bluuebunny/crossref_metadata_2025 huggingface dataset:
Community Based Tourism for the Concept of Village Tourism Facility Development in Papan Island
Authors: Arief Irdinal , Thahir Harifuddin
Published: June 2020

Community based tourism can create employment opportunities for local communities, and reduce poverty, where tourism income is from tourist services to tourists. In the Planning of facilities and infrastructure is needed the concept of development with the location of the local natural environment. It to be developed must be integrated. At the stage of development of tourism facilities, as natural resources and man-made resources are absolutely needed by tourists in their travels in tourist destinations, such as: roads, electricity, water, telecommunications, terminals, bridges and so forth. With the pattern of community-based tourism does not mean that people will run their own tourism business. The level of tourism implementation should be seen as part of integrated development planning that will be carried out in Papan Island of Kadoda Village Talatakoh Subdistrict of Togean Islands, which is designated as the national tourism development and the regional tourism master plan of Tojo Una-Una Regency. One of the strategies is development of marine tourism attraction in Strategic area of National Togean Archipelago, consisting of 50 national tourism destinations. The following spatial concepts that actually include many studies in planning and architecture but this process has included analysis of community-based tourism.
Characterization of Liquid Volatile Matter Rice Husk Using Gas Chromatography
Authors: Ilmawati Wa Ode Sitti , Mashuni Muhammad Jahiding , Kinanti
Published: June 2020

Rice husk is one type of organic waste that has not been used optimally. Rice husks contain cellulose, hemicellulose and lignin, so they are potentially processed as liquids volatile matter (LVM). The purpose of this study was to determine the effect of pyrolysis temperature on the density and chemical composition of rice husk LVM. This study began with the collection of rice husks. Rice husk is dried and then heated with high temperature 400°C, 500°C, and 600°C. The heating temperature is maintained for 15 minutes, respectively. The process of pyrolysis of rice husk produces charcoal, tar, and smoke. Condensed smoke is called rice husk LVM. The density of rice husk LVM at each pyrolysis temperature is different, namely 0.416 g/cm3, 0.714 g/cm3, and 1.139 g/cm3. The rice husk LVM is characterized using gas chromatography. Characterization results showed that the chemical composition of rice husk LVM consisted of ammonia, propanone, acetic acid, hexane, furfural, phenol, etc.
Hybrid Method Analysis of Variance (ANOVA) and Loss Function to Analyzed Optimizing Composition of Fiber Baggase and Fly Ash
Authors: Laome Lilis , Hasbi Muh.
Published: June 2020

Research on the utilization of baggase fiber as a composite material has been done, but still has shortcomings in the composite material brilliance. Therefore, the use of baggase fiber combined with coal ash can be an alternative to make a composite material. The purpose of this research is to know the effect of baggase fiber composition and fly ash composition to tensile stress and bending stress. This paper discusses the application of Analysis of Variance (ANOVA) on composite material data. There are two variables measured are variable of tensile stress and variable of bending stress. The result obtained that there is influence composition of baggase fiber and composition of fly ash at tensile stress and bending stress. Furthermore, further tests using Tukey method showed that the different composition pairs significantly were 10% -30%, 10% -40% and 20% -40% in both compositions of the two variables studied. In the determination of loss function with Signal-to-Noise (SN) Ratio with larger-is-the-better criteria, the composition of 40% baggase fiber, 10% fly ash composition and 50% matrix can produce optimal tensile and bending strength.
Fuzzy Analysis to Determine Potential Catching Areas of Skipjack Tuna on Southeast Sulawesi Waters
Authors: Ningrum Ika Purwanti , Sari Jayanti Yusmah , Saputra Rizal Adi , Sutardi  , Yushar Ismail
Published: June 2020

Southeast Sulawesi is one of the catching fisheries bases in the Eastern Indonesia Region which deals directly with the Banda Sea. Skipjack Tuna (Katsuwonus pelamis) is classified as an important economic pelagic fish resource and is one of the export commodities. The existence of skipjack tuna is certainly influenced by the condition of the ocean. The parameters used in the analysis of the determination of skipjack fish catches are Sea Surface Temperature, the distribution of chlorophyll-a and catches. The purpose of this study was to analyze the catching area of skipjack fish around the waters of the Southeast Sulawesi. To determine of skipjack tuna fishing area is supported by Fuzzy Mamdani method. The results showed that the catching area of skipjack fish on the peak catching season in the waters around Southeast Sulawesi May was in position 03008’30.2 S / 122025’17.4 E to 03009’48.8 S / 122042’32.7 E. In June the potential area is at point 03009’47.4 S / 1220 41’02.3 E and on July potential area at point 03005’50.8 S / 122041’16.3 E.
Composition Chemistry And Distribution to Quality of Essential Oil From Rhizome E.elatior and E.calophyris By Gas Chromatography-Mass Spectrometry (GC-MS)
Authors: Aswan Muhammad , Arafah Nur , Sahidin I. , Imran  , Suryani  , Ngkoimani La Ode
Published: June 2020

The composition chemistry and distribution of essential oil from the rhizome of two plants family Zingiberaceae is Etlingera species include E.elatior and E.calophyris from South East Sulawesi. The aim of this study is to determine the chemical composition of rhizomes two plants and compared the contain essential oils of the rhizome. The rhizome of the plants was extracted by hydrodistillation and analyzed was by Gas Chromatography-Mass Spectrometry (GC-MS). The essential oils from rhizome E.elatior and E.calophyris had a different compound among, with 25 compounds for E.elatior and 27 compounds identified for E.calphyris. The rhizome of E.elatior had the highest yield essential oils are dodecanal (36,09 %) and Dodecanoic acid (15, 54 %) and rhizome of E.calophyris is n-Decanal (34, 09 %) and Dodecanoic acid (14,5 %) into the mayor compound. While the compound minor for E.elatior had the highest 2-Undecanon (0,61%) and 2-Tridicanon (0,51 %) and E.calophyris is (-) Caryophyllene oxide (0,95 %) and 2-Undecanon (0,71%).
Design of Prototype System for Monitoring Air Quality for Smart City Implementation
Authors: Koedoes Yuni Aryani , Jie Samuel , Anshari Nur Muh. Nadzirin , Bunyamin  , Astari Alwan
Published: June 2020

Air pollution can be caused by natural sources and human activity. Now many say the polluted air around us. Carbon monoxide (CO) and carbon dioxide (CO2) is a parameter for determining the quality of clean air and polluted. If levels of these two substances excessive inhaled by humans, can be detrimental to health. By using the Arduino Mega 2560, air quality monitoring system in this study using LM35 sensor to determine the temperature of the air, MQ-7 sensor to determine the levels of CO and sensor MQ-135 to determine the levels of CO2 that is in the room. Sensor MQ-7 will be equipped with red and green LED indicator as the level of air quality is polluted or not polluted. If the levels of CO < 5 ppm, the green LED turns on and vice versa CO > 5 ppm, the red LED lights up. Likewise, CO2 levels <350 ppm, the green LED turns on and vice versa CO> 350 ppm, the red LED lights up. Research and simulation results show that the system works well. In the application of smart city, one of the important parameters is the monitoring system, in this research will be designed air quality monitoring system for the application of smart city.
Dynamic Behavior of Human Tympanic Membrane Perforation Using Finite Element Method
Authors: Hidayat  , Sudarsono  , Othman Rozaini
Published: June 2020

Human tympanic membrane also known as an eardrum is a thin membrane that separtes the outer ear and middle ear. The tympanic membrance perforation can cause longer lasting hearing loss. The purpose of this research is to simulate the dynamic behavior of tympanic membrane perforation using finite element method. In this paper, two types analysis model, namely normal tympanic membrane and tympanic membrane perforation were developed. Firstly, the geometrics model of human tympanic membrane was generated by CAD Software (Solidworks) using physical properties reported by other researchers. Then, eigenvalue analysis was carried out to simulate the dynamic behavior of two types of human tympanic membrane. As for the boundary conditions of human tympanic membrane, torsional springs were used for the rotational motion around one axis of the local coordinate frame on the boundary of tympanic membrane. Finally, the simulation of dynamic behavior of two types of tympanic membrane were compared.
Effect of Current Density on Hardness of Low Carbon Steel Electroplated by Copper, Nickel and Copper-Nickel
Authors: Sudarsono  , Aminur  , Nurjannah Irma , Hidayat  , Othman Rozaini
Published: June 2020

Coating process of metal surface undergoes rapid development, especially in electroplating method. This study aims to investigate effect of current density on hardness of low carbon steel plates electroplated by copper, nickel and copper-nickel. Low carbon steel plate coated with copper, nickel and copper-nickel using electroplating process with current variation (6, 9, 12 A for copper coating), (2.5, 3.5, 5 for nickel coating) and (2.5, 3.5, 5, 6, 9, 12 A for copper-nickel coating). Electroplating time for the three processes is 20 minutes in 5-liter solution at temperature range of 55-60°C. The electroplated steel plates are characterized with micro vickers hardness test. The results of this study indicated that the highest hardness is 290 kg/mm2 for nickel coating at current density of 5 A. Contrary, the lowest hardness is 111 kg/mm2 in copper coating at current density of 12 A, while the hardness for copper-nickel coating is 252 kg/mm2 at current densities of 12 A and 5 A.
Analysis of Islamic Center Planning with Ecological Architecture Approach in Kendari City
Authors: Ratna Adelila Haksika Fisika , Nurjannah Irma
Published: June 2020

Indonesian religion plays an important role in people’s lives, based on Indonesian ideology, Pancasila. Kendari City is one of the cities in Indonesia, which majorities are Muslim. Year by year population of Muslim in Kendari City have increased, but the increase is not directly proportional with the existing means of worship, for example like Islamic Center. Basic from status, Islamic Center in Kendari City consists of two types, they are Islamic Private Center and Government Islamic Center. The Government Islamic Centre, located in Abdullah Silondae street, but the building has been destroyed and turn into Head Office of PT Bank Sultra. Therefore, it is necessary to plan a new Islamic Center building for the people in Kendari. The Islamic Center planning was designed by applying the Ecological Architecture approach. The method used is descriptive analysis carried out by collecting data, then analyzed based on the theory of ecological architecture. The results of the analysis are micro and macro site processing which has minimal impact with the environment, and the application of a rectangle as a form of building and the use of sloping roofs to cover buildings. This form can maximize the lighting and the building’s effect on the thermal comfort of the building user.
Application of Under-Frequency Relay (UFR) in Load Shedding Scheme for System Stability (A Case Study on PT. PLN Kendari)
Authors: Tachrir  , Jie Samuel , Bunyamin  , Djohar Abdul
Published: June 2020

A reliable electric power system must maintain its operation in stable conditions with the support of various protection system during normal operation or when a fault occurs. To minimize the frequency of blackouts in the system due to interference, transient conditions, or the increased load, this study simulated the load shedding scheme using under-frequency relays (UFR). The analysis was done in ETAP 12.6.0 software using the Transient Stability Analysis feature. In this simulation, discontinuation occurs in the CB (Circuit Breaker) generator which causes the generator to escape from the system in two conditions, namely Peak Load Time (PLT) and Off-Peak Load Time (OPLT). The study simulated scenarios where circuit breakers (CB) tripped due to a fault, which causing a power plant to be disconnected from the grid. The scenarios were simulated in two conditions, during the peak load and off-peak load. The results show that during the peak load, the simulated Load Shedding Scheme 1 to 3 was occurred on the frequency of 49.3918 Hz, 48.72 Hz, and 48.0195 Hz, respectively. The respective disconnected loads on Scheme 1 to 3 were 4.529 MW, 41.84MW, and 59,072 MW while the recovery times were 2.432 s, 0.081 s, and 0.626 s, respectively Meanwhile, in the off-peak load, the UFR tripped at the frequency of 49.3958 Hz, 48.5855 Hz, and 47.75 Hz, the disconnected loads were 3.652 MW, 30.627 MW, and 43.93 MW, and the recovery time were 2.934 s, 0.588 s, and 0.592 s for Load Shedding Scheme 1 to 3, respectively.
Space utilization optimization of new campus of Halu Oleo University
Authors: Hasan La Ode Amrul , Hartono Yudhi Dwi , Saleh Arif , Bahri Alim
Published: June 2020

The New Campus of Halu Oleo University (UHO) is one of the state universities included in the term of the largest university in Eastern Indonesia with an area of more than 252 Ha. Located in the central government development area, UHO’s New Campus has become an attractive campus, shown by the increasing number of prospective students from year to year. This increasing number causes the university to provide educating facilities as the main need. The existing buildings and future development projects have not considered the concept of good spatial planning. This threatens the availability of land, especially the availability of open space and also affects the arrangement of related elements such as vehicle circulation, building utilities, drainage systems and mechanical-electrical. The purpose of this research is to provide a recommendation about the design of the UHO campus spatial layout which optimizes 60% open space availability proportionally with a more directed structuring concept. This research employed a qualitative method and data was collected through questionnaires and observations. The results indicate that the current space utilization is not well arranged, therefore affects other elements. Through the concept of cluster eco, campus area will be more organized.
Evaluation of Bottom Ash Composition on Modified Hollow Brick Design with Sago Husk as Filler
Authors: Ornam Kurniati , Kimsan Masykur , Ngkoimani La Ode , Amri Siti Belinda , Santi  , Amsyar Syafrianto
Published: June 2020

Improvement of hollow brick models demands profound analysis in terms of their behavior on mechanical properties as some shape variations provide different characteristics on stress concentration. Additional waste filler i.e. sago husk and utilization of bottom ash are expected to deliver better results based on strength, weight and economic factor. This paper aims to analyze experimentally and analytically those 7 shapes variations of modified hollow bricks design with additional admixtures which consists 1,1% of sago husk and 4 composition of bottom ash i.e. 0%; 10%; 20%; and 25%. Some works were conducted in laboratory, and followed by mathematical stress analysis of hollow shape characteristics. The results show that 10 – 20% bottom ash composition share maximum value of compressive strength, with model 1 is the greatest (17.8 Mpa). Mathematical analysis provides similar results as well, where the stress concentration of model 1 was not amplified with subsequent hollow position. In conclusion, all model still appropriate to be utilized for housing, especially in element selection for lightweight bricks that meet the requirements for strength.
Indonesian License Plate Detection Using Morphological Operation
Authors: Pasrun Y P , Muchtar M , Basyarah A N , Noorhasanah
Published: June 2020

Technological developments have enabled the use of vehicle number plate recognition in various fields such as parking systems, e-toll payments, handling motor vehicle theft cases, traffic violations and so on. Vehicle number plate characteristics in each country have characteristics that are not the same. Each country has a standard numbering system in its writing method, colour, language and size of the license plate, so that to take the research standards for license plate numbers from other countries is not effective. Special research is needed in accordance with the format of the number plate used by the country, in this case Indonesia. This research applies simple method, morphological operations in detecting vehicle plates in Indonesia. Morphological results will be segmented to get the image of the plate character separately. The test results show that the method applied can provide a maximum accuracy of up to 100% on taking plate images with a distance of 1.5 meters.
Tribological behavior of borocarburized layer on low-carbon steel treated by double glow plasma surface alloying
Authors: Yang Zhengang , Liang Wenping , Miao Qiang , Ding Zheng , Zuo Shiwei
Published: June 2020

In this paper, the borocarburized layer was fabricated on the surface of low-carbon steel via double glow treatment to enhance the wear resistance. Benefited by the gradient structure of an outermost boride layer and inner carburized layer, the bonding strength of the protective coating was improved. The novel design improved the mechanical properties at the coating-substrate interface and extended the service life of the coating. The microstructure and composition of borocarburized layer were analyzed by SEM, XRD, XPS. The tribological properties of substrate and borocarburized layer under dry sliding against ZrO2 ball were investigated. The results indicated that borocarburized layer consisted of a 38 μm boride layer with main phase of Fe2B and a 75 μm carburized layer with main phase of Fe5C3. The microhardness of borocarburized layer emerged in gradient distribution attributed to the double glow plasma surface alloying technique, and the maximum value was around 1700 HV. In addition, the major wear mechanisms of low carbon steel were fatigue and abrasive wear, which transformed to abrasive and adhesive wear with the load increased. The wear mechanisms of borocarburized layer were abrasive and adhesive wear. During wear process, borocarburized layer with high hardness against ZrO2 ball due to the decreased real contact areas. Therefore, the borocarburized layer fabricated on low carbon steel enhanced the wear resistance effectively.
Salinity affects pH and lead availability in two mangrove plant species
Authors: Cabañas-Mendoza María del Refugio , Santamaría Jorge M , Sauri-Duch Enrique , Escobedo-GraciaMedrano Rosa María , Andrade José Luis
Published: June 2020

Some tropical coastal areas that include mangroves are highly polluted by heavy metals, where lead (Pb) is prevalent. Few studies document how environment affects soil physicochemical characteristics and the availability of heavy metals. This study evaluated how different salt concentrations influenced the accumulation of Pb in plants of Avicennia germinans and Laguncularia racemosa and how salinity modified the substrate pH. Under unsalted conditions, Pb accumulation occurred continuously, mainly in L. racemosa, which was more tolerant to its toxic effects. Salt led to a decreased Pb uptake by the roots and an increase in the substrate pH. In addition, salinity also caused an increase in the translocation of Pb to the leaves. Because L. racemosa was tolerant to Pb, this species could be a better candidate for possible remediation and restoration programs in mangrove areas.
Nematic liquid crystal/dimethylsulphoxide mixture based tuning condenser
Authors: Parveen Ariba , Varshney Depanshu , Prakash Jai
Published: June 2020

Here, we demonstrate experimentally the existence of temporally variable dielectric behavior of a nematic liquid crystal (NLC), the most widely used liquid crystal (LC) phase among all LCs materials, by mixing dimethylsulphoxide (DMSO) into former. The intermolecular interactions and nanosegregation of the molecular LC structures have influenced their self-assembly by mixing DMSO into it. We mainly examined the dielectric parameters such as dielectric permittivity, dielectric loss factor, and absorption/energy dissipation and observed that the NLC/DMSO mixture shows a nearly dielectric-conductor (D-C) transition as time passes. The presence of DMSO in this analysis was confirmed by Fourier transform infrared spectroscopy while time-dependent dielectric studies were carried out using dielectric spectroscopic techniques. The promising idea of showing D-C transition is truly proven that may open the possibilities for real-time variable and supercapacitors.
Graphite fabric reinforced PAEK composites by novel impregnation-co-film technique
Authors: Marathe Umesh , Padhan Meghashree , Bijwe Jayashree
Published: June 2020

High performance polymers such as Poly(ether ether ketone) (PEEK), Poly(aryl ether ketone) (PAEK), Poly(ether ketone ketone) (PEKK), etc exhibit high melting points, 343 °C, 373 °C and 338 °C respectively and very high melt viscosity. They do not have appropriate solvents, which could open the ways to process their fabric reinforced composites; by impregnation technique followed by compression molding. Film stacking and powder sprinkling are the only possible techniques, which lead to weak crossover points due to non-wetting by the resin and finally resulting in inferior mechanical and interfacial properties and high amount of voids. In order to solve these problems, a novel technique called impregnation-co-film (ICF) is explored in this work. Polyetherimide (PEI) (10 wt% in dichloromethane solution) pre-impregnated graphite fabric prepregs were used before applying film technique followed by compression molding. The study compares properties such as density, void content, flexural strength, impact strength, Interlaminar shear strength (ILSS), thermal stability (in air) and interface by field emission scanning electron microscopy for the composite prepared with film stacking technique and that by impregnation-co-film stacking technique. It was confirmed that the new ICF technique proved to be significantly promising than the older technique almost in all aspects with 120% improvement in ILSS, 127% in flexural strength and 200% decrease in void content.
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
Authors: Sarkar Hirak , Srivastava Avi , Bravo Héctor Corrada , Love Michael I , Patro Rob
Published: June 2020

Motivation

Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects.

Results

We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result.

Availability and implementation

Terminus is implemented in Rust, and is freely available and open source. It can be obtained from https://github.com/COMBINE-lab/Terminus.

Supplementary information

Supplementary data are available at Bioinformatics online.
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction
Authors: Stamboulian Moses , Guerrero Rafael F , Hahn Matthew W , Radivojac Predrag
Published: June 2020

Motivation

The computational prediction of gene function is a key step in making full use of newly sequenced genomes. Function is generally predicted by transferring annotations from homologous genes or proteins for which experimental evidence exists. The ‘ortholog conjecture’ proposes that orthologous genes should be preferred when making such predictions, as they evolve functions more slowly than paralogous genes. Previous research has provided little support for the ortholog conjecture, though the incomplete nature of the data cast doubt on the conclusions.

Results

We use experimental annotations from over 40 000 proteins, drawn from over 80 000 publications, to revisit the ortholog conjecture in two pairs of species: (i) Homo sapiens and Mus musculus and (ii) Saccharomyces cerevisiae and Schizosaccharomyces pombe. By making a distinction between questions about the evolution of function versus questions about the prediction of function, we find strong evidence against the ortholog conjecture in the context of function prediction, though questions about the evolution of function remain difficult to address. In both pairs of species, we quantify the amount of information that would be ignored if paralogs are discarded, as well as the resulting loss in prediction accuracy. Taken as a whole, our results support the view that the types of homologs used for function transfer are largely irrelevant to the task of function prediction. Maximizing the amount of data used for this task, regardless of whether it comes from orthologs or paralogs, is most likely to lead to higher prediction accuracy.

Availability and implementation

https://github.com/predragradivojac/oc.

Supplementary information

Supplementary data are available at Bioinformatics online.
Joint modeling and multiple comparisons with the best of data from a SMART with survival outcomes
Authors: Chao Yan-Cheng , Tran Qui , Tsodikov Alex , Kidwell Kelley M
Published: June 2020

A dynamic treatment regimen (DTR) is a sequence of decision rules that can alter treatments or doses based on outcomes from prior treatment. In the case of two lines of treatment, a DTR specifies first-line treatment, and second-line treatment for responders and treatment for non-responders to the first-line treatment. A sequential, multiple assignment, randomized trial (SMART) is one such type of trial that has been designed to assess DTRs. The primary goal of our project is to identify the treatments, covariates, and their interactions result in the best overall survival rate. Many previously proposed methods to analyze data with survival outcomes from a SMART use inverse probability weighting and provide non-parametric estimation of survival rates, but no other information. Other methods have been proposed to identify and estimate the optimal DTR, but inference issues were seldom addressed. We apply a joint modeling approach to provide unbiased survival estimates as a mechanism to quantify baseline and time-varying covariate effects, treatment effects, and their interactions within regimens. The issue of multiple comparisons at specific time points is addressed using multiple comparisons with the best method.
Appropriateness of Antibiotic Prescribing for Acute Sinusitis in Primary Care: A Cross-sectional Study
Authors: Truitt Katie N , Brown Tiffany , Lee Ji Young , Linder Jeffrey A
Published: June 2020

The proportion of sinusitis visits that meet antibiotic prescribing criteria is unknown. Of 425 randomly selected sinusitis visits, 50% (214) met antibiotic prescribing criteria. There was no significant difference in antibiotic prescribing at visits that did (205/214 [96%]) and did not (193/211 [92%]; P = .07) meet antibiotic prescribing criteria.
Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective
Authors: Bar-Yoseph Haggai , Carasso Shaqed , Shklar Shlomit , Korytny Alexander , Even Dar Razi , Daoud Haneen , Nassar Roni , Maharshak Nitsan , Hussein Khetam , Geffen Yuval , Chowers Yehuda , Geva-Zatorsky Naama , Paul Mical
Published: June 2020

Background

Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and aimed to explain failure or success through microbiome analyses.

Methods

In this prospective cohort study, all consenting eligible CPE carriers received oral capsulized FMT for 2 days. Primary outcome was CPE eradication at 1 month, defined by 3 consecutive negative rectal swabs, the last also negative for carbapenemase gene by polymerase chain reaction. Comprehensive metagenomics analysis of the intestinal microbiome of donors and recipients before and after FMT was performed.

Results

Fifteen CPE carriers received FMT, 13 of whom completed 2 days of treatment. CPE eradication at 1 month was successful in 9/15 and 9/13, respectively. Bacterial communities showed significant changes in both beta and alpha diversity metrics among participants who achieved CPE eradication that were not observed among failures. Post-FMT samples’ beta-diversity clustered according to the treatment outcome, both in taxonomy and in function. We observed a significant decrease in beta diversity in participants who received post-FMT antibiotics. Enterobacteriaceae abundance decreased in post-FMT samples of the responders but increased among failures. Functionally, a clear demarcation between responders (who were similar to the donors) and failures was shown, driven by antimicrobial resistance genes.

Conclusions

Our study provides the biological explanation for the effect of FMT against CPE carriage. Decolonization of CPE by FMT is likely mediated by compositional and functional shifts in the microbiome. Thus, FMT might be an efficient strategy for sustained CPE eradication.

Clinical Trials Registration

NCT03167398.
mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
Authors: Yang Fenglong , Zou Quan
Published: June 2020

Due to the concerted efforts to utilize the microbial features to improve disease prediction capabilities, automated machine learning (AutoML) systems aiming to get rid of the tediousness in manually performing ML tasks are in great demand. Here we developed mAML, an ML model-building pipeline, which can automatically and rapidly generate optimized and interpretable models for personalized microbiome-based classification tasks in a reproducible way. The pipeline is deployed on a web-based platform, while the server is user-friendly and flexible and has been designed to be scalable according to the specific requirements. This pipeline exhibits high performance for 13 benchmark datasets including both binary and multi-class classification tasks. In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the GMrepo database. The repository involves 120 microbiome-based classification tasks for 85 human-disease phenotypes referring to 12 429 metagenomic samples and 38 643 amplicon samples. The mAML pipeline and the GMrepo ML repository are expected to be important resources for researches in microbiology and algorithm developments.

Database URL: http://lab.malab.cn/soft/mAML
Three-dimensional right ventricular shape and strain in congenital heart disease patients with right ventricular chronic volume loading
Authors: Moceri Pamela , Duchateau Nicolas , Gillon Stéphane , Jaunay Lolita , Baudouy Delphine , Squara Fabien , Ferrari Emile , Sermesant Maxime
Published: June 2020

Aims

Right ventricular (RV) function assessment is crucial in congenital heart disease patients, especially in atrial septal defect (ASD) and repaired Tetralogy of Fallot (TOF) patients with pulmonary regurgitation (PR). In this study, we aimed to analyse both 3D RV shape and deformation to better characterize RV function in ASD and TOF-PR.

Methods and results

We prospectively included 110 patients (≥16 years old) into this case–control study: 27 ASD patients, 28 with TOF, and 55 sex- and age-matched healthy controls. Endocardial tracking was performed on 3D transthoracic RV echocardiographic sequences and output RV meshes were post-processed to extract local curvature and deformation. Differences in shape and deformation patterns between subgroups were quantified both globally and locally. Curvature highlights differences in RV shape between controls and patients while ASD and TOF-PR patients are similar. Conversely, strain highlights differences between controls and TOF-PR patients while ASD and controls are similar [global area strain: −31.5 ± 5.8% (controls), −34.1 ± 7.9% (ASD), −24.8 ± 5.7% (TOF-PR), P < 0.001, similar significance for longitudinal and circumferential strains]. The regional and local analysis highlighted differences in particular in the RV free wall and the apical septum.

Conclusion

Chronic RV volume loading results in similar RV shape remodelling in both ASD and TOF patients while strain analysis demonstrated that RV strain is only reduced in the TOF group. This suggests a fundamentally different RV remodelling process between both conditions.
Comparing traditional aortic valve surgery and transapical approach to transcatheter aortic valve implant
Authors: Buzzatti Nicola , Sala Alessandra , Alfieri Ottavio
Published: June 2020

During the last 15 years, transcatheter aortic valve implant (TAVI) has become a valid alternative to surgical aortic valve replacement in symptomatic patients with severe aortic stenosis, and high or intermediate operative risk. Transcatheter aortic valve implant could be approached through various access sites, among which the transapical has long been one of the most popular. Through the years, this procedure has shown results similar to the standard surgical approach, but not as good as the same procedure via the transfemoral approach. For this reason, along with continuous technological advances, the transfemoral approach is used, presently, in 90% of the patient, while the transapical route has been limited, progressively, to a minority of patients. Currently the Heart Team should decide, in every single patient, between conventional surgery and TAVI. In clinical practice, TAVI is favoured in high-risk patients, and in the elderly at intermediate surgical risk with favourable anatomical features. In patients in whom TAVI is preferable to surgery, but have ‘non-usable’ femoral approach, alternative routes, such as transaxillary or transapical, could be considered.
Atrial fibrillation ablation in heart failure
Authors: Balla Cristina , Cappato Riccardo
Published: June 2020

Atrial fibrillation (AF) and heart failure (HF) commonly coexist in the same patient and either condition predisposes to the other. Several mechanisms promote the pathophysiological relationship between AF and HF, reducing quality of life, increasing the risk of stroke, and worsening HF progression. Although restoration and maintenance of sinus rhythm would be ideal for those patients, several trials comparing rhythm and rate control failed to show a benefit of rhythm control strategy, achieved with pharmacological therapy, in terms of hospitalization for HF or death. Catheter ablation is a well-established option for symptomatic AF patients, resistant to drug therapy, with normal cardiac function. Several recent studies have shown an improvement in clinical outcomes after AF ablation in HF patients highlighting the emerging role of the invasive approach in this subset of patients. However, several concerns regarding patients’ selection and standardization of the procedure still remain to be addressed.
How important is blood pressure variability?
Authors: Rosei Enrico Agabiti , Chiarini Giulia , Rizzoni Damiano
Published: June 2020

Arterial blood pressure (BP) is a continuous variable, with a physiology characterized by significant variability stemming from the complex interaction among haemodynamic factors, neuronal reflexes, as well as hormonal, behavioural, and environmental stimuli. The homoeostatic response accounts for the physiologic variability in BP in normotensive individuals, which is more evident in hypertensive patients. Blood pressure variability is a complex phenomenon, which could be classified in various types: very short term (beat to beat), short term (during 24 h), mid-term (day by day), long term (<5 years), and very long term (>5 years). Accurate measurement of BP variability represents a complex and often controversial endeavour, despite several methodological approaches are available. Albeit a prognostic significance has been demonstrated for some indicators of BP variability, the clinical significance of this measurement is still uncertain. In fact, none of the indicators presently available for BP variability, including early morning BP rise, substantially affects, and redefines, the cardiovascular risk of the hypertensive patient, over and beyond the mere BP values. Accordingly, in defining the cardiovascular risk, the focus should be on the absolute BP values, which remain the most relevant risk factor, and the one more susceptible to modification with both non-pharmacologic and pharmacologic treatment.
Right ventricular electromechanical abnormalities in Brugada syndrome: is this a cardiomyopathy?
Authors: Pappone Carlo , Monasky Michelle M , Micaglio Emanuele , Ciconte Giuseppe
Published: June 2020

Brugada syndrome (BrS) has been often described as a purely electrical disease. However, current dogma surrounding this concept has shifted to accept that BrS is associated with structural abnormalities. Brugada syndrome is now associated with epicardial surface and interstitial fibrosis, reduced gap junction expression, increased collagen, and reduced contractility. The ventricular arrhythmias observed in BrS have been linked to an arrhythmogenic substrate (AS) located rather consistently in the right ventricular outflow tract, sparking much debate as to the significance of this anatomical position. The size of the AS is dynamic and can be altered due to a number of factors. A larger AS is associated with reduced contractility, and this impaired mechanical function may be responsible for syncopal episodes in BrS patients in the absence of arrhythmic events. While BrS is generally regarded as a channelopathy, recent studies have now identified also mutations in genes encoding for sarcomeric proteins to be associated with BrS. Future studies should evaluate electromechanical coupling in BrS, including calcium handling and sarcomeric alterations, and evaluate whether BrS should be classified as a cardiomyopathy.
The revolution of the anti-diabetic drugs in cardiology
Authors: Verdecchia Paolo , Angeli Fabio , Cavallini Claudio , Aita Adolfo , Turturiello Dario , Reboldi Gianpaolo
Published: June 2020

Beginning in December 2008, under the auspices of Food and Drug Administration, numerous controlled clinical trial were planned, and in part completed, concerning the cardiovascular (CV) effects of hypoglycaemic drug in patients with Type 2 diabetes mellitus. At least 9 studies have been concluded, 13 are still open, and 4 have been initiated and closed ahead of time. Of the nine completed studies, three concerned inhibitor of the dipeptidyl peptidase 4 (inhibitors of DPP-4), four the glucagon-like peptide 1 agonist (GLP-1 agonist), and two the inhibitor of sodium-glucose co-transporter-2 (inhibitors of SGLT-2). Only four studies demonstrated the superiority, and not the mere ‘non-inferiority’, of the anti-diabetic drugs compared to placebo, in addition to standard treatment, in terms of reduction of the primary endpoint (CV death, non-fatal myocardial infarction, and non-fatal stroke). Two of the four studies regarded GLP-1 analogues (liraglutide and semaglutide), and two inhibitors of SGLT-2 (empaglifozin and canaglifozin). As a whole, these studies provided solid data supporting major beneficial CV effects of anti-diabetic drugs. During the next 3–4 years, an equal number of studies will be completed and published, so we will soon have the ‘final word’ on this issue. In the meantime, the clinical cardiologist should become familiar with these drugs, selecting the patients able to gain the best clinical advantage from this treatment, also by establishing a close relationship with the diabetologist.
To whom recommend intensive treatment for hypertension?
Authors: Volpe Massimo , Gallo Giovanna
Published: June 2020

Arterial hypertension is the main identifiable cardiovascular risk factor, and although the benefit of blood pressure reduction is universally acknowledged, the scientific community has long been divided over the therapeutic blood pressure targets to be reached, also considering the estimated overall cardiovascular risk and the presence of individual risk factors and associated comorbidities. During the last few years, numerous clinical studies and meta-analyses, in particular, the SPRINT study, have been published, demonstrating the advantages of an intensive antihypertensive treatment, over a target blood pressure value (<140/90 mmHg), in the reduction of major cardiovascular events, myocardial infarction, stroke, heart failure, and all-causes cardiovascular mortality. Stemming from these results the major International Guidelines revisited the therapeutic objectives, recommending blood pressure value <130/80 mmHg for the vast majority of hypertensive patients until the age of 65 and suggesting a reduction of the target also in the elderly. Numerous studies and meta-analyses demonstrated that the reduction of the risk of coronary or cerebral events, and of all-causes cardiovascular mortality, is independent from the baseline value of blood pressure and the individual estimated risk. It has been also demonstrated that an early institution of antihypertensive treatment is associated with a faster realization of the recommended targets, and consequent significant benefits in terms of reduction of the incidence of myocardial infarction, heart failure, and major cardiovascular events, particularly when blood pressure control is achieved during the first 6 months of treatment, and even better during first 3 months. Other studies outlined that combination therapy with two or more drugs, mainly in a single pill configuration, are superior in reaching the recommended therapeutic targets. This is the reason why this strategy is strongly supported by the European Society of Cardiology/European Society of Hypertension (ESC/ESH) 2018 Guidelines, specifically the use of renin–angiotensin–aldosterone system inhibitors [angiotensin-converting enzyme (ACE) inhibitors and Sartans], in combination with calcium antagonist and/or thiazide diuretics, with the option to add antagonist of mineralcorticoid receptors, when an adequate blood pressure control has not been reached, or other classes of drugs, such as beta-blockers, when specific clinical indications are present, first and foremost ischaemic cardiomyopathy or heart failure. The newly proposed therapeutic goals are particularly important in high-risk patients, such as patients with previous cardiovascular events, diabetes mellitus, renal insufficiency, and patients older than 65 years of age.
Patenting a living microbial cell: 40th anniversary of US Supreme Court decision Diamond versus Chakrabarty
Authors: Silver Simon
Published: June 2020

Patents for microbiology and biotechnology are generally for a process (for example DNA cloning; and polymerase chain reaction, PCR) and not for the microbe itself. The patent for oil degrading bacteria was different in that it covered the modified microbial cell itself, a Pseudomonas strain with laboratory-assembled plasmids that encoded the bacterial degradation of multiple components of crude oil. It was first applied for in 1972, initially refused by the patent office on the basis that it was a living organism, and then eight years later in June 1980 allowed by the US Supreme Court ruling that this did not matter and the only issue was whether it was a novel manufactured product.
Virulence factors regulation by the quorum-sensing and Rsm systems in the marine strain Pseudomonas aeruginosa ID4365, a natural mutant in lasR
Authors: Cocotl-Yañez Miguel , Soto-Aceves Martín Paolo , González-Valdez Abigail , Servín-González Luis , Soberón-Chávez Gloria
Published: June 2020

Pseudomonas aeruginosa is an opportunistic human pathogen that is able to produce several virulence factors such as pyocyanin, rhamnolipids and elastase. In the clinical reference strain PAO1, synthesis of these virulence factors is regulated transcriptionally by quorum sensing (QS) and post-transcriptionally by the Rsm system. Herein, we investigated the role of these systems in the control of the pyocyanin, rhamnolipids and elastase production in the marine strain ID4365. We found that this strain carries a nonsense mutation in lasR that makes it a natural mutant in the Las QS system. However, its QS response is still functional with the Rhl system activating virulence factors synthesis. We found that the Rsm system affects virulence factors production, since overexpression of RsmA reduces pyocyanin production whereas RsmY overexpression increases its synthesis. Unexpectedly, and in contrast to the type strain PAO1, inactivation of rsmA increases pyocyanin but reduces elastase and rhamnolipids production by a reduction of RhlR levels. Thus, QS and Rsm systems are involved in regulating virulence factors production, but this regulation is different to the PAO1 strain even though their genomes are highly conserved. It is likely that these differences are related to the different ecological niches in which these strains lived.
Geometric controls on megathrust earthquakes
Authors: Plescia Steven M , Hayes Gavin P
Published: June 2020

The role of subduction zone geometry in the nucleation and propagation of great-sized earthquake ruptures is an important topic for earthquake hazard, since knowing how big an earthquake can be on a given fault is fundamentally important. Past studies have shown subducting bathymetric features (e.g. ridges, fracture zones, seamount chains) may arrest a propagating rupture. Other studies have correlated the occurrence of great-sized earthquakes with flat megathrusts and homogenous stresses over large distances. It remains unclear, however, how subduction zone geometry and the potential for great-sized earthquakes (M 8+) are quantifiably linked—or indeed whether they can be. Here, we examine the potential role of subduction zone geometry in limiting earthquake rupture by mapping the planarity of seismogenic zones in the Slab2 subduction zone geometry database. We build from the observation that historical great-sized earthquakes have preferentially occurred where the surrounding megathrust is broadly planar, and we use this relationship to search for geometrically similar features elsewhere in subduction zones worldwide. Assuming geometry exerts a primary control on earthquake propagation and termination, we estimate the potential size distribution of large (M 7+) earthquakes and the maximum earthquake magnitude along global subduction faults based on geometrical features alone. Our results suggest that most subduction zones are capable of hosting great-sized earthquakes over much of their area. Many bathymetric features previously identified as barriers are indistinguishable from the surrounding megathrust from the perspective of slab curvature, meaning that they either do not play an important role in arresting earthquake rupture or that their influence on slab geometry at depth is not resolvable at the spatial scale of our subduction zone geometry models.