bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimised TSO–DSO interaction in unbalanced networks through frequency‐responsive EV clusters in virtual power plants
Authors: Sanchez Gorostiza Francisco , Gonzalez‐Longatt Francisco
Published: October 2020

The increased penetration of distributed energy resources (DERs) installed in distribution networks via power electronic converters reduces the overall rotating inertia of the power system, causing faster frequency dynamics after a large disturbance. However, these DERs coupled with energy storage systems (ESSs) can be managed to provide valuable grid support functions such as fast frequency response (FFR) and assist the transmission system operator (TSO) in frequency control. In this study, single‐ and three‐phase clusters of electric vehicles (EVs), acting as mobile‐ESSs, are grouped together as virtual power plants (VPPs) to centralise the provision of FFR for the distribution system operator (DSO) whilst considering network unbalance. Furthermore, the parameters of the EV clusters within each VPP are optimised to minimise the inertia‐weighed maximum frequency deviation following a disturbance whilst adhering to network security and power quality constraints. To this aim, a variant of the metaheuristic optimisation algorithm called improved harmony search is used for the optimisation process. Finally, the merits of the proposed methodology are shown with an illustrative example of an unbalanced three‐phase transmission and distribution network modelled in DIgSILENT PowerFactory. The results show that clusters of EVs grouped as VPPs effectively improve frequency support via the TSO–DSO interaction.
Galerkin method‐based model predictive control for mid‐long term voltage stability enhancement
Authors: Xia Bingqing , Wu Hao , Shen Danfeng , Zheng Xiang , Hua Wen , Song Yonghua
Published: October 2020

Mid‐long term voltage stability refers to voltage stability concerning the dynamics of the slow dynamic elements and protection devices in power systems. To improve the mid‐long term voltage stability, this paper proposes a scheme of model predictive control (MPC) based on Galerkin method. The basic principle of MPC is to solve the optimization problem regarding voltage stability control based on the prediction model periodically. By applying the optimal control scheme to power systems, the mid‐long term voltage stability can be enhanced. The Galerkin method‐based polynomial approximation approximates the relationship between mid‐long term trajectories and control parameters by a polynomial function. The polynomial function acts as a prediction model to predict future system trajectories under different values of control parameters in MPC. The advantage of the proposed method is that its prediction accuracy is relatively high and thus the control efficiency of MPC is improved, as the polynomial function can embody the non‐linear characteristics of the power system. In the case study, the 3‐machine 10‐bus system and the New England 39‐bus system are taken as examples to compare the MPC based on the proposed method and the trajectory sensitivity method in terms of prediction accuracy, computation time and control results.
Feeder‐corridor‐based distribution network planning model with explicit reliability constraints
Authors: Li Zihao , Wu Wenchuan , Zhang Boming , Tai Xue
Published: October 2020

Most distribution network planning models rely on predefined candidate electric line routes (branches), i.e. the planning model is to select a subset of the candidate branches to form a network with minimal investment cost and guarantee the power supply to consumers with specified reliability. However, the manually presented candidate branch set may be thoughtless while the exhaustively generated a large set of candidate branches may make the planning model intractable. In this study, the authors propose a distribution network planning model based on feeder corridors instead of the candidate branches, since feeder corridors are commonly given in municipal planning. Based on the graph model formulated by feeder corridors, the proposed planning model can generate the network with minimal investment cost while meeting the specific reliability requirement. Furthermore, since post‐fault load restoration strategies between feeders are fully incorporated, the proposed model is applicable for mesh networks. The planning model is formulated as a mixed‐integer linear programming (MILP) problem and can be effectively solved by off‐the‐shelf software. Simulation results show the effectiveness and flexibility of the proposed method.
Accident‐related cost analysis and decision‐making support through econometric modelling
Authors: Catalano Mario , Galatioto Fabio , Shaikh Nabeel
Published: October 2020

This study illustrates the early results of on‐going research started under a recent project sponsored by the United Kingdom Government Transport Department to investigate the principal factors influencing road accidents as well as develop an internet application for the prediction of road accident‐related effects at different scales. In particular, accident modelling, analysis of socio–economic, land use, infrastructural and contextual factors of road safety, as well as decision‐making support are the focus of this work. In particular, an application in the United Kingdom of a model framework potentially transferable to other contexts is described. This application resulted in an extensive analysis of road safety factors as well as the development of a simulation web‐based platform that uses microeconometric models to estimate the frequency of road accident along with the number and severity of injuries. These models proved considerable accuracy at the national level. In the end, the potential benefit of the simulation platform for road safety decision‐making is showcased on a micro‐scale with an application to a medium‐sized town in South East England.
Design and analysis of customised pulse width modulation based dc–dc converter for EV battery charging application
Authors: Srivastava Manaswi , Verma Arun Kumar , Singh Tomar Pavan
Published: October 2020

This study presents the full‐bridge dc–dc converter (FBDC) operated with customised pulse width modulation (cPWM) for electric vehicle (EV) battery charging. The proposed cPWM retains all the benefits of the popular conventional phase shifted modulation (PSM) with minimal modification in the pulse width while further achieving the zero voltage switching for the active switches of the converter. The cPWM gating technique results in minimal circulating loss and switch conduction loss in comparison to PSM gating technique and higher efficiency. The detailed operation of the converter is presented with analysis. The theoretical waveforms of the converter and power loss analysis are discussed. A 540 W, 80 kHz experimental prototype is developed to validate the theoretical analysis. Finally, the comparison between PSM and cPWM is presented.
Photovoltaic cell defect classification using convolutional neural network and support vector machine
Authors: Ahmad Ashfaq , Jin Yi , Zhu Changan , Javed Iqra , Maqsood Asim , Akram Muhammad Waqar
Published: October 2020

Automatic defect classification in photovoltaic (PV) modules is gaining significant attention due to the limited application of manual/visual inspection. However, the automatic classification of defects in crystalline silicon solar cells is a challenging task due to the inhomogeneous intensity of cell cracks and complex background. The present study is carried out for automatic defects classification of PV cells in electroluminescence images. Two machine learning approaches, features extraction‐based support vector machine (SVM) and convolutional neural network (CNN) are used for the solar cell defect classifications. Suitable hyperparameters, algorithm optimisers, and loss functions are used to achieve the best performance. Solar cell defects are divided into seven classes such as one non‐defective and six defective classes. Feature extraction algorithms such as histograms of oriented gradients (HOG), KAZE, Scale‐Invariant Feature Transform (SIFT) and speeded‐up‐robust features (SURF) are used to train the SVM classifier. Finally, the performance results are compared. It is concluded that CNN's accuracy for solar cell defect classification is 91.58% which outperforms the state‐of‐the‐art methods. With features extraction‐based SVM, accuracies of 69.95, 71.04, 68.90, and 72.74% are obtained for HOG, KAZE, SIFT, and SURF, respectively. The present study may contribute to making a PV system more efficient for classifying defects to improve the power system efficiency.
Application of recent nature‐inspired meta‐heuristic optimisation techniques to small permanent magnet DC motor parameters identification problem
Authors: Karnavas Yannis L.
Published: October 2020

In this study, an attempt is made to find an effective solution on the small direct current (DC) motor's parameters identification problem by employing two recently introduced stochastic nature‐inspired techniques. The first one is called ‘salp swarm algorithm’ (SSA) while the second one is called ‘ant‐lion optimiser’ (ALO). These algorithms have been inspired by the interaction strategy between the ocean salps and the ants and ant‐lions, respectively, in nature. To appraise the effectiveness of these algorithms, a DC motor model has been appropriately implemented and its performance is evaluated by using speed step responses, while all model's parameters are considered unknown and therefore search variables. Integral of the square of the error (ISE), integral absolute error and integral in time of absolute error have been adopted as objective functions for the algorithms’ evaluation. In order to judge the acceptability of these algorithms, the simulation results are compared with those of another one similar technique, namely the ‘grey wolf optimiser’ (GWO). The obtained results reveal very satisfactory performance and confirm that the examined SSA, ALO and GWO algorithms can identify accurately the DC motor parameters and can be applied effectively to the specific problem. Another finding is that SSA combined with ISE criterion seems to be the most appropriate technique among the three algorithms.
The solar gravitational redshift from HARPS-LFC Moon spectra
Authors: González Hernández J. I. , Rebolo R. , Pasquini L. , Lo Curto G. , Molaro P. , Caffau E. , Ludwig H.-G. , Steffen M. , Esposito M. , Suárez Mascareño A. , Toledo-Padrón B. , Probst R. A. , Hänsch T. W. , Holzwarth R. , Manescau A. , Steinmetz T. , Udem Th. , Wilken T.
Published: October 2020

Context. The general theory of relativity predicts the redshift of spectral lines in the solar photosphere as a consequence of the gravitational potential of the Sun. This effect can be measured from a solar disk-integrated flux spectrum of the Sun’s reflected light on Solar System bodies.

Aims. The laser frequency comb (LFC) calibration system attached to the HARPS spectrograph offers the possibility of performing an accurate measurement of the solar gravitational redshift (GRS) by observing the Moon or other Solar System bodies. Here, we analyse the line shift observed in Fe absorption lines from five high-quality HARPS-LFC spectra of the Moon.

Methods. We selected an initial sample of 326 photospheric Fe lines in the spectral range between 476–585 nm and measured their line positions and equivalent widths (EWs). Accurate line shifts were derived from the wavelength position of the core of the lines compared with the laboratory wavelengths of Fe lines. We also used a CO5BOLD 3D hydrodynamical model atmosphere of the Sun to compute 3D synthetic line profiles of a subsample of about 200 spectral Fe lines centred at their laboratory wavelengths. We fit the observed relatively weak spectral Fe lines (with EW< 180 mÅ) with the 3D synthetic profiles.

Results. Convective motions in the solar photosphere do not affect the line cores of Fe lines stronger than about ∼150 mÅ. In our sample, only 15 Fe I lines have EWs in the range 150< EW(mÅ) < 550, providing a measurement of the solar GRS at 639 ± 14 m s−1, which is consistent with the expected theoretical value on Earth of ∼633.1 m s−1. A final sample of about 97 weak Fe lines with EW < 180 mÅ allows us to derive a mean global line shift of 638 ± 6 m s−1, which is in agreement with the theoretical solar GRS.

Conclusions. These are the most accurate measurements of the solar GRS obtained thus far. Ultrastable spectrographs calibrated with the LFC over a larger spectral range, such as HARPS or ESPRESSO, together with a further improvement on the laboratory wavelengths, could provide a more robust measurement of the solar GRS and further testing of 3D hydrodynamical models.
Different sodium enhancements among multiple populations of Milky Way globular clusters
Authors: Piatti Andrés E.
Published: October 2020

We searched for clues to understand the different Na abundances measured in first and second generation stars of ancient Milky Way globular clusters. For that purpose, from the recent literature, we gathered the aforementioned Na abundances, orbital parameters, and structural and internal dynamical properties and ages in a homogeneous scale of 28 globular clusters. We found that the intra-cluster Na enrichment, which is measured by the difference of Na abundances between first and second generation stars, exhibits a trend as a function of the Na abundances of first generation stars, in the sense that the more Na-poor the first generation stars are, the larger the Na enrichment is. By using the inclinations of the globular clusters’ orbits, the analyzed Na enrichments also hinted at a boundary at ∼0.3 dex to differentiate globular clusters with an accreted or in situ origin, the accreted globular clusters having larger Na enrichments. Because relatively larger intra-cluster Na enhancements are seen in accreted globular clusters and small Na enhancements are observed in globular clusters formed in situ, although not exclusively, we speculate that the amplitude of the Na enrichment may be linked with the building block paradigm. Globular clusters at the time of formation of first and second generation stars would seem to keep a memory of this hierarchical galaxy formation process.
Fractal Dimension Analysis of Three-Point Bending Concrete Test Specimens
Authors: Sobek Jakub , Frantík Petr , Trčka Tomáš , Lehký David
Published: October 2020

The paper deals with the analysis of the fractal dimension of fracture surfaces of concrete specimens tested in a three-point bending configuration. Fifteen representative specimens were chosen out of a bigger set for the fractal dimension analysis. Their fracture surfaces were scanned by 2D optical profilometry and analysed by the FracDiM software created in the Java programming language. The resulting values of fractal dimensions for specimens of three different sizes are presented.
Strengthening of RC plates with mineral-bonded composite layers for enhanced impact safety
Authors: Hering Marcus , Curbach Manfred
Published: October 2020

The presented paper deals with a series of impact experiments conducted in the drop tower facility of the Otto Mohr Laboratory (OML) at the Technische Universität Dresden. The presented research results were generated in three projects. A number of reinforced concrete (RC) plates which were subsequently strengthened on the not-impacted side were produced and tested. As basic materials for the RC plates, a normal strength concrete (C35/45) and conventional BSt500 reinforcement steel were used. Different material combinations, cement-bonded composites were chosen for the subsequently applied strengthening layer. The paper presents the experimental program, the used test facility, and the results of the experiments and their interpretation.
Klinik Unternehmen: AUF-/Absteiger des Monats
Authors: Schmidt Hartmut
Published: October 2020

Börsenexperte Hartmut Schmidt analysiert für kma die Jahresabschlüsse ausgewählter Kliniken
Europäischer Gesundheitskongress München 2020: Mut zur Zukunft
Authors: Hillebrand Ralf-Thomas
Published: October 2020

Diesmal ist alles anders beim Europäischen Gesundheitskongress München: Das üblicherweise von über 1 000 Entscheidern aus Gesundheitspolitik und -wirtschaft besuchte Event wird Ende Oktober erstmals als kostenlose Digitalveranstaltung ausgerichtet.
Rapid Recovery: Schnell auf die Beine
Authors: Kohrs Jens
Published: October 2020

Das Rapid-Recovery-Konzept verspricht viel: kürzere Verweildauer, schnellere Mobilität und weniger Komplikationen nach orthopädischen Operationen. Die Sana Kliniken Sommerfeld setzen es seit 2014 um – und sind mittlerweile Vorbild für alle Häuser des Konzerns.
High-power few-cycle THz generation at MHz repetition rates in an organic crystal
Authors: Buchmann Tobias Olaf , Railton Kelleher Edmund John , Jazbinsek Mojca , Zhou Binbin , Seok Jin-Hong , Kwon O-Pil , Rotermund Fabian , Jepsen Peter Uhd
Published: October 2020

Ultrafast terahertz (THz) spectroscopy is a potent tool for studying the fundamental properties of matter. Limitations of current THz sources, however, preclude the technique being applied in certain advanced configurations or in the measurement of, e.g., strongly absorbing samples. In response to this problem, here we demonstrate the generation of 1.38 mW broadband THz radiation at 10 MHz repetition rate by combining the highly efficient nonlinear organic crystal HMQ-TMS with ultrafast pump pulses generated using a simple and stable external pulse compression of a high power, near-infrared (NIR) femtosecond ytterbium-doped fiber (Yb:fiber) laser. Utilizing spectral broadening in a large core, polarization maintaining photonic crystal fiber and a pair of SF11 prisms, we achieve a tenfold pulse compression of the Yb:fiber laser, yielding compressed 0.35 µJ pulses with a full-width at half maximum pulse duration of 22 fs, exerting a peak power of 13.8 MW at a repetition rate of 10 MHz. THz generation through optical rectification of the NIR pulses is explored in two distinct thicknesses of the organic crystal, leading to a maximum conversion efficiency of ∼5.5 · 10−4, an order of magnitude higher than that achieved with inorganic nonlinear crystals, e.g., gallium phosphide, for similar pump parameters. The focused THz beam has a peak on-axis field strength greater than 6.4 kV cm−1 in unpurged atmosphere. We believe that our moderately strong-field THz source is well suited to a variety of applications in ultrafast THz spectroscopy, in particular THz-enabled scattering-type near-field, and scanning tunneling spectroscopy, where multi-MHz repetition rate sources are required.
Spatial epidemiology of Toxoplasma gondii seroprevalence in sentinel feral chickens (Gallus gallus) in Kaua‘i, Hawai‘i
Authors: Chalkowski Kayleigh , Fiedler Kathryn , Lucey William G. , Zohdy Sarah , Lepczyk Christopher A.
Published: October 2020

Toxoplasma gondii is a globally prevalent coccidian parasite that fatally infects a wide range of endangered avian and mammalian hosts in Hawai‘i including the Hawaiian Monk Seal (llio holo I ka uaua; Monachus schauinslandi), Hawaiian Goose (Nēnē; Branta sandvicensis) and Hawaiian Crow (‘Alalā; Corvus hawaiiensis). Thus, identifying environmental factors that predict or impact T. gondii exposure is important for mitigating disease risks. The island of Kaua‘i is a good model system to study spatial and environmental covariates of T. gondii prevalence due to (1) high landscape heterogeneity spanning a small geographical area, (2) the presence of an ideal sentinel species, the feral chicken (Gallus gallus), and (3) recent evidence that T. gondii contributes to local declines of Hawai‘i’s endemic bird and mammal species. Despite these compelling opportunities, little is known about the prevalence or distribution of T. gondii in Hawai‘i. In this study, 294 Kaua‘i feral chickens were tested for T. gondii using ELISA IgG immunoassays, of which 117 chickens (39.8%) tested seropositive – indicating infection with the parasite – and nearly every sampled site contained chickens with positive seroprevalence. Prevalence varied among the 34 sampled localities and was significantly, positively correlated with proximity to the coast. These findings reveal that T. gondii is prevalent across Kaua‘i. Furthermore, this variability offers insight to the factors that might predict T. gondii seropositivity across the landscape, and likewise predict exposure risks for endangered wildlife.
Dynamical structure factors of dynamical quantum simulators
Authors: Baez Maria Laura , Goihl Marcel , Haferkamp Jonas , Bermejo-Vega Juani , Gluza Marek , Eisert Jens
Published: October 2020

Significance

Quantum simulators promise to offer new insights into strongly correlated matter beyond what is accessible by means of classical computers. We propose dynamical quantum simulators (DQSs) as a method to simulate dynamical structure factors (DSFs) for system sizes considerably larger than what classical simulations can compute and provide complexity-theoretic evidence that they cannot be classically efficiently computed. Based on state-of-the-art experimental setups, we show how results from DQSs can be directly compared to experiments exploring properties of quantum materials. At the same time, we explore long-ranged spin systems: In particular, we show that the DSFs in DQSs can exhibit the signatures of excitation confinement in long-ranged models for which a comprehensive understanding is lacking.
Dynamic and reversible shape response of red blood cells in synthetic liquid crystals
Authors: Nayani Karthik , Evans Arthur A. , Spagnolie Saverio E. , Abbott Nicholas L.
Published: October 2020

Significance

Red blood cells are soft and pliable, which allows them to deform through small capillaries. We have found that red blood cells, if dispersed in a synthetic liquid crystal, are squeezed into complex shapes via the viscoelastic environment created by the liquid crystal. The strained shapes exhibited by individual red blood cells in liquid crystals reveal cell mechanical properties and unmask a high level of cell-to-cell variation across a population of cells. The sharing of strain between liquid crystals and soft mammalian cells is general and provides approaches for quantifying variations in cell mechanical properties, including during aging and diseases such as malaria and sickle cell anemia.
Reduced volume and reflection for bright optical tweezers with radial Laguerre–Gauss beams
Authors: Béguin J.-B. , Laurat J. , Luan X. , Burgers A. P. , Qin Z. , Kimble H. J.
Published: October 2020

Significance

Nanoscale dielectric devices are capable of mediating long-range atom–atom interactions using guided mode photons, as well as long-range photon–photon interactions mediated by lattices of atoms. Such systems have the potential to provide new tools for quantum science. However, an outstanding challenge is the delivery of single atoms to optical traps near nanophotonic devices. We introduce a capability that could increase fidelity for atom-lattice assembly near nanophotonic structures. Other applications include imaging strategies.
Nociceptors protect sickle cell disease mice from vaso-occlusive episodes and chronic organ damage
Authors: Xu Chunliang , Gulinello Maria , Frenette Paul S.
Published: October 2020

Sickle cell disease (SCD) is a common hereditary hematologic disorder. SCD patients suffer from acute vaso-occlusive episodes (VOEs), chronic organ damage, and premature death, with few therapeutic options. Although severe pain is a major clinical manifestation of SCD, it remains unknown whether nociception plays a role in SCD pathogenesis. To address this question, we generated nociceptor-deficient SCD mice and found, unexpectedly, that the absence of nociception led to more severe and more lethal VOE, indicating that somatosensory nerves protect SCD mice from VOE. Mechanistically, the beneficial effects of sensory nerves were induced by the neuropeptide calcitonin gene–related peptide (CGRP), which acted on hematopoietic cells. Additionally, oral capsaicin consumption, which can activate somatosensory nerves by binding to TRPV1, dramatically alleviated acute VOE and significantly prevented chronic liver and kidney damage in SCD mice. Thus, the manipulation of nociception may provide a promising approach to treat SCD.
Understanding immersion in zinc fixed-point cells using factorial design of experiments
Authors: da Silva Rodrigo , Pearce Jonathan
Published: October 2020

The objective of this study was to investigate the ‘lift-off effect’ in zinc open cells, where an anomalously large change in temperature is observed when the standard platinum resistance thermometer (SPRT) is lifted off the bottom of the re-entrant tube during an immersion profile measurement. The goal was to determine the most important influences and hence what measures could be taken to mitigate it. The influences investigated were the filling gas, re-entrant tube material, re-entrant tube exterior surface condition, and the SPRT design. For each of these influence variables, three options were chosen. Since testing all combinations of different configurations arising would be extremely time consuming, the authors employed the optimal ‘design of experiments’ method using orthogonal arrays described by the Taguchi method, which is commonly used in manufacturing to optimise processes. Nine test configurations were identified, giving the necessary information on the interrelation between all influence variables. According to these results, the ideal configuration that yields the optimum immersion profile is a borosilicate tube, with full sandblasting and using nitrogen as filling gas for the cell. In addition, one particular SPRT design was found to be the least sensitive to the lift-off effect.
Functional Heterogeneity in Superorganisms: Emerging Trends and Concepts
Authors: O’Shea-Wheller Thomas A , Hunt Edmund R , Sasaki Takao
Published: October 2020

Social insects are biological benchmarks of self-organization and decentralized control. Their integrated yet accessible nature makes them ideal models for the investigation of complex social network interactions, and the mechanisms that shape emergent group capabilities. Increasingly, interindividual heterogeneity, and the functional role that it may play, is seen as an important facet of colonies’ social architecture. Insect superorganisms present powerful model systems for the elucidation of conserved trends in biology, through the strong and consistent analogies that they display with multicellular organisms. As such, research relating to the benefits and constraints of heterogeneity in behavior, morphology, phenotypic plasticity, and colony genotype provides insight into the underpinnings of emergent collective phenomena, with rich potential for future exploration. Here, we review recent advances and trends in the understanding of functional heterogeneity within social insects. We highlight the scope for fundamental advances in biological knowledge, and the opportunity for emerging concepts to be verified and expanded upon, with the aid of bioinspired engineering in swarm robotics, and computational task allocation.
Reactive Eosinophil Proliferations in Tissue and the Lymphocytic Variant of Hypereosinophilic Syndrome
Authors: King Rebecca L , Tan Brent , Craig Fiona E , George Tracy I , Horny Hans-Peter , Kelemen Katalin , Orazi Attilio , Reichard Kaaren K , Rimsza Lisa M , Wang Sa A , Zamo Alberto , Quintanilla-Martinez Leticia
Published: October 2020

Objectives

The 2019 Society for Hematopathology and European Association for Haematopathology Workshop reviewed the spectrum of neoplastic, nonneoplastic, and borderline entities associated with reactive eosinophilia in tissue.

Methods

The workshop panel reviewed 46 cases covered in 2 workshop sessions.

Results

The 46 cases were presented with their consensus diagnoses during the workshop. Reactive eosinophilia in lymph nodes and other tissues may be accompanied by or be distinct from peripheral blood eosinophilia. Reactive etiologies included inflammatory disorders such as Kimura disease and IgG4-related disease, which may show overlapping pathologic features and reactions to infectious agents and hypersensitivity (covered in a separate review). Hodgkin, T-cell, and B-cell lymphomas and histiocytic neoplasms can result in reactive eosinophilia. The spectrum of these diseases is discussed and illustrated through representative cases.

Conclusions

Reactive eosinophilia in lymph nodes and tissues may be related to both nonneoplastic and neoplastic lymphoid proliferations and histiocytic and nonhematolymphoid processes. Understanding the differential diagnosis of reactive eosinophilia and the potential for overlapping clinical and pathologic findings is critical in reaching the correct diagnosis so that patients can be treated appropriately.
Development of standardized regression-based formulas to assess meaningful cognitive change in early Parkinson’s disease
Authors: Combs Hannah L , Wyman-Chick Kate A , Erickson Lauren O , York Michele K
Published: October 2020

Objective

Longitudinal assessment of cognitive and emotional functioning in patients with Parkinson’s disease (PD) is helpful in tracking progression of the disease, developing treatment plans, evaluating outcomes, and educating patients and families. Determining whether change over time is meaningful in neurodegenerative conditions, such as PD, can be difficult as repeat assessment of neuropsychological functioning is impacted by factors outside of cognitive change. Regression-based prediction formulas are one method by which clinicians and researchers can determine whether an observed change is meaningful. The purpose of the current study was to develop and validate regression-based prediction models of cognitive and emotional test scores for participants with early-stage idiopathic PD and healthy controls (HC) enrolled in the Parkinson’s Progression Markers Initiative (PPMI).

Methods

Participants with de novo PD and HC were identified retrospectively from the PPMI archival database. Data from baseline testing and 12-month follow-up were utilized in this study. In total, 688 total participants were included in the present study (NPD = 508; NHC = 185). Subjects from both groups were randomly divided into development (70%) and validation (30%) subsets.

Results

Early-stage idiopathic PD patients and healthy controls were similar at baseline. Regression-based models were developed for all cognitive and self-report mood measures within both populations. Within the validation subset, the predicted and observed cognitive test scores did not significantly differ, except for semantic fluency.

Conclusions

The prediction models can serve as useful tools for researchers and clinicians to study clinically meaningful cognitive and mood change over time in PD.
Ecological and social drivers of neighbor recognition and the dear enemy effect in a poison frog
Authors: Tumulty James P , Bee Mark A
Published: October 2020

Navigating social relationships frequently rests on the ability to recognize familiar individuals using phenotypic characteristics. Across diverse taxa, animals vary in their capacities for social recognition, but the ecological and social sources of selection for recognition are often unclear. In a comparative study of two closely related species of poison frogs, we identified a species difference in social recognition of territory neighbors and investigated potential sources of selection underlying this difference. In response to acoustic playbacks, male golden rocket frogs (Anomaloglossus beebei) recognized the calls of neighbors and displayed a “dear enemy effect” by responding less aggressively to neighbors’ calls than strangers’ calls. In contrast, male Kai rocket frogs (Anomaloglossus kaiei) were equally aggressive to the calls of neighbors and strangers. This species difference in behavior is associated with key differences in reproductive ecology and characteristics of territories. Golden rocket frogs defend reproductive resources in the form of bromeliads, which is expected to create a threat asymmetry between neighbors and strangers favoring decreased aggression to neighbors. In contrast, Kai rocket frogs do not defend reproductive resources. Further, compared with Kai rocket frog territories, golden rocket frog territories occur at higher densities and are defended for longer periods of time, creating a more complex social environment with more opportunities for repeated but unnecessary aggression between neighbors, which should favor the ability to recognize and exhibit less aggression toward neighbors. These results suggest that differences in reproductive ecology can drive changes in social structure that select for social recognition.
kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes
Authors: Cao Chen , Kwok Devin , Edie Shannon , Li Qing , Ding Bowei , Kossinna Pathum , Campbell Simone , Wu Jingjing , Greenberg Matthew , Long Quan
Published: October 2020

The power of genotype–phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation methods. Transcriptome-wide association studies (TWAS) represent a set of emerging methods that select variants based on their effect on gene expressions, providing pretrained linear combinations of variants for downstream association mapping. In contrast to this, kernel methods such as sequence kernel association test (SKAT) model genotypic and phenotypic variance use various kernel functions that capture genetic similarity between subjects, allowing nonlinear effects to be included. From the perspective of machine learning, these two methods cover two complementary aspects of feature engineering: feature selection/pruning and feature aggregation. Thus far, no thorough comparison has been made between these categories, and no methods exist which incorporate the advantages of TWAS- and kernel-based methods. In this work, we developed a novel method called kernel-based TWAS (kTWAS) that applies TWAS-like feature selection to a SKAT-like kernel association test, combining the strengths of both approaches. Through extensive simulations, we demonstrate that kTWAS has higher power than TWAS and multiple SKAT-based protocols, and we identify novel disease-associated genes in Wellcome Trust Case Control Consortium genotyping array data and MSSNG (Autism) sequence data. The source code for kTWAS and our simulations are available in our GitHub repository (https://github.com/theLongLab/kTWAS).
Unpaired data empowers association tests
Authors: Gong Mingming , Liu Peng , Sciurba Frank C , Stojanov Petar , Tao Dacheng , Tseng George C , Zhang Kun , Batmanghelich Kayhan
Published: October 2020

Motivation

There is growing interest in the biomedical research community to incorporate retrospective data, available in healthcare systems, to shed light on associations between different biomarkers. Understanding the association between various types of biomedical data, such as genetic, blood biomarkers, imaging, etc. can provide a holistic understanding of human diseases. To formally test a hypothesized association between two types of data in Electronic Health Records (EHRs), one requires a substantial sample size with both data modalities to achieve a reasonable power. Current association test methods only allow using data from individuals who have both data modalities. Hence, researchers cannot take advantage of much larger EHR samples that includes individuals with at least one of the data types, which limits the power of the association test.

Results

We present a new method called the Semi-paired Association Test (SAT) that makes use of both paired and unpaired data. In contrast to classical approaches, incorporating unpaired data allows SAT to produce better control of false discovery and to improve the power of the association test. We study the properties of the new test theoretically and empirically, through a series of simulations and by applying our method on real studies in the context of Chronic Obstructive Pulmonary Disease. We are able to identify an association between the high-dimensional characterization of Computed Tomography chest images and several blood biomarkers as well as the expression of dozens of genes involved in the immune system.

Availability and implementation

Code is available on https://github.com/batmanlab/Semi-paired-Association-Test.

Supplementary information

Supplementary data are available at Bioinformatics online.
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis
Authors: Wang Shixiang , Tao Ziyu , Wu Tao , Liu Xue-Song
Published: October 2020

Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes.

Availability and implementation

Sigflow is an open source software under academic free license v3.0 and it is freely available at https://github.com/ShixiangWang/sigflow or https://hub.docker.com/r/shixiangwang/sigflow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hourly modelling of Thermal Hydrogen electricity markets
Authors: Moore Jared , Meeks Noah
Published: October 2020

The hourly operation of Thermal Hydrogen electricity markets is modelled. The economic values for all applicable chemical commodities are quantified (syngas, ammonia, methanol and oxygen) and an hourly electricity model is constructed to mimic the dispatch of key technologies: bi-directional power plants, dual-fuel heating systems and plug-in fuel-cell hybrid electric vehicles. The operation of key technologies determines hourly electricity prices and an optimization model adjusts the capacity to minimize electricity prices yet allow all generators to recover costs. We examine 12 cost scenarios for renewables, nuclear and natural gas; the results demonstrate emissions-free, ‘energy-only’ electricity markets whose supply is largely dominated by renewables. The economic outcome is made possible in part by seizing the full supply-chain value from electrolysis (both hydrogen and oxygen), which allows an increased willingness to pay for (renewable) electricity. The wholesale electricity prices average $25–$45/MWh, or just slightly higher than the assumed levelized cost of renewable energy. This implies very competitive electricity prices, particularly given the lack of need for ‘scarcity’ pricing, capacity markets, dedicated electricity storage or underutilized electric transmission and distribution capacity.
Marmoset Brain ISH Data Revealed Molecular Difference Between Cortical Folding Patterns
Authors: Li Xiao , Liu Tao , Li Yujie , Li Qing , Wang Xianqiao , Hu Xintao , Guo Lei , Zhang Tuo , Liu Tianming
Published: October 2020

Literature studies have demonstrated the structural, connectional, and functional differences between cortical folding patterns in mammalian brains, such as convex and concave patterns. However, the molecular underpinning of such convex/concave differences remains largely unknown. Thanks to public access to a recently released set of marmoset whole-brain in situ hybridization data by RIKEN, Japan; this data’s accessibility empowers us to improve our understanding of the organization, regulation, and function of genes and their relation to macroscale metrics of brains. In this work, magnetic resonance imaging and diffusion tensor imaging macroscale neuroimaging data in this dataset were used to delineate convex/concave patterns in marmoset and to examine their structural features. Machine learning and visualization tools were employed to investigate the possible transcriptome difference between cortical convex and concave patterns. Experimental results demonstrated that a collection of genes is differentially expressed in convex and concave patterns, and their expression profiles can robustly characterize and differentiate the two folding patterns. More importantly, neuroscientific interpretations of these differentially expressed genes, as well as axonal guidance pathway analysis and gene enrichment analysis, offer novel understanding of structural and functional differences between cortical folding patterns in different regions from a molecular perspective.
Association Between Minimum Inhibitory Concentration, Beta-lactamase Genes and Mortality for Patients Treated With Piperacillin/Tazobactam or Meropenem From the MERINO Study
Authors: Henderson A , Paterson D L , Chatfield M D , Tambyah P A , Lye D C , De P P , Lin R T P , Chew K L , Yin M , Lee T H , Yilmaz M , Cakmak R , Alenazi T H , Arabi Y M , Falcone M , Bassetti M , Righi E , Rogers B A , Kanj S S , Bhally H , Iredell J , Mendelson M , Boyles T H , Looke D F M , Runnegar N J , Miyakis S , Walls G , Khamis M A I , Zikri A , Crowe A , Ingram P R , Daneman N , Griffin P , Athan E , Roberts L , Beatson S A , Peleg A Y , Cottrell K , Bauer M J , Tan E , Chaw K , Nimmo G R , Harris-Brown T , Harris P N A ,   MERINO Trial Investigators and the Australasian Society for Infectious Disease Clinical Research Network (ASID-CRN), Newton Peter , Wren Heather , Graham Maryza , Korman Tony , Aljohani Sameera M , Alalwan Bassam , Sultana Khizra , Sartor Assunta , Welch Darren , Kahlmeter Gunnar
Published: October 2020

Introduction

This study aims to assess the association of piperacillin/tazobactam and meropenem minimum inhibitory concentration (MIC) and beta-lactam resistance genes with mortality in the MERINO trial.

Methods

Blood culture isolates from enrolled patients were tested by broth microdilution and whole genome sequencing at a central laboratory. Multivariate logistic regression was performed to account for confounders. Absolute risk increase for 30-day mortality between treatment groups was calculated for the primary analysis (PA) and the microbiologic assessable (MA) populations.

Results

In total, 320 isolates from 379 enrolled patients were available with susceptibility to piperacillin/tazobactam 94% and meropenem 100%. The piperacillin/tazobactam nonsusceptible breakpoint (MIC >16 mg/L) best predicted 30-day mortality after accounting for confounders (odds ratio 14.9, 95% confidence interval [CI] 2.8–87.2). The absolute risk increase for 30-day mortality for patients treated with piperacillin/tazobactam compared with meropenem was 9% (95% CI 3%–15%) and 8% (95% CI 2%–15%) for the original PA population and the post hoc MA populations, which reduced to 5% (95% CI −1% to 10%) after excluding strains with piperacillin/tazobactam MIC values >16 mg/L. Isolates coharboring extended spectrum β-lactamase (ESBL) and OXA-1 genes were associated with elevated piperacillin/tazobactam MICs and the highest risk increase in 30-day mortality of 14% (95% CI 2%–28%).

Conclusions

After excluding nonsusceptible strains, the 30-day mortality difference from the MERINO trial was less pronounced for piperacillin/tazobactam. Poor reliability in susceptibility testing performance for piperacillin/tazobactam and the high prevalence of OXA coharboring ESBLs suggests that meropenem remains the preferred choice for definitive treatment of ceftriaxone nonsusceptible Escherichia coli and Klebsiella.
Low Health Literacy Exists in the Inflammatory Bowel Disease (IBD) Population and Is Disproportionately Prevalent in Older African Americans
Authors: Dos Santos Marques Isabel C , Theiss Lauren M , Baker Samantha J , Liwo Amandiy , Wood Lauren N , Cannon Jamie A , Morris Melanie S , Kennedy Gregory D , Fouad Mona N , Davis Terry C , Chu Daniel I
Published: October 2020

Background

Low health literacy is common in general populations, but its prevalence in the inflammatory bowel disease (IBD) population is unclear. The objective of this study was to assess the prevalence of low health literacy in a diverse IBD population and to identify risk factors for low health literacy.

Methods

Adult patients with IBD at a single institution from November 2017 to May 2018 were assessed for health literacy using the Newest Vital Sign (NVS). Demographic and socioeconomic data were also collected. Primary outcome was the prevalence of low health literacy. Secondary outcomes were length-of-stay (LOS) and 30-day readmissions after surgical encounters. Bivariate comparisons and multivariable regression were used for analyses.

Results

Of 175 IBD patients, 59% were women, 23% were African Americans, 91% had Crohn disease, and mean age was 46 years (SD = 16.7). The overall prevalence of low health literacy was 24%. Compared to white IBD patients, African Americans had significantly higher prevalence of low health literacy (47.5% vs 17.0%, P < 0.05). On multivariable analysis, low health literacy was associated with older age and African American race (P < 0.05). Of 83 IBD patients undergoing abdominal surgery, mean postoperative LOS was 5.5 days and readmission rate was 28.9%. There was no significant difference between LOS and readmissions rates by health literacy levels.

Conclusions

Low health literacy is present in IBD populations and more common among older African Americans. Opportunities exist for providing more health literacy-sensitive care in IBD to address disparities and to benefit those with low health literacy.
Linker histone H1.5 is an underestimated factor in differentiation and carcinogenesis
Authors: Behrends Marthe , Engmann Olivia
Published: October 2020

Human histone H1.5, in mice called H1b, belongs to the family of linker histones (H1), which are key players in chromatin organization. These proteins sit on top of nucleosomes, in part to stabilize them, and recruit core histone modifying enzymes. Through subtype-specific deposition patterns and numerous post-translational modifications, they fine-tune gene expression and chromatin architecture, and help to control cell fate and homeostasis. However, even though it is increasingly implicated in mammalian development, H1.5 has not received as much research attention as its relatives. Recent studies have focused on its prognostic value in cancer patients and its contribution to tumorigenesis through specific molecular mechanisms. However, many functions of H1.5 are still poorly understood. In this review, we will summarize what is currently known about H1.5 and its function in cell differentiation and carcinogenesis. We will suggest key experiments that are required to understand the molecular network, in which H1.5 is embedded. These experiments will advance our understanding of the epigenetic reprogramming occurring in developmental and carcinogenic processes.