bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of oxidative ageing on the thermophysical and electrical properties of the nanofluid with statistical analysis of AC breakdown voltage
Authors: Maharana Mrutyunjay , Baruah Niharika , Nayak Sisir Kumar , Sahoo Niranjan
Published: August 2018

In this study, the prediction of the breakdown probability of a new batch of nanofluid (NF), namely exfoliated hexagonal boron nitride based NF is performed. Weibull two‐parameter model distribution function has been used to predict the AC breakdown voltage (ACBDV) probability percentage at 5, 10, 50 and 63.2% of failure. To verify the effect of ageing on the other allied properties like dielectric dissipation factor, resistivity, interfacial tension, acid number and thermal conductivity of the insulating NF, oxidative ageing test has been performed at three different ageing durations and compared with the existing mineral oil (MO). It is observed that the new batch of NF has the superior properties to be new age insulating oil compared to the MO. A significant enhancement in the ACBDV and thermal conductivity of the NF compared to MO is observed. Hydrophobic nature of the nanoparticle (NP) which has the minimum affinity towards the polar contamination hinders early ageing degradation in the NF. The enhancement in ACBDV of NF is due to the stimulated charge accumulation on the surface of the NP of the NF. The high aspect ratio of the exfoliated NP surface enhances the heat transfer capabilities in the NF.
Massive star population of the Virgo Cluster galaxy NGC4535
Authors: Spetsieri Z. T. , Bonanos A. Z. , Kourniotis M. , Yang M. , Lianou S. , Bellas-Velidis I. , Gavras P. , Hatzidimitriou D. , Kopsacheili M. , Moretti M. I. , Nota A. , Pouliasis E. , Sokolovsky K. V.
Published: August 2018

We analyzed the massive star population of the Virgo Cluster galaxy NGC 4535 using archival Hubble Space Telescope Wide Field Planetary Camera 2 images in filters F555W and F814W, equivalent to Johnson V and Kron-Cousins I. We performed high precision point spread function fitting photometry of 24353 sources including 3762 candidate blue supergiants, 841 candidate yellow supergiants, and 370 candidate red supergiants. We estimated the ratio of blue to red supergiants as a decreasing function of galactocentric radius. Using Modules for Experiments in Stellar Astrophysics (MESA) isochrones at solar metallicity, we defined the luminosity function and estimated the star formation history of the galaxy over the last 60 Myr. We conducted a variability search in the V and I filters using three variability indexes: the median absolute deviation, the interquartile range, and the inverse von-Neumann ratio. This analysis yielded 120 new variable candidates with absolute magnitudes ranging from MV = −4 to −11 mag. We used the MESA evolutionary tracks at solar metallicity to classify the variables based on their absolute magnitude and their position on the color-magnitude diagram. Among the new candidate variable sources are eight candidate variable red supergiants, three candidate variable yellow supergiants and one candidate luminous blue variable, which we suggest for follow-up observations.
Solar flares and Kelvin-Helmholtz instabilities: A parameter survey
Authors: Ruan W. , Xia C. , Keppens R.
Published: August 2018

Context. Hard X-ray (HXR) sources are frequently observed near the top of solar flare loops, which are also bright in soft X-ray (SXR) and extreme ultraviolet (EUV) wavebands. We revisit a recent scenario proposed by Fang et al. (2016) to trigger loop-top turbulence in flaring loops, which can help explain variations seen in SXR and EUV brightenings and potentially impact and induce HXR emission. It is conjectured that evaporation flows from flare-impacted chromospheric footpoints interact with each other near the loop top and produce turbulence via the Kelvin–Helmholtz instability (KHI).

Aims. By performing a rigorous parameter survey, in which we vary the duration, total amount, and asymmetry of the energy deposition at both footpoints, we assess the relevance of the KHI in triggering and sustaining loop-top turbulence. We synthesize SXR and EUV emission and discuss the possibility of HXR emission through bremsstrahlung or inverse Compton processes, which scatter SXR photons to HXR photons via the inverse Compton mechanism.

Methods. We performed 2.5D numerical simulations in which the magnetohydrodynamic model incorporates a realistic photosphere to coronal stratification, parametrized heating, radiative losses, and field-aligned anisotropic thermal conduction. We focus on the trigger of the KHI and the resulting turbulence, as well as identify various oscillatory patterns that appear in the evolutions.

Results. We find that a M2.2-class related amount of energy should be deposited in less than four minutes to trigger a KHI interaction. Slower deposition, or lesser energy (< 0.33 × 1029 ergs) rather leads to mere loop-top compression sites bounded by shocks, without KHI development. Asymmetry in the footpoint deposition determines whether the KHI turbulent zone gets produced away from the apex, and asymmetric cases can show a slow-mode mediated, periodic displacement of the turbulent zone. Our reference simulation further demonstrates a clear 25 s periodicity in the declining phase of the SXR light curve, wherein compressional effects dominate.

Conclusions. When turbulence is produced in the loop apex, an index of −5/3 can be found in the spectra of velocity and magnetic field fluctuations. Typical values for M-class flares routinely show KHI development. The synthesized SXR light curve shows a clear periodic signal related to the sloshing motion of the vortex pattern created by the KHI.
Survival following Multimodality Treatment Including Surgery for Stage IA–IIIB Small-Cell Lung Cancer
Authors: Weckler Barbara Christine , Baldes Natalie , Schirren Joachim
Published: August 2018

Background Prognosis in limited disease small-cell lung cancer (SCLC) after concurrent chemoradiotherapy is poor. While some studies show better survival after multimodality treatment including surgery, other trials failed to prove a surgery-related survival benefit. Therefore, this study investigated survival in stage IA–IIIB SCLC following surgery combined with chemotherapy and/or thoracic radiotherapy.

Methods We retrospectively reviewed all stage IA–IIIB SCLC patients without supraclavicular lymph node involvement at a single institution between January 1999 and August 2016 after multimodality treatment with curative intent. This comprised surgery consisting of primary tumor resection and systematic lymph node dissection combined with chemotherapy, chemoradiotherapy, or thoracic radiotherapy. Survival was determined using the Kaplan–Meier method, and differences were compared using log-rank tests. The risk of locoregional relapse was calculated.

Results A total of 47 patients (29 men, 18 women; mean age: 62 years) were included. Thirty-day mortality was 0%. Overall median survival was 56 months, and 2-, 3-, 5-, and 10-year survival rates were 69, 54, 46, and 30%, respectively. The only significant prognostic factor (p = 0.006) was R0 resection (n = 40) increasing median survival to 64 versus 17 months in case of technical inoperability (n = 5). The risk of locoregional relapse was 2.5% (n = 1) after R0 resection.

Conclusions Multimodality treatment including surgery was safe and led to considerable survival. R0 resection was the only factor extending survival. It could be achieved in most patients and was associated with a low risk of locoregional relapse. Prospective randomized controlled studies are needed to define best practice in stage IA–IIIB SCLC.
Understanding how China is championing climate change mitigation
Authors: Engels Anita
Published: August 2018

This comment deals with the question of how current political regimes could effectively contribute to the mitigation of climate change—and why this might happen. Against the backdrop of the US government’s announcement to withdraw from the Paris agreement, the rise of populist governments across the globe, and the slow progress of energy transformation projects in pluralistic countries, this paper focuses on China’s potential role in climate change mitigation. Since 2008, the Chinese government has switched to a proactive stance on climate governance and low-carbon development. Due to significant improvements in CO2 efficiency and a clear slow-down in the rise of its annual total CO2 emissions, China is increasingly perceived as a new low-carbon champion and appears to be in a position to take over global climate mitigation leadership. This comment examines the drivers behind current low-carbon developments in China and tests the assumption that China’s state-led non-participatory authoritarianism will effectively offer a solution to the global climate problem. Any switch to low-carbon development rests on complex societal preconditions and requirements. This paper discusses the reasons why the likelihood that the Chinese authoritarian regime will be effective over the long-term in lowering greenhouse gas emissions is uncertain at best—because of internal contestations, low public and private-business participation, and countervailing strategies to secure China’s global market positions. Understanding the foundations and nature of China’s climate change mitigation championship has important implications for fostering low-carbon developments in all political regimes.
First principle investigation of electronic transport properties of the edge shaped graphene-porphine molecular junction device
Authors: Kole Abhisek , Ang Diing Shenp
Published: August 2018

There has been considerable interest in engaging porphyrin, which plays a central role in a variety of biological processes, as a molecular device for bio-inspired system application. This paper is focused on molecular junctions made up of porphine, the metal-free counterpart of porphyrin, and graphene electrode. Electronic properties are elucidated using the density functional theory and non-equilibrium Green’s function method. Excellent coupling between the porphine molecule and graphene electrode is obtained by carbon-carbon covalent bonding and has been analyzed by the electron difference density. The current-voltage curve and the evolution of the transmission spectrum with applied voltage bias have also been investigated. A noteworthy observation is the pronounced negative differential resistance (NDR) behavior, obtained when a benzene ring precisely bridges two porphine molecules. The projected device density of states and the potential profile along with the charge distribution at various applied voltages have been analyzed to understand the NDR behavior. The study confirms that the excess current in the NDR region can be attributed to resonant tunneling through the potential barrier.
Compound fault extraction method via self-adaptively determining the number of decomposition layers of the variational mode decomposition
Authors: Zhang Ziying , Zhang Xi , Zhang Panpan , Wu Fengbiao , Li Xuehui
Published: August 2018

Local mean decomposition (LMD) is a self-adaptive method, which has been widely applied to extract early fault signals from bearings. However, mode mixing occurs during the decomposition process. Moreover, in processing signals with strong noise, false frequency components can be generated by variational mode decomposition (VMD). To address these problems, a weak fault extraction method based on VMD is proposed for rolling bearings. This method regards LMD and the combination production function (CPF) as prefilters for VMD. First, LMD is used for denoising the original signal, and then the CPF components that contain the fault information are combined into a new signal. Second, this method determines the decomposition level K of the VMD from the spectral peaks of the recombined signal. Finally, this method decomposes the recombined signal using the VMD. The main contributions of the proposed method are (i) the CPF method is employed for adaptively de-noising, and the power of the fault feature can be improved; (ii) the decomposition level K of the VMD can be determined adaptively. After processing a simulated signal, fault information of the gears and rolling elements is successfully extracted, thereby demonstrating the feasibility of the presented method. Moreover, the feasibility of the proposed method is further demonstrated in a comparison of results with those obtained from the MOMEDA (Multipoint Optimal Minimum Entropy Deconvolution Adjusted) algorithm.
A novel analytical solution to estimate residual saturation of the displaced fluid in a capillary tube by matching time-dependent injection pressure curves
Authors: Adibifard Meisam
Published: August 2018

Characterizing two-phase flow in a capillary tube is of great importance in many branches of engineering such as petroleum, civil, medicine, CO2 capture and sequestration, and polymer processing. Accurate estimation of the residual saturation in a multi-phase flow will aid engineers to optimize the investigated two-phase flow by altering the flow parameters. The main goal of this study is to develop a new analytical model to estimate the amount of the residual saturation solely by matching the injection pressure versus time data for the times before breakthrough. The proposed model is based on decomposing the total pressure drop into Poiseuille and Young-Laplace terms and assuming a linear decrease in the radius of the front with the traveled distance from the inlet. An optimization technique is required to find the slope of the linear function through matching the inlet pressure data. The saturation-time data can be reconstructed after obtaining a fair match over the pressure-time data. Results of the proposed model were compared with the outcomes of a numerical finite volume simulator, for wide ranges of Ca (Capillary) numbers and two different wetting systems. Observations showed a maximum relative error of around 11% over the predicted residual saturation for both oil-wetting and water-wetting mediums. Based on the phase-diagram, the developed model is applicable for both capillary and viscous fingering flow regimes. Moreover, the introduced model accurately predicts the changes in the front velocity with time, for all investigated Ca numbers, which demonstrates that outcomes of the proposed technique are physically reliable.
AlGaN/GaN high-electron-mobility transistor pH sensor with extended gate platform
Authors: Pyo Ju-Young , Jeon Jin-Hyeok , Koh Yumin , Cho Chu-young , Park Hyeong-Ho , Park Kyung-Ho , Lee Sang Woon , Cho Won-Ju
Published: August 2018

In this paper, we fabricated an AlGaN/GaN high electron mobility transistor (HEMT) pH sensor with an extended-gate (EG). As the carrier mobility of the transducer that is used as the biosensor is increased, the electrical signal conversion efficiency of the biomaterials is improved. Therefore, the HEMT is a more suitable transducer platform than the conventional silicon-based transistor. The fabricated AlGaN/GaN device showed an electron density of 9.0 × 1012 cm-2, and an electron mobility of 1,990 cm2/V-s. In order to reduce the gate leakage current, which is a drawback of conventional HEMT devices, we deposited a 3-nm thick Al2O3 layer as a top-gate oxide by the atomic layer deposition (ALD) method; the fabricated HEMT has a metal–insulator semiconductor (MIS) structure. In addition, we used the EG to implement the disposable biosensor. Although the EG (a sensing membrane) is contaminated and destroyed, the HEMT (a transducer) can be reused. We evaluated the pH sensing characteristics using a pH sensor, which was implemented by connecting the HEMT and EG. The EG HEMT pH sensor showed a sensitivity of 57.6 mV/pH, which is close to the Nernst limit (approximately 59 mV/pH), and a linearity of 98.93%. To verify the stability and reliability of the implemented EG HEMT pH sensor, we measured the real-time response. The EG HEMT pH sensor has an error of only 2.39% of the signal. Therefore, we expect that the EG-based AlGaN/GaN HEMT pH sensor will be a suitable next-generation biosensor platform for a high electrical signal change efficiency of biomaterials, disposable, and point-of-care systems.
What to call a dog? A review of the common names for Australian free-ranging dogs
Authors: Kreplins T. L. , Gaynor A. , Kennedy M. S. , Baudains C. M. , Adams P. , Bateman P. W. , Fleming P. A.
Published: August 2018

Wildlife research is informed by human values and interests, and these are reflected in, and reinforced by, the language used to describe particular species and animals. Examining factors that influence the use of common names of contentious taxa such free-ranging dogs is important, as naming can influence the design and reception of scientific studies. There are a range of common names for free-ranging dogs in Australian scientific literature but the most common names are ‘dingoes’ and ‘wild dogs’. This review investigated influences on the terminology used to describe Australian free-ranging dogs in scientific studies from October 1952 to January 2018. Using a multidimensional scaling analysis, we tested the effects of several potential factors on terminology around Australian free-ranging dogs. We found a significant correlation between studies that reported on ‘wild dog’ control within livestock production–focussed papers and the use of the term ‘dingo’ and discussion of mesopredator release in conservation-related papers. There was a bias associated with author employment, with studies funded by a livestock production organisation more likely to employ ‘wild dog’ terminology. Year of publication and dingo purity within the locale of the study made a lesser contribution to differences in terminology. Our study explores the contextual factors that influence the choice of common names in scientific papers. Although referring to the same species, this review highlights that common terminology within scientific papers is reliant on the discussion of mesopredators release, control programs and the paper’s context.
Screening for depression in young Indigenous people: building on a unique community initiative
Authors: Harriss Linton R. , Kyle Mary , Connolly Katrina , Murgha Edward , Bulmer Merton , Miller Darren , Munn Paul , Neal Paul , Pearson Kingsley , Walsh Melanie , Campbell Sandra , Berger Maximus , McDermott Robyn , McDonald Malcolm
Published: August 2018

Gurriny Yealamucka Health Service Aboriginal Corporation (GYHSAC) is an Indigenous community-controlled health organisation providing comprehensive primary care to the people of Yarrabah in far north Queensland, Australia. GYHSAC conducts an annual Young Person’s Health Check (YPC) for people aged 15–25 years based on the Medical Benefits Schedule Item 715. However, the YPC is constantly evolving to meet the needs of the community, and in 2016, in response to concerns about psychological risk among Indigenous youth, GYHSAC teamed up with James Cook University to trial an adapted PHQ-9 depression screening tool (aPHQ-9) as part of the YPC. This study describes the 2016 YPC event, reports the prevalence of depressive symptoms, examines local issues related to the use of the screening tool and proposes recommendations for future health screening. Experienced health professionals conducted the aPHQ-9 assessment in a private area of the clinic. One-in-five young people were found to have moderate–severe symptoms or self-harm ideation in the previous 2 weeks; they were referred to the mental health service. The aPHQ-9 screening process was found to be straightforward and well accepted by staff and youth. Importantly, it provided valuable ‘space’ to facilitate communication on sensitive issues and was a conduit for speedy referral and follow up by trained staff. Based on our experience, we recommend dedicated depression screening in future routine community health checks for young people and adults.
Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor–microtubule interaction strength
Authors: Mitra Aniruddha , Ruhnow Felix , Girardo Salvatore , Diez Stefan
Published: August 2018

Significance

Microtubules consist of parallel protofilament lanes for motor-based intracellular transport. While most motors translocate along individual protofilaments, members of the kinesin-8 family have been reported to sidestep. However, the mechanism of sidestepping is currently not understood. Here, we track the 3D motion of single kinesin-8 motors on freely suspended microtubules. We find that individual motors sidestep with a bias to the left, the probability of which is increased with the time taken per forward step. We relate this behavior to a bifurcation in the step cycle of kinesin-8. Experiments on a kinesin-1 with an elongated neck linker suggest that sidestepping is intrinsic to all processive kinesins possessing long neck linkers, potentially helping them to circumnavigate obstacles on the microtubule.
Characterisation of secondary phases in Ni-base superalloy Rene 65
Authors: Wojcik Tomasz , Rath Markus , Kozeschnik Ernst
Published: August 2018

The Ni-base superalloy Rene 65 is a newly introduced cast and wrought alloy, used for turbine disc applications in aero-engines. The fine-grained and γ′-strengthened alloy was developed to increase service temperatures up to over 700°C and therefore, enhance the efficiency of aerospace turbines.

In this work, the phases occurring in the as-received material as well as after continuous cooling experiments are characterised by transmission electron microscopy (TEM). In the as-received material, a tri-modal γ′ size distribution is found, ranging from a few nanometres up to approx. 5 µm. In addition, borides are found preferentially at grain boundaries with a size of approx. 1 µm. For different cooling rates, a change in morphology and size distribution of γ′ precipitates is found.

This is part of a thematic issue on Nanoscale Materials Characterisation and Modeling by Advances Microscopy Methods - EUROMAT.
The shared role of the Rsr1 GTPase and Gic1/Gic2 in Cdc42 polarization
Authors: Kang Pil Jung , Miller Kristi E. , Guegueniat Julia , Beven Laure , Park Hay-Oak
Published: August 2018

The Cdc42 GTPase plays a central role in polarity development in many species. In budding yeast, Cdc42 is essential for polarized growth at the proper site and also for spontaneous cell polarization in the absence of spatial cues. Cdc42 polarization is critical for multiple events in the G1 phase prior to bud emergence, including bud-site assembly, polarization of the actin cytoskeleton, and septin filament assembly to form a ring at the new bud site. Yet the mechanism by which Cdc42 polarizes is not fully understood. Here we report that biphasic Cdc42 polarization in the G1 phase is coupled to stepwise assembly of the septin ring for bud emergence. We show that the Rsr1 GTPase shares a partially redundant role with Gic1 and Gic2, two related Cdc42 effectors, in the first phase of Cdc42 polarization in haploid cells. We propose that the first phase of Cdc42 polarization is mediated by positive feedback loops that function in parallel—one involving Rsr1 via local activation of Cdc42 in response to spatial cues and another involving Gic1 or Gic2 via reduction of diffusion of active Cdc42.
The leucine-rich region of Flightless I interacts with R-ras to regulate cell extension formation
Authors: Arora P. D. , He T. , Ng K. , McCulloch C. A.
Published: August 2018

Flightless I (FliI) is a calcium-dependent, actin severing and capping protein that localizes to cell matrix adhesions, contributes to the generation of cell extensions, and colocalizes with Ras. Currently, the mechanism by which FliI interacts with Ras to enable assembly of actin-based cell protrusions is not defined. R-Ras, but not K-ras, H-ras, or N-ras, associated with the leucine-rich region (LRR) of FliI. Mutations of the proline-rich region of R-ras (P202A, P203A) prevented this association. Knockdown of Ras GTPase-activating SH3 domain-binding protein (G3BP1) or Rasgap120by small interfering RNA inhibited the formation of cell extensions and prevented interaction of R-ras and G3BP1 in FliI wild-type (WT) cells. Pull-down assays using G3BP1 fusion proteins showed a strong association of R-ras with the C-terminus of G3BP1 (amino acids 236–466), which also required the LRR of FliI. In cells that expressed the truncated N-terminus or C-terminus of G3BP1, the formation of cell extensions was blocked. Endogenous Rasgap120interacted with the N-terminus of G3BP1 (amino acids 1–230). We conclude that in cells plated on collagen FliI-LRR interacts with R-ras to promote cell extension formation and that FliI is required for the interaction of Rasgap120with G3BP1 to regulate R-ras activity and growth of cell extensions.
CRISPR/Cas9-based gene targeting using synthetic guide RNAs enables robust cell biological analyses
Authors: Su Kuan-Chung , Tsang Mary-Jane , Emans Neil , Cheeseman Iain M.
Published: August 2018

A key goal for cell biological analyses is to assess the phenotypes that result from eliminating a target gene. Since the early 1990s, the predominant strategy utilized in human tissue culture cells has been RNA interference (RNAi)-mediated protein depletion. However, RNAi suffers well-documented off-target effects as well as incomplete and reversible protein depletion. The implementation of CRISPR/Cas9-based DNA cleavage has revolutionized the capacity to conduct functional studies in human cells. However, this approach is still underutilized for conducting visual phenotypic analyses, particularly for essential genes that require conditional strategies to eliminate their gene products. Optimizing this strategy requires effective and streamlined approaches to introduce the Cas9 guide RNA into target cells. Here we assess the efficacy of synthetic guide RNA transfection to eliminate gene products for cell biological studies. On the basis of three representative gene targets (KIF11, CENPN, and RELA), we demonstrate that transfection of synthetic single guide RNA (sgRNA) and CRISPR RNA (crRNA) guides works comparably for protein depletion as cell lines stably expressing lentiviral-delivered RNA guides. We additionally demonstrate that synthetic sgRNAs can be introduced by reverse transfection on an array. Together, these strategies provide a robust, flexible, and scalable approach for conducting functional studies in human cells.
Effects of human sex chromosome dosage on spatial chromosome organization
Authors: Jowhar Ziad , Shachar Sigal , Gudla Prabhakar R. , Wangsa Darawalee , Torres Erin , Russ Jill L. , Pegoraro Gianluca , Ried Thomas , Raznahan Armin , Misteli Tom
Published: August 2018

Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples
Authors: Andrusch Andreas , Dabrowski Piotr W , Klenner Jeanette , Tausch Simon H , Kohl Claudia , Osman Abdalla A , Renard Bernhard Y , Nitsche Andreas
Published: August 2018

Motivation

Next generation sequencing (NGS) has provided researchers with a powerful tool to characterize metagenomic and clinical samples in research and diagnostic settings. NGS allows an open view into samples useful for pathogen detection in an unbiased fashion and without prior hypothesis about possible causative agents. However, NGS datasets for pathogen detection come with different obstacles, such as a very unfavorable ratio of pathogen to host reads. Alongside often appearing false positives and irrelevant organisms, such as contaminants, tools are often challenged by samples with low pathogen loads and might not report organisms present below a certain threshold. Furthermore, some metagenomic profiling tools are only focused on one particular set of pathogens, for example bacteria.

Results

We present PAIPline, a bioinformatics pipeline specifically designed to address problems associated with detecting pathogens in diagnostic samples. PAIPline particularly focuses on userfriendliness and encapsulates all necessary steps from preprocessing to resolution of ambiguous reads and filtering up to visualization in a single tool. In contrast to existing tools, PAIPline is more specific while maintaining sensitivity. This is shown in a comparative evaluation where PAIPline was benchmarked along other well-known metagenomic profiling tools on previously published well-characterized datasets. Additionally, as part of an international cooperation project, PAIPline was applied to an outbreak sample of hemorrhagic fevers of then unknown etiology. The presented results show that PAIPline can serve as a robust, reliable, user-friendly, adaptable and generalizable stand-alone software for diagnostics from NGS samples and as a stepping stone for further downstream analyses.

Availability and implementation

PAIPline is freely available under https://gitlab.com/rki_bioinformatics/paipline.
Comparative assessment of content overlap between written documentation and verbal communication: an observational study of resident sign-outs
Authors: Abraham Joanna , Ihianle Imade , Ward Charlotte E , Arora Vineet M , Kannampallil Thomas G
Published: August 2018

Objective

Effective sign-outs involve verbal communication supported by written or electronic documentation. We investigated the clinical content overlap between sign-out documentation and face-to-face verbal sign-out communication.

Methods

We audio-recorded resident verbal sign-out communication and collected electronically completed (“written”) sign-out documentation on 44 sign-outs in a General Medicine service. A content analysis framework with nine sign-out elements was used to qualitatively code both written and verbal sign-out content. A content overlap framework based on the comparative analysis between written and verbal sign-out content characterized how much written content was verbally communicated. Using this framework, we computed the full, partial, and no overlap between written and verbal content.

Results

We found high a high degree of full overlap on patient identifying information [name (present in 100% of sign-outs), age (96%), and gender (87%)], past medical history [hematology (100%), renal (100%), cardiology (79%), and GI (67%)], and tasks to-do (97%); lesser degree of overlap for active problems (46%), anticipatory guidance (46%), medications/treatments (15%), pending labs/studies/procedures (7%); and no overlap for code status (<1%), allergies (0%) and medical record number (0%).

Discussion and Conclusion

Three core functions of sign-outs are transfer of information, responsibility, and accountability. The overlap—highlighting what written content was communicated—characterizes how these functions manifest during sign-outs. Transfer of information varied with patient identifying information being explicitly communicated and remaining content being inconsistently communicated. Transfer of responsibility was explicit, with all pending and future tasks being communicated. Transfer of accountability was limited, with limited discussion of written contingency plans.
Pediatric Tetanus in Central Pennsylvania
Authors: Ahmed Bilaal S , Beck Michael J , Williamson Gregory , Ericson Jessica E , Kumar Parvathi
Published: August 2018

Approximately 20% of the nationally reported tetanus infections in children aged 0 to 14 years that occurred in the United States between 2005 and 2015 were treated at Penn State Children’s Hospital. With an electronic medical record search, we identified 5 cases of pediatric tetanus; 100% of these cases occurred in unimmunized children. Their median length of stay was 10 days, and the costs were significant.
Evolution and Mental Disorders
Authors: Del Giudice Marco
Published: August 2018

The chapter discusses the definition of mental disorder, reviews the biological explanations for vulnerability to disease, and presents a detailed taxonomy of undesirable conditions that may be regarded as disorders in a broad sense (whether or not they involve genuine dysfunctions). After detailing the main evolutionary and developmental processes that can lead to psychopathology, the chapter addresses some important questions about the structure and classification of disorders and the nature of psychiatric comorbidity. The chapter also considers the strengths and weaknesses of other emerging approaches: computational psychiatry, the network approach to psychopathology, the Research Domain Criteria (RDoC), and transdiagnostic models such as the Hierarchical Taxonomy of Psychopathology (HiTOP).
The Bipolar Spectrum
Authors: Del Giudice Marco
Published: August 2018

The chapter discusses disorders in the bipolar spectrum. Bipolar disorders (BDs) and cyclothymic disorder are marked by mania, a state of abnormally high energy and activity coupled with persistently elevated, expansive, or irritable mood. After an overview of these disorders, their developmental features, and the main risk factors identified in the epidemiological literature, the chapter critically reviews existing evolutionary models and suggests new directions for research. The final section applies the criteria developed earlier in the book to classify the disorders within the fast-slow-defense (FSD) model and identify functionally distinct subtypes. The author proposes to tentatively distinguish between two subtypes of BDs: a high-frequency fast spectrum subtype (F-BD) with strong links to schizophrenia and a low-frequency slow spectrum subtype (S-BD) marked by higher comorbidity with autism.
Generalized Anxiety Disorder
Authors: Del Giudice Marco
Published: August 2018

The chapter discusses generalized anxiety disorder (GAD), a chronic state of excessive, uncontrollable anxiety and worry about a number of different events and activities. Generalized anxiety co-occurs with depression at very high rates and shares the same genetic risk factors. After an overview of this disorder, its developmental features, and the main risk factors identified in the epidemiological literature, the chapter critically reviews existing evolutionary models and suggests new directions for research. The final section applies the criteria developed earlier in the book to classify the disorder within the fast-slow-defense (FSD) model. The author concludes that GAD can be classified as a defense activation (D-type) condition.
Posttraumatic Stress Disorder
Authors: Del Giudice Marco
Published: August 2018

The chapter discusses posttraumatic stress disorder (PTSD). PTSD is a severe, prolonged response to witnessing or experiencing traumatic events that may manifest with a variety of cognitive, affective, and physiological symptoms, from irritability and hypervigilance to recurrent dreams and flashbacks. After an overview of this disorder, its developmental features, and the main risk factors identified in the epidemiological literature, the chapter critically reviews existing evolutionary models and suggests new directions for research. The final section applies the criteria developed earlier in the book to classify the disorder within the fast-slow-defense (FSD) model. The author concludes that PTSD can be classified as a defense activation (D-type) condition.
What Is Authentic Self-Esteem and Why Does It Matter?
Authors: Mruk Christopher J.
Published: August 2018

Chapter 1 deals with the crucial issue of defining self-esteem to set solid foundations for the rest of the book. The chapter describes all three major ways that social scientists, mental health professionals, and people in general define self-esteem. Then this section shows how defining self-esteem in terms of a relationship between competence and worthiness is best for two reasons. First, this approach reflects John Milton’s original use of the term, which bases self-esteem on doing that which is just and right rather than simply on feeling good about oneself. Second, this definition gives people a sense of where to go when facing life’s challenges and how to make healthier decisions. The chapter includes a description of the basic types of self-esteem, namely, low, defensive, and authentic self-esteem, and various self-esteem related problems.
Self-Esteem and Individual Well-Being
Authors: Mruk Christopher J.
Published: August 2018

Chapter 5 focuses on understanding the connection between self-esteem and positive psychology. It begins by looking at self-esteem in relation to two theories of mental health and then moves on to explore research concerning two forms of happiness, namely, hedonic and eudaimonic well-being. The chapter also highlights the relationship between self-esteem and basic human values that positive psychologists have associated with the good life in an Aristotelian sense. This material includes appreciating the importance of identifying one’s own intrinsic values concerning such things as wisdom, compassion, balance, beauty, courage, and more. Special attention is given to the idea that making these types of values a greater part of one’s life may increase a sense of purpose and meaning or well-being. Practical suggestions and activities round out this chapter to make its concepts more useful.
Session Ten: Posttraumatic Growth
Authors: Rashid Tayyab , Seligman Martin
Published: August 2018

Following trauma, some individuals develop posttraumatic stress disorder (PTSD), a serious condition requiring serious treatment. However, following trauma, most people also develop what is called posttraumatic growth (PTG). PTG entails a change of insight into the meaning of life and the importance of relationships. Session Ten invites clients to explore their deep feelings and thoughts about a traumatic experience that continues to bother them. The central positive psychotherapy practice covered in this session is Expressive Writing.
Session Eleven: Slowness and Savoring
Authors: Rashid Tayyab , Seligman Martin
Published: August 2018

Clients report that despite doing many things each day, most of which are done quickly, they still feel stressed, underaccomplished, and tired. Despite speeding up almost everything, including human maturation, we are not any happier or healthier. That is why the “Slow Movement” is attracting attention. In Session Eleven, clients learn how to deliberately slow down and develop an awareness of how to savor. In so doing, they learn to attend mindfully to the positives. The central positive psychotherapy (PPT) practices covered in this session are Slow and Savor.
Session Thirteen: Positive Communication
Authors: Rashid Tayyab , Seligman Martin
Published: August 2018

In Session Thirteen, clients learn about four styles of responding to good news (active-constructive, active-destructive, passive-constructive, and passive-destructive). Of these styles, only Active Constructive Responding—the central practice covered in this session—predicts relationship satisfaction. Self-disclosure of positive events is critical for secure bonding and for the development of intimacy.
Defeaters and Disqualifiers
Authors: Muñoz Daniel
Published: August 2018

Justification depends on context: even if E on its own justifies H, still it might fail to justify in the context of D. This sort of effect, epistemologists think, is due to defeaters, which undermine or rebut a would-be justifier. I argue that there is another fundamental sort of contextual feature, disqualification, which doesn't involve rebuttal or undercutting, and which cannot be reduced to any notion of screening-off. A disqualifier makes some would-be justifier otiose, as direct testimony sometimes does to distal testimony, and as manifestly decisive evidence might do to gratuitous evidence on the same team. Basing a belief on disqualified evidence, moreover, is distinctively irrational. One is not necessarily irresponsible. Instead one is turning down a free upgrade to a sleeker, stabler basis for one's beliefs. Such an upgrade would prevent wastes of epistemic effort, since someone who bases her belief on a disqualified proposition E will need to remember E and rethink her belief should E ever be defeated. The upgrade might also reduce reliance on unwieldy evidence, if E is relevant only thanks to some labyrinthine argument; and if even ideal agents should doubt their ability to follow such arguments, even they should care about disqualifiers.
Knowability Relative to Information
Authors: Berto Francesco , Hawke Peter
Published: August 2018

We present a formal semantics for epistemic logic, capturing the notion of knowability relative to information (KRI). Like Dretske, we move from the platitude that what an agent can know depends on her (empirical) information. We treat operators of the form (‘B is knowable on the basis of information A’) as variably strict quantifiers over worlds with a topic- or aboutness-preservation constraint. Variable strictness models the non-monotonicity of knowledge acquisition while allowing knowledge to be intrinsically stable. Aboutness-preservation models the topic-sensitivity of information, allowing us to invalidate controversial forms of epistemic closure while validating less controversial ones. Thus, unlike the standard modal framework for epistemic logic, KRI accommodates plausible approaches to the Kripke-Harman dogmatism paradox which bear on non-monotonicity or on topic-sensitivity. KRI also strikes a better balance between agent idealization and a non-trivial logic of knowledge ascriptions.
Self-similar galaxy dynamics below the de Sitter scale of acceleration
Authors: van Putten Maurice H P M
Published: August 2018

Radial accelerations α in galaxy dynamics are now observed over an extended range in redshift that includes model calculations on galactic distributions of cold dark matter (CDM) in lambda cold dark matter (ΛCDM). In a compilation of data of the Spitzer Photometry and Accurate Rotation Curves (SPARC) catalogue, the recent sample of Genzel et al. (2017) and the McMaster Unbiased Galaxy Simulations 2 (MUGS2), we report on effective self-similarity in the variable ζ = aN/adS, given by the Newtonian acceleration aN based on baryonic matter content over the de Sitter scale of acceleration adS = cH, where c is the velocity of light and H is the Hubble parameter. SPARC, MUG2, and theory satisfy ${a_\mathrm{ N}}/{\alpha } \simeq 2.1\, \zeta ^\frac{1}{2}$ asymptotically at small accelerations (ζ < <1). At ζ = 1, however, aN/α ≃ 0.78 in MUGS2 galaxies falls short by 6σ of aN/α ≃ 1 in SPARC galaxies in transition to Newtonian gravity (ζ > >1) that eluded previous studies. This gap poses a novel challenge to CDM in ΛCDM against the apparent C0 galaxy dynamics observed in SPARC. We attribute the latter to reduced inertia below the de Sitter scale of acceleration (ζ < 1), based on a causality constraint imposed by the cosmological horizon ${\cal H}$.
Cost-Benefit Analysis of Transitional Care in Neurosurgery
Authors: Liu Jingyi , Gormley Natalia , Dasenbrock Hormuzdiyar H , Aglio Linda S , Smith Timothy R , Gormley William B , Robertson Faith C
Published: August 2018

BACKGROUND

Transitional care programs (TCPs) coordinate care to improve safety and efficiency surrounding hospital discharge. While TCPs have the potential to reduce hospital length of stay and readmissions, their financial implications are less well understood.

OBJECTIVE

To perform a cost-benefit analysis of a previously published neurosurgical TCP implemented at an urban academic hospital from 2013 to 2015.

METHODS

Patients received intensive preoperative education and framing of expectations for hospitalization, in-hospital discharge planning and medication reconciliation with a nurse educator, and a follow-up phone call postdischarge. The cost-benefit analysis involved program costs (nurse educator salary) and total direct hospital costs within the 30-d perioperative window including readmission costs.

RESULTS

The average cost of the TCP was $435 per patient. The TCP was associated with an average total cost reduction of 17.2% (95% confidence interval [CI]: 7.3%-26.7%, P = .001). This decrease was driven by a 14.3% reduction in the average initial admission cost (95% CI: 6.2%-23.7%, P = .001), largely attributable to the 16.3% decrease in length of stay (95% CI: 9.93%-23.49%, P < .001). Thirty-day readmissions were significantly decreased in the TCP group, with a 5.5% readmission rate for controls and 2.4% for TCP enrollees (P = .04). The average cost of readmission was decreased by 71.3% (95% CI: 58.7%-74.7%, P < .01).

CONCLUSION

This neurosurgical TCP was associated with decreased costs of initial admissions, 30-d readmissions, and total costs of hospitalization alongside previously published decreased length of stay and reduced 30-d readmission rates. These results underscore the clinical and financial feasibility and impact of transitional care in a surgical setting.
Correlation of commercially available quantitative MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation scores and GBM patient survival
Authors: Dovek Laura , Nguyen Nhung T , Ozer Byram H , Li Ning , Elashoff Robert M , Green Richard M , Liau Linda , Nghiemphu P Leia , Cloughesy Timothy F , Lai Albert
Published: August 2018

Background

Between 2011 and 2016, O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation testing at University of California Los Angeles (UCLA) was performed through LabCorp, using a threshold of 2 to distinguish MGMT methylated from unmethylated tumors. In this study, we sought to determine whether the magnitude of the methylation score correlated with outcome.

Methods

We identified 165 newly diagnosed glioblastoma (GBM) isocitrate dehydrogenase (IDH) wild-type and temozolomide-treated upfront patients at UCLA and Kaiser Permanente Los Angeles with LabCorp-derived quantitative MGMT scores obtained on pretreatment tissue samples. Using LabCorp’s threshold, we found 102 unmethylated and 63 methylated patients. We then further substratified each group based on the magnitude of the score, and performed Kaplan-Meier and Cox regression analyses of overall survival (OS) and progression-free survival (PFS).

Results

We validated that the standard LabCorp threshold of 2 could separate our cohort by survival, showing longer OS and PFS for MGMT methylated patients vs unmethylated patients. Cox regression analysis confirmed that MGMT (<1) patients had worse outcome, with OS and PFS hazard ratios of 2.375 (P = .053) and 2.463 (P = .023), respectively, when compared to the MGMT (1-1.99) patients. Contrary to our expectation, when we substratified the ≥2 (methylated) group, we did not find a dose-dependent relationship between the magnitude of MGMT methylation and improved survival.

Conclusions

The MGMT unmethylated group contains a partially methylated group (greater than 1) that shares survival benefits similar to the methylated group. However, we did not demonstrate an association of very high methylation scores with increased survival. These findings will require validation in additional independent clinical data sets.