bluuebunny/crossref_metadata_2025 huggingface dataset:
New interpretation and techniques of transcreation
Authors: Du Chen
Published: July 2020

This article points out some “loopholes” in the traditional Chinese-English translation theories, and proposes
several transcreation theories to countermeasure the “loopholes”, illustrating non-equivalences. In particular, the article
proposes a novel translation/transcreation theory that incorporates the writing field, in both the source and target languages,
into the traditional translation field. This is for the purpose of cultural transmission and integration. In addition, the article
illustrates the relationship between translation and writing by dissecting the translation/transcreation process into two
processes: understanding and writing. Moreover, it suggests that the transcreation field develop some criteria, such as: fidelity,
flexibility and creativity, and that all the science, social science and humanities subareas in the transcreation field are
categorized according to these criteria. In order to support the transcreation theories and multidisciplinary translation theories
proposed in this article, some typical examples and transcreation techniques that push the envelope of existing transcreation
theories are provided. This article may shed new light on the limitations of, and possible solutions to, machine translation. It
may also answer questions like: “Is understanding unimportant to machine translation?”
The commitment to sustainable tourism and the development of indigenous tourism in Chile.
Authors: de la Maza Francisca , Calfucura Enrique
Published: July 2020

This chapter offers a critical analysis of tourism development policy in Chile. It specifically analyses the commitment of public policy to sustainability as a pillar of indigenous tourism and highlights the contradictions of tourism development under the country's economic model. It is acknowledged that there are contradictions between promotion of the indigenous world as part of what the country offers in terms of sustainable tourism and the difficulties in the political recognition of its indigenous peoples. The chapter documents that in various parts of the country tourism has developed massively and with little regulation, and that indigenous territories have become natural and cultural attractions with little control over their territories and implementation of their specific rights. It is concluded that it is difficult to put into practice a type of tourism that is governed by the principles of sustainability as well as the recognition of the needs and desires of the indigenous population.
Development and validation of an economical uric acid-Fe3+/Fe2+-ferrozine-based colorimetric assay to estimate uric acid level of pure and biological samples
Authors: Akram Maryam , Asghar Muhammad Nadeem , Saleem Khan Maria , Shahid Sammia , Abdur Rahman Hafiz Muhammad , Nadeem Iram
Published: July 2020

This work presents the development and validation of a simple, rapid, and cost-effective spectrophotometric method for quantitative analysis of uric acid in biological samples. The method relies upon uric acid-led reduction of Fe(III) to Fe(II) of sample/standard solutions which stoichiometrically engages ferrozine to form a magenta-colored complex. Different parameters including pH, metal and chelator concentrations, temperature, etc., were optimized for the maximum intensity and stability of the complex. The uric acid concentrations of synthetic/plasma solutions were determined by comparing the color intensity of Fe(ferrozine)32+ complex produced by test solution with the standard curve formed by known uric acid concentrations. The method was validated in accordance with ICH guidelines and subjected to human plasma analysis. The results obtained were compared with a reference (enzymatic) method which revealed that there was no significant difference between the two methods at 95% confidence level. The method is highly specific, precise, linear, accurate, and robust.
Sirtuin 6 protects human retinal pigment epithelium cells from LPS-induced inflammation and apoptosis partly by regulating autophagy
Authors: Liu Jingjing , Liu Dan
Published: July 2020

Lipopolysaccharides (LPS)-induced retinal inflammation is an important factor in retinal diseases. This study was aimed to investigate the effect of Sirt6 on LPS-induced retinal injury. ARPE-19 cells were incubated with LPS to induce inflammation. The cell viability was determined using CCK-8 assay. The mRNA level and protein expression of corresponding genes was detected using qRT-PCR and western blot, respectively. The production of inflammatory cytokines was measured using ELISA kit. The levels of oxidative stress-related factors were measured using their detection kits. Cell apoptosis was observed using TUNEL assay. The results showed that Sirt6 was downregulated after LPS treatment. Sirt6 strengthened LPS-induced autophagy by promoting the expression of LC3II/I, beclin1 and ATG5. Sirt6 treatment significantly inhibited LPS-induced inflammation, oxidative stress and cell apoptosis, which was then partly abolished by 3 MA. These results suggest Sirt6 to be an important regulator for LPS-induced inflammation, oxidative stress, and apoptosis partly by regulating cell autophagy.
Spin-bath polarization via disentanglement
Authors: Rao D D Bhaktavatsala , Ghosh Arnab , Gelbwaser-Klimovsky David , Bar-Gill Nir , Kurizki Gershon
Published: July 2020

The occurrence of any physical process is restricted by the constraints imposed by the laws of thermodynamics on the energy and entropy exchange involved. A prominent class of processes where thermodynamic constraints are crucial involve polarization of nuclear spin baths that are at the heart of magnetic resonance imaging, nuclear magnetic resonance (NMR), quantum information processing. Polarizing a spin bath, is the key to enhancing the sensitivity of these tools, leading to new analytical capabilities and improved medical diagnostics. In recent years, significant effort has been invested in identifying the far-reaching consequences of quantum modifications to classical thermodynamics for such processes. Here we focus on the adverse role of quantum correlations (entanglement) in the spin bath that can impede its cooling in many realistic scenarios. We propose to remove this impediment by modified cooling schemes, incorporating probe-induced disentanglement or, equivalently, alternating non-commuting probe–bath interactions to suppress the buildup of quantum correlations in the bath. The resulting bath polarization is thereby exponentially enhanced. The underlying quantum thermodynamic principles have far-reaching implications for a broad range of quantum technological applications.
Visible-light all-fiber vortex lasers based on mode selective couplers*
Authors: Dong Chuchu , Zou Jinhai , Wang Hongjian , Yao Han , Zeng Xianglong , Bu Yikun , Luo Zhengqian
Published: July 2020

We demonstrate visible-light all-fiber vortex lasers by incorporating the home-made mode selective couplers (MSCs). The MSC at green or red wavebands is fabricated by specially designing and fusing a single-mode fiber (SMF) and a few-mode fiber (FMF). The MSCs inserted into visible fiber cavities act as power splitters and mode converters from the LP01 to LP11 mode at green and red wavelengths, respectively. The red-light all-fiber vortex laser is formed by a 10-cm Pr3+/Yb3+:ZBLAN fiber, a fiber Bragg grating, a fiber end-facet mirror and the MSC at 635 nm, which generates vortex beams with OAM±1 at 634.4 nm and an output power of 13 mW. The green-light all-fiber vortex laser consists of a 12-cm Ho3+:ZBLAN fiber, two fiber pigtail mirrors, and the MSC at 550 nm, which generates vortex beams with OAM±1 at 548.9 nm and an output power of 3 mW.
Determination of Ethanol in a Distillate Sample of Arenga pinnata by UV-Visible Spectrophotometry
Authors: Febriani Y , Ihsan E A
Published: July 2020

This research aimed to determinate ethanol in a distillate sample of Arenga pinnata. We have determined, by the means of spectrophotometer UV/VIS, ethanol contained by the distillation process of a series of samples. The results of these researches will analyse the ethanol contained in a distillate sample, qualitatively. Experiment method with 12 samples of Arenga pinnata series has been done. The samples found by varying day of the fermentation process and continued with the distillation process. Further, a distillate sample has been measured by UV-VIS Spectrophotometry. Wavelength 277 nm found as maximum wavelength with absorbance range (0.1 A-0.5 A). Samples in day 2nd to day 17th have these data. This means that a sample in day 2nd to day 17th of samples contained ethanol. Furthermore, the percentage of ethanol in a series of samples and the pharmacology effect of palm sugar as hypoglycaemic are still investigating in this research.
Design and Development of Automotive Workshop Application Based on Android and IOS Using Dart Programming Language
Authors: Candra P Baiq Andriska , Ahmad Ramli
Published: July 2020

During this time, most vehicle service can only be done in a garage where every customer who wants to make repairs to them vehicle must bring the vehicle directly to the service shop. Under these conditions it need the use of the latest technology that can facilitate two-way communication between vehicle service providers with consumers. The solution offered in this study is in the form of applications based on Android and IOS that are connected to the internet and GPS (Global Positioning System) for vehicle repair services. With the development of the application services can be done anywhere, and users who need services can easily find out the nearest location of the vehicle service to the point of position of consumers at that real time. With the existence of this application the user does not have to go to the vehicle service shop, but the service can be done at the office, at home even in an emergency on the road though. So the application making it easier to service the user’s vehicle also helped in terms of time.
The Development of E-Learning Use MOODLE as A Multimedia Learning Medium
Authors: Arianti Baiq Desi Dwi , Kholisho Yosi Nur , Sujatmiko Sigit Budi
Published: July 2020

The success of a nation lies in the quality of education that can improve the quality of its human resources. We need human resources who can respond to the development of science and technology. There are many supporting factors to enhance the quality of education; one of them is the use of science and technology. One of the technology utilization in education is using E-learning as a learning medium. Using E-learning in vocational schools is very lacking. Therefore, it is necessary to develop an E-learning as a learning medium for a vocational school. This research aims to develop learning medium using Moodle as a development platform. We use Research and Development (R&D) as a development model. This study focusing on phase 4 (Design validation) of R&D model, two experts involved to validating this product. The results of the validation by experts show that the product qualifies for the next level, with a feasibility percentage of 74.33%.
Implementation of simplex algorithm to optimize toddler’s balanced nutrition needs with minimum costs
Authors: Ruhimat Q A A , Riftana R J , Dharmawan T
Published: July 2020

Nutrition is an important element needed by humans, including toddlers. The unfulfilled nutritional needs can cause several diseases, such as malnutrition and stunting. It was caused because of human inability to fullfill the nutrition needs of all family members with good quality and the lack of parental knowledge about nutritious food ingredients and how to feed properly. It is necessary to optimize the fulfillment of food nutrition for infants with a minimum cost. One of the efforts is to make the right combination of food ingredients with cost minimum so that it can be reached by all levels of society. This research was analyzed using Simplex algorithm with QM for Windows software. The results was obtained in the form of the amount of food that can be consumed by user to fullfill the nutritional intake needs along with the minimum cost.
Learning Device Development with Cooperative Model Of Productive Creative Type To Improve Students’ Motivation
Authors: Hayati Nila , Marlita Linda , Waluyo Edy
Published: July 2020

This study aims to produce mathematical learning tools with a productive creative type cooperative model to increase motivation and mathematical ability of students of class VIII SMP that are valid, practical, and effective. This type of research is development research. This research develops learning tools including Learning Implementation Plan (RPP), Student Worksheet (LKPD), and Learning Outcomes Test (THB) by using the ADDIE development model (Analysis, Design, Development, Implementation, and Evaluation). The research subjects were students of class VIII MTs. NW Lepak. Data analysis was performed by converting the total actual scores obtained into five scale qualitative data. From the results of expert validation, teacher assessment scores, student assessments, and learning achievement tests show that the learning tools developed are valid, effective, and practical.
Use of Information Technology Media on Physical Activities of Students
Authors: Suryansah  , Hariadi  , Suryadi Lalu Erpan
Published: July 2020

Where physical activity is very important for the health of every human being in carrying out daily activities as well as unexpected activities. Activities that are less mobile due to too often playing the virtual world such as online and offline games, internet, watching television too much will lead to the risk of obesity / obesity. Overweight / obesity is considered as a frightening specter and risk factors for various diseases, such as heart disease, hypertension and many others. One effort that is considered to reduce the risk of obesity is to increase physical activity. Physical activity is not only limited to special sports activities, but also other activities that require physical work, such as cleaning the house, sweeping, mopping, washing, walking, dancing, painting, hoeing, walking and so on. This study aims to determine whether there is an influence and how much information technology users on the physical activity of students of SMAN 1 Mantang. This research is a non-experimental research. The subjects in this study were students of class X SMAN 1 Mantang by using cluster random sampling consisting of 5 classes with a total poulasi of 141 students / students categorized as 69 male students and 72 female students. And from the cluster random sampling results obtained 5 classes with a total sample of 100 students. From the results of statistical calculations, it can be concluded that there is no significant effect between the use of information technology on students’ physical activities. Because the data testing carried out shows that r count is smaller than r count table (-.717)> r table (0.197).
The Comparison of Cooperative Learning Method of Rotating Trio Exchange Type and Think Pair Share Type
Authors: Gazali Muhammad , Haiban Hirzi Ristu
Published: July 2020

This study aimed to know which gave better learning outcomes between Rotating Trio Exchange (RTE) and Think Pair Share (TPS) cooperative learning methods on student mathematics learning outcomes. This research used the experiment method. The population in this research was all VII grade students of MTs NW Ketangga Suela in the 2018/2019 school year. The technique of random sampling determined the research sample. Grade of VII-B of MTs NW Ketangga Suela as the experiment class, meanwhile VII-C grade of MTs NW Ketangga Suela as the experiment class 2. The research design used was Randomized Post test Only Comparison Group Design. Data collection technique used learning result test. The data were analyzed using the two-party t test with pollen variants method, Hypothesis results showed that thitung > ttabel that was (4,513> 2,074) namely that Ho is rejected and Ha is accepted, So it could be concluded that there was a difference between the Rotating Trio Exchange (RTE) learning method and the Think Pair Share (TPS) method. Based on the average got, the Rotating Trio Exchange (RTE) method with an average of 77,661 had better learning achievement than the Think Pair Share (TPS) method with an average of 71,217.
The Influence of Audio Visual Based Learning Media on Learning Temboyak Dance
Authors: Hafiz Alwan , Kaelani Aswan
Published: July 2020

The aims of this research is to find out whether there were significant differences between student achievement which is taught using a visual audio media with student achievement in teaching without using media audio visual media in learning pemboyaq dance for VIII grade student in junior high school 2 Keruak in the 2016/2017 academic year. This is an actual experimental research which conducted at class VIII grade in junior high school that consist of 5 classes. The sample in this research were student of class VIII.1 as an experimental group with 28 students consist of 12 boys and 16 girls, and class VIII.2 as a control group with 26 students consist of 11 boys and 15 girls. The sampling technique with random sampling and data analysis using inferential statistic. The test results using statistic obtained number which shows that t-count > t-table or (2.247) > t-table value (2.0095). This hypothesis proposed in chapter II is acceptable. Thus, there is an influence on pemboyaq dance for eight grade students in junior high school.
Exploring Students Mental Computing Based On Number Sense At 7thGrade Junior High School In Ponorogo
Authors: Marga S A , Kusmayadi T A , Fitriana L
Published: July 2020

The ability of number sense possessed by students will affect the performance of these students in determining the strategies used in solving a mathematical problem. Students who have a good number sense will show the mental characteristics of computing possessed. According to Markovits and Shower (1994), there are four levels of mental computation in the way students of solving numbers problems, namely: standard, transition, non-standard without reformulation, and non-standard with reformulation. Therefore this study aims to categorize how to answer students in solving numbers problems based on the ability of number sense possessed. This type of research is descriptive qualitative. Subjects selection use the purposive sampling method obtained three subjects that represent the number sense category owned by students. The results of this research indicate the students who have high number sense abilities tend to have computational mental with non-standard categories with reformulation while students who have medium and low number sense abilities tend to have standard category mental computation.
Advancing Learning Math Industry Era 4.0
Authors: Mahmudah Rifa’atul , Yazid Muh.
Published: July 2020

The emergence of the industrial era 4.0 is a challenge in welcoming and preparing mathematics learning. The purpose of this study was to determine the components in welcoming mathematics learning in the industrial era 4.0. This type of research uses descriptive qualitative with the method used is the study of literature/literature review from 2012 to 2019. From the results of the literature review, it is concluded that there are 3 components in welcoming mathematics learning in the industrial era 4.0. 1) HR Literacy, covering aspects; critical thinking, creative thinking, reflective thinking, mathematical imagination, mathematical reasoning, mathematical communication, and problem-solving. 2) Data literacy, including system aspects cyber-physical, internet of things, cognitive computing, and cloud computing. 3)Technology literacy, including aspects; Technology for doing mathematics, Technology for practicing skills, and Technology for developing conceptual understanding.
High School Students’ Responses in Solving Linear Program Problems Based on SOLO Taxonomy Viewed from Mathematical Disposition
Authors: Claudia L F , Kusmayadi T A , Fitriana L
Published: July 2020

In mathematics learning, students need a cognitive domain that is supported by an equivalent affective domain. One of the factors students can master or like math is that they must have an interest and curiosity in learning mathematics. Interest of students can solve mathematics problems more efficiently. The combination of affinity and interest in learning mathematics will form a positive attitude which is often called a mathematical disposition. Mathematical disposition is students’ beliefs and attitudes about mathematics that support the tendency to see mathematics as reasonable and useful as well as the role he or she believes diligence plays in solving mathematical tasks. SOLO taxonomy can be classified into five levels ranging from simple to high levels, pre-structural, uni-structural, multi-structural, relational, and extended abstract. This study uses descriptive qualitative research that has the purpose of describing level response of students who have high, medium, and low mathematical disposition categories. The subjects in this study were senior high school students in the City of Kediri with a purposive sampling technique in a class of 35 students and obtained three subjects which represent every category of mathematical disposition. The results of this study are (1) Student with high mathematical disposition is at the extended abstract level, (2) Student with medium mathematical disposition is at the multi-structural level, (3) Student with low mathematical disposition is at the pre-structural level.
No perfect storm for crop yield failure in Germany
Authors: Webber Heidi , Lischeid Gunnar , Sommer Michael , Finger Robert , Nendel Claas , Gaiser Thomas , Ewert Frank
Published: July 2020

Large-scale crop yield failures are increasingly associated with food price spikes and food insecurity and are a large source of income risk for farmers. While the evidence linking extreme weather to yield failures is clear, consensus on the broader set of weather drivers and conditions responsible for recent yield failures is lacking. We investigate this for the case of four major crops in Germany over the past 20 years using a combination of machine learning and process-based modelling. Our results confirm that years associated with widespread yield failures across crops were generally associated with severe drought, such as in 2018 and to a lesser extent 2003. However, for years with more localized yield failures and large differences in spatial patterns of yield failures between crops, no single driver or combination of drivers was identified. Relatively large residuals of unexplained variation likely indicate the importance of non-weather related factors, such as management (pest, weed and nutrient management and possible interactions with weather) explaining yield failures. Models to inform adaptation planning at farm, market or policy levels are here suggested to require consideration of cumulative resource capture and use, as well as effects of extreme events, the latter largely missing in process-based models. However, increasingly novel combinations of weather events under climate change may limit the extent to which data driven methods can replace process-based models in risk assessments.
Structure factors and x-ray diffraction intensities in molten alkali halides
Authors: Abramo Maria C , Costa Dino , Malescio Gianpietro , Munaò Gianmarco , Pellicane Giuseppe , Prestipino Santi , Caccamo Carlo
Published: July 2020

We show by extensive molecular dynamics simulations that rather accurate predictions of structure factors and x-ray diffraction intensities of molten alkali halides can be achieved in terms of the Born-Huggins-Mayer-Fumi-Tosi rigid ion potential description of these systems. Specifically, the partial structure factors of six ionic melts, namely NaCl, RbCl, LiCl, LiF, NaF and KF, are computed by Fourier inversion of the radial distribution functions obtained from simulation; the x-ray diffraction intensity is then obtained from the calculated partial structure factors. We perform a comparison between the molecular dynamics results and the experimental data obtained via neutron and/or x-ray diffraction. We also determine the total number density and total charge structure factors and document that, in all the salts examined, the peaks in the x-ray intensities fall at wavevectors practically coincident with those of the partial and total structure factors. We then show how to improve upon some limits emerging in the adopted model when applied to molten fluorides. We finally comment on the opportunity to extend to other molten alkali halides, for which experimental x-ray diffraction intensities are available, the assessment of structural predictions according to the scheme outlined here.
Time-dependent relaxation of observables in complex quantum systems
Authors: Volya Alexander , Zelevinsky Vladimir
Published: July 2020

We consider time-dependent relaxation of observables in quantum systems of chaotic and regular type. Using statistical arguments and exact numerical solutions we show that the spread of the initial wave function in the Hilbert space and the main characteristics of evolution of observables have certain generic features. The study compares examples of regular dynamics, a completely chaotic case of the Gaussian orthogonal ensemble, a bosonic system with random interactions, and a fully realistic case of the time evolution of various initial non-stationary states in the nuclear shell model. In the case of the Gaussian orthogonal ensemble we show that the survival probability obtained analytically also fully defines the relaxation timescale of observables. This is not the case in general. Using the realistic nuclear shell model and the quadrupole moment as an observable we demonstrate that the relaxation time is significantly longer than defined by the survival probability of the initial state. The full analysis does not show the presence of an analog of the Lyapunov exponent characteristic for examples of classical chaos.
Chimera states formed via a two-level synchronization mechanism
Authors: Provata A
Published: July 2020

We introduce an oscillatory toy-model with variable frequency governed by a 3rd order equation to shed light on the formation of chimera states in systems of coupled oscillators. The toy-oscillators are constructed as bistable units and depending on the initial conditions their frequency may result in one of the two attracting fixed points,

and

(two-level synchronization). Numerical simulations demonstrate that when these oscillators are nonlocally coupled in networks, they organize in domains with alternating frequencies. In each domain the oscillators synchronize, while sequential domains follow different modes of synchronization. The border elements between two consecutive domains form the asynchronous domains as they are influenced by both frequencies. This way chimera states are formed via a two-level synchronization scenario. We investigate the influence of the frequency coupling constant and of the coupling range on the chimera morphology and we show that the chimera multiplicity decreases as the coupling range increases.

The frequency spectrum is calculated in the coherent and incoherent domains of this model. In the coherent domains single frequencies (

or

) are observed, while in the incoherent domains both

and

as well as their superpositions appear. This mechanism of creating domains of alternating frequencies offers a reasonable generic scenario for chimera state formation.
Effect of Mg doping on the improvement of photoluminescence and magnetic properties of NiO nanoparticles
Authors: Panigrahi U K , Sathe V , Babu P D , Mitra A , Mallick P
Published: July 2020

NiO nanoparticles doped with different concentration of Mg were synthesized by a low cost wet chemical method. XRD characterization indicated that the fcc structure of NiO is not affected with Mg doping. TEM analysis further reveals the Mg doping induced reduction in grain agglomeration along with the spherical shape transformation in NiO. Significant enhancement of UV emission in Mg doped NiO nanoparticles is evident from photoluminescence characterization. Magnetic characterization of the samples showed that all the samples show weak ferromagnetism along with the dominance of background antiferromagnetism at room temperature. The perseverance of background antiferromagnetic order is further probed through Raman characterization. All the samples show first order antiferromagnetic to weak ferromagnetic transition along with the presence of shape memory effect as evident by the negative slope in Arrott plot. The Ni0.9Mg0.1O sample with much enhanced UV emission and magnetization could find the usefulness in UV optoelectronic device, spintronic device etc.
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities
Authors: Zhang He , Zhang Liang , Mathews David H , Huang Liang
Published: July 2020

Motivation

RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more severe than cubic-time free energy minimization due to a substantially larger constant factor in runtime.

Results

Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna RNAfold and CONTRAfold (e.g. 2.5 days versus 1.3 min on a sequence with length 32 753 nt). More interestingly, the resulting base-pairing probabilities are even better correlated with the ground-truth structures. LinearPartition also leads to a small accuracy improvement when used for downstream structure prediction on families with the longest length sequences (16S and 23S rRNAs), as well as a substantial improvement on long-distance base pairs (500+ nt apart).

Availability and implementation

Code: http://github.com/LinearFold/LinearPartition; Server: http://linearfold.org/partition.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting mechanism of action of cellular perturbations with pathway activity signatures
Authors: Ren Yan , Sivaganesan Siva , Clark Nicholas A , Zhang Lixia , Biesiada Jacek , Niu Wen , Plas David R , Medvedovic Mario
Published: July 2020

Motivation

Misregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures (TSeses) a difficult problem.

Results

We developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the Library of Integrated Network-based Cellular Signature TSes of genetic perturbations of pathway genes and the TS of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only the TS of the perturbation fail.

Availability and implementation

Open source R package paslincs is available at https://github.com/uc-bd2k/paslincs.

Supplementary information

Supplementary data are available at Bioinformatics online.
Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples
Authors: Ilieva Nina I , Galvanetto Nicola , Allegra Michele , Brucale Marco , Laio Alessandro
Published: July 2020

Motivation

Single-molecule force spectroscopy (SMFS) experiments pose the challenge of analysing protein unfolding data (traces) coming from preparations with heterogeneous composition (e.g. where different proteins are present in the sample). An automatic procedure able to distinguish the unfolding patterns of the proteins is needed. Here, we introduce a data analysis pipeline able to recognize in such datasets traces with recurrent patterns (clusters).

Results

We illustrate the performance of our method on two prototypical datasets: ∼50 000 traces from a sample containing tandem GB1 and ∼400 000 traces from a native rod membrane. Despite a daunting signal-to-noise ratio in the data, we are able to identify several unfolding clusters. This work demonstrates how an automatic pattern classification can extract relevant information from SMFS traces from heterogeneous samples without prior knowledge of the sample composition.

Availability and implementation

https://github.com/ninailieva/SMFS_clustering.

Supplementary information

Supplementary data are available at Bioinformatics online.
Adaptive multiorientation resolution analysis of complex filamentous network images
Authors: Kittisopikul Mark , Vahabikashi Amir , Shimi Takeshi , Goldman Robert D , Jaqaman Khuloud
Published: July 2020

Motivation

Microscopy images of cytoskeletal, nucleoskeletal and other structures contain complex junctions of overlapping filaments with arbitrary geometry. Yet, state-of-the-art algorithms generally perform single orientation analysis to segment these structures, resulting in gaps near junctions, or assume particular junction geometries to detect them.

Results

We developed a fully automated image analysis approach to address the challenge of determining the number of orientations and their values at each point in space to detect both lines and their junctions. Our approach does not assume any fixed number of orientations or any particular geometry in the case of multiple coincident orientations. It is based on analytically resolving coincident orientations revealed by steerable ridge filtering in an adaptive manner that balances orientation resolution and spatial localization. Combining this multiorientation resolution information with a generalization of the concept of non-maximum suppression allowed us to then identify the centers of lines and their junctions in an image. We validated our approach using a wide array of synthetic junctions and by comparison to manual segmentation. We also applied it to light microscopy images of cytoskeletal and nucleoskeletal networks.

Availability and implementation

https://github.com/mkitti/AdaptiveResolutionOrientationSpace.

Supplementary information

Supplementary information is available at Bioinformatics online.
In Their Own Words: Gene E. Likens
Authors: Verdier James M
Published: July 2020

In Their Own Words chronicles the stories of scientists who have made great contributions to their fields, particularly within the biological sciences. These short oral histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and on our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This oral history is with Dr. Gene E. Likens, emeritus president of the Cary Institute of Ecosystem Studies and a distinguished professor at the University of Connecticut. He also served as president of the American Institute of Biological Sciences.

Note: Both the text and audio versions have been edited for clarity and length.
An International Prospective Cohort Study To Validate 2 Prediction Rules for Infections Caused by Third-generation Cephalosporin-resistant Enterobacterales
Authors: Deelen J W Timotëus , Rottier Wouter C , Giron Ortega José A , Rodriguez-Baño Jesús , Harbarth Stephan , Tacconelli Evelina , Jacobsson Gunnar , Zahar Jean-Ralph , van Werkhoven Cornelis H , Bonten Marc J M ,   ESBL-PREDICT Study Team
Published: July 2020

Background

The possibility of bloodstream infections caused by third-generation cephalosporin-resistant Enterobacterales (3GC-R-BSI) leads to a trade-off between empiric inappropriate treatment (IAT) and unnecessary carbapenem use (UCU). Accurately predicting 3GC-R-BSI could reduce IAT and UCU. We externally validate 2 previously derived prediction rules for community-onset (CO) and hospital-onset (HO) suspected bloodstream infections.

Methods

In 33 hospitals in 13 countries we prospectively enrolled 200 patients per hospital in whom blood cultures were obtained and intravenous antibiotics with coverage for Enterobacterales were empirically started. Cases were defined as 3GC-R-BSI or 3GC-R gram-negative infection (3GC-R-GNI) (analysis 2); all other outcomes served as a comparator. Model discrimination and calibration were assessed. Impact on carbapenem use was assessed at several cutoff points.

Results

4650 CO infection episodes were included and the prevalence of 3GC-R-BSI was 2.1% (n = 97). IAT occurred in 69 of 97 (71.1%) 3GC-R-BSI and UCU in 398 of 4553 non–3GC-R-BSI patients (8.7%). Model calibration was good, and the AUC was .79 (95% CI, .75–.83) for 3GC-R-BSI. The prediction rule potentially reduced IAT to 62% (60/97) while keeping UCU comparable at 8.4% or could reduce UCU to 6.3% (287/4553) while keeping IAT equal. IAT and UCU in all 3GC-R-GNIs (analysis 2) improved at similar percentages. 1683 HO infection episodes were included and the prevalence of 3GC-R-BSI was 4.9% (n = 83). Here model calibration was insufficient.

Conclusions

A prediction rule for CO 3GC-R infection was validated in an international cohort and could improve empirical antibiotic use. Validation of the HO rule yielded suboptimal performance.
From micro- to macroevolution: brood parasitism as a driver of phenotypic diversity in birds
Authors: Medina Iliana , Kilner Rebecca M , Langmore Naomi E
Published: July 2020

A fundamental question in biology is how diversity evolves and why some clades are more diverse than others. Phenotypic diversity has often been shown to result from morphological adaptation to different habitats. The role of behavioral interactions as a driver of broadscale phenotypic diversity has received comparatively less attention. Behavioral interactions, however, are a key agent of natural selection. Antagonistic behavioral interactions with predators or with parasites can have significant fitness consequences, and hence act as strong evolutionary forces on the phenotype of species, ultimately generating diversity between species of both victims and exploiters. Avian obligate brood parasites lay their eggs in the nests of other species, their hosts, and this behavioral interaction between hosts and parasites is often considered one of the best examples of coevolution in the natural world. In this review, we use the coevolution between brood parasites and their hosts to illustrate the potential of behavioral interactions to drive evolution of phenotypic diversity at different taxonomic scales. We provide a bridge between behavioral ecology and macroevolution by describing how this interaction has increased avian phenotypic diversity not only in the brood parasitic clades but also in their hosts.
Case report of an isolated myocarditis due to COVID-19 infection in a paediatric patient
Authors: Fischer Quentin , Brillat-Savarin Nina , Ducrocq Grégory , Ou Phalla
Published: July 2020

Background

Cardiovascular complications of COVID-19 have been reported in the adult population including myocarditis. However, less is known about the myocardial involvement in paediatric patients.

Case summary

A 15-year-old boy was admitted to our intensive cardiac care unit with COVID-19 and an isolated acute myocarditis, confirmed on cardiac magnetic resonance imaging. No pulmonary lesion was observed on the chest CT scan. We report here the initial presentation, medical care, and clinical course of this patient.

Discussion

In the context of the acute COVID-19 outbreak, screening for COVID-19 infection should be performed in children presenting with myocardial injury in an inflammatory context.
Cost-utility of ticagrelor plus aspirin in diabetic patients with stable coronary artery disease
Authors: Wu Bin , Shi Lizheng
Published: July 2020

Aims

Ticagrelor plus aspirin could reduce the risks of major adverse cardiac events in diabetic patients with stable coronary artery disease (SCD), and yet it also increases bleeding risk. This study would compare the cost and effectiveness of aspirin and ticagrelor plus aspirin therapies in diabetic patients with SCD from a US healthcare sector perspective.

Methods and results

A state-transition Markov model was developed to project probabilities of myocardial infarction, ischaemic stroke, bleeding, and death with and without ticagrelor among all diabetic patients with SCD as the overall population, and those with a history of previous percutaneous coronary intervention (PCI) as a sub-population. Model inputs were extracted from published sources. Lifetime costs and quality-adjusted life-years (QALYs) were measured. The clinical benefits and bleeding risk of ticagrelor added to aspirin were translated into additional 0.08 QALYs at incremental costs of $19 580 in the overall population, yielding an incremental cost-utility ratio (ICUR) of $260 032/QALY. In the sub-population with an additional 0.43 QALYs at an incremental cost of $20 189, the ICUR was $46 426/QALY. Two-way sensitivity showed the clinical benefits of ticagrelor plus aspirin was counterbalanced by its risk of major bleeding. One-way sensitivity and probabilistic sensitivity analysis demonstrated that the results were generally robust except the all-cause death reduction.

Conclusion

The results indicated that ticagrelor plus aspirin is likely to be a cost-effective option in the diabetic patients with a history of PCI. Diabetes management can be improved by carefully prescribing ticagrelor to individuals with low risk of bleeding and high risk of ischaemic events.
Anatomical feasibility of a new off-the-shelf inner branch stent graft (E-nside) for endovascular treatment of thoraco-abdominal aneurysms
Authors: Bilman Victor , Cambiaghi Tommaso , Grandi Alessandro , Carta Niccolò , Melissano Germano , Chiesa Roberto , Bertoglio Luca
Published: July 2020

OBJECTIVES

The aim of this study was to evaluate the proportion of thoraco-abdominal aortic aneurysms (TAAAs) that could theoretically be treated with the JOTEC® E-nside® Thoracoabdominal Branch Endoprosthesis off-the-shelf multibranched endograft.

METHODS

Preoperative computed tomography scans of patients with atherosclerotic TAAA treated between 2007 and 2019 were reviewed, and the anatomical feasibility of the E-nside graft was verified by a retrospective study (clinicaltrials.gov: NCT03959670) based on the investigational manufacturer instructions for use. The anatomical factors determining overall feasibility were divided into vascular access (AC) feasibility, aortic (AO) feasibility and visceral vessels (VV) feasibility.

RESULTS

Two hundred sixty-eight patients with thoraco-abdominal aneurysms were analysed: the overall treatment feasibility was 43%. AC feasibility was 78%, AO feasibility 60% and VV feasibility 79%. An iliac diameter <8.5 mm excluded 21% of the patients. Aortic feasibility was limited by infrarenal aortic diameter (16%) and size of aortic lumen at the level of visceral vessels (14%). Visceral vessels feasibility was mainly limited by inadequate number (8%) or diameter (12%) of target vessels. Height and orientation of target vessels were adequate in 97% of the cases. Overall feasibility was negatively influenced by female gender (Odds ratio: 3.89; 95% confidence interval 2.03–7.44; P < 0.001): the limiting factors in this subgroup being iliac diameter, infrarenal aortic diameter and visceral vessels diameter.

CONCLUSIONS

The E-nside off-the-shelf stent graft can be theoretically employed in almost half of the cases from an all-comers cohort of patients with TAAA. Improvement of device profile and creation of a dedicated infrarenal component are warranted to increase overall feasibility. Female gender significantly affects the overall feasibility.

Clinicaltrials.gov

NCT03959670.
Differences in substrate use linked to divergent carbon flow during litter decomposition
Authors: Albright Michaeline B N , Thompson Jaron , Kroeger Marie E , Johansen Renee , Ulrich Danielle E M , Gallegos-Graves La Verne , Munsky Brian , Dunbar John
Published: July 2020

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.
Liver microRNA-29b-3p positively correlates with relative enhancement values of magnetic resonance imaging and represses liver fibrosis
Authors: Gong Xijun , Wang Xiaolin , Zhou Fangfang
Published: July 2020

This study aims to identify potential microRNAs (miRNAs) contribute to liver fibrosis progression and investigate how the miRNA is involved. We recruited totally 58 patients. Magnetic resonance imaging was employed to detect fibrosis. Classification of liver fibrosis was carried out by Ishak scoring system. Cell viability was tested using cell counting kit-8. Measurements of mRNA and protein expressions were conducted using real-time quantitative polymerase chain reaction and western blotting. Luciferase reporter assay was recruited for determination of miR-29b-3p targets. We found that relative enhancement (RE) values were reduced with the increases in fibrosis stages and was negatively associated with Ishak scores. In comparison with patients without liver fibrosis, miR-29b-3p level was remarkably reduced in those with liver fibrosis. Its level was found to be positively associated with RE values. Transforming growth factor beta 1 (TGF-β1)-induced hepatic stellate cell (HSC) activation significantly decreased miR-29b-3p expression. However, miR-29b-3p overexpression repressed TGF-β1-induced collagen I protein and alpha-smooth muscle actin (α-SMA) expression. As expected, its overexpression also reduced cell viability. We found that miR-29b-3p directly bind to signal transducer and activator of transcription 3 (STAT3) and suppressed its expression. Our study demonstrates that low expression of miR-29b-3p may contribute to the progression of liver fibrosis by suppressing STAT3.