bluuebunny/crossref_metadata_2025 huggingface dataset:
Upgrade of the ALICE inner tracking system: Construction and commissioning
Authors: Fantoni Alessandra
Published: July 2020

ALICE (A Large Ion Collider Experiment) is the CERN LHC experiment optimized for the study of the strongly interacting matter produced in heavy-ion collisions, in particular the characterization of the quark-gluon plasma. After the successful operation of the experiment during the first two runs of the LHC, the ALICE collaboration is currently working on a major upgrade of its detectors, to be installed during the 2019–2020 Long Shutdown (LS2). The main goal is to increase the readout capabilities and allow recording of Pb–Pb minimum bias events at rates in excess of 50 kHz, which is the expected Pb–Pb interaction rate at the LHC after LS2. One key part of the upgrade is the construction of a new Inner Tracking System (called ITS2) that will significantly improve the impact parameter resolution of the tracks, tracking efficiency, and readout capacity which enables precise measurements of low momentum charged particles. The ITS2 consists of seven approximately-cylindrical detector layers of CMOS Monolithic Active Pixel Sensors (MAPS) with the sensor matrix and readout integrated on a single chip, named ALPIDE (ALice PIxel DEtector), covering an area of 10 m2 and containing about 12.5 billion pixels. All layers are mounted on ultra-lightweight carbon support structures with an embedded cooling system. This allows a reduction of the material budgets down to about 0.3% X0 for the inner layers and 1% X0 for the outer layers, with respect to the previous ITS system. After a brief overview of the upgrade motivation, details of the overall layout will be given as well as the construction and commissioning status and plans.
Wearable multichannel haptic device for encoding proprioception in the upper limb
Authors: Sagastegui Alva Patrick G , Muceli Silvia , Farokh Atashzar S , William Lucie , Farina Dario
Published: July 2020

Objective. We present the design, implementation, and evaluation of a wearable multichannel haptic system. The device is a wireless closed-loop armband driven by surface electromyography (EMG) and provides sensory feedback encoding proprioception. The study is motivated by restoring proprioception information in upper limb prostheses. Approach. The armband comprises eight vibrotactile actuators that generate distributed patterns of mechanical waves around the limb to stimulate perception and to transfer proportional information on the arm motion. An experimental study was conducted to assess: the sensory threshold in eight locations around the forearm, the user adaptation to the sensation provided by the device, the user performance in discriminating multiple stimulation levels, and the device performance in coding proprioception using four spatial patterns of stimulation. Eight able-bodied individuals performed reaching tasks by controlling a cursor with an EMG interface in a virtual environment. Vibrotactile patterns were tested with and without visual information on the cursor position with the addition of a random rotation of the reference control system to disturb the natural control and proprioception. Main results. The sensation threshold depended on the actuator position and increased over time. The maximum resolution for stimuli discrimination was four. Using this resolution, four patterns of vibrotactile activation with different spatial and magnitude properties were generated to evaluate their performance in enhancing proprioception. The optimal vibration pattern varied among the participants. When the feedback was used in closed-loop control with the EMG interface, the task success rate, completion time, execution efficiency, and average target-cursor distance improved for the optimal stimulation pattern compared to the condition without visual or haptic information on the cursor position. Significance. The results indicate that the vibrotactile device enhanced the participants’ perceptual ability, suggesting that the proposed closed-loop system has the potential to code proprioception and enhance user performance in the presence of perceptual perturbation.
Antibacterial activity of ZnO nanoparticle coatings formed by electrophoretic deposition
Authors: Uribe P A , Ruiz J , Ortiz C C , Blanco S I , Gutierrez J A
Published: July 2020

The scientific community is focused on the development and use of new nanomaterials to create novel devices and systems that can be useful to solve problems or provide services. Among all nanomaterials, semiconductors allow improving optical, electrical, and catalytic properties of several surfaces, including the corrosion resistance of the materials; corrosion causes several problems and economic losses in the food, pharmaceutical, and hospital industries because the materials selected must be durable, economic, and as innocuous as possible. Zinc oxide (ZnO) is one of the most interesting materials, is a photo-chemically active n-type semiconductor and has particular defects into intrinsic lattices, such as Zn and O vacancies. Herein, we use electrophoretic deposition (EPD) for the synthesis of nanostructured films composed of ZnO nanoparticles (ZnONPs) as a protective coating on low-alloy carbon steel. The electrochemical stability of the coated steel was evaluated and compared with the response of the bare steel. This work used NPs formed in homogeneous media and in reverse micelles (RMs) formed in our previous published report. The coatings were synthesized on the surface of SAE 1020 carbon steel electrodes with 12 mm diameter. As results, two different colloidal systems were formed, by RMs we synthesized high mono-dispersed and spherical 3-5 nm ZnONPs, and by homogeneous media anisotropic 20-100 nm ZnONPs, both systems with excellent fluorescence emission at different excitation wavelengths. The electrochemical evaluation confirms the stability of the coatings obtained, improving the corrosion resistance of the low-alloy carbon steel. We found that the coating obtained with the smallest particles shows better protective properties; the difference between both coatings could be related to the force balance during the electrophoretic deposition, where the friction force, that is against the electrophoretic movement, is proportional to the particle size, reducing the amount of deposited material.
Variation of Structural and Hyperfine Parameters of (Fe0.70Al0.30)1-xNbx, with x=0, 0.05, 0.10 and 0.20 System
Authors: Rodríguez R R , Pérez Alcázar G A , Colorado H , Zamora L E
Published: July 2020

Fe0.70Al0.30 alloy is a bcc and ferromagnetic phase, being the Al atoms magnetic dilutor. In this work, we study the effect of the Nb on the structural and hyperfine behavior of the Fe0.70Al0.30 alloy when atoms of Nb substitute atoms of Fe or Al. The nanostructured system of (Fe0.70Al0.30)1-xNbx (x = 0, 0.05, 0.10, 0.20, at. %) was obtained by alloying Fe, Al and Nb powders in a planetary ball mill during 12 h, 24 h and 36 h, and a ball mass to powder mass relation of 10:1. The magnetic and hyperfine properties of the samples were studied by X-ray diffraction (XRD) and Mössbauer Spectrometry (MS) at room temperature, respectively. The X-ray diffraction patterns for x=0 showed the bcc-α FeAl structure and its lattice parameter is approximately constant with milling times (∼ 2.91 Å). For x=0.05, 0.10 and 0.20 the patterns showed the coexistence of the α-FeAl, Nb(Fe,Al)2 structural phases with an amorphous component. The Mössbauer spectra of x=0 samples were fitted using hyperfine magnetic field distributions (HMFDs), and the obtained mean hyperfine fields (MHF) were 23.4, 24.2, and 24.3 T for 12, 24, and 36 h of milling time, respectively, which correspond to the α-FeAl structure. The spectra of the samples with x=0.05 and 0.10 were fitted using a model with two components, the first one is a HMFD attributed to the bcc-FeAlNb structure and the second with two doublets attributed to the Nb(Fe,Al)2 structure. When atomic percentage of Nb increases up to 20 at. % the ferromagnetic behavior is diluted due to substitution of Fe-atoms by Nb and Al atoms in the bcc-FeAlNb structure. The magnetic behavior becomes paramagnetic at x=0.20, the spectra were fitted with three doublets, one of them related with bcc-FeAlNb structure and the others to the Nb(Fe,Al)2 structural phase. The alloying of Nb to the Fe0.70Al0.30 system destroyed the magnetism due the substitution of Fe by Nb atoms and generates an amorphization into the system.
Chemical and morphological analysis of formation of rGO/ZnO composite obtained by microwave-assisted hydrothermal method
Authors: Merlano Aura S , Pérez F R , Cabanzo Rafael , Mejía Enrique , Hoyos Lina M , Salazar Ángel
Published: July 2020

A chemical synthesis route for facile, fast and economical production of reduced graphene oxide/zinc oxide composites (rGO/ZnO) via a microwave-assisted hydrothermal method is presented. For a particular concentration (124 mM) of zinc acetate di-hydrate (Zn(CH3COO)2.2H2O) acting as precursor of Zn, different microwave irradiation times of the order of seconds were tested in order to select the more adequate time. Furthermore, with the selected irradiation time (40 s), different concentrations (31, 62 and 124 mM) were then considered and chemical and morphological properties of the obtained composites were evaluated. For their characterizations SEM, EDS, FTIR, Raman spectroscopy and XRD were employed. Experimental results confirm that the proposed synthesis route for the fabrication of rGO/ZnO is efficient, environmentally friendly and cost-effective.
Electroencephalography based Emotion Recognition using Fisher’s Linear Discriminant Analysis on Support Vector Machine
Authors: Yulita I N , Novita D , Sholahuddin A , Emilliano
Published: July 2020

Emotions as intense feelings for reactions to something affect someone in interacting with others such as in determining choices, actions, and perceptions. The emotional state of an individual can be seen clearly through facial expression and tone of speech. Apart from facial features or voice features, identification of emotions can also be done through brain waves. This study used an electroencephalogram signal as an input to recognize types of emotions. The electroencephalogram signal was chosen because it can record the true emotions of individuals. The recognition of emotions based on Support Vector Machine (SVM). To improve the performance, this method was combined with Fisher’s Linear Discriminant Analysis (FLDA). The experiments showed the SVM performance increased above 30%. As a comparison, this research also implemented Multi-Layer Perceptron (MLP). The results showed that the performances of SVM and FLDA-SVM were higher than MLP or FLDA-MLP. It showed that FLDA-SVM was the best method of this research in recognizing emotions.
Fuzzy Logic System Implementation with Mamdani Method in Computer-Based Intelligence Quotient Test to Determining the Type of Intelligence Dimension
Authors: Putri G N , Dirgantoro B , Aulia P , Setianingsih C
Published: July 2020

A person of a thing can cultivate intelligence in areas of interest, sometimes many people complain because the results of their intelligence quotient test (IQ) show unsatisfactory results. Because they are still looking only lies in those abilities. Intelligence quotient tests are used to explore knowledge about certain individual skills and intelligence. To determine someone’s intelligence, it takes a long time to analyze and get the test output from calculations by certain methods manually. The determination of a person’s dimension intelligence can be done by certain method, this research is one way to make a fuzzy model for the type of intelligence dimension support system based on standardization in psychology The result of this research is expected to explain how to modeling the fuzzy logic system with Mamdani method in a support system to determine the types of intelligence dimensions, namely the festigung / exact or flexibilitat / non-exact.
Detecting the Burned Area in Volcanic Region by Using Multitemporal Landsat-8 OLI (Case Study: Mt. Sumbing, Central Java)
Authors: Prasasti I , Triyono D , Suwarsono
Published: July 2020

Biomass burning is one of the natural agents that most change terrestrial ecosystems and has a key ecological role in a huge piece of the Earth’s surface. Biomass burning has numerous socio-economic implications, particularly in developed countries where the developing urbanization of forested regions tends to increase accidents related with extraordinary fire occasions. Wildland fire mapping has been a subject vital for the international community over the recent two decades. Since fire is a major threat to forests and wooded areas in the tropical environment of Kalimantan, methodical regional fire observing is a need. Remote sensing methods are recognized as the efficient source of information for mapping burned areas from regional-national up to global scale. This study investigated the use of multitemporal Landsat-8 OLI (Operational Land Imager) data, to identify the burned area, in the tropical region of Indonesia, during 2019 fire season. A pair of Landsat-8 OLI, collected before and after fires, has been used to delineate the boundaries of sample location of burned area. Then, the difference of reflectance and Normalized Burn Ratio were analyzed. Fire incident causes landcover changes from vegetated land to bareland. This changes can affect the reflectance detected from Landsat-8 OLI. The result showed that biomass burning on volcanic region has caused high decreasing values on band 5 and there were high increasing on band 7. The NBR was better used to extracted burned area rather than NDVI or single spectral band. This method based on multitemporal optical data, creates a valuable tool for identifying and interpreting burned area following a fire event on volcanic region.
Shallot Quality Classification using HSV Color Models and Size Identification based on Naive Bayes Classifier
Authors: Susanto A , Dewantoro Z H , Sari C A , Setiadi D R I M , Rachmawanto E H , Mulyono I U W
Published: July 2020

This research proposes a method of classification of shallots based on quality using the Naïve Bayes Classifier. The Naïve Bayes classifier is a classifier based on statistics and simple probabilities that are widely used in many sophisticated learning methods today. Shallots are classified into three classes, namely good, medium, and poor quality. To get good classification results, appropriate extraction of features is needed, in this case, color feature extraction is selected with the hue saturation value (HSV) model and to identify the size the area, metric and perimeter calculations are used. To get the right size, some morphological operations such as filling holes and opening are performed. Based on the experimental results on 60 training data and 60 testing data classification shallot quality using Naïve Bayes Classifier produces an accuracy of up to 91.67%.
Securing Text Messages using the Beaufort-Vigenere Hybrid Method
Authors: Sugiarto E , Setiadi D R I M , Fahmi A , Rachmawanto E H , Sari C A , Sarker Md K , Widjajanto B
Published: July 2020

Beaufort and Vigenere are fast and strong substitution encryption methods against brute force attacks if they have good key quality. But both of these methods by default can not produce a good avalanche effect. Avalanche effect is a measuring tool that can determine the strength of encryption from differential attacks. This research proposes hybrid techniques of Beaufort and Vigenere algorithms to optimize the security of text message encryption by modifying key generators. With this method, the encryption process can be done by input text messages and keys. The key is processed with a key generator to produce two new keys that are used for encryption using the Beaufort and Vigenere hybrid methods. Based on the test results, the Avalanche effect value rose significantly compared to the standard method, and the value of the avalanche effect was more stable and close to ideal compared to the previous method. The time required is also relatively very fast for the encryption or decryption process, experimental result shows it takes less than 0.1 seconds for more than 43 thousand of characters in the text message.
Wireless communication design of internet of things based on FPGA and WiFi Module
Authors: Wibowo F W
Published: July 2020

The implementation of the internet of things (IoT) has been many researched. Some applications have their own designs and special uses. Low-cost designs and multi-usage are always targeted on the implementation either using a microcontroller or field programmable gate arrays (FPGAs). The reconfigurable device of FPGA in some cases has advantages in its uses. This paper has designed the communication of the radio frequency (RF) for the IoT using wireless communication based on the FPGA and wireless fidelity (WiFi) of the ESP8266 WiFi module. The research methodology used in this paper was a simulation using Xilinx ISE software for the device of the Xilinx Spartan-3E FPGA that has been configured using Very High Speed Integrated Circuit Hardware Description Language (VHDL). The result of the ESP8266 driver based on the FPGAs is sent to the JSON based website.
Design of Phishing Simulation Dashboard Using Analytic Data Concepts
Authors: Septiana R , Julian R K
Published: July 2020

Security awareness is the main concern of phishing attack prevention. Every internet user will deal with a serious issue. Phishing is the falsification of messages that aims to retrieve important information from the recipient of the message. In a company, phishing becomes a serious problem because it can come to all employees suddenly. Employees who do not understand the dangers of phishing are the most dangerous threats because they are likely to be the main supporters of the success of phishing attacks. Understanding of phishing attack can be seen from the way the worker responds to incoming messages. A company makes a phishing simulation to find out the handling of the employee on a fake message came. One of the phishing simulation tools is web forgery. In this research, phishing simulations attack every employee in a company. The employee will receive a message that contains a field. The result will show a percentage of employee that successfully attacked. The results will be displayed on a dashboard after being processed using an analytic data concept. The processes of data analytic involve business intelligent software called QlikView. The software gives a percentage of the employee who opens the fake message and fills some data in the fields is about 13.9%.
Development of Web-based Research and Community Service Database at Universitas Negeri Surabaya
Authors: Warju  , Cahyaningrum S E , Nurkholis  , Saksono L , Nudin S R , Ariyanto S R
Published: July 2020

One of the data used as a benchmark for determining the progress of a university can be seen from the productivity of research and community service. The research objectives are to (1) analyze Unesa lecturer research based on the distribution of faculties/departments/study programs; (2) analyzing trends in the research focus of Unesa lecturers; (3) analyzing the achievement of Unesa lecturer research outcomes compared with the target research outcomes; and (4) analyzing the profile of the service to the Unesa lecturer community based on the distribution of faculties/departments/study programs. The reference used in analyzing is from 2015-2019. The development model used is the Waterfall model with a linear development system. The research subject used was the procedure of developing Sistem Informasi Riset dan Pengabdian Kepada Masyarakat (SIRIP) in Higher Education. Data analysis techniques were carried out in three stages, namely pre-development, development, and post-development. Based on the results and discussion, the conclusions in this study are as follows. The results of the trial of Sistem Informasi Riset dan Pengabdian Kepada Masyarakat (SIRIP) using the black box testing method in accordance with 18 functional requirements of the system can run successfully. The profile of research in Unesa from 2015-2019 experienced a significant increase and decrease (fluctuation). The number of research titles funded from 2015-2019 was as many as 250 titles, 585 titles, 700 titles, 480 titles, and 447 titles. Meanwhile, the number of community service titles funded from 2015-2019 was 46 titles, 51 titles, 29 titles, 22 titles, and 338 titles, respectively.
Energy Management Methodology for Sustainable Water Development and Servicing, Considering the POET Based Concept
Authors: Ngancha P B , Kusakana K , Markus E D
Published: July 2020

This paper aims at analysing the energy management activities for commercial bulk water development and servicing in South Africa. The energy efficiency, in terms of performance, operation, equipment and technology (POET), is reviewed. The sustainability of a general energy management program is discussed within this POET framework. As an application of this discussion to the commercial bulk water development scenario, the POET efficiency of an energy system is a measure of energy efficiency, which is determined by external but deterministic system indicators, such as production period, energy sources, environmental impact and technical indicators, amongst others. The case study concludes that the POET, based framework does not only cover all major energy management activities, but further identifies energy efficiency improvement opportunities.
IoT Water Monitor Implementation Strategy
Authors: Gericke G A , Kuriakose R B
Published: July 2020

Water scarcity is a serious threat that is directly impacting the lives of over four billion people globally every month. While phenomenon’s like global climate change and pattern droughts contribute to this challenge, they are beyond human control to an extent. However, the challenge of water wastage due to water leaks is one that can and should be controlled. Majority of water leaks are only reported within 4-8 hours of their occurrence and take even longer to be fixed. This paper proposes an implementation strategy for monitoring water leakages in real time by connecting IoT enabled controllers onto the water main lines and automatically/remotely control the water main lines to limit the amount of water wastage. The key results of the study show that with the proposed system, water leaks can be detected and reported within an hour of their occurrence and with timeous intervention can prevent water loss of up to 50000 liters.
The greenhouse gas emissions, water consumption, and heat emissions of global steam-electric power production: a generating unit level analysis and database
Authors: Raptis C E , Oberschelp C , Pfister S
Published: July 2020

Steam-electric power dominates global electricity production. Mitigating its environmental burdens relies on quantifying them globally, on a high resolution. Here, with an unprecedented combination of detail and coverage, the Rankine cycle was individually modelled for >21 000 geocoded steam-electric generating units globally. Accounting for different cooling systems and fuels enabled the calculation of three major environmental stressors on a generating unit level. Geographical, chronological, and technological patterns are examined, as are trade-offs and improvement scenarios. Greenhouse gases (GHG) emissions from young (>2000) Chinese coal-fuelled generating units are equal to the sum of GHG emissions from all steam-electric power plants of all ages in the U.S. and Europe, and occupy 5% of all GHG emissions from the entire global economy. Twenty-four per cent of freshwater consumed from steam-electric power originates from nuclear power units from the 1970s/1980s, mainly in the U.S. and Europe. One per cent of steam-electric generating units is responsible for 50% of global heat emissions to freshwater. The median carbon intensity of Indian coal-fired units (≥50 MW) is 7%–16% higher than that in any other region globally. As concerns GHGs, technology-related efficiency differences (Rankine cycle, cooling system) play a small role compared to the fuel, which dominates the carbon intensity (GHGs/GJ el.). With the highest shares of cogeneration, 1 GJ electricity from tower-cooled coal units in Russia consumes on average 8%–49% less freshwater compared to respective units globally. There is a small margin for improvement based on alternative steam-electric technologies: retiring inefficient units and replacing their demand by ramping up more efficient ones with the same fuel, within the same country results in, respectively, ∼1%, 6%, and 11% fewer GHG emissions, freshwater consumption, and heat emissions globally. The full environmental benefits of completely retiring old units (<1970) consist of 9% fewer GHG emissions, 7% less freshwater consumed, and 18% fewer thermal emissions globally.
Effect of WWTP size on grey water footprint—Czech Republic case study
Authors: Ansorge Libor , Stejskalová Lada , Dlabal Jiří
Published: July 2020

The number of wastewater treatment plants (WWTPs) in the Czech Republic is increasing. Wastewater, which was previously disposed of in other ways (e.g. septic tanks, cesspits etc), is now entering the surface water (after treatment at a WWTP). Billions of Czech crowns have been invested in the construction of new WWTPs or reconstruction and intensification of existing ones. This money had been invested to meet discharge standards for individual pollutants. However, the overall level of pollution associated with wastewater discharges has not been assessed. The indicator of grey water footprint was used to assess whether there was an increase in pollution load discharged from WWTPs between 2002 and 2018. Discharged pollution data from 4115 industrial and municipal WWTPs were analysed. The analysis of such a large data set has not been carried out yet and brings new knowledge concerning the effect of WWTP size on the grey water footprint. Overall, the total value of the grey water footprint (and thus of the discharged pollution level) decreased in the monitored period. Grey water footprint caused by the largest WWTPs decreased, while the grey water footprint of small WWTPs increased, due to the increase in their number. The decisive pollutants that determine the value of the grey water footprint are total phosphorus and ammonium nitrogen. Measures targeting these two main pollutants can significantly reduce the overall level of pollution load discharged from WWTPs.
Surface erosion behaviour over NiCrBSi-Al2O3 composite coatings
Authors: Senapati Pragyan , Sutar Harekrushna
Published: July 2020

For hydro turbine components High Velocity Oxy Fuel (HVOF) thermal spraying process was adopted for three different types of coatings i.e NiCrBSi-5%Al2O3 (N5A), NiCrBSi-10%Al2O3 (N10A) and NiCrBSi-15%Al2O3 (N15A) on Grade 420 Stainless steel, the coatings being characterized by Scanning Electron Microscope (SEM), x-ray Diffraction (XRD) and optical microscope. With measurements of surface roughness, thickness, micro hardness and porosity of the coatings, the erosion tests were conducted in a slurry-jet erosion tester at 30°, 60° and 90 ° impingement angles, jet velocity of 20 m s−1 and erodent size of 200 μm. The optical microscopy images of the coated samples exhibited lamella structure of the coatings. The N15A coating exhibits highest micro hardness value of 715 ± 31 HV0.3 followed by N10A (557 ± 22 HV0.3) and N5A (407 ± 15 HV0.3). The grade 420ss shows the lowest micro hardness value (272 ± 5 HV0.3). The surface morphology of the eroded samples was studied using SEM. The mechanisms involved in erosion of all the coated surfaces are removal of splats, lip formation, ploughing action and micro cutting whereas of bare steel, ploughing action, micro cutting and lip formation along with appearance of pores and craters. It was found that amongst the three coatings NiCrBSi-15%Al2O3 exhibited the lowest erosion and all the coatings offered better wear resistance than the uncoated steel.
A novel mechanism for the retention of Golgi membrane proteins mediated by the Bre5p/Ubp3p deubiquitinase complex
Authors: Wang Peng , Ye Ziyun , Banfield David K.
Published: July 2020

A novel mechanism required for the retention of Golgi resident integral membrane proteins in budding yeast is described that involves a deubiquitinase and the vesicle coat complex COPI-coatomer.
AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data
Authors: Peng Xiyu , Dorman Karin S
Published: July 2020

Motivation

Next-generation amplicon sequencing is a powerful tool for investigating microbial communities. A main challenge is to distinguish true biological variants from errors caused by amplification and sequencing. In traditional analyses, such errors are eliminated by clustering reads within a sequence similarity threshold, usually 97%, and constructing operational taxonomic units, but the arbitrary threshold leads to low resolution and high false-positive rates. Recently developed ‘denoising’ methods have proven able to resolve single-nucleotide amplicon variants, but they still miss low-frequency sequences, especially those near more frequent sequences, because they ignore the sequencing quality information.

Results

We introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets. AmpliCI considers the quality information and allows the data, not an arbitrary threshold or an external database, to drive conclusions. AmpliCI estimates a finite mixture model, using a greedy strategy to gradually select error-free sequences and approximately maximize the likelihood. AmpliCI has better performance than three popular denoising methods, with acceptable computation time and memory usage.

Availability and implementation

Source code is available at https://github.com/DormanLab/AmpliCI.

Supplementary information

Supplementary material are available at Bioinformatics online.
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data
Authors: Ghosh Roy Gourab , Geard Nicholas , Verspoor Karin , He Shan
Published: July 2020

Motivation

Inferring gene regulatory networks (GRNs) from expression data is a significant systems biology problem. A useful inference algorithm should not only unveil the global structure of the regulatory mechanisms but also the details of regulatory interactions such as edge direction (from regulator to target) and sign (activation/inhibition). Many popular GRN inference algorithms cannot infer edge signs, and those that can infer signed GRNs cannot simultaneously infer edge directions or network cycles.

Results

To address these limitations of existing algorithms, we propose Polynomial Lasso Bagging (PoLoBag) for signed GRN inference with both edge directions and network cycles. PoLoBag is an ensemble regression algorithm in a bagging framework where Lasso weights estimated on bootstrap samples are averaged. These bootstrap samples incorporate polynomial features to capture higher-order interactions. Results demonstrate that PoLoBag is consistently more accurate for signed inference than state-of-the-art algorithms on simulated and real-world expression datasets.

Availability and implementation

Algorithm and data are freely available at https://github.com/gourabghoshroy/PoLoBag.

Supplementary information

Supplementary data are available at Bioinformatics online.
Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
Authors: Freed Nikki E , Vlková Markéta , Faisal Muhammad B , Silander Olin K
Published: July 2020

Rapid and cost-efficient whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with Cq values between 20 and 31, we show that high-quality genomes can be generated with as few as 10 000 reads (∼5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.
UPLC-ESI/Q-TOF MS/MS Method for Determination of Vildagliptin and its Organic Impurities
Authors: Ferrazza Alves Giordani Camila , Campanharo Sarah , Ribeiro Wingert Nathalie , Maronesi Bueno Lívia , Wittckind Manoel Joanna , Virginia Garcia Cássia , Maria Volpato Nadia , Dineck Iop Gabrielle , de Azevedo Mello Paola , Marlon de Moraes Flores Erico , Eva Scherman Schapoval Elfrides , Steppe Martin
Published: July 2020

Vildagliptin (VLG) corresponds to a drug used for the treatment of diabetes mellitus. This disease requires continuous treatment, and so the control of impurities present in it is important to assure the quality of this drug. Thus, it is necessary to use sensitive and selective detection techniques and the ultra-performance liquid chromatography is a better option compared with high-performance liquid chromatography because it enhances the separation efficiency with a shorter analysis time and an increased resolution. This research analysis was accomplished by using liquid chromatography/tandem mass spectrometry, and the quantification was performed by using an extracted ion from the VLG drug and its main organic impurities of synthesis. During the validation process, following international standards, the method proved to be linear for the tree substances (R2 = 0.997–0.998) and the analysis of variance showed a non-significant linearity deviation (P > 0.05). Three critical factors were selected to evaluate method robustness with a full factorial experimental design, and the changes in the parameters were found to be not significant for the quantification of VLG and its impurities. The ultra-performance liquid chromatography-tandem mass spectrometry for the determination of impurities in VLG was precise, accurate and robust proving to be effective for analysis in the pharmaceutical industry and to improve the quality, safety and effectiveness of the new drug developed.
Clinical Application of Multiple Reaction Monitoring-Mass Spectrometry to Human Epidermal Growth Factor Receptor 2 Measurements as a Potential Diagnostic Tool for Breast Cancer Therapy
Authors: Do Misol , Kim Hyunsoo , Yeo Injoon , Lee Jihyeon , Park In Ae , Ryu Han Suk , Kim Youngsoo
Published: July 2020

Background

Human epidermal growth factor receptor 2 (HER2) is often overexpressed in breast cancer and correlates with a worse prognosis. Thus, the accurate detection of HER2 is crucial for providing the appropriate measures for patients. However, the current techniques used to detect HER2 status, immunohistochemistry and fluorescence in situ hybridization (FISH), have limitations. Specifically, FISH, which is mandatory for arbitrating 2+ cases, is time-consuming and costly. To address this shortcoming, we established a multiple reaction monitoring-mass spectrometry (MRM-MS) assay that improves on existing methods for differentiating HER2 status.

Methods

We quantified HER2 expression levels in 210 breast cancer formalin-fixed paraffin-embedded (FFPE) tissue samples by MRM-MS. We aimed to improve the accuracy and precision of HER2 quantification by simplifying the sample preparation through predicting the number of FFPE slides required to ensure an adequate amount of protein and using the expression levels of an epithelial cell-specific protein as a normalization factor when measuring HER2 expression levels.

Results

To assess the correlation between MRM-MS and IHC/FISH data, HER2 quantitative data from MRM-MS were divided by the expression levels of junctional adhesion molecule A, an epithelial cell-specific protein, prior to statistical analysis. The normalized HER2 amounts distinguished between HER2 2+/FISH-negative and 2+/FISH-positive groups (AUROC = 0.908), which could not be differentiated by IHC. In addition, all HER2 status were discriminated by MRM-MS.

Conclusions

This MRM-MS assay yields more accurate HER2 expression levels relative to immunohistochemistry and should help to guide clinicians toward the proper treatment for breast cancer patients, based on their HER2 expression.
Breeding success of Eleonora’s Falcon in Cyprus revisited using survey techniques for cliff-nesting species
Authors: Hadjikyriakou Thomas G , Kassinis Nikolaos , Skarlatos Dimitrios , Charilaou Pantelis , Kirschel Alexander N G
Published: July 2020

The global breeding population of Eleonora’s Falcon (Falco eleonorae) is distributed from the Canary Islands in the west, across the Mediterranean Sea, to Cyprus in the east. The remoteness of nesting colonies, which are predominantly located on sea cliffs and islets, renders breeding success estimation a challenging task, requiring a composite approach to assess each of the breeding stages. Early estimates of the breeding success of Eleonora’s Falcon suggested that the Akrotiri colony in Cyprus had the lowest breeding success among all the colonies throughout the species’ breeding range, at a level seemingly unsustainable, suggesting the colony might have been in danger of gradual extinction. Here we use a diversity of survey methods including boat, ground, and aerial surveys, with the incorporation of photography and photogrammetry, to reassess the breeding success and the effect of nest characteristics on the Eleonora’s Falcon breeding population in Cyprus. During a 6-yr study, we found that Cyprus hosts ~138 ± 8 breeding pairs and that breeding success equals 1.54 ± 0.85 fledglings per breeding pair, and thus is considerably higher than previous estimates. In addition, by analyzing temporal variation in breeding and nest characteristics, we found that early breeding and reuse of nests positively influence breeding success, but physical nest characteristics have a limited effect on colony productivity. The range of survey methods employed, as well as the array of photography techniques utilized, enhanced the efficiency and accuracy of this study, allowing us to overcome the challenge of inaccessibility of nesting cliffs.
Intervention Outcomes, Anxiety, Self-Esteem, and Self-Efficacy With DHH Students in Universities
Authors: Pandya Samta P
Published: July 2020

This article reports the impact of an online spiritual counseling (OSC) program in mitigating anxiety and building self-esteem and academic self-efficacy among deaf and hard-of-hearing (DHH) students in universities. Compared to online relaxation sessions, the OSC was more effective. Male DHH students and those whose parents were highly qualified exhibited less anxiety and higher self-esteem and self-efficacy at pretest (T1). Post-test (T2) male students having better educated parents responded better to the OSC. T2 anxiety was lower and self-esteem and academic self-efficacy was higher for liberal arts students and having stay-at-home parents compared with science and commerce students and whose parents worked outside home. Self-esteem was also positively moderated by better economic class and presence of siblings. Intervention compliance in terms of regular attendance and self-practice mediated the relationship between sociodemographic predictors and outcomes. Results support the biopsychosocial model and encourage the implementation of the OSC with DHH university students.
Effects of Vocal Training on Thyroarytenoid Muscle Neuromuscular Junctions and Myofibers in Young and Older Rats
Authors: Shembel Adrianna C , Lenell Charles , Chen Sophia , Johnson Aaron M
Published: July 2020

The purpose of this investigation was to determine the effects of vocal training on neuromuscular junction (NMJ) morphology and muscle fiber size and composition in the thyroarytenoid muscle, the primary muscle in the vocal fold, in younger (9-month) and older (24-month) Fischer 344 × Brown Norway male rats. Over 4 or 8 weeks of vocal training, rats of both ages progressively increased their daily number of ultrasonic vocalizations (USVs) through operant conditioning and were then compared to an untrained control group. Neuromuscular junction morphology and myofiber size and composition were measured from the thyroarytenoid muscle. Acoustic analysis of USVs before and after training quantified the functional effect of training. Both 4- and 8-week training resulted in less NMJ motor endplate dispersion in the lateral portion of the thyroarytenoid muscle in rats of both ages. Vocal training and age had no significant effects on laryngeal myofiber size or type. Vocal training resulted in a greater number of USVs with longer duration and increased intensity. This study demonstrated that vocal training induces laryngeal NMJ morphology and acoustic changes. The lack of significant effects of vocal training on muscle fiber type and size suggests vocal training significantly improves neuromuscular efficiency but does not significantly influence muscle strength changes.
Vaginal neutrophils eliminate sperm by trogocytosis
Authors: Olivera-Valle I , Latorre M C , Calvo M , Gaspar B , Gómez-Oro C , Collazos A , Breton A , Caballero-Campo P , Ardoy M , Asensio F , Sánchez-Mateos P , Pérez-Millan F , Relloso M
Published: July 2020

STUDY QUESTION

What is the vaginal polymorphonuclear (PMN) spermicidal mechanism to reduce the excess of sperm?

SUMMARY ANSWER

We show that PMNs are very efficient at killing sperm by a trogocytosis-dependent spermicidal activity independent of neutrophil extracellular traps (NETs).

WHAT IS KNOWN ALREADY

Trogocytosis has been described as an active membrane exchange between immune cells with a regulatory purpose. Recently, trogocytosis has been reported as a mechanism which PMNs use to kill tumour cells or Trichomonas vaginalis.

STUDY DESIGN, SIZE, DURATION

We used in vivo murine models and human ex vivo sperm and PMNs to investigate the early PMN–sperm response.

PARTICIPANTS/MATERIALS, SETTING, METHODS

We set up a live/dead sperm detection system in the presence of PMNs to investigate in vivo and ex vivo PMN-spermicidal activity by confocal microscopy, flow cytometry and computer-assisted sperm analysis (SCA).

MAIN RESULTS AND THE ROLE OF CHANCE

We revealed that PMNs are highly efficient at killing sperm by way of a NETs-independent, contact-dependent and serine proteases-dependent engulfment mechanism. PMNs ‘bite’ sperm and quickly reduce sperm motility (within 5 min) and viability (within 20 min) after contact.

LARGE SCALE DATA

N/A

LIMITATIONS, REASONS FOR CAUTION

This study was conducted using murine models and healthy human blood PMNs; whether it is relevant to human vaginal PMNs or to cases of infertility is unknown.

WIDER IMPLICATIONS OF THE FINDINGS

Vaginal PMNs attack and immobilize excess sperm in the vagina by trogocytosis because sperm are exogenous and may carry pathogens. Furthermore, this mechanism of sperm regulation has low mucosal impact and avoids an exacerbated inflammatory response that could lead to mucosal damage or infertility.

STUDY FUNDING/COMPETING INTEREST(S)

This work was partially supported by Ministry of Economy and Competitiveness ISCIII-FIS grants, PI16/00050, and PI19/00078, co-financed by ERDF (FEDER) Funds from the European Commission, ‘A way of making Europe’ and IiSGM intramural grant II-PI-MRC-2017. M.R. holds a Miguel Servet II contract (CPII14/00009). M.C.L. holds IiSGM intramural contract. There are no competing interests.
The Effects of Roughness and Wetness on Salamander Cling Performance
Authors: O’Donnell Mary Kate , Deban Stephen M
Published: July 2020

Synopsis

Animals clinging to natural surfaces have to generate attachment across a range of surface roughnesses in both dry and wet conditions. Plethodontid salamanders can be aquatic, semi-aquatic, terrestrial, arboreal, troglodytic, saxicolous, and fossorial and therefore may need to climb on and over rocks, tree trunks, plant leaves, and stems, as well as move through soil and water. Sixteen species of salamanders were tested to determine the effects of substrate roughness and wetness on maximum cling angle. Substrate roughness had a significant effect on maximum cling angle, an effect that varied among species. Substrates of intermediate roughness (asperity size 100–350 µm) resulted in the poorest attachment performance for all species. Small species performed best on smooth substrates, while large species showed significant improvement on the roughest substrates (asperity size 1000–4000 µm), possibly switching from mucus adhesion on a smooth substrate to an interlocking attachment on rough substrates. Water, in the form of a misted substrate coating and a flowing stream, decreased cling performance in salamanders on smooth substrates. However, small salamanders significantly increased maximum cling angle on wetted substrates of intermediate roughness, compared with the dry condition. Study of cling performance and its relationship to surface properties may cast light onto how this group of salamanders has radiated into the most speciose family of salamanders that occupies diverse habitats across an enormous geographical range.
Resolution of the identity ofPinnotheres latipesHombron & Jacquinot, 1846 and description of a new species ofViridotheresManning, 1996 (Decapoda: Brachyura: Pinnotheridae): two symbionts of bivalve molluscs
Authors: Ahyong Shane T
Published: July 2020

Pinnotherid crabs are well known as obligate associates of other marine invertebrates, frequently bivalve molluscs. Knowledge of the Australian pinnotherid crab fauna is expanded by description of a new species of Viridotheres Manning, 1996, representing the first record of the genus from Western Australia. The new species of Viridotheres is most similar to V. gracilis (Bürger, 1895) from the Philippines and V. takedai Ahyong, Komai & Watanabe, 2012 from Japan, but is unique in the genus in the elongated maxilliped 3 palp that distinctly overreaches the propodal apex. The identity of the poorly known northern Australian species, Pinnotheres latipes Hombron & Jacquinot, 1846, originally described from the Northern Territory, is resolved by designation of a neotype that places the species in the genus Nepinnotheres Manning, 1993. Nepinnotheres latipescomb. nov. is widespread in northern Australia and commonly hosted by the bivalve mollusc Pinna Linnaeus, 1758. Previous Australian records of Nepinnotheres cardii (Bürger, 1895) and N. edwardsi (De Man, 1888) from Australia are referable to N. latipes. Nepinnotheres latipes is one of only five known pinnotherids having androgynous males. Few pinnotherids are known from males, so estimating the extent of androgyny in Pinnotheridae must await discovery of males of additional species.