bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal and combustion characteristics of a double ring burner with different swirling flow patterns
Authors: Saad H E , Kamal M , Adel A
Published: October 2019

The swirling effect on the gas hob of double ring domestic LPG burner was investigated using 4 patterns of swirl orientation: Co swirl, Counter swirl, Star pattern swirl and, the radial flow as a Benchmarking cooker burner. To improve future domestic gas burners thermal efficiency and CO emissions of these burners are compared using LPG. The influence of Reynolds number and the pan height above the flame (as normalized by the Burner outer diameter) has been studied. The results showed that using swirl motion increased both the thermal efficiency and CO emissions, except for the Star pattern burner whereby the thermal efficiency increased while the CO emissions decreased. Increasing the pan height to the burner outer diameter decreased the thermal efficiency and CO emissions under all operating conditions due to lower pigmentation of the flame to the pan bottom which reduces the heat transfer from the flames to the heated pan. For the counter flow burner, the efficiency increased by 2.1% from the radial one while it increased by 1.7% and 0.9 % for the co swirl and star pattern respectively. On the other hand, the CO emission decreased by 33% for the star pattern burner from the benchmark one.
Automated unsupervised change detection technique from RGB color image
Authors: Gomaa M , hamza E , Elhifnawy H
Published: October 2019

Change detection is an important process for many applications such as monitoring the effects of environmental hazards, landslides, rock fall and city development projects. RGB images are commonly used as commercial sources of data for monitoring changes visually because they have powerful descriptive information for different features. Automation of detected changes from two RGB images is a challenge because the two images are usually captured in different environments, as temperature, sun angle, clouds, capturing time …etc. The objective of this research is to introduce an automated technique for detecting changes from RGB image based on color channels. The image pixel is represented as a set of its color channels values, R, G and B which is called color signature of image pixel. A real data is used to fulfil the research objective without pre-knowledge about the changes. The correlation coefficients are calculated between color signatures of each two associated pixels from two different registered high resolution satellite images for the same area of study. The detected pixels of changes are identified based on specific correlation value that is identified based on degree of change sensitivity. The degree of sensitivity is based on the importance of detection procedure that is considered as a main part of decision making for risk and crisis management system. The proposed technique is unsupervised and fully automated. It can be applied through a real time process based on the processing capabilities, size and resolution of input images. This technique is easy to use and gives accurate results with neglecting the effects of atmospheric effects.
Theoretical and experimental study of underwater explosion performance of selected explosive compositions
Authors: Hawass Ahmed , Elbeih Ahmed , Mostafa Hosam E.
Published: October 2019

Measurements of underwater explosion parameters and their effects are still the major problem for naval designer. In this study, thermo-chemical calculations have been carried out using EXPLO5 code to determine the underwater explosion parameters for different selected explosive mixtures. Preparation of the different types of explosive mixtures based on melt cast explosive (TNT) and plastic bonded explosives (PBXs) based on polyurethane binder system were presented. The effect of different aluminum weight percentage for the selected explosive mixture has been investigated with respect to the impulse and the resulted deformation. Underwater experimental measurements of the prepared explosive mixtures based on steel plate’s deformation were determined and compared. It was concluded that PBX based on RDX in addition to 25 wt% aluminum and 30wt% ammonium perchlorate produces the highest underwater explosion performance from all the tested samples. This explosive mixture is candidate to replace the traditional well known TNT in the underwater explosive applications.
Crystal structure and optical properties of 1D-bi based organic-inorganic hybrid perovskite
Authors: Kandeel Mohamed F. , Abdel-Aal Seham K. , El-Sherif Ashraf F. , Ayoub H. S. , Abdel-Rahman Ahmed S.
Published: October 2019

In the pages that follow,the structure of the crystal, unit cell dimension and complete structure information will be shown by single crystal x-ray diffraction and measuring some physical properties of 1D propylene diammonium pentachloro bismuthate [(NH3)2(CH2)3]BiCl5 organic-inorganic hybrid perovskites (OIHs).Slow evaporation method is used to prepared the synthesis. The process of preparation occurred by mixing ethanolic solution of equimolar ratios (1:1) of its basic components (organic / inorganic). The Bi hybrid crystallized in orthorhombic non centro-symetric Pca21 structure with 8 molecules per unit cell.The unit cell parameters are a = 19.8403 (7) Å, b = 6.3303 (2) Å, c = 19.0314 (7) Å. The average C-C bond lengths are 1.50Å. The average N-C bond lengths are 1.47Å. The connection between organic parts to inorganic part is via hydrogen bond (H. Bond). Raman spectroscopy and also Fourier transform infrared spectroscopy (FTIR) have been used to study the vibrational spectra that shows the main diffraction peaks and their assignment. Diffuse reflectance spectra (DRS) method is used to study the optical properties and show that there is a strong absorption in the UV region for Bi hybrid. Kubelka–Munk equation has been used to calculate the band gap energy and indicates that the band gap for the present investigated hybrid is equals 3.15 eV.
Enhanced Grayscale Image Transmission Over HF Channel
Authors: Mashaly Ahmed S. , Mekkawy Tamer
Published: October 2019

Image transmission over HF communication is suitable for long-distance coverage beyond the line of sight and across intercontinental. Unfortunately, the channel condition is degraded with low Signal to Noise Ratio (SNR) and multi-path spreading. In this paper, we aim to transmit images over HF channel and introduce some techniques to improve the received noisy images. First, a Least square estimation technique is applied to estimate the channel state information, then we propose an enhanced filter to reduce image noise effect and improve the received image appearance. This proposed enhanced filter is based on our enhanced version of the Median Filter (MF) and the Mathematical Morphology (MM). Simulation results assess the performance of the proposed filter compared with the performance of some popular filters, we conclude that the proposed enhanced filter can be used for any further detection and recognition operations, and it introduces promising results which can be used for real-time implementation with different computer vision applications.
Structural behaviour of inflatable PVC fabric cylindrical tubes
Authors: Okda Sherif , Akl Wael , Elsabbagh Adel
Published: October 2019

Inflatable structures are light weight structures that have often been proposed for aerospace applications. They are light in weight, easily manufacturable and foldable. Thus, they can be easily transported and deployed in space. However, the proper characterization for their properties of these structures is still missing.

The work done in this paper aims at studying the structural properties of inflatable cylindrical tubes, manufactured from PVC fabric. The cylindrical tubes are fixed as cantilever beams and subjected to a load at the beam tip. Samples of different sizes are tested under different inflation pressures and loads. Load-deflection curves are recorded for each test. Results show that the beam stiffness increases with the increase of inflation pressure and beam cross sectional area. The inflatable beams show linear behaviour up to a certain critical load at which wrinkling occurs. Beyond this load the behaviour of the beam becomes nonlinear and can be unstable. Hysteresis phenomenon is also observed during the unloading of the beam. In addition, Free vibration analysis was conducted to study the effect of inflation pressure on the beam natural frequency. This work is a part of project aiming to design and manufacture an inflatable wind turbine blade to overcome the drawbacks of conventional blades.
A proposed index to assess commonality among aircraft product families
Authors: Heikal Eman A. , El-Kharbotly Amin K. , El-Beheiry Mohammed M.
Published: October 2019

Market increasing competition escalate the challenges facing aeronautics companies to satisfy the diversity of aircrafts applications while keeping design and manufacturing cost of Aircrafts as low as possible. Modularity and commonality in Aircrafts design have been recognized as solution for the stated challenge. Commonality in aeronautics result in offering different aircrafts models at lower costs that broader the use of aircrafts. For modular product design the need to assess the degree of modularity or commonality arises, and many researchers have been motivated for designing various commonality indices for specific focus to assess commonality to evaluate the benefits and compare between the degree of commonality among various product families. This paper proposes new commonality index within design concern that take into account products production quantities. Commonality is assessed for different products quantities patterns using one of previous design concern index (e.g DCI) and using developed CPF. CPF give consistent commonality assessment unlike any design focus commonality index such DCI. Consequently, it is concluded that commonality assessment must be based on the actual production quantity of common modules used unlike previous approaches that based their commonality assessment on the number of times common modules can be used in the fixed design of products within product family. Therefore, the developed index could assess the commonality across various Aircrafts product families more effectively than previous measures.
Design and Implementation of an Advanced Radar Signal Processor with Waveform Generator and BIST Unit on a Single FPGA Chip
Authors: Abdel Razek Ahmed M. , Ahmed Fathy M. , Kamel Hazem , Mahfouz Wael , Moustafa K. H.
Published: October 2019

Field Programmable Gate Arrays (FPGAs) are best suited for signal processing applications that require real-time processing. Therefore, it is preferred over DSP processors in implementing radar receivers that processes incoming continuous stream of data. In the past, implementing complex arithmetic operations in floating point representation was a monopoly on DSP processors and the designers had to work around the sequential nature of the DSP processor to make it suitable for real-time applications by using buffered and multi-clocking designs. But nowadays, the great advances in FPGA design technology minimized this design effort since it is capable of performing these complex algorithms in real time. This paper represents the design and implementation of an advanced radar signal processor for binary phase-coded pulsed radar incorporating a time range side lobes suppression technique on a single FPGA chip. The proposed hardware design includes a waveform generator, an advanced signal processing unit, and a built-in self-test (BIST). Design aspects and hardware details for each part is introduced thoroughly.
Modeling and prediction of aerodynamic characteristics of free fall rotating wing based on experiments
Authors: Zakaria Mohamed Y. , dos Santos Carlos R. , Dayhoum Abdallah , Marques Flávio D. , Hajj Muhammad R.
Published: October 2019

The unsteady vortex lattice method (UVLM) is used to model the aerodynamic loading on different Samara leaves (Maple seed) during their steady state flight. Experiments is performed to verify the analytical results. Parameters including the drop speed, angular velocity and coning angle for different sets of Maple Samaras were determined from experiments. The aerodynamic loads were calculated using UVLM against the forces required for maintaining a steady state flight as obtained from the experiment. Consequently, the UVLM approach yields adequate aerodynamic modelling features that can be used for more accurate flight stability analysis of the Samara flight or of decelerator devices inspired by such flight.
Automatic fire fighting robot with notification
Authors: Jalani J , Misman D , Sadun A S , Hong L C
Published: October 2019

In real life, fire accidents can happen anytime and anywhere that usually hardly controllable. Fire accidents can damage the buildings, kill human and may cause unpredictable losses. In addition, death not only due to the fire but also from smoke inhalation and toxic gases. Therefore the fire security is important to human life. Note that the human is difficult to detect the fire in the location that is hard to reach or see by a human. Moreover, the human also may take a lot of time to extinguish fire due to the fact that finding a water source can be troublesome. Therefore, an automatic firefighting robot has been designed and proposed in this study. This robot used 3 flame sensors to detect the fire. It also equipped with 3 ultrasonic sensors for obstacle avoiding which protecting the robot and the internal components from any obstacles. Each sensor on the robot is controlled by the Arduino. Apart from the sensors, the robot is also equipped with the water tank that provides water once the fire is detected. The robot will move randomly in the room when the power is on. When the flame sensors detected the fire, the robot will move to the fire source and send a warning message to the user. Once the robot reached the burning area, it will stop at a certain distance and extinguish the fire by using water.
Discussion on the welding performance of automatic welding of industrial robot and manual welding
Authors: Yan Zhang
Published: October 2019

Since the introduction of industrial robots and their widespread application in manufacturing, the production quality and efficiency of manufacturing have been affected their automated welding performance directly. In this paper the author provides a useful basis for improving welding quality and promoting production efficiency through the analysis of industrial robot automatic welding technology standards and welding performance.
Flexible flow shop scheduling problem with setup times and blocking constraint via genetic algorithm and simulation
Authors: Zhang Meng
Published: October 2019

Flexible flow shop scheduling problem (FFSP) is recognized as an important class of problems in manufacturing systems. To consider more actual production factors, such as transportation time, setup times, blocking constraint, etc., we solved the FFSP using the improved genetic algorithm (GA) and discrete event simulation (DES). Firstly, a mathematical model for FFSP with the objective of minimizing total completion time was established. Besides, a GA mixed with Palmer heuristic algorithm was proposed to solve the mathematical model. Moreover, a DES software-plant simulation-was used to establish a more realistic production model, and an actual production workshop was modeled and optimized. After optimization, the total completion time and equipment utilization were greatly improved compared with the original scheduling. It shows the effectiveness and rationality of the proposed method to solve the actual FFSP.
Extending Blade-Element Model to Contra-Rotating Configuration
Authors: Gur Ohad
Published: October 2019

Blade element model is one of the most popular models for rotating-wing analysis and design. Many legacy tools are based on blade-element and capable of analysing only a single-rotating configuration. The current scope suggests a simple and effective method for extending such applications to contra-rotating configurations. The model based on the classic axial-momentum theory and assumes rigid wake. The method is validated versus results from propeller, hovering rotor, and prop-fan experiments. The experiments present both single and dual-rotating wing configuration, which share the same blade geometry and test facilities. This enables the isolation of the single-versus dual-rotating configuration influences, thus validating the suggested model with high level-of-confidence. The validation shows that the same trends of the single-rotating model appears in the dual-rotating analyses. Moreover, the difference between single and dual rotating configuration is replicated accurately compared to the test results. This proves the validity of the suggested model extension. The model validation also exhibits the differences between the accuracy of the forward and rear rotating disk in the contra-rotating configuration. The rear disk contributes by the no-swirled wake and exhibits accurate results compared to the forward disk which operate similar to a single rotating wing, hence suffers from the same inaccuracies.
Residual inflammatory risk after contemporary lipid lowering therapy
Authors: Riaz Haris , Khan Safi U , Lateef Noman , Talluri Swapna , Khan Muhammad Shahzeb , Desai Milind Y
Published: October 2019

Background

Recently, there has been an increasing interest in targeting inflammation to reduce major adverse cardiovascular events (MACE) in patients with cardiovascular risk. Statins, PCSK9 inhibitors, and ezetimibe have been shown to reduce MACE owing to reduction in low-density lipoproteins cholesterol (LDL-c). Herein, we investigate whether the intensity of these agents is associated with (i) discernible reduction in inflammation measured by the levels of high-sensitivity C-reactive protein (hsCRP); (ii) reduction in MACE; (iii) if there is an association between the baseline hsCRP and MACE.

Methods and results

Electronic databases were searched for randomized controlled trials (RCTs) that compared statins, ezetimibe, PCSK9 inhibitors with placebos/active controls and reported MACEs and hsCRP (mg/L). Studies were stratified based on baseline hsCRP (<2, 2–3, >3) with subgroup analysis conducted across each stratum. Fourteen RCTs including 133 109 patients randomized into more intensive therapy (MIT) and less intensive therapy were selected. Meta-analysis did not demonstrate any significant differences between use of MIT and hsCRP levels (mean difference, −0.02; CI, −0.06, 0.02; P = 0.31). The MIT significantly reduced the risk of MACE (RR, 0.82; CI, 0.75, 0.91; P < 0.001). The relative risk and absolute risk remained consistent across the strata. However, there was a 0.5% statistically significant absolute risk reduction in all-cause mortality in patients with higher hsCRP (RD, −0.005; CI, −0.009, −0.001; P = 0.01).

Conclusion

Overall, LDL-c lowering therapies reduce relative risk of MACEs particularly in patients with higher baseline hsCRP. However, there appears to be a residual inflammatory risk despite the use of contemporary lipid lowering agents.
NLRP3 Inflammasome Inhibition by MCC950 in Aged Mice Improves Health via Enhanced Autophagy and PPARα Activity
Authors: Marín-Aguilar Fabiola , Castejón-Vega Beatriz , Alcocer-Gómez Elísabet , Lendines-Cordero Debora , Cooper Matthew A , de la Cruz Patricia , Andújar-Pulido Eloísa , Pérez-Alegre Mónica , Muntané Jordi , Pérez-Pulido Antonio J , Ryffel Bernhard , Robertson Avril A B , Ruiz-Cabello Jesús , Bullón Pedro , Cordero Mario D
Published: October 2019

The NLRP3 inflammasome has emerged as an important regulator of metabolic disorders and age-related diseases in NLRP3-deficient mice. In this article, we determine whether, in old mice C57BL6J, the NLRP3 inflammasome inhibitor MCC950 is able to attenuate age-related metabolic syndrome to providing health benefits. We report that MCC950 attenuates metabolic and hepatic dysfunction in aged mice. In addition, MCC950 inhibited the Pi3K/AKT/mTOR pathway, enhanced autophagy, and activated peroxisome proliferator-activated receptor-α in vivo and in vitro. The data suggest that MCC950 mediates the protective effects by the mammalian target of rapamycin inhibition, thus activating autophagy and peroxisome proliferator-activated receptor-α. In conclusion, pharmacological inhibition of NLRP3 in aged mice has a significant impact on health. Thus, NLRP3 may be a therapeutic target of human age-related metabolic syndrome.
The Path of the Boomerang: Human Rights Campaigns, Third-Party Pressure, and Human Rights
Authors: Allendoerfer Michelle Giacobbe , Murdie Amanda , Welch Ryan M
Published: October 2019

How can information campaigns of nongovernmental human rights organizations (HROs) to “name and shame” human rights violators improve human rights conditions? Is the effect direct—does HRO targeting induce violating states to change their behavior? Or is the effect indirect—does pressure by third parties mediate the relationship between HRO actions and changes in human rights practices? The boomerang and spiral models suggest HRO activity provokes third parties, such as other states and international organizations, to pressure violating states. This pressure, in turn, drives violating states to improve human rights conditions. On the other hand, recent empirical work finds third-party pressure can further degrade human rights conditions. In this paper we provide a comprehensive analysis of how these individual factors—HRO activities and pressure from third parties—work together in the larger chain of causal events influencing human rights conditions. Using a causal mediation model, we examine whether HRO campaigning improves human rights directly or if the effect is mediated by costs imposed by powerful actors through sanctions and military interventions. We find that, although HRO activities have an overall positive effect on human rights conditions, the negative effects of third-party pressure somewhat diminish the positive effects.
Associative effects of wet distiller’s grains plus solubles and tannin-rich peanut skin supplementation on in vitro rumen fermentation, greenhouse gas emissions, and microbial changes1
Authors: Min Byeng Ryel , Castleberry Lana , Allen Heather , Parker David , Waldrip Heidi , Brauer David , Willis William
Published: October 2019

Two sets of in vitro rumen fermentation experiments were conducted to determine effects of diets that included wet distiller’s grains plus solubles (WDGS) and tannin-rich peanut skin (PS) on the in vitro digestibility, greenhouse gas (GHG) and other gas emissions, fermentation rate, and microbial changes. The objectives were to assess associative effects of various levels of PS or WDGS on the in vitro digestibility, GHG and other gas emissions, fermentation rate, and microbial changes in the rumen. All gases were collected using an ANKOM Gas Production system for methane (CH4), carbon dioxide (CO2), nitrous oxide (N2O), and hydrogen sulfide (H2S) analyses. Cumulative ruminal gas production was determined using 250 mL ANKOM sampling bottles containing 50 mL of ruminal fluid (pH 5.8), 40 mL of artificial saliva (pH 6.8), and 6 g of mixed diets after a maximum of 24 h of incubation. Fermenters were flushed with CO2 gas and held at 39 °C in a shaking incubator for 24 h. Triplicate quantitative real-time polymerase chain reaction (qPCR) analyses were conducted to determine microbial diversity. When WDGS was supplied in the diet, in the absence of PS, cumulative CH4 production increased (P < 0.05) with 40% WDGS. In the presence of PS, production of CH4 was reduced but the reduction was less at 40% WDGS. In the presence of PS, ruminal lactate, succinate, and acetate/propionate (A/P) ratio tended to be less with a WDGS interaction (P < 0.01). In the presence of PS and with 40% WDGS, average populations of Bacteroidetes, total methanogens, Methanobrevibacter sp. AbM4, and total protozoa were less. The population of total methanogens (R2 = 0.57; P < 0.01), Firmicutes (R2 = 0.46: P < 0.05), and Firmicutes/Bacteroidetes (F/B) ratio (R2 = 0.46; P < 0.03) were strongly correlated with ruminal CH4 production. Therefore, there was an associative effect of tannin-rich PS and WDGS, which suppressed methanogenesis both directly and indirectly by modifying populations of ruminal methanogens.
Self-Organizing Maps to Validate Anti-Pollution Policies
Authors: Arroyo Ángel , Cambra Carlos , Herrero Álvaro , Tricio Verónica , Corchado Emilio
Published: October 2019

This study presents the application of self-organizing maps to air-quality data in order to analyze episodes of high pollution in Madrid (Spain’s capital city). The goal of this work is to explore the dataset and then compare several scenarios with similar atmospheric conditions (periods of high Nitrogen dioxide concentration): some of them when no actions were taken and some when traffic restrictions were imposed. The levels of main pollutants, recorded at these stations for eleven days at four different times from 2015 to 2018, are analyzed in order to determine the effectiveness of the anti-pollution measures. The visualization of trajectories on the self-organizing map let us clearly see the evolution of pollution levels and consequently evaluate the effectiveness of the taken measures, after and during the protocol activation time.
In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae)
Authors: Salamatian Iman , Moshaverinia Ali , Razmyar Jamshid , Ghaemi Mehran
Published: October 2019

Avian influenza virus (AIV) H9N2 emerged in the 1990s as an economically important disease in poultry and occasionally infects humans and other mammals. The aim of this study was to evaluate the acquisition and retention of H9N2 AIV on and within the house fly, Musca domestica (Linnaeus 1758), under laboratory conditions. In first experiment, 100 adult house flies were divided into control and treatment groups equally. Treatment group was fed with a meal containing H9N2 virus, while control group was supplied with an identical meal without virus. Fifteen minutes after exposure in each group, flies were washed twice to remove surface particles, disinfected and then homogenized for testing. The two external body surface washes and the homogenate samples were tested for H9N2 to distinguish exterior from interior viral load. Second experiment was performed likewise but five flies from each group were taken at 0, 6, 24, 48, 72, 96, and 120 h post-exposure. All samples were subjected to real-time reverse-transcription polymerase chain reaction (RRT-PCR) for detecting H9-Specific viral RNA. Results of the first experiment showed that viral RNA was detectable in both of external surface and homogenates samples. Second experiment revealed that persistence of H9N2 AIVs on external body surface and within the body of M. domestica were 24 and 96 h, respectively. Moreover, viral RNAs concentration declined during the time after exposure to AIV H9N2 either outside or within house flies. Overall, house fly was able to acquire and preserve H9N2 AIV experimentally, which may contribute the spread of virus among poultry farms.
Developing a Music-Based Selective Attention Training Program for Toddlers with Developmental Disabilities
Authors: Lantigua Katherine
Published: October 2019

The purpose of this article was to describe the development of a music-based selective attention training (MSAT) program to improve selective attention in toddlers with developmental disabilities. Selective attention is the ability to attend despite distractors, and it is a developmentally appropriate skill for toddlers because they have the neural connections to begin selectively attending. Music can potentially impact selective attention due to overlapping neural processing areas for both selective attention and music engagement (i.e., listening to and playing music). The MSAT program development involved several steps, including observations, reviewing literature to outline the Therapeutic Function of Music (TFM), participating in training, offering parent and teacher information sessions, designing session evaluation forms, and facilitating 19 weeks of group and individual sessions at an early intervention setting. Program development resulted in an MSAT program manual designed to improve selective attention in toddlers with developmental disabilities. The clinician found that specific auditory and visual distractors that are familiar and preferred by toddlers could be used to practice selective attention. Introducing distractors at predictable time points within the music experience gave toddlers multiple opportunities to practice ignoring the distractors and focusing on the target task. Evaluation of this MSAT program, its utility for stakeholders such as music therapists and early childhood professionals, and implications for the development of future music-based programs in early intervention are discussed.
NPInter v4.0: an integrated database of ncRNA interactions
Authors: Teng Xueyi , Chen Xiaomin , Xue Hua , Tang Yiheng , Zhang Peng , Kang Quan , Hao Yajing , Chen Runsheng , Zhao Yi , He Shunmin
Published: October 2019

Noncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database (http://bigdata.ibp.ac.cn/npinter). Since the last version of NPInter was issued, a rapidly growing number of studies have reported novel interactions and accumulated numerous high-throughput interactome data. We have therefore updated NPInter to its fourth edition in which are integrated 600 000 new experimentally identified ncRNA interactions. ncRNA–DNA interactions derived from ChIRP-seq data and circular RNA interactions have been included in the database. Additionally, disease associations were annotated to the interacting molecules. The database website has also been redesigned with a more user-friendly interface and several additional functional modules. Overall, NPInter v4.0 now provides more comprehensive data and services for researchers working on ncRNAs and their interactions with other biomolecules.
Antimicrobial Stewardship Review of Automated Candidemia Alerts Using the Epic Stewardship Module Improves Bundle-of-Care Adherence
Authors: Pettit Natasha N , Han Zhe , Nguyen Cynthia T , Choksi Anish , Charnot-Katsikas Angella , Beavis Kathleen G , Tesic Vera , Pisano Jennifer
Published: October 2019

Background

Antimicrobial stewardship interventions utilizing real-time alerting through the electronic medical record enable timely implementation of the bundle of care (BOC) for patients with severe infections, such as candidemia. Automated alerting for candidemia using the Epic stewardship module has been in place since July 2015 at our medical center. We sought to assess the impact of these alerts.

Methods

All adult inpatients with candidemia between April 1, 2011, and March 31, 2012 (pre-intervention), and June 30, 2016, and July 1, 2017 (post-intervention), were evaluated for BOC adherence. We also evaluated the impact on timeliness to initiate targeted therapy, length of stay (LOS), and 30-day mortality.

Results

Eighty-four patients were included, 42 in the pre- and 42 in the post-intervention group. Adherence to BOC was significantly improved, from 48% (pre-intervention) to 83% (post-intervention; P = .001). The median time to initiation of therapy was 4.8 hours vs 3.3 hours (P = .58), the median LOS was 24 and 18 days (P = .28), and 30-day mortality was 19% and 26% (P = .60) in the pre- and post-intervention groups, respectively.

Conclusions

Antimicrobial stewardship program review of automated alerts identifying patients with candidemia resulted in significantly improved BOC adherence and was associated with a 1.5-hour reduction in time to initiation of antifungal therapy. No significant change was observed with 30-day mortality or LOS.
Evaluation of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry and ClinPro Tools as a Rapid Tool for Typing Streptococcus pyogenes
Authors: Tadros Manal , Cabrera Ana , Matukas Larissa M , Muller Matthew
Published: October 2019

Background

Timely strain typing of group A Streptococci (GAS) is necessary to guide outbreak recognition and investigation. We evaluated the use of (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) combined with cluster analysis software to rapidly distinguish between related and unrelated GAS isolates in real-time.

Methods

We developed and validated a typing model using 177 GAS isolates with known emm types. The typing model was created using 43 isolates, which included 8 different emm types, and then validated using 134 GAS isolates of known emm types that were not included in model generation.

Results

Twelve spectra were generated from each isolate during validation. The overall accuracy of the model was 74% at a cutoff value of 80%. The model performed well with emm types 4, 59, and 74 but showed poor accuracy for emm types 1, 3, 12, 28, and 101. To evaluate the ability of this tool to perform typing in an outbreak situation, we evaluated a virtual outbreak model using a “virtual outbreak strain; emm74” compared with a non-outbreak group or an “outgroup “ of other emm types. External validation of this model showed an accuracy of 91.4%.

Conclusions

This approach has the potential to provide meaningful information that can be used in real time to identify and manage GAS outbreaks. Choosing isolates characterized by whole genome sequencing rather than emm typing for model generation should improve the accuracy of this approach in rapidly identifying related and unrelated GAS strains.
Thirty years after water privatization—is the English model the envy of the world?
Authors: Helm Dieter
Published: October 2019

The paper considers whether water privatization 30 years ago has delivered the promised superior performance to nationalization, which remains the dominant model in Europe. The paper sets out the arguments at privatization, in particular in relation to efficiency, the managerial incentives, the role of private-sector balance sheets in facilitating investment, and the impacts on the cost of capital. Alternative explanations of relative performance, notably the regulation model adopted, are highlighted, and the paper concludes by outlining an alternative model of water regulation which better marries up public responsibilities and private incentives.
Longitudinal clusters of pain and stiffness in polymyalgia rheumatica: 2-year results from the PMR Cohort Study
Authors: Muller Sara , Whittle Rebecca , Hider Samantha L , Belcher John , Helliwell Toby , Morton Chris , Hughes Emily , Lawton Sarah A , Mallen Christian D
Published: October 2019

Objectives

To investigate potential subgroups of primary care–diagnosed patients with PMR based on self-reported pain and stiffness severity over time.

Methods

A total of 652 people with an incident PMR diagnosis were recruited from English general practices and completed a baseline postal questionnaire. They were followed up with a further six questionnaires over a 2 year period. A total of 446 people completed the 2 year follow-up. Pain and stiffness were reported on a 0–10 numerical rating scale. Latent class growth analysis was used to estimate the joint trajectories of pain and stiffness over time. A combination of statistical and clinical considerations was used to choose the number of clusters. Characteristics of the classes were described.

Results

Five clusters were identified. One cluster represented the profile of ‘classical’ PMR symptoms and one represented sustained symptoms that may not be PMR. The other three clusters displayed a partial recovery, a recovery followed by worsening and a slow, but sustained recovery. Those displaying classical PMR symptoms were in better overall health at diagnosis than the other groups.

Conclusion

PMR is a heterogeneous condition, with a number of phenotypes. The spectrum of presentation, as well as varying responses to treatment, may be related to underlying health status at diagnosis. Future research should seek to stratify patients at diagnosis to identify those likely to have a poor recovery and in need of an alternative treatment pathway. Clinicians should be aware of the different experiences of patients and monitor symptoms closely, even where there is initial improvement.
Heart Failure Self-care Associated With Brain Injury in Executive Control Regions
Authors: Choi Sarah , Roy Bhaswati , Kumar Rajesh , Fonarow Gregg C. , Woo Mary A.
Published: October 2019

Background:

Inadequate self-care is linked to poor health outcomes in heart failure (HF). Self-care depends on decision-making abilities, but links between self-care and brain injury to executive decision-making regulatory areas (prefrontal cortices) are unclear.

Objective:

We investigated the relationships between HF self-care and status of prefrontal cortices.

Methods:

Magnetic resonance imaging–based diffusion tensor imaging was performed in 21 patients with HF (age, 53.8 ± 7.9 years; 15 men; left ventricular ejection fraction, 25.1% ± 6.1%), and self-care and executive function were measured with the Self-care of Heart Failure Index (SCHFI) and Trail Making Test B. Using diffusion tensor imaging data, mean diffusivity (MD) maps were calculated and region-of-interest analyses were performed on the left and right prefrontal brain areas. Statistical analyses consisted of partial correlations (covariates, age, and gender).

Results:

The mean ± SD SCHFI scores were 70.78 ± 11.37 for maintenance, 70 ± 17.32 for management, and 74.91 ± 15.76 for confidence. The mean ± SD Trail Making Test B score was 90.2 ± 73.3 seconds. The mean ± SD MD values (higher values indicate tissue injury) of the left and right prefrontal cortices were 1.46 ± 0.16 (×10−3 mm2/s) and 1.44 ± 0.14 (×10−3 mm2/s), respectively. Significant negative correlations emerged between prefrontal MD values and SCHFI maintenance (left/right, r = −0.64/−0.70; P < .003) and SCHFI management (r = −0.93/−0.86; P < .003). Significant positive correlations were observed between prefrontal MD values and Trail Making Test B (r = 0.71/0.74; P < .001). A nonsignificant correlation emerged between prefrontal MD values and SCHFI confidence scores.

Conclusions:

Brain tissue integrity in executive function regulatory regions is associated with HF self-care for maintenance and management. The findings indicate that protection and brain injury repair in executive control areas may improve HF self-care.
Interaction of the Motor Protein SecA and the Bacterial Protein Translocation Channel SecYEG in the Absence of ATP
Authors: Winkler Klemens , Karner Andreas , Horner Andreas , Hannesschlaeger Christof , Knyazev Denis , Siligan Christine , Zimmermann Mirjam , Kuttner Roland , Pohl Peter , Preiner Johannes
Published: October 2019

Translocation of many secretory proteins through the bacterial plasma membrane is facilitated by a complex of the SecYEG channel with the motor protein SecA. The ATP-free complex is unstable in detergent, raising the question how SecA may perform several rounds of ATP hydrolysis without being released from the membrane embedded SecYEG. Here we show that dual recognition of (i) SecYEG and (ii) vicinal acidic lipids confers an apparent nanomolar affinity. High-speed atomic force microscopy visualizes the complexes between monomeric SecA and SecYEG as being stable for tens of seconds. These long-lasting events and complementary shorter ones both give rise to single ion channel openings of equal duration. Furthermore, luminescence resonance energy transfer reveals two conformations of the SecYEG-SecA complex that differ in the protrusion depth of SecA’s two-helix finger into SecYEG’s aqueous channel. Such movement of the finger is in line with the power stroke mechanism of protein translocation.
Parallel 1024-ch Cyclic Voltammetry on Monolithic CMOS Electrochemical Detector Array
Authors: White Kevin A. , Mulberry Geoffrey , Kim Brian N.
Published: October 2019

Large-scale microelectrode arrays offers enhanced spatiotemporal resolution in electrophysiology studies.. In this paper, we discuss the design and performance of an electrochemical detector array which is capable of 1024-ch parallel cyclic voltammetry (CV) as well as other electrochemical measurements. The electrochemical detector is fabricated using a custom-designed CMOS chip which integrates both the circuity and on-chip microelectrode array, to operate and record from electrochemical measurements. For parallel 1024-ch recordings, 1024 capacitor-based integrating transimpedance amplifiers (TIA) are designed and integrated. The TIA design features the bipolar capabilities for measuring both negative and positive electrochemical currents due to reduction and oxidation of molecules. The resulted dynamic range of this TIA is −700 pA – 1968 pA. CV can be used to examine the quality of electrochemical electrodes by measuring the double-layer capacitance. Double-layer capacitance forms at the electrode-electrolyte interface and is a function of the effective area of the electrode. Thus, a contaminated electrode can have smaller effective area resulting in smaller double-layer capacitance. Using the parallel CV capability of the monolithic CMOS device, the double layer capacitance of all 1024 electrodes are simultaneously measured to examine the status of the electrodes’ surface in real time. The initial measurement of the electrode array showed a mean capacitance of 466 pF. After plasma treatment to remove contamination on the electrode’s surface, the increased capacitance was 1.36nF nearly tripling the effective surface area. We have successfully developed of 1024-ch electrochemical detector array using the monolithic CMOS sensor. The CV functionality was validated by measuring the double-layer capacitance of the on-chip electrode array. This method can accelerate the characterization of a massive electrode array before analytical experiments to provide well-controlled electrochemical electrodes, which is crucial in conducting reliable electrochemical measurements.
Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics
Authors: Grishin Dennis , Raisaro Jean Louis , Troncoso-Pastoriza Juan Ramón , Obbad Kamal , Quinn Kevin , Misbach Mickaël , Gollhardt Jared , Sa Joao , Fellay Jacques , Church George M. , Hubaux Jean-Pierre
Published: October 2019

The growing number of health-data breaches, the use of genomic databases for law enforcement purposes and the lack of transparency of personal-genomics companies are raising unprecedented privacy concerns. To enable a secure exploration of genomic datasets with controlled and transparent data access, we propose a novel approach that combines cryptographic privacy-preserving technologies, such as homomorphic encryption and secure multi-party computation, with the auditability of blockchains. This approach provides strong security guarantees against realistic threat models by empowering individual citizens to decide who can query and access their genomic data and by ensuring end-to-end data confidentiality. Our open-source implementation supports queries on the encrypted genomic data of hundreds of thousands of individuals, with minimal overhead. Our work opens a path towards multi-functional, privacy-preserving genomic-data analysis.

One Sentence Summary

A citizen-centered open-source response to the privacy concerns that hinder population genomics, based on modern cryptography.
TEsorter: lineage-level classification of transposable elements using conserved protein domains
Authors: Zhang Ren-Gang , Wang Zhao-Xuan , Ou Shujun , Li Guang-Yuan
Published: October 2019

Transposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs.

Availability

The code in Python is freely available at https://github.com/zhangrengang/TEsorter.
Adaptive time scales in recurrent neural networks
Authors: Quax Silvan C. , D’Asaro Michele , van Gerven Marcel A. J.
Published: October 2019

Recurrent neural network models have become widely used in computational neuroscience to model the dynamics of neural populations as well as in machine learning applications to model data with temporal dependencies. The different variants of RNNs commonly used in these scientific fields can be derived as discrete time approximations of the instantaneous firing rate of a population of neurons. The time constants of the neuronal process are generally ignored in these approximations, while learning these time constants could possibly inform us about the time scales underlying temporal processes and enhance the expressive capacity of the network. To investigate the potential of adaptive time constants, we compare the standard Elman approximation to a more lenient one that still accounts for the time scales at which processes unfold. We show that such a model with adaptive time scales performs better on predicting temporal data, increasing the memory capacity of recurrent neural networks, and allows recovery of the time scales at which the underlying processes unfold.
Association between breastfeeding and DNA methylation over the life course: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC)
Authors: Hartwig Fernando Pires , Smith George Davey , Simpkin Andrew J , Victora Cesar Gomes , Relton Caroline L. , Caramaschi Doretta
Published: October 2019

Background

Breastfeeding is associated with short and long-term health benefits. Long-term effects might be mediated by epigenetic mechanisms, yet a recent systematic review indicated that the literature on this topic is scarce. We performed the first epigenome-wide association study of infant feeding, comparing breastfed vs non-breastfed children. We measured DNA methylation in children from peripheral blood collected in childhood (age 7, N=640) and adolescence (age 15-17, N=709) within the Accessible Resource for Integrated Epigenomic Studies (ARIES) project, part of the larger Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Cord blood methylation (N=702) was used as a negative control for potential pre-natal residual confounding.

Results

Two differentially-methylated sites presented directionally-consistent associations with breastfeeding at ages 7 and 15-17, but not at birth. Twelve differentially-methylated regions in relation to breastfeeding were identified, and for three of them there was evidence of directional concordance between ages 7 and 15-17, but not between birth and age 7.

Conclusions

Our findings indicate that DNA methylation in childhood and adolescence may be predicted by breastfeeding, but further studies with sufficiently large samples for replication are required to identify robust associations.
raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML
Authors: Edler Daniel , Klein Johannes , Antonelli Alexandre , Silvestro Daniele
Published: October 2019

RaxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to set up and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML and built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML Next Generation. RaxmlGUI facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.