration. The numerical examples illustrate that greater negative or positive forces on the two cylindrical particles emerge by adjusting the phase difference, the distance, or the amplitudes of the two Airy beams, which make it easier to separate the particles. The values of the torques will also increase or change between the positive and the negative, which increase the particles’ rotation velocity or change the particles’ rotation direction. This work will be conducive to the development of acoustic tweezers for polymer drugs separation (or cells separation) in medical domain.
Instability in a relativistic magnetized plasma
Authors: Liu Xu , Chen Lunjin
Published: April 2019

We present a general relativistic linear growth rate formula of electromagnetic waves for any wave normal angle and a general distribution function in a uniform magnetized plasma with a dominant cold plasma component and a tenuous hot plasma component. Such a general linear growth rate formula can be applied to different plasma environments, such as the Jovian Magnetosphere and laboratory plasma. The relativistic resonant condition for different wave modes is discussed and summarized. Then, the formula is applied to a parametric study for local instability of Earth's plasmaspheric hiss. We study the effects of the electron temperature, electron temperature anisotropy, types of distribution functions, plasma density, background magnetic field, and wave normal angle on the relativistic linear growth rate of the whistler mode. We find that (1) the energetic electrons with larger energy resonate with the lower frequency wave. The relativistic effect becomes significant for the electron with energy >100 keV. (2) The anisotropy only increases the growth rate and expands the growth wave band. (3) The high density and low background magnetic field tend to decrease the wave frequency and increase the growth rate. (4) The field-aligned growth rate is larger than the oblique growth rate, and the lower frequency whistler waves are easier to propagate obliquely.
Oxygen-dependent contraction and degradation of the extracellular matrix mediated by interaction between tumor and endothelial cells
Authors: Yoshino Daisuke , Funamoto Kenichi
Published: April 2019

Understanding the mechanisms of cancer development and metastasis requires comprehensive analyses of interactions between normal and tumor cells and the extracellular matrix (ECM) in hypoxic tumor microenvironments. However, the scope of many tumor microenvironment studies is limited to verifying the development and performance of microenvironment-producing cell culture platforms. This study describes the effects of co-culture and hypoxia on contraction and degradation of the ECM. Collagen type I gel was placed in the gel channel of an oxygen tension–controllable microfluidic device as a tumor tissue substrate. MDA-MB-231 human breast cancer cells and/or human umbilical vein endothelial cells (HUVECs) were cultured inside the gel or on the adjacent media channels, respectively. Changes in the collagen gel were evaluated by generating normoxic (21% O2) or hypoxic (1% O2) conditions via variation of the supply of gas mixture. HUVECs induced collagen gel contraction and degradation more strongly than MDA-MB-231 cells. Although interaction between co-cultured MDA-MB-231 cells and HUVECs promoted gel contraction and degradation, hypoxia attenuated the effect. Immunofluorescence staining indicated decreased expression of secretory matrix metalloproteinase-7 (MMP-7) inside the collagen gel under hypoxic conditions, but no morphologic changes in cells were observed. Separate Western blot analyses using cells cultured on cell culture dishes confirmed reduced endogenous MMP expression in hypoxia-exposed HUVECs. These results demonstrate that hypoxic conditions affect collagen gel contraction and degradation by altering the expression of MMP-7 in co-cultured MDA-MB-231 cells and HUVECs.
A new full-dimensional ab initio intermolecular potential energy surface and vibrational states for (HF)2 and (DF)2
Authors: Huang Jing , Yang Dongzheng , Zhou Yanzi , Xie Daiqian
Published: April 2019

We present a new full-dimensional ab initio potential energy surface (PES) of a hydrogen fluoride dimer [(HF)2] using the supermolecular approach. The calculations were performed at the coupled-cluster single double triple level, with an augmented correlation-consistent polarized valence quadruple-zeta basis set plus bond functions. The basis set superposition error was corrected by a full counterpoise procedure. With the exchange symmetry of the two HF molecules, the permutation invariant polynomial neural network approach was used to fit the hypersurface with a root-mean-square-error of 0.465 cm−1 for about 110 000 points. The ab initio noise of intermolecular potential in the long range was smoothed by the long-range coefficients method. The equilibrium configuration of the complex was found to be a Cs structure located at two equivalent minima with the well depth of 1573.495 cm−1. The eigenstates were calculated by employing a symmetry-adapted Lanczos propagation algorithm in the mixed radical discrete variable representation/angular finite basis representation. The tunneling splitting for the ground state of (HF)2 is 0.665 cm−1, agreeing well with experimental value of 0.65869 cm−1. Vibrational fundamentals are also very close to the observed values. The results of vibrational states calculations demonstrate the high accuracy of our new PES.
Catalyzed chemical polishing of SiO2 glasses in pure water
Authors: Toh Daisetsu , Bui Pho Van , Isohashi Ai , Kidani Naotaka , Matsuyama Satoshi , Sano Yasuhisa , Morikawa Yoshitada , Yamauchi Kazuto
Published: April 2019

A catalytically assisted etching system was developed for the ultra-precision fabrication of optical components, such as X-ray mirrors and extreme-ultraviolet mask blanks. This study demonstrates that an atomically smooth surface with a sub-Angstrom root-mean-square roughness could be achieved on a SiO2 glass substrate using pure water and Pt as the etching solution and catalyst, respectively. Density functional theory calculations confirmed that the mechanistic pathway was involved in catalyzed hydrolysis. The significant roles of the catalyst were clarified to be the dissociation of water molecules and the stabilization of a meta-stable state, in which a hypervalent silicate state is induced, and the Si–O backbond is elongated and loosened. To confirm the role of the catalyst, the Pt metal was replaced by Au, and the observed drastic difference in the removal rate was attributed to the degree of stabilization of the metastable state.
Simultaneous measurement of temperature and RI based on an optical microfiber coupler assembled by a polarization maintaining fiber
Authors: Zhao Li , Zhang Yundong , Chen Yunhao , Wang Jinfang
Published: April 2019

A temperature and refractive index simultaneous measurement sensor based on an optical microfiber coupler (OMC) combined with a polarization maintaining fiber (PMF) is proposed and experimentally demonstrated. The OMC-PMF sensor is fabricated by inserting a section of PMF between two output ports of the OMC. The interference spectrum of the OMC-PMF sensor has different responses to temperature and refractive index variations. Temperature and the refractive index can be measured by monitoring the dip intensity variation and the dip wavelength shift of the interference spectrum, respectively. The experimental results show that the refractive index sensitivity is 12 020 nm/RIU, and the temperature sensitivity is 0.88 dB/°C upon increasing temperature from 35 °C to 41 °C.
Implementation science approaches to enhance uptake of complex interventions in surgical settings
Authors: Byrnes Angela , Mudge Alison , Clark David
Published: April 2019

Achieving practice change in the complex healthcare environment is difficult. Effective surgical care requires coordination of services across the continuum of care, involving interdisciplinary collaboration across multiple units, with systems and processes that may not connect effectively. Principles of enhanced recovery after surgery (ERAS) are increasingly being incorporated into facility policies and practice, but the literature reports challenges with both initial adherence and mid- to long-term sustainability. Greatest adherence is typically observed for the intraoperative elements, which are within the control of a single discipline, with poorest adherence reported for postoperative processes occurring in the complex ward environment. Using ERAS as an example, this perspective piece describes the challenges associated with implementation of complex interventions in the surgical setting, highlighting the value that implementation science approaches can bring to practice change initiatives and providing recommendations as to suggested course of action for effective implementation.
Attenuated post-fire fauna succession: the effects of surrounding landscape context on post-fire colonisation of fauna
Authors: Simms Angela , Scott Meaghan , Watson Simon , Leonard Steve
Published: April 2019

Context
After fire, immigration from outside burnt areas is important for the recovery of faunal communities. However, for recovery to occur, the matrix around the fire must support source populations of immigrants. Therefore, the landscape context of fires may be a critical determinant of the species pool available for (re)colonisation, hence post-fire community composition. Increasingly, fires occur in fragmented systems, and there is limited knowledge of how the surrounding landscape interacts with post-fire community recovery.

Aim
The present study aimed to examine how landscape context influences faunal communities after large wildfires.

Methods
Three reserves burnt by wildfire were examined ~18 months before the study in the Mallee region of south-eastern Australia. In all cases the burnt area consisted of natural mallee woodland. Two fires occurred within a matrix of extensive natural vegetation, while the third fire burnt >80% of a reserve situated within a highly fragmented, largely agricultural landscape. Birds, reptiles and mammals were surveyed at 90 sites inside and outside the fire boundaries, and relationships of species occurrence to reserve location, burnt versus unburnt status and distance from fire edge were all examined.

Key results
Post-fire faunal communities reflected the species in the surrounding unburnt landscape. Notably, open habitat specialists, invasive species and species that can persist in small habitat patches were prominent within the fragmented system. Post-fire fauna communities were also influenced by variation of the natural vegetation surrounding the fire. The occurrence of species with low dispersal ability (i.e. reptiles) was influenced by local (patch scale) vegetation structure.

2Conclusions
The landscape context of fires is a major driver of the composition of post-fire faunal communities. Our results highlight the potential loss of species sensitive to fragmentation from fire-prone natural vegetation within modified landscapes, and that a reduced pool of potential immigrants leads to ‘attenuated succession’, compromising recovery of the pre-fire community.

Implications
Post-fire colonists reflect the surrounding landscapes species pool, such that reserves surrounded by fragmented or otherwise low quality habitat are at risk of attenuated succession after fire. Landscape context should be incorporated into conservation planning in fire-prone ecosystems, including consideration of surrounding habitat quality and connectivity and protecting long unburnt vegetation.
Predators attacking virtual prey reveal the costs and benefits of leadership
Authors: Ioannou Christos C. , Rocque Florence , Herbert-Read James E. , Duffield Callum , Firth Josh A.
Published: April 2019

Significance

Across a wide range of animals, it is assumed that leading from the front of a group exposes individuals to greater predation risk, generating a cost that explains variation between individuals in their tendencies to lead and follow. Remarkably, there is scant empirical evidence to support this, and there are no experimental tests. By presenting real predators with a simulation of collective behavior, we were able to exclude any correlation between social behavior and other traits that could confound effects on predation risk. We show that virtual prey leading others were preferentially attacked, but leaders were still safer than solitary prey. Leaders benefit from being followed, and they should act to maintain group cohesion and avoid splitting from their followers.
Cystine/glutamate antiporter xCT (SLC7A11) facilitates oncogenic RAS transformation by preserving intracellular redox balance
Authors: Lim Jonathan K. M. , Delaidelli Alberto , Minaker Sean W. , Zhang Hai-Feng , Colovic Milena , Yang Hua , Negri Gian Luca , von Karstedt Silvia , Lockwood William W. , Schaffer Paul , Leprivier Gabriel , Sorensen Poul H.
Published: April 2019

Significance

RAS
genes are among the most mutated proto-oncogenes in human cancer. The mechanisms supporting RAS transformation are not fully understood, particularly regarding the relative contributions of oxidant versus antioxidant pathways. Here, we report that the cystine/glutamate transporter xCT is essential for RAS-induced tumorigenicity by enhancing antioxidant glutathione synthesis. Our findings uncover that RAS controls
xCT
transcription by downstream activation of ETS-1 to synergize with ATF4. This has clinical relevance since
xCT
expression is upregulated in human cancers exhibiting an activated RAS pathway. Therefore, oncogenic RAS transformation is supported by induction of an antioxidant program, highlighting xCT as a potential vulnerability for therapeutic targeting.
Revisiting the procedure for characterising mechanical properties in welded joints through nanoindentation
Authors: Chang Chao , Xiao Gesheng , Liu Erqiang , Lin Jinbao , Zhang Xuexia , Long Xu , Zhang Le-le
Published: April 2019

Owing to the microstructural inhomogeneities and residual stresses that are generated during welding, welded joints are the weakest parts of structures. Nanoindentation, a non-destructive technique, is commonly used to analyse the local mechanical properties and residual stresses in welded joints. However, the pile-up effect is often neglected during the nanoindentation procedure, which results in inaccurate measurements. In this study, an alternative procedure, based on a previous study, was used to measure the local mechanical properties and residual stresses in metal inert gas (MIG) welded joints. Moreover, a new equation is proposed for estimating the residual stresses.
Structural confirmation of the 24-item Environmental Attitude Inventory / Confirmación estructural del Inventario de Actitudes Ambientales de 24 ítems
Authors: Ajdukovic Ivan , Gilibert Daniel , Fointiat Valérie
Published: April 2019

Despite an ever-increasing use of the Environmental Attitude Inventory (EAI), few studies have aimed at checking the dimensional structure of its 24-item version and particularly the structure of the subdimensions and its two main dimensions: utilization and preservation of the environment. Structural analyses confirmed the strength of the structure. Pro-environmental behaviours can be predicted by this scale, mainly through the dimension of preservation. Lastly, two of the ideological and emotional subdimensions of preservation appeared not to be highly specific in the French context of our study: environmental movement activism and ecocentrism, which cover ecological behaviour and the support for interventionist conservation policies. If the objective of the scale is not to study those two dimensions, we suggest a shorter version of the EAI, more balanced, coherent and structured into 20 items comprising 10 clearly distinct subdimensions.
Bile acids inhibit human purinergic receptor P2X4 in a heterologous expression system
Authors: Ilyaskin Alexandr V. , Sure Florian , Nesterov Viatcheslav , Haerteis Silke , Korbmacher Christoph
Published: April 2019

We recently demonstrated that bile acids, especially tauro-deoxycholic acid (t-DCA), modify the function of the acid-sensing ion channel ASIC1a and other members of the epithelial sodium channel (ENaC)/degenerin (DEG) ion channel family. Surprisingly, ASIC1 shares a high degree of structural similarity with the purinergic receptor P2X4, a nonselective cation channel transiently activated by ATP. P2X4 is abundantly expressed in the apical membrane of bile duct epithelial cells and is therefore exposed to bile acids under physiological conditions. Here, we hypothesize that P2X4 may also be modulated by bile acids and investigate whether t-DCA and other common bile acids affect human P2X4 heterologously expressed in Xenopus laevis oocytes. We find that application of either t-DCA or unconjugated deoxycholic acid (DCA; 250 µM) causes a strong reduction (∼70%) of ATP-activated P2X4-mediated whole-cell currents. The inhibitory effect of 250 µM tauro-chenodeoxycholic acid is less pronounced (∼30%), and 250 µM chenodeoxycholic acid, cholic acid, or tauro-cholic acid did not significantly alter P2X4-mediated currents. t-DCA inhibits P2X4 in a concentration-dependent manner by reducing the efficacy of ATP without significantly changing its affinity. Single-channel patch-clamp recordings provide evidence that t-DCA inhibits P2X4 by stabilizing the channel’s closed state. Using site-directed mutagenesis, we identifiy several amino acid residues within the transmembrane domains of P2X4 that are critically involved in mediating the inhibitory effect of t-DCA on P2X4. Importantly, a W46A mutation converts the inhibitory effect of t-DCA into a stimulatory effect. We conclude that t-DCA directly interacts with P2X4 and decreases ATP-activated P2X4 currents by stabilizing the closed conformation of the channel.
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays
Authors: Reith Frank , Verboom William , Pate John , Chittleborough David
Published: April 2019

Background and Aims

Previous studies have described the laying down of specific B horizons in south-western Australian ecosystems. This paper presents biomolecular, morphological and physicochemical analyses elucidating the roles of specific woody plant taxa and rhizosphere bacteria in producing these phenomena.

Methods

Clayey deposits within lateral root systems of eucalypts and appropriate background soil samples were collected aseptically at multiple locations on sand dunes flanking Lake Chillinup. Bacterial communities were profiled using tagged next-generation sequencing (Miseq) of the 16S rRNA gene and assigned to operational taxonomic units. Sedimentation, selective dissolution and X-ray diffraction analyses quantitatively identified clay mineral components. Comparisons were made of pedological features between the above eucalypt systems, giant podzols under proteaceous woodland on sand dunes at the study site of Jandakot and apparently similar systems observed elsewhere in the world.

Key Results

Bacterial communities in clay pods are highly diverse, resolving into 569 operational taxonomic units dominated by Actinobacteria at 38.0–87.4 % of the total reads. Multivariate statistical analyses of community fingerprints demonstrated substrate specificity. Differently coloured pods on the same host taxon carry distinctive microfloras correlated to diversities and abundances of Actinobacteria, Acidobacteria, Firmicutes and Proteobacteria. A number of these microbes are known to form biominerals, such as phyllosilicates, carbonates and Fe-oxides. A biogenic origin is suggested for the dominant identified mineral precipitates, namely illite and kaolinite. Comparisons of morphogenetic features of B horizons under eucalypts, tree banksias and other vegetation types show remarkably similar developmental trajectories involving pods of precipitation surrounding specialized fine rootlets and their orderly growth to form a continuous B horizon.

Conclusions

The paper strongly supports the hypothesis that B-horizon development is mediated by highly sophisticated interactions of host plant and rhizosphere organisms in which woody plant taxa govern overall morphogenesis and supply of mineral elements for precipitation, while rhizosphere microorganisms execute biomineralization processes.
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA
Authors: Gong Sha , Zhang Chengxin , Zhang Yang
Published: April 2019

Motivation

Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search.

Results

We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments.

Availability and implementation

https://zhanglab.ccmb.med.umich.edu/RNA-align/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda)
Authors: Kerkhove Thomas R H , Boyen Jens , De Backer Annelies , Mol Jan H , Volckaert Filip A M , Leliaert Frederik , De Troch Marleen
Published: April 2019

The recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
Healing through Connection: An Aboriginal Community Designed, Developed and Delivered Cultural Healing Program for Aboriginal Survivors of Institutional Child Sexual Abuse
Authors: Black Carlina , Frederico Margarita , Bamblett Muriel
Published: April 2019

The wrongs experienced by Aboriginal people have caused life-long and intergenerational impacts that demand culturally grounded healing approaches, yet this is not experienced by Aboriginal people in mainstream services. This article details a culturally informed approach by sharing the findings of a Cultural Healing Program (CHP) designed, developed and delivered by an Aboriginal Community Controlled Organisation. The program was for Aboriginal survivors of institutional child sexual abuse who had also experienced cultural abuse having been forcibly removed from their families as children and in the process disconnected from their communities, culture and land. This study of the development, implementation and evaluation of the CHP included a review of literature, interviews with survivors and facilitators, pre- and post-participant surveys, facilitator journals, participant–observer reflections and short films exploring impacts. The study drew upon the experiences of the survivors and facilitators to identify outcomes of the program. Connection with culture and the collective approach were key to healing for all survivors. The paper identifies key learnings that can inform social work practice and discusses implications regarding program design and implementation.
Public Health Importance of Invasive Methicillin-sensitive Staphylococcus aureus Infections: Surveillance in 8 US Counties, 2016
Authors: Jackson Kelly A , Gokhale Runa H , Nadle Joelle , Ray Susan M , Dumyati Ghinwa , Schaffner William , Ham David C , Magill Shelley S , Lynfield Ruth , See Isaac
Published: April 2019

Background

Public health and infection control prevention and surveillance efforts in the United States have primarily focused on methicillin-resistant Staphylococcus aureus (MRSA). We describe the public health importance of methicillin-susceptible S. aureus (MSSA) in selected communities.

Methods

We analyzed Emerging Infections Program surveillance data for invasive S. aureus (SA) infections (isolated from a normally sterile body site) in 8 counties in 5 states during 2016. Cases were considered healthcare-associated if culture was obtained >3 days after hospital admission; if associated with dialysis, hospitalization, surgery, or long-term care facility (LTCF) residence within 1 year prior; or if a central venous catheter was present ≤2 days prior. Incidence per 100 000 census population was calculated, and a multivariate logistic regression model with random intercepts was used to compare MSSA risk factors with those of MRSA.

Results

Invasive MSSA incidence (31.3/100 000) was 1.8 times higher than MRSA (17.5/100 000). Persons with MSSA were more likely than those with MRSA to have no underlying medical conditions (adjusted odds ratio [aOR], 2.06; 95% confidence interval [CI], 1.26–3.39) and less likely to have prior hospitalization (aOR, 0.70; 95% CI, 0.60–0.82) or LTCF residence (aOR, 0.37; 95% CI, 0.29–0.47). MSSA accounted for 59.7% of healthcare-associated cases and 60.1% of deaths.

Conclusions

Although MRSA tended to be more closely associated with healthcare exposures, invasive MSSA is a substantial public health problem in the areas studied. Public health and infection control prevention efforts should consider MSSA prevention in addition to MRSA.
Clinical practice and implementation of guidelines for the prevention, diagnosis and management of cardiac implantable electronic device infections: results of a worldwide survey under the auspices of the European Heart Rhythm Association
Authors: Traykov Vassil , Bongiorni Maria Grazia , Boriani Giuseppe , Burri Haran , Costa Roberto , Dagres Nikolaos , Deharo Jean-Claude , Epstein Laurence M , Erba Paola Anna , Snygg-Martin Ulrika , Nielsen Jens Cosedis , Poole Jeanne E , Saghy Laszlo , Starck Christoph , Strathmore Neil , Blomström-Lundqvist Carina
Published: April 2019

Aims

Cardiac implantable electronic device (CIED) infection rates are increasing. Worldwide compliance and disparities to published guidelines for the prevention, diagnosis and management of these conditions are not well elucidated. The purpose of this survey, therefore, was to clarify these issues through an inquiry to arrhythmia-related associations and societies worldwide.

Methods and results

A questionnaire comprising 15 questions related to CIED infections was distributed among members of seven arrhythmia societies worldwide. A total of 234 centres in 62 countries reported implantation rates of which 159 (68.0%) performed more than 200 device implantations per year and 14 (6.0%) performed fewer than 50 implantations per year. The reported rates of CIED infections for 2017 were ≤2% in 78.7% of the centres, while the infection rates exceeded 5% in 7.8% of the centres. Preventive measures for CIED infection differed from published recommendations and varied among different regions mainly in terms of pocket irrigation and administering post-operative antimicrobial therapy the use of which was reported by 39.9% and 44% of the respondents, respectively. Antibacterial envelopes were used by 37.7% of the respondents in selected circumstances. In terms of pocket infection management, 62% of the respondents applied complete system removal as an initial step. Diagnostic pocket needle aspiration and pocket surgical debridement were reported by 15.8% and 11.8% of centres, respectively.

Conclusion

Clinical practices for prevention and management of CIED do not fully comply with current recommendations and demonstrate considerable regional disparities. Further education and programmes for improved implementation of guidelines are mandatory.
Characterizing the first wave of fish and invertebrate colonization on a new offshore petroleum platform
Authors: Todd Victoria L G , Williamson Laura D , Cox Sophie E , Todd Ian B , Macreadie Peter I
Published: April 2019

Offshore Oil & Gas (O&G) infrastructure creates artificial reef complexes that support marine communities in oceans. No studies have characterized the first wave of colonization, which can reveal information about habitat attraction and ecological connectivity. Here we used opportunistically-collected industrial Remotely Operated Vehicles (ROVs) to investigate fish and invertebrate colonization on a new North Sea O&G platform and trenching of an associated pipeline. We observed rapid colonization of fish communities, with increases in species richness (S), abundance (N), and diversity (H′) over the first four days (the entire study period). By contrast, there was minimal change in motile invertebrate communities over the survey period. After trenching, invertebrate S, N and H′ decreased significantly, whilst fish S, N and H′ increased. This study is the first to report on the pioneer wave of fish and invertebrate colonization on O&G infrastructure, thereby providing rare insight into formation of new reef communities in the sea. These short and opportunistic data are valuable in terms of showing what can be discovered from analysis of ‘pre-installation’ ROV footage of O&G structures, of which there are terabytes of data held by O&G companies waiting to be analyzed by environmental scientists.
The variable effectiveness of hedging strategies
Authors: Ciorciari John D
Published: April 2019

Governments often adopt hedging strategies to mitigate risks they face in international affairs. They hedge in the conventional, financial sense of the term by seeking to offset risks in global markets. They also adopt strategies to hedge against international security hazards by preserving strategic ambiguity, forging limited security alignments, and cultivating modest self-protection in case potential threats materialize. Both types of hedging typically are seen as prudent behavior. However, hedging strategies sometimes fail. Risks can be difficult to calculate, and the measures needed to hedge against them can be costly. Hedging international security risks can be particularly challenging, as governments sometimes lack access to adequate protective options at any price. This article illustrates the argument with two contrasting cases: relatively successful Southeast Asian hedging against the risk of financial calamity after the 1997 crisis and less effective efforts by some of the same states to hedge against the security risk of Chinese encroachment in the South China Sea.
Four versus six weeks of antibiotic therapy for osteoarticular infections after implant removal: a randomized trial
Authors: Benkabouche Mohamed , Racloz Guillaume , Spechbach Hervé , Lipsky Benjamin A , Gaspoz Jean-Michel , Uçkay Ilker
Published: April 2019

Background

The optimal duration of antibiotic therapy for treating orthopaedic implant infections after surgical drainage and complete implant removal is unknown.

Methods

This was a single-centre, unblinded, prospective trial randomizing (1:1) eligible patients to either 4 or 6 weeks of systemic, pathogen-targeted antibiotic therapy. Clinical trial registration number: ClinicalTrials.gov (NCT0362209).

Results

We analysed 123 eligible patients (62 in the 4 week antibiotic arm and 61 in the 6 week arm) in the ITT analysis. The patients’ median age was 64 years, 75 (61%) were men and 38 (31%) were immunocompromised. The most common types of infection treated included: two-stage exchange procedure for prosthetic joint infection (n = 38); orthopaedic plate infection (44) and infected nail implants (11). The median duration of post-explant intravenous antibiotic therapy was 4 days. Overall, 120 episodes (98%) were cured microbiologically and 116 (94%) clinically after a median follow-up period of 2.2 years. During follow-up, four patients had a clinical recurrence with a pathogen other than the initial causative agent. We noted recurrence of clinical infection in four patients in the 4 week arm and three patients in the 6 week arm (4/62 versus 3/61; χ2 test; P = 0.74); in all cases, this occurred at around 2 months following the end of antibiotic treatment.

Conclusions

We found no statistically significant difference in the rates of clinical or microbiological remission between patients randomized to only 4 compared with 6 weeks of systemic antibiotic therapy after removal of an infected osteoarticular implant.
Deontic modals and hyperintensionality
Authors: Faroldi Federico L G
Published: April 2019

In this paper I argue that deontic modals are hyperintensional, i.e. logically equivalent contents cannot be substituted in their scope. I give two arguments, one deductive and the other abductive. First, I show that the contrary thesis (that deontic modals are not hyperintensional) leads to falsity; second, I argue that a hyperintensional theory of deontic modals fares better than its rivals in terms of elegance, theoretical simplicity and explanatory power (e.g. Ross’s paradox, the Gentle Murderer, The Good Samaritan, Free Choice Permission and the Miners’ Paradox disappear). I then propose a philosophical analysis of this thesis and outline some consequences. In Section 1 I introduce and define deontic modality and hyperintensionality. In Section 2 I give a reductio for the hyperintensionality of deontic modals. If the argument is sound, a useful corollary is that deontic modals are also non-intensional, and therefore possible-world semantics accounts are illfitted for them. I then show how the main result can be strengthened or weakened by varying the definition of logical validity. In Section 3 I give an abductive argument for the hyperintensionality of deontic modals, arguing that with a single move we are able to solve many paradoxes and puzzles traditionally troubling deontic logic. I present a version of a hyperintensional deontic logic in an appendix, which I prove is sound and complete with respect to a version of truthmaker semantics.
Proof theory for quantified monotone modal logics
Authors: Negri Sara , Orlandelli Eugenio
Published: April 2019

This paper provides a proof-theoretic study of quantified non-normal modal logics (NNML). It introduces labelled sequent calculi based on neighbourhood semantics for the first-order extension, with both varying and constant domains, of monotone NNML, and studies the role of the Barcan formulas in these calculi. It will be shown that the calculi introduced have good structural properties: invertibility of the rules, height-preserving admissibility of weakening and contraction and syntactic cut elimination. It will also be shown that each of the calculi introduced is sound and complete with respect to the appropriate class of neighbourhood frames. In particular, the completeness proof constructs a formal derivation for derivable sequents and a countermodel for non-derivable ones, and gives a semantic proof of the admissibility of cut.
Dose–volume parameters and local tumor control in cervical cancer treated with central-shielding external-beam radiotherapy and CT-based image-guided brachytherapy
Authors: Okazaki Shohei , Murata Kazutoshi , Noda Shin-ei , Kumazaki Yu , Hirai Ryuta , Igari Mitsunobu , Abe Takanori , Komatsu Shuichiro , Nakano Takashi , Kato Shingo
Published: April 2019

Definitive radiotherapy for cervical cancer consists of external-beam radiotherapy (EBRT) and brachytherapy. In EBRT, a central shield (CS) reduces the dose to the rectum and bladder. The combination of whole-pelvic (WP)- and CS-EBRT and brachytherapy is the standard radiotherapy protocol in Japan. Despite clinical studies, including multi-institutional clinical trials, showing that the Japanese treatment protocol yields favorable treatment outcomes with low rates of late radiation toxicities, dose–volume parameters for the Japanese treatment protocol remain to be established. We conducted a retrospective dose–volume analysis of 103 patients with uterine cervical cancer treated with the Japanese protocol using computed tomography–based adaptive brachytherapy. The 2-year overall survival and 2-year local control rates according to FIGO stage were 100% and 100% for Stage I, 92% and 94% for Stage II, and 85% and 87% for Stage III–IV, respectively. Late adverse effects in the rectum and bladder were acceptable. Receiver operating characteristic analysis discriminated recurrence within the high-risk clinical target volume (HR-CTV) (n = 5) from no local recurrence (n = 96), with the optimal response obtained at a dose of 36.0 GyEQD2 for HR-CTV D90 and 28.0 GyEQD2 for HR-CTV D98. These values were used as cut-offs in Fisher exact tests to show that high HR-CTV D90 and HR-CTV D98 doses for brachytherapy sessions were significantly associated with tumor control within the HR-CTV. These data suggest a contribution of brachytherapy to local tumor control in WP- and CS-EBRT and brachytherapy combination treatment, warranting validation in multi-institutional prospective studies.
Towards a Refugee Livelihoods Approach: Findings from Cameroon, Jordan, Malaysia and Turkey
Authors: Wake Caitlin , Barbelet Veronique
Published: April 2019

This note from the field explores the purpose, process and value of using a sustainable-livelihoods framework and operational map to study refugee livelihoods. The current absence of a livelihoods framework specifically tailored to refugees has created a gap not only in research, but in policy development and application. This article reflects on the utility of this methodology to generate insight into the lives of refugees in four diverse contexts: Central African Republic (CAR) refugees in Cameroon; Rohingya refugees in Kuala Lumpur, Malaysia; Syrian refugees in Zarqa, Jordan; and Syrian refugees in Istanbul, Turkey. The framework was helpful in that it enabled us to explore how refugees perceive their context, risks and possibilities as well their objectives, actions and strategies. As per Levine’s methodology, starting with refugees and their perceptions unlocked a new way of looking at the environment within which refugees try to sustain themselves and a deeper understanding of how refugees’ perceptions dictate their livelihood goals, strategies and actions. This article extends analysis to consider the broader policy implications that this specific methodological approach supports.
The Wandering Palestinian as Reflected in the Novel Imra’at Al-Risāla by The Palestinian Writer Rajā’ Bakriyya
Authors: Gottesfeld Dorit
Published: April 2019

The article examines the writing of Rajā’ Bakriyya, who is considered a prominent new generation Palestinian woman writer in Israel, focusing on her latest novel, Imra’at al-risāla (The Letter Woman, 2007). It points to the way Bakriyya feminizes the novel from every possible aspect, even the national-political dimension which is integrated into the novel, creating a narrative which is truly her own. The article focuses on the integration of the national-political reality into the text, especially the female protagonist’s journey of wandering between homeland and exile, which is presented as a metaphor for the wandering Palestinian. Bakriyya articulates this journey in a unique way, as a journey between the beloved and a lover. Leaving the homeland is described as leaving the beloved while returning to the homeland is described as a returning to the eternal beloved one. The uniqueness of the novel lies in the innovative and unconventional way in which it describes this journey.
Mortality associated with Blastomyces dermatitidis infection: A systematic review of the literature and meta-analysis
Authors: Carignan Alex , Denis Mélina , Abou Chakra Claire Nour
Published: April 2019

Published case fatality in blastomycosis patients ranges between 4% and 78%. This study aimed to assess mortality associated with blastomycosis and identify its associated risk factors. We conducted a systematic review of publications related to Blastomyces dermatitidis available in PubMed and Scopus databases. Studies that reported data on blastomycosis mortality and that were published from inception through February 2018 were assessed and included in the analysis. Using the R meta package, a random-effect model meta-analysis was used to calculate pooled and stratified estimates of case-fatality proportions and risk ratios. Of 1553 publications, we included 20 studies reporting on a total of 2820 cases of blastomycosis between 1970 and 2014 and three case series reports with 10, 21, and 36 patients. The mean or median ages ranged from 28 to 59 years. Mortality was defined as attributable mortality caused by blastomycosis in 13 studies. Among 14 studies with a standard error ≤0.05, the overall pooled mortality was 6.6% (95% confidence interval [CI], 4.9–8.2) with 57% heterogeneity. The mortality rate was 37% (95% CI, 23–51) in immunocompromised patients and 75% (95% CI, 53–96) in patients who developed an acute respiratory distress syndrome (ARDS) (n = 3 studies each). ARDS was the only identified risk factor in general patients (risk ratio = 10.2). The overall mortality was significantly higher in studies involving immunocompromised patients and ARDS patients. Our analysis showed considerable heterogeneity among studies. Inconsistent mortality definitions may have contributed to the observed heterogeneity. Further research is needed to assess potential risk factors for mortality.
On the geometry of the X-ray emission from pulsars: the changing aspect of the Be/X-ray pulsar SXP348
Authors: Cappallo R , Laycock S G T , Christodoulou D M , Coe M J , Zezas A
Published: April 2019

The X-ray source SXP348 is a high-mass X-ray binary system in the Small Magellanic Cloud. Since its 1998 discovery by BeppoSAX, this pulsar has exhibited a spin period of ∼340−350 s. In an effort to determine the orientation and magnetic geometry of this source, we used our geometric model Polestar to fit 71 separate pulse profiles extracted from archival Chandra and XMM-Newton observations over the past two decades. During 2002, pulsations ceased being detectable for nine months despite the source remaining in a bright state. When pulsations resumed, our model fits changed, displaying a change in accretion geometry. Furthermore, in 2006, detectable pulsations again ceased, with 2011 marking the last positive detection of SXP348 as a point source. These profile fits will be released for public use as part of the database of Magellanic Cloud pulsars.
Influence of galactic arm scale dynamics on the molecular composition of the cold and dense ISM – II. Molecular oxygen abundance
Authors: Wakelam V , Ruaud M , Gratier P , Bonnell I A
Published: April 2019

Molecular oxygen has been the subject of many observational searches as chemical models predicted it to be a reservoir of oxygen. Although it has been detected in two regions of the interstellar medium, its rarity is a challenge for astrochemical models. In this paper, we have combined the physical conditions computed with smoothed particle hydrodynamics simulations with our full gas–grain chemical model Nautilus, to study the predicted O2 abundance in interstellar material forming cold cores. We thus follow the chemical evolution of gas and ices in parcels of material from the diffuse interstellar conditions to the cold dense cores. Most of our predicted O2 abundances are below 10−8 (with respect to the total proton density) and the predicted column densities in simulated cold cores are at maximum a few 10−14 cm−2, in agreement with the non-detection limits. This low O2 abundance can be explained by the fact that, in a large fraction of the interstellar material, the atomic oxygen is depleted on to the grain surface (and hydrogenated to form H2O) before O2 can be formed in the gas-phase and protected from ultraviolet photodissociations. We could achieve this result only because we took into account the full history of the evolution of the physical conditions from the diffuse medium to the cold cores.