bluuebunny/crossref_metadata_2025 huggingface dataset:
A tuning method based on the coupled mode frequencies in biperiodic coupled-cavity linear accelerator
Authors: Zhou Bowen , Li Wenliang , Zhang Pengjiao , Zhang Liping , Li Bolin , Ke Yijing , Zhang Hong , Zhao Lei , Li Junzhou , Hou Rui , An Sun
Published: December 2018

A coupled-cavity linac (CCL) is widely used around the world in many fields. The radio frequency design is always a fundamental and crucial problem in CCL. In biperiodic structures, especially side-coupled structures, entirely different structures between accelerating cavities (ACs) and coupled cavities (CCs) will cause different frequency drops (δf) with the introduction of coupling slots. In order to achieve precise and consistent frequencies in each cell, the rule of individual cavity frequency drops should be figured out. A model of lumped resonant circuits is chosen to provide accurate prediction for normal mode frequencies. Through solving equivalent circuit equations, a parameter called frequency gap difference (ΔFg) is proposed, whose value is directly proportional to the frequency difference (df) between AC and CC and the ratio is one-to-one when AC frequency ( fa) is close to CC frequency ( fc). Based on the property of ΔFg, a simplified method on how to design and tune a triplet CCL is proposed; instead of tuning each individual cell, the new method only requires measuring the frequencies of the coupled normal modes, which considerably simplifies the tuning process and reduces the turn-around time. The particular design flow and tuning method have been successfully applied in the Nanjing University CCL Project. In addition, through comparing cavities with and without coupling slots, the value of frequency drops with different coupling coefficients is revealed and analyzed.
Early pathological characterization of murine dissecting abdominal aortic aneurysms
Authors: Phillips Evan H. , Lorch Adam H. , Durkes Abigail C. , Goergen Craig J.
Published: December 2018

We report here on the early pathology of a well-established murine model of dissecting abdominal aortic aneurysms (AAAs). Continuous infusion of angiotensin II (AngII) into apolipoprotein E-deficient mice induces the formation of aortic dissection and expansion at some point after implantation of miniosmotic pumps containing AngII. While this model has been studied extensively at a chronic stage, we investigated the early pathology of dissecting AAA formation at multiple scales. Using high-frequency ultrasound, we screened 12-week-old male mice daily for initial formation of these aneurysmal lesions between days 3 and 10 post-implantation. We euthanized animals on the day of diagnosis of a dissecting AAA or at day 10 if no aneurysmal lesion developed. Aortic expansion and reduced vessel wall strain occurred in animals regardless of whether a dissecting AAA developed by day 10. The aortas of mice that did not develop dissecting AAAs showed intermediate changes in morphology and biomechanical properties. RNA sequencing and gene expression analysis revealed multiple proinflammatory and matrix remodeling genes to be upregulated in the suprarenal aorta of AngII-infused mice as compared to saline-infused controls. Histology and immunohistochemistry confirmed that extracellular matrix remodeling and inflammatory cell infiltration, notably neutrophils and macrophages, occurred in AngII-infused mice with and without dissecting AAAs but not saline-infused controls. Understanding early disease processes is a critical step forward in translating experimental results in cardiovascular disease research. This work advances our understanding of this well-established murine model with applications for improving early diagnosis and therapy of acute aortic syndrome in humans.
Direct access to the moments of scattering distributions in x-ray imaging
Authors: Modregger Peter , Endrizzi Marco , Olivo Alessandro
Published: December 2018

The scattering signal obtained by phase-sensitive x-ray imaging methods provides complementary information about the sample on a scale smaller than the utilised pixels, which offers the potential for dose reduction by increasing pixel sizes. Deconvolution-based data analysis provides multiple scattering contrasts but suffers from time consuming data processing. Here, we propose a moment-based analysis that provides equivalent scattering contrasts while speeding up data analysis by almost three orders of magnitude. The availability of rapid data processing will be essential for applications that require instantaneous results such as medical diagnostics, production monitoring, and security screening. Further, we experimentally demonstrate that the additional scattering information provided by the moments with an order higher than two can be retrieved without increasing exposure time or dose.
Enhancing the critical current of YBa2Cu3O7 thin films by substrate nanoengineering
Authors: Jones A. , Lam S. K. H. , Du J. , Rubanov S. , Pan A. V.
Published: December 2018

The critical current density, Jc, can be increased by introducing defects throughout YBa2Cu3O7 superconducting thin films. We propose a new approach of substrate nanoengineering to produce well-controlled defects. LaAlO3 substrates have been ion-etched with different 34 nm deep patterns prior to the deposition of the films. An annealing step at 1000 °C after substrate etching has been undertaken to negate the Ar-ion damage to the surface. The Jc of the so-prepared samples measured at different temperatures has been compared to thin films deposited on plain substrates at the same time. In general, an increase in Jc is observed across all temperatures and fields as a result of both patterning and annealing. In particular, at zero field and 85 K, the largest enhancement of >40% has been recorded for circle and triangle patterns. This new substrate nanoengineering technique is very promising for flux trapping of superconducting devices, particularly because an increase to critical current (Ic) also occurs. Further optimization of depth, size, and shape of the patterns is expected to produce further improvements to Jc.
Compressed sensing based sub-Nyquist sampling of multiple sinusoids with dual rate channels
Authors: Dai Zhijian , Chen Yu , Wen Weifeng , Zheng Yanze
Published: December 2018

In this paper, we propose a reconstruction approach for a multiple-sinusoidal signal. The signal reconstruction requires a small number of samples and is based on a sub-Nyquist sampling scheme with dual rate channels. In the proposed sampling scheme, the samples are grouped into multiple cosets. To obtain enough different cosets to reconstruct a signal, the sampling rates of channels are required to be relative coprime. For each coset, the Whittaker–Shannon interpolation formula is employed to construct the relation between the sub-Nyquist samples and the original signal, which is used to construct the measurement matrix. Since the multiple-sinusoidal signal is sparse in the frequency domain, compressed sensing theory can be adopted to reconstruct the signal. Simulation results are reported to demonstrate the feasibility and effectiveness of the proposed approach.
Modifying the linear and nonlinear optical susceptibilities of coupled quantum dot-metallic nanosphere systems with the Purcell effect
Authors: Evangelou Sofia
Published: December 2018

We study the modification of the linear, third-order, and fifth-order susceptibilities of a quantum dot that is coupled to a spherical metallic nanoparticle. We calculate the susceptibilities with a density matrix approach and calculate the modified spontaneous emission rate of the quantum dot due to the Purcell effect next to the metallic nanosphere using a boundary element method. We show that the strong variation of the spontaneous decay rates of the quantum dot near the metallic nanosphere can be used for tailoring the linear, third-order, and fifth-order susceptibilities. Specifically, the Purcell modified spontaneous decay rate leads to strong alteration (enhancement or suppression) of the linear and the nonlinear susceptibilities. The specific type of alteration depends on the distance of the quantum dot from the surface of the nanosphere and the direction of the electric dipole moment of the quantum dot. The strong influence of the pure dephasing rate of the quantum dot on the modification of the optical susceptibilities is also analyzed.
A finite element model for magnetohydrodynamic squeeze-film flows
Authors: Wagner Jordan R. , Higgs C. Fred
Published: December 2018

A computational model is developed to analyze magnetohydrodynamic (MHD) squeeze-film flows featuring an electrically conducting fluid subjected to imposed magnetic and electric fields. The model is based on the so-called MHD Reynolds equation for squeeze-films—an extension of the classical hydrodynamic Reynolds equation. A complete derivation of the MHD Reynolds equation is performed by applying thin-film and quasi-steady assumptions to the Maxwell/Navier-Stokes system coupled by the Lorentz force. The resulting equation is a two-dimensional and variable-coefficient Poisson equation for pressure, which reduces to the purely hydrodynamic form in the limit of vanishing Hartmann number. A geometric calculus formulation facilitates the reduction of the mathematical system into two dimensions, which is a challenge in standard vector calculus due to the cross product. The model permits realistic geometrical representations of the constraining squeeze-surfaces, and we demonstrate the use of a multi-variate Weierstrass-Mandelbrot fractal to numerically generate scale-invariant surface roughness profiles. Ultimately, the governing equation is solved with the Galerkin finite element method. Several numerical examples are conducted to highlight some of the model’s capabilities. MHD forces—as well as the roughness, geometry, and topology of the squeeze surfaces—are shown to significantly influence flow characteristics.
Towards the description of adsorption of water in slit-like pores with walls covered by molecular brushes
Authors: Trejos Víctor M. , Pizio Orest , Sokołowski Stefan
Published: December 2018

The density profiles, adsorption isotherms, and phase behavior of a water model in a slit-like pore with walls modified by pre-adsorbed tethered chain molecules have been studied in the framework of a density functional theory. Each chain is bonded to the surface by its terminal segment, and the surface density of grafted chains is the same for each wall. The model for water taken from the work of Clark et al. [Mol. Phys. 104, 3561 (2006)] reproduces successfully a bulk equation of state. The mean field approach has been used to describe the effects of attractive interactions. The chemical association effects are taken into account by using the first-order thermodynamic perturbation theory of Wertheim. We have found that the presence of molecular brushes on the pore walls has important consequences for the adsorption and phase behavior of confined water. If the brush segments do not attract water molecules strongly, the vapor-liquid coexistence envelope shrinks upon increasing brush density, but the critical temperature is weakly affected. Alteration from capillary condensation to evaporation is observed with changes in the brush density, number of segments of tethered chains, and/or chemical identity of segments. The crossover temperature is affected by all these factors. Moreover, we have shown that affinity of water to segments of tethers is an important factor determining adsorption of water vapor and the entire phase diagram.
Lattice models provide fast and accurate way to simulate DNA self-assembling
Authors: Liebendorfer Adam
Published: December 2018

Lattice modeling coupled with Monte Carlo methods allows accurate and logistically feasible computational simulations of DNA folding.
New, scalable, reproducible method to make high-sensitivity optomechanical magnetometers
Authors: Patrick Chris
Published: December 2018

Sputter coating a magnetostrictive film onto a microcavity fabricates high-sensitivity optomechanical magnetometers without degrading optical quality factor or magnetostrictive performance.
White clover or nitrogen fertiliser for dairying under nitrate leaching limits?
Authors: Chapman David , Pinxterhuis Ina , Ledgard Stewart , Parsons Tony
Published: December 2018

As the pressure intensifies to reduce nitrogen (N) losses to the environment from pasture-based dairy systems, interest in reducing N-fertiliser inputs and returning to grass–clover mixtures, where more N for pasture growth is supplied by biological N fixation (BNF), have been revived. However, the following question then arises: is BNF fundamentally different from fertiliser N with respect to N losses, especially nitrate-N leaching risk? The present paper addresses this question by reviewing empirical evidence in the context of N-cycling processes and the efficiency of N use for herbage production. Nitrate leaching data from studies comparing different sward treatments at the same level of total N inputs (fertiliser plus BNF) provide no evidence to suggest that leaching differs when N is supplied solely by fixation in mixtures, by fixation plus fertiliser in mixtures, or solely as a fertiliser to grass monoculture. Increasing clover content in mixed grass–clover pastures is likely to increase N leaching due to a lower ratio of soluble sugar and starch to N in herbage than the common companion grass species perennial ryegrass, and, therefore, a higher partitioning of N eaten to urine. Counteracting this effect, mixed grass–clover pastures may offer some potential for increasing N-use efficiency and reducing the whole-farm N surplus compared with grass-dominant pasture receiving high rates of N fertiliser. While there are undeniable benefits for the productivity of dairy systems from maintaining strong grass–clover mixtures, it is the total amount of N entering the system, rather than the form of N (BNF or fertiliser), that influences nitrate leaching rates.
Electronic Spectra of the Triacetylene Cation (HC6H+) and Protonated Triacetylene (HC6H2+) Tagged with Ar
Authors: Jacovella Ugo , Muller Giel , Catani Katherine J. , Bartlett Nastasia I. , Bieske Evan J.
Published: December 2018

Polyacetylene cations (HC2nH+) play important roles in combustion processes and in the chemistry of planetary atmospheres and interstellar clouds. Here we report the electronic spectrum for the triacetylene cation (HC6H+) recorded over the 300–610nm range by photodissociating mass-selected ions tagged with argon atoms in a tandem mass spectrometer. The spectrum shows three band systems that are assigned to (origin transition 16665cm−1), (origin transition 23916cm−1), and (origin transition 29920cm−1). Although the band system is well known, the and band systems are observed for the first time in the gas phase. In addition, the electronic spectrum of the protonated triacteylene cation tagged with an argon atom (HC6-Ar) is reported, providing the first gas-phase spectrum for this species.
Path-dependent institutions drive alternative stable states in conservation
Authors: Tekwa Edward W. , Fenichel Eli P. , Levin Simon A. , Pinsky Malin L.
Published: December 2018

Understanding why some renewable resources are overharvested while others are conserved remains an important challenge. Most explanations focus on institutional or ecological differences among resources. Here, we provide theoretical and empirical evidence that conservation and overharvest can be alternative stable states within the same exclusive-resource management system because of path-dependent processes, including slow institutional adaptation. Surprisingly, this theory predicts that the alternative states of strong conservation or overharvest are most likely for resources that were previously thought to be easily conserved under optimal management or even open access. Quantitative analyses of harvest rates from 217 intensely managed fisheries supports the predictions. Fisheries’ harvest rates also showed transient dynamics characteristic of path dependence, as well as convergence to the alternative stable state after unexpected transitions. This statistical evidence for path dependence differs from previous empirical support that was based largely on case studies, experiments, and distributional analyses. Alternative stable states in conservation appear likely outcomes for many cooperatively managed renewable resources, which implies that achieving conservation outcomes hinges on harnessing existing policy tools to navigate transitions.
Adjective-noun order in Papiamento-Dutch code-switching
Authors: Pablos Leticia , Parafita Couto M. Carmen , Boutonnet Bastien , de Jong Amy , Perquin Marlou , de Haan Annelies , Schiller Niels O.
Published: December 2018

In Papiamento-Dutch bilingual speech, the nominal construction is a potential ‘conflict site’ if there is an adjective from one language and a noun from the other. Adjective position is pre-nominal in Dutch (cf.rode wijn‘red wine’) but post-nominal in Papiamento (cf.biña kòrá‘wine red’). We test predictions concerning the mechanisms underpinning word order in noun-adjective switches derived from three accounts: (i) the adjective determines word order (Cantone & MacSwan, 2009), (ii) the matrix language determines word order (Myers-Scotton, 1993,2002), and (iii) either order is possible (Di Sciullo, 2014). An analysis of spontaneous Papiamento-Dutch code-switching production (Parafita Couto & Gullberg, 2017) could not distinguish between these predictions. We used event-related brain potentials (ERPs) to measure online comprehension of code-switched utterances. We discuss how our results inform the three theoretical accounts and we relate them to syntactic coactivation and the production-comprehension link.
Recovery of left ventricular function following in vivo reexpression of cardiac myosin binding protein C
Authors: Giles Jasmine , Patel Jitandrakumar R. , Miller Adam , Iverson Elizabeth , Fitzsimons Daniel , Moss Richard L.
Published: December 2018

The loss of cardiac myosin binding protein C (cMyBP-C) results in left ventricular dilation, cardiac hypertrophy, and impaired ventricular function in both constitutive and conditional cMyBP-C knockout (MYBPC3 null) mice. It remains unclear whether the structural and functional phenotypes expressed in the MYBPC3 null mouse are reversible, which is an important question, since reduced expression of cMyBP-C is an important cause of hypertrophic cardiomyopathy in humans. To investigate this question, we generated a cardiac-specific transgenic mouse model using a Tet-Off inducible system to permit the controlled expression of WT cMyBP-C on the MYBPC3 null background. Functional Tet-Off mice expressing WT cMyBP-C (FT-WT) were generated by crossing tetracycline transactivator mice with responder mice carrying the WT cMyBP-C transgene. Prior to dietary doxycycline administration, cMyBP-C was expressed at normal levels in FT-WT myocardium, which exhibited similar levels of steady-state force and in vivo left ventricular function as WT mice. Introduction of dietary doxycycline for four weeks resulted in a partial knockdown of cMyBP-C expression and commensurate impairment of systolic and diastolic function to levels approaching those observed in MYBPC 3 null mice. Subsequent withdrawal of doxycycline from the diet resulted in the reexpression of cMyBP-C to levels comparable to those observed in WT mice, along with near-complete recovery of in vivo ventricular function. These results show that the cardiac phenotypes associated with MYBPC3 null mice are reversible. Our work also validates the use of the Tet-Off inducible system as a means to study the mechanisms underlying hypertrophic cardiomyopathy.
Analyzing Components of Productivity Growth Using the Bennet‐Lowe Indicator: An Application to Welsh Sheep Farms
Authors: Ang Frederic
Published: December 2018

This article introduces the Bennet‐Lowe Total Factor Productivity (TFP) indicator. The proposed measure is difference‐based, additively complete, and transitive. We also develop a general nonparametric framework to exhaustively decompose all Bennet‐type TFP indicators, including the one introduced here, into technical change, technical efficiency change, scale efficiency change, and mix efficiency change. This decomposition provides a powerful tool for policy makers to guide financial decisions on research and development, extension, subsidies, and price support. The empirical application focuses on the Welsh sheep sector for the years 2001–2014. The results show that in this 14‐year period, Welsh sheep farms increased their TFP by 30.28% on average (2.33% p.a.). However, the exhaustive decomposition shows that TFP growth is not distributed equally across all farms, with an increasing divergence between front‐runners and laggards. The negative values of scale efficiency change and mix efficiency change cast doubt on the current subsidy policies.
Against Kripke’s solution to the problem of negative existentials
Authors: Hausmann Marco
Published: December 2018

In this paper, I try to show that Kripke’s proposed solution to the problem of negative existentials fails. I try to show that Kripke’s proposal fails because it entails that anybody who has (or had) good reasons to believe that there are no propositions has (or had) also good reasons to believe that he or she does not exist. However, there were philosophers (most notably Quine) who had good reasons to believe that there are no propositions even though they didn’t have good reasons to believe that they do not exist. I conclude that Kripke’s proposed solution to the problem of negative existentials fails.
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data
Authors: Poell Jos B , Mendeville Matias , Sie Daoud , Brink Arjen , Brakenhoff Ruud H , Ylstra Bauke
Published: December 2018

Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing, but analysis is hampered by the lack of knowledge on absolute DNA copy numbers and tumor purity. Here, we describe an analytical tool for Absolute Copy number Estimation, ACE, which scales relative copy number signals from chromosomal segments to optimally fit absolute copy numbers, without the need for additional genetic information, such as SNP data. In doing so, ACE derives an estimate of tumor purity as well. ACE facilitates analysis of large numbers of samples, while maintaining the flexibility to customize models and generate output of single samples.

Availability and implementation

ACE is freely available via www.bioconductor.org and at www.github.com/tgac-vumc/ACE.

Supplementary information

Supplementary data are available at Bioinformatics online.
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning
Authors: Li Xiangtao , Zhang Shixiong , Wong Ka-Chun
Published: December 2018

Motivation

In recent years, single-cell RNA sequencing enables us to discover cell types or even subtypes. Its increasing availability provides opportunities to identify cell populations from single-cell RNA-seq data. Computational methods have been employed to reveal the gene expression variations among multiple cell populations. Unfortunately, the existing ones can suffer from realistic restrictions such as experimental noises, numerical instability, high dimensionality and computational scalability.

Results

We propose an evolutionary multiobjective ensemble pruning algorithm (EMEP) that addresses those realistic restrictions. Our EMEP algorithm first applies the unsupervised dimensionality reduction to project data from the original high dimensions to low-dimensional subspaces; basic clustering algorithms are applied in those new subspaces to generate different clustering results to form cluster ensembles. However, most of those cluster ensembles are unnecessarily bulky with the expense of extra time costs and memory consumption. To overcome that problem, EMEP is designed to dynamically select the suitable clustering results from the ensembles. Moreover, to guide the multiobjective ensemble evolution, three cluster validity indices including the overall cluster deviation, the within-cluster compactness and the number of basic partition clusters are formulated as the objective functions to unleash its cell type discovery performance using evolutionary multiobjective optimization. We applied EMEP to 55 simulated datasets and seven real single-cell RNA-seq datasets, including six single-cell RNA-seq dataset and one large-scale dataset with 3005 cells and 4412 genes. Two case studies are also conducted to reveal mechanistic insights into the biological relevance of EMEP. We found that EMEP can achieve superior performance over the other clustering algorithms, demonstrating that EMEP can identify cell populations clearly.

Availability and implementation

EMEP is written in Matlab and available at https://github.com/lixt314/EMEP

Supplementary information

Supplementary data are available at Bioinformatics online.
Modeling human prostate cancer progression in vitro
Authors: Liu Teresa T , Ewald Jonathan A , Ricke Emily A , Bell Robert , Collins Colin , Ricke William A
Published: December 2018

Detailed mechanisms involved in prostate cancer (CaP) development and progression are not well understood. Current experimental models used to study CaP are not well suited to address this issue. Previously, we have described the hormonal progression of non-tumorigenic human prostate epithelial cells (BPH1) into malignant cells via tissue recombination. Here, we describe a method to derive human cell lines from distinct stages of CaP that parallel cellular, genetic and epigenetic changes found in patients with cancers. This BPH1-derived Cancer Progression (BCaP) model represents different stages of cancer. Using diverse analytical strategies, we show that the BCaP model reproduces molecular characteristics of CaP in human patients. Furthermore, we demonstrate that BCaP cells have altered gene expression of shared pathways with human and transgenic mouse CaP data, as well as, increasing genomic instability with TMPRSS2–ERG fusion in advanced tumor cells. Together, these cell lines represent a unique model of human CaP progression providing a novel tool that will allow the discovery and experimental validation of mechanisms regulating human CaP development and progression. This BPH1-derived Cancer Progression (BCaP) model represents different stages of cancer. The BCaP model reproduces molecular characteristics of prostate cancer. The cells have altered gene expression with TMPRSS2-ERG fusion representing a unique model for prostate cancer progression.
The Association of Antibiotic Stewardship With Fluoroquinolone Prescribing in Michigan Hospitals: A Multi-hospital Cohort Study
Authors: Vaughn Valerie M , Gandhi Tejal , Conlon Anna , Chopra Vineet , Malani Anurag N , Flanders Scott A
Published: December 2018

Background

Fluoroquinolones increase the risk of Clostridioides difficile infection and antibiotic resistance. Hospitals often use pre-prescription approval or prospective audit and feedback to target fluoroquinolone prescribing. Whether these strategies impact aggregate fluoroquinolone use is unknown.

Methods

This study is a 48-hospital, retrospective cohort of general-care, medical patients hospitalized with pneumonia or positive urine culture between December 2015–September 2017. Hospitals were surveyed on their use of pre-prescription approval and/or prospective audit and feedback to target fluoroquinolone prescribing during hospitalization (fluoroquinolone stewardship). After controlling for hospital clustering and patient factors, aggregate (inpatient and post-discharge) fluoroquinolone (ciprofloxacin, levofloxacin, moxifloxacin) exposure was compared between hospitals with and without fluoroquinolone stewardship.

Results

There were 11 748 patients (6820 pneumonia; 4928 positive urine culture) included at 48 hospitals. All hospitals responded to the survey: 29.2% (14/48) reported using pre-prescription approval and/or prospective audit and feedback to target fluoroquinolone prescribing. After adjustment, fluoroquinolone stewardship was associated with fewer patients receiving a fluoroquinolone (37.1% vs 48.2%; P = .01) and fewer fluoroquinolone treatment days per 1000 patients (2282 vs 3096 days/1000 patients; P = .01), driven by lower inpatient prescribing. However, most (66.6%) fluoroquinolone treatment days occurred after discharge, and hospitals with fluoroquinolone stewardship had twice as many new fluoroquinolone starts after discharge as hospitals without (15.6% vs 8.4%; P = .003).

Conclusions

Hospital-based stewardship interventions targeting fluoroquinolone prescribing were associated with less fluoroquinolone prescribing during hospitalization, but not at discharge. To limit aggregate fluoroquinolone exposure, stewardship programs should target both inpatient and discharge prescribing.
Fast and furious: a retrospective study of catheter-associated bloodstream infections with internal jugular nontunneled hemodialysis catheters at a tropical center
Authors: Agrawal Varun , Valson Anna T , Mohapatra Anjali , David Vinoi George , Alexander Suceena , Jacob Shibu , Bakthavatchalam Yamuna Devi , Prakash John Anthony Jude , Balaji Veeraraghavan , Varughese Santosh
Published: December 2018

Background

Nontunneled hemodialysis catheters (NTHCs) remain the preferred vascular access at hemodialysis (HD) initiation in developing countries. We studied the incidence, risk factors and microbiological spectrum of jugular NTHC-associated bloodstream infections (CABSIs) at a tertiary care center in South Asia.

Methods

In this retrospective cohort study, all adult (≥18 years) incident patients who underwent jugular NTHC insertion for HD between January 2016 and June 2017, had no prior history of temporary vascular access insertion and were followed up for ≥14 days were included.

Results

A total of 897 patients underwent NTHC insertion during the study period and 169 patients fulfilled the inclusion criteria and contributed 7079 patient days of follow-up. CABSI incidence was 7.34 episodes per 1000 catheter days and median infection-free survival and time to CABSI were 96 and 24.5 days, respectively. In multivariate Cox regression analysis, immunosuppressive medication {hazard ratio [HR] 2.87 [95% confidence interval (CI) 1.09–7.55]; P = 0.033} and intravenous cefazolin use [HR 0.51 (95% CI 0.28–0.94); P = 0.031] was independently associated with CABSI. The cumulative hazard of CABSI was 8.3, 13.3, 17.6 and 20.9% at Weeks 1, 2, 3 and 4, respectively. Gram-negative organisms were the most common etiological agents (54.7%) and 40.3% of CABSIs were caused by drug-resistant organisms. Gram-negative and Gram-positive CABSIs were associated with neutrophil left shift and higher procalcitonin compared with coagulase-negative staphylococcal CABSIs.

Conclusion

In South Asia, NTHC-associated CABSIs occur early and are predominantly Gram negative. We hypothesize that poor hygiene practices may play a role in this phenomenon.
A data-limited method for assessing cumulative fishing risk on bycatch
Authors: Zhou Shijie , Daley Ross M , Fuller Michael , Bulman Cathy M , Hobday Alistair J
Published: December 2018

To assess fishing effects on data-poor species, impact can be derived from spatial overlap between species distribution and fishing effort and gear catchability. Here, we enhance the existing sustainability assessment for fishing effect method by estimating gear efficiency and heterogeneous density from sporadic catch data. We apply the method to two chondrichthyan bycatch species, Bight Skate and Draughtboard Shark in Australia, to assess cumulative fishing mortality (Fcum) from multiple fisheries. Gear efficiency is estimated from a Bayesian mixture distribution model and fish density is predicted by a generalized additive model. These results, combined with actual fishing effort, allow estimation of fishing mortality in each sector and subsequently, the Fcum. Risk is quantified by comparing Fcum with reference points based on life history parameters. When only the point estimates were considered, our result indicates that for the period 2009 and 2010 Bight Skate caught in 14 fisheries was at high cumulative risk (Fcum ≥ Flim) while Draughtboard Shark caught by 19 fisheries was at low cumulative risk (Fcum ≤ Fmsy). Because of the high cost of conducting cumulative risk assessments, we recommend examining the distribution of fishing effort across fisheries before carrying out the assessments.
Granulysin- and granzyme-dependent elimination of myeloid cells by therapeutic ova-specific type 1 regulatory T cells
Authors: Guipouy Delphine , Gertner-Dardenne Julie , Pfajfer Laurène , German Yolla , Belmonte Nathalie , Dupré Loïc
Published: December 2018

The intrinsic immunosuppressive properties of regulatory T (Treg) cells can be harnessed for therapeutic approaches aiming at down-modulating harmful immune reactions. In this context, expanded type 1 Treg cells (Tr1 cells) specific for ovalbumin (ova-Tr1 cells) have been tested for clinical efficacy in the treatment of autoimmune disorders such as refractory Crohn’s disease (CD). The clinical use of these therapeutic products warrants exploration of their mechanism of action. Here, we identified a relationship between the CD activity index and the expression of lytic molecules by the ova-Tr1 cells administered in the previously reported First-in-Man study [Crohn’s And Treg cells Study 1 (CATS1) study]. Accordingly, ova-Tr1 cells were found to carry granules containing high levels of lytic molecules, including multiple granzymes and granulysin. These cells displayed a T-cell receptor (TCR)-independent cytotoxic activity, which was preferentially directed toward myeloid cell lines and monocyte-derived dendritic cells. Upon contact with myeloid cells, ova-Tr1 cells induced their apoptosis via a perforin-independent and a granulysin/granzyme-dependent mechanism. As compared to CD8+ cytotoxic T cells, ova-Tr1 cells required more time to lyse target cells and displayed a more gradual lytic activity over time. Notably, this activity was sustained over days resulting in the control of myeloid cell populations at a relatively low ratio. Our study reveals that ova-Tr1 cells are endowed with a sustained cytotoxic activity that relies on a unique combination of granulysin and granzymes and that preferentially eliminates myeloid target cells in a TCR-independent manner.
Recent advances and novel approaches in laboratory-based diagnostic mycology
Authors: White P Lewis
Published: December 2018

The field of diagnostic mycology represents much more than culture and microscopy and is rapidly embracing novel techniques and strategies to help overcome the limitations of conventional approaches. Commercial molecular assays increase the applicability of PCR testing and may identify markers of antifungal resistance, which are of great clinical concern. Lateral flow assays simplify testing and turn-around time, with potential for point of care testing, while proximity ligation assays embrace the sensitivity of molecular testing with the specificity of antibody detection. The first evidence of patient risk stratification is being described and together with the era of next generation sequencing represents an exciting time in mycology.
New Wave Consequentialism
Authors: Seidel Christian
Published: December 2018

Consequentialism is a focal point of discussion in moral philosophy, although it is unclear what, exactly, consequentialism is. Taking seriously the idea that “consequentialism” is a term of art in moral theorizing that has been shaped in response to objections against utilitarianism, this chapter retraces the debate on consequentialism in section 1.1. It shows that (a) a trend to design consequentialist theories at increasingly higher levels of abstraction has triggered an emerging new wave consequentialism which is extremely flexible and characteristically associated with a “resort to abstraction” and a “turn to reasons”; and that (b) the concept of consequentialism itself has become increasingly general by incremental conceptual emancipations from certain characteristic marks. Section 1.2 explains the structure of the volume, summarizes the essays, and outlines the relation between them. By identifying emerging topics for further exploration, section 1.3 provides a brief outlook on the prospects of new wave consequentialism.
Summing Up
Authors: Achinstein Peter
Published: December 2018

This chapter provides a summary of the results of this investigation into the meaning, legitimacy, and importance of speculating within and about science.
After the Projects
Authors: Vale Lawrence J.
Published: December 2018

At a time when lower-income Americans face a desperate struggle to find affordable rental housing in many cities, After the Projects investigates the contested spatial politics of public housing development and redevelopment. Public housing practices differ markedly from city to city and, collectively, reveal deeply held American attitudes about poverty and how the poorest should be governed. The book exposes the range of outcomes from the US federal government’s HOPE VI program for public housing transformation, focused on nuanced accounts of four very different ways of implementing this same national initiative—in Boston, New Orleans, Tucson, and San Francisco. It draws upon more than two hundred interviews, analysis of internal documents about each project, and nearly fifteen years of visits to these neighborhoods. The central aim is to understand how and why some cities, when redeveloping public housing, have attempted to minimize the presence of the poorest residents in their new mixed-income communities, while other cities have instead tried to serve the maximum number of extremely low-income households. The book shows that these socially and politically revealing decisions are rooted in distinctly different kinds of governance constellations—each yielding quite different sorts of community pressures. These have been forged over many decades in response to each city’s own struggle with previous efforts at urban renewal. In contrast to other books that have focused on housing in a single city, this volume offers comparative analysis and a national picture, while also discussing four emblematic communities with an unprecedented level of detail.
Introduction
Authors: Avi Astor Ron , Benbenishty Rami
Published: December 2018

This introduction chapter presents the historical, personal, and academic background that led to this book that examines a model of school violence in context. The chapter presents the book chapters: a revised model of school violence in evolving contexts; the definition of bullying and school violence; exploring similarities and differences between groups in base rates of victimization and in the structures of victimization types; the multiple ways of exposure to a range of weapons on school grounds, focusing on school-level analysis; sexual victimization and its association with cultural groups; suicide and its relations with bullying both on the individual and school levels; the victimization of teachers by students and of students by their teachers and their interrelationships on a student and school-level; multiple forms of cyberbullying and their relationships with “traditional” bullying; school climate, its definitions, and relationships with victimization and academic achievement over time; policy and intervention implications.
Weapons and Schools
Authors: Avi Astor Ron , Benbenishty Rami
Published: December 2018

This chapter presents conceptualization and empirical evidence regarding weapons in schools. The chapter suggests that instead of limiting the discussion to mass shootings, scholars need to examine multiple forms of weapons exposure including bringing a weapon to school, using a weapon to threaten or hurt a student, or witnessing a weapon in schools. Distinctions should also be drawn between various types of weapons. The chapter draws attention to the disconnect between the literature on bullying and weapons and discussions of the presence of gangs in school. The chapter also conceptualizes weapons in school from a multilevel perspective, of both student- and school-level. A multilevel analysis of weapons in all high schools in California is used to examine these issues empirically. The chapter discusses implications for policy and practices, such as the need to employ a public health approach and reassess zero tolerance policies.
Sexual Victimization
Authors: Avi Astor Ron , Benbenishty Rami
Published: December 2018

This chapter examines issues of sexual victimization in schools. It discusses the complexity of definitions of sexual victimization in light of shifting societal norms and expectations. The chapter takes a nuanced approach to issues of sexual assault, victimization due to sexual orientation or gender identity, and sexual humiliation or sexual predatory behaviors as they relate to various forms of bullying, harassment, victimization, and discrimination. It discusses the interrelations between school climate and sexual harassment, the vulnerability of certain groups to being targeted for such harassment (e.g., sexual minorities such as lesbian, gay, bisexual, transgender, and queer [LGBTQ]). The chapter also explores issues of sexual harassment in schools as they relate to issues of patriarchal and religious cultures and examines differences in sexual victimization among cultural groups in Israel, both on the level of the individual student and on the school level.
Teacher–Student and Student–Teacher Victimization and their Interrelationship
Authors: Avi Astor Ron , Benbenishty Rami
Published: December 2018

This chapter examines the victimization of teachers by students and victimization of students by teachers and explores their interrelationships. The chapter reviews the literature on these issues and notes the paucity of research in education on the prevalence and consequences of victimization of students by teachers—this, in contrast to a recent worldwide interest in the victimization of teachers by students. The chapter examines cultural beliefs and shifting norms with regards to corporal punishment of students. A study of student–teacher mutual victimization as reported by Israeli students from several cultural groups. The chapter suggests that students’ reports of being victimized by their teachers are associated with their reports of victimizing teachers, both on the student and school level (especially with regard to more physical and sexual types of victimization) and for all three cultural groups. The chapter explores the role of teacher unions in teacher perpetration and victimization.
Can Interventions to Increase Schooling and Incomes Reduce HIV Incidence Among Young Women in Sub-Saharan Africa?
Authors: Baird S , Ahner-McHaffie T , Özler B
Published: December 2018

This chapter provides insights into resolving the social issues that have led to the pre-existent disparity of young females are far more likely than young males to be infected by HIV. In this case, the structural-level problem is centered on inequitable access to education in sub-Saharan Africa. The chapter examines the impact of conditional and unconditional cash transfers on risk factors related to HIV among girls. After summarizing the existing evidence, the chapter provides a detailed description of two studies: the Schooling, Income and Health Risk study in Malawi and the Empowerment and Livelihood study in Uganda. A final section of the chapter gives recommendations for policy and future research.
Enhancing Access to Safe and Secure Housing
Authors: Dickson-Gomez J , Quinn K
Published: December 2018

This chapter reviews the global pervasiveness of being homeless or unstably housed as an antecedent to risk of HIV acquisition and as a barrier to global efforts directed toward treatment as prevention. Emphasis on youth is provided, as they experience a vast disparity in this regard. Subsequently, this chapter addresses key structural-level intervention designed to provide stable living environments for persons living with HIV/AIDS. Several possible public health response options are provided, with an emphasis on feasibility and sustainability. Topics covered include the multidimensional definitions of housing status and stability, the global housing crisis and how it relates to HIV, structural interventions to address the link between housing and HIV, and future directions for research.
Evidence-Based Structural Interventions for HIV Prevention
Authors: Sherman S , Hunter K
Published: December 2018

Microenterprise approaches have been used in the context of both HIV prevention and treatment (e.g., adherence to antiretroviral therapy) with several highly vulnerable populations including women, female sex workers, and low-income HIV-positive individuals. This chapter defines and describes different approaches to microenterprise in the context of HIV prevention. The chapter also includes several case studies with vulnerable populations to evaluate the effectiveness of structural approaches to HIV prevention, including the IMAGE study, the Undarga study, the JEWEL study, and the Chennai study. The chapter concludes by outlining directions for future policy and research, including gaps and principles in research on HIV prevention.
Economic Strengthening Approaches with Female Sex Workers
Authors: Mantsios A , Kerrigan D , Mbwambo J , Likindikoki S , Shembilu C
Published: December 2018

This chapter examines different strategies for addressing the economic vulnerability that puts female sex workers (FSW) at increased risk of acquiring HIV. After presenting various theoretical approaches to economic interventions with FSW, the chapter provides examples of interventions employing different approaches. The focus is placed on interventions using a community empowerment approach. The authors argue that it is through this type of approach that FSW can confront their economic vulnerability at the community level, rather than through programs focused on increasing individual income alone. An applied example is provided by an in-depth look at community savings groups among FSW in Tanzania.
Integrating Treatment for Opioid Use Disorders and HIV Services into Primary Care
Authors: El-Bassel N , Marotta P. L , Gilbert L , Wu E , Springer S , Goddard-Eckrich D , Hunt T
Published: December 2018

The public health crisis of opiate use disorder (OUD) and HIV infection in the United States demands solutions incorporating structural-level factors to accessing and engaging in drug abuse treatment and HIV care. After providing a review of evidence-based programs that have been used in integrated approaches to treating opioid addiction for persons living with HIV, the chapter provides models of integrating treatments for OUD with services for the prevention and management of HIV infection in primary care. The chapter concludes by reviewing multiple structural barriers to integration of substance use treatment into primary care and offering structural strategies to overcoming and implementing integrated OUD-HIV services in primary care settings.
Getting to 40!
Authors: Nutland W
Published: December 2018

There remains a lack of consensus about the extent to which pre-exposure prophylaxis (PrEP) contributed to the recent dramatic and stunning declines in HIV incidence occurring in the United Kingdom. This chapter describes the potential role of PrEP in this decline and offers insights into how this occurred despite a lack of formal, government-sponsored support for PrEP. Further, the chapter describes the development of a new PrEP movement in England as well as contributing factors, such as the leadership of a new wave of HIV activists, access to global generic markets, innovative supply chains, and the use of social media and the Internet. The “U-turn” and subsequent court cases are also described.