bluuebunny/crossref_metadata_2025 huggingface dataset:
The Structural and Optical Band Gap Energy Evaluation of TiO2-Fe2O3 Composite
Authors: Iqbal Rendy Muhamad , Pramoda Wardani Dyah Ayu , Hakim Luqman , Damsyik Akhmad , Safitri Riaa , Fansuri Hamzah
Published: July 2020

Solar cells, one of which is Dye Sensitizer Solar Cell (DSSC), are promising alternative energy in the 2000s. Compared to many other energy sources, solar cell does not emit waste (clean energy). An important component that generates electricity in DSSC is photoanode. TiO2, the most widely used materials as photoanodes in the current era, is widely used photoanode although the energy gap of the TiO2 band is quite large (3.43 eV). This study aims to reduce the energy gap of TiO2 band by forming composites with Fe2O3. Various compositions of TiO2 and Fe2O3 fine powders mixtures were dispersed in methanol and stirred until homogeneous in order to synthesize the photoanode. The methanol was then evaporated to obtain a dried mixture of solids, followed by calcination to form composites. The resulted composites were characterized by XRD and Diffuse Reflectance UV-Vis Spectrophotometer. XRD analysis results showed that the composites are composed of TiO2 and Fe2O3 mixtures. Diffuse Reflectance UV-Vis analysis results showed that there was a change in bandgap energy due to the mixing of TiO2 with Fe2O3. The lowest band gap energy is 2.67 eV at 1: 4 ratios. The smallest and largest refractive index values calculated by the Ravindra relation are 2.0725 and 2.4286, respectively. The refractive index value is the reversely proportional of the band gap energy value, the greater the band gap energy, the smaller the refractive index value.
Effect of sonication frequency in synthesis of silica aerogel-activated carbon nanocomposite
Authors: Muthomimah Siti , Rahayu Widi , Nazriati  , Aliyatulmuna Adilah
Published: July 2020

The silica adsorption capacity can be improved by composing it with activated carbon. The study aims to know the effect of sonication frequency in the nanocomposite silica aerogel-activated carbon synthesis using sol-gel method with TMCS (trimethylchlorosilane) and HMDS (hexamethyldisilazane) as modifying agents. Synthesized nanocomposites were further characterized by means of functional groups analysis using FTIR (Fourier Transform Infrared Spectrophotometry) method, morphological analysis using SEM (Scanning Electron Microscopy) method, and surface area analysis using BET (Brunauer-Emmet-Teller) method. The results of functional group analysis using FTIR shows that nanocomposite has a group of Si - OH, Si - O - Si, Si – C, C - H, C = O, C – O, the peaks around of 3300 cm−1, 1051 cm−1 - 1180 cm−1, 1253 cm−1, 2960 cm−1, 1649 cm−1, 1417 cm−1; morphological analysis using SEM indicates that nanocomposite synthesis with 42 kHz frequency sonication has a smaller particle size than 35 kHz frequency, where are the surface area analysis using BET method obtained 674.897 m! / g at frequency of 42 kHz and 486.909 m2 / g synthesis at frequency of 35 kHz.
Optical Emission Spectroscopy Study of the Electron Temperature and Electron Density Dependence on the Pressure Chamber for the Carbon Deposition Produced by Argon Plasma Sputtering
Authors: Pambudi D R S , Hanif M A , Santjojo D J D H , Padaga M C , Masruroh
Published: July 2020

An investigation of the Optical Emission Spectroscopy (OES) to study the effect of the pressure chamber to the chemical species, electron temperature (Te) and electron density (Ne) was performed on RF 2 MHz plasma sputtering for carbon deposition. A carbon target and argon (Ar) gas were used to deposit carbon films. The carbon deposition was carried out at pressure chamber of 10, 15 and 20 Pa, and the RF voltage, flow rate and substrate temperature were kept at 120 volts, 60 ml/min, and 200°C, respectively. The emission spectrum of Ar plasma was monitored by OES in order to analyze the chemical species present in the plasma during the deposition process. The atomic spectroscopy data center (NIST) database was used to determine the species in the plasma and to calculate the Te and Ne. The OES emission shows the peak intensity which indicates the Ar I (Ar*) and Ar II (Ar+ ion). The electron temperature was calculated using the Boltzmann Plot while the electron density was calculated using Stark Broadening. The results show that both Te and Ne decreased on the increasing of the pressure chamber. The emission line measurements with Boltzmann Plot resulted in the electron temperature dependence of pressure is approximately 0.487±0.005, 0.481±0.006, and 0.474±0.011 eV, respectively. Moreover, the calculation of electron density resulted in approximately (5.495 ± 0.407) × 1018, (4.825 ± 0.384) × 1018, and (4.515 ± 1.037) × 1018 cm−3.
The Effect of SrO Impregnation on The Characteristics of Cobalt Ferrite (CoFe2O4) Nanoparticles Synthesized by Coprecipitation
Authors: Primadi Thutug Rahardiant , Santoso Aman , Fajaroh Fauziatul
Published: July 2020

Cobalt Ferrite (CoFe2O4) nanoparticles are magnetic materials that have greater hardness than Fe3O4. CoFe2O4 is widely applied in many fields, including as a heterogeneous catalyst in various chemical reactions such as photocatalysis, phenol degradation, and transesterification reactions. This is supported by the thermal and chemical stability possessed by CoFe2O4. Coating or impregnation of non-magnetic material on the surface of the ferrite, on one side will reduce its magnetism and possibly its surface area. But on the other hand, the positive impact of coating or impregnation is the increase in particle monodispersity. Weakening the magnetism of the particles will reduce the interaction of attraction between particles, so that the particles are getting more monodisperse. This will optimize its potential as a heterogeneous catalyst. In this research impregnation of strontium oxide (SrO) would be carried out on the surface of CoFe2O4. After that, the characters were compared with CoFe2O4 before being impregnated. The CoFe2O4 synthesis was carried out through the coprecipitation method, followed by wet impregnation with SrO. The results showed that the impregnation of SrO on CoFe2O4 increased the zeta potential of the particles which indicated the stability of the particles in the dispersion.
Effect of Sonication Time on Characteristics of Synthesized Silica Aerogel Activated Carbon Nanocomposite Based on Bagasse Ash
Authors: Rahayu Widi , Muthomimah Siti , Sumari Sumari , Nazriati Nazriati
Published: July 2020

The purpose of this research was to identify the effect of sonication time on the characteristics of silica aerogel activated carbon (SA-AC) nanocomposite produced based on bagasse ash. SA-AC nanocomposites was synthesized by sol-gel method at ambient pressure. The silicic acid solution was mixed with activated carbon and the surface modifying agent (TMCS and HDMS). The mixture was then put in an ultrasonic bath at the varying sonication time of 5, 10, 15, and 20 seconds on frequency of 42 kHz. SA-AC nanocomposites were characterized by using FTIR, SEM, and BET. The results showed that SA-AC is formed, indicated by the wave number FTIR spectra of Si-O-Si (1076.28 cm−1), Si-C (1253.73 cm−1), C-H (2960.73 cm−1), C-O (1087.85 cm−1), C=C (2113.98 cm−1), and C=O (1942.32 cm−1). SA-AC nanocomposites synthesized by sonication assistence has a smaller agglomerate than that of without sonication. The largest surface area of SA-AC nanocomposite of 677.719 m2/g and the biggest pore volume of 0.6338 m3/g is obtained when the nanocomposite is synthesized at sonication time of 10 seconds
Inexpensive solar cell using TiO2/coffee composite as photon absorbing material
Authors: Rahman D Y , Utami F D , Margaretta D O , Amalia N , Sulistyowati R , Abdullah M
Published: July 2020

Solar cell using TiO2/coffee composite as photon absorbing material has been successfully fabricated. A suspension of TiO2/coffee was dropped on Fluorine Tin Oxide substrate which was previously heated on a hotplate with temperature of 100 °C. The fraction of coffee was varied from 10, 20, 30, 40, and 50 %, compared to the mass of TiO2. PVA-LiOH electrolyte polymer was functionalized as the hole transport medium. The highest efficiency of 0.76 % was achieved with 40% of coffee fraction. The solar cell is promising to be developed in the future due to the easy method and cheap materials used.
Preparation of Silver-Incorporated Rhynchospora corymbosa (L.) Cellulose via in-situ Green Reduction and Its Antibacterial Study
Authors: Rosdiana Fitri , Falahudin Aswin , Wibowo Risky Hadi , Yudha S. Salprima , Gustian Irfan
Published: July 2020

Silver incorporated R. corymbosa (L.) cellulose was obtained through the direct attachment (insertion) of silver ions to natural cellulose, followed by the green reduction of ions to metallic silver, using aqueous extract of fresh R. corymbosa (L.). In addition, Fourier transform infra-red (FTIR) analysis of the isolated cellulose showed some peaks at 3330 cm−1, 2890 cm−1, 1320 cm−1, 1030 cm−1, 895 cm−1 corresponding to OH stretching, methylene (-CH2-) stretching, OH bonding, C-O bonding, and 1,4 β-glycoside, respectively. The silver incorporated R. corymbosa (L.) cellulose was prepared by impregnating silver ions obtained from silver nitrate solution, followed by ion reduction to the metallic silver in-situ. Furthermore, another interesting outcome of this study is seen in the products’ ability to show inhibition zones in the growth medium of Escherichia coli.
Impedance Spectrum of QCM Sensor Coated With 18-Crown-6-Ether Solved in THF, Chloroform and Toluene
Authors: Setiana Mira , Zafirah Tyas N. , Masruroh  , Istiroyah  , Sakti Setyawan P.
Published: July 2020

Crown ether is a form of ethylene oxide cyclo-oligomer. Crown ether has a strong ability to form a complex with cations. The crown ether has been used as part of the electrochemical sensor and optical sensor because of its selectivity to several cations. There was no report on the use of the 18-crown-6-ether as a single coating layer on the QCM sensor. This work investigates the loading effect of the 18-crown-6-ether as a selective coating for QCM sensors as a pre-requirement for a selective coating layer. The impedance spectrum of the QCM sensor coated with 18-crown-6-ether at different concentrations solved in three different solvents was measured. The effects of solvents and 18-crown-6-ether concentrations to the calculated thickness and the effect of the QCM sensor impedance was investigated. The solvents used are Toluene, Tetrahydrofuran (THF), and Chloroform. The results show that the film behaves like a rubber material, which is shown by the impedance value of the sensor at the series resonance frequency. It can be concluded that the thickness of the 18-crown-6-ether layer must be maintained less than one μm to avoid damping on the QCM sensor.
Effect of sulfur and sodium sulfate on phase transformation and microstructure on carbothermic reduction of Indonesian ilmenite
Authors: Setiawan Agung , Harjanto Sri
Published: July 2020

Utilization of ilmenite and pulverized biomass of palm kernel shell is a beneficial solution to deal with the depletion of high-grade titanium minerals and manage of palm oil waste. The purposes of this research are to analysis the phase transformation and microstructure with additive addition. Sulfur and sodium sulfate have used an additive with an additional dosage of 0%, 1.5%, 3.0%, and 4.5%, and the reductant was the pulverized palm kernel shell biomass. The ilmenite concentrate was reduced at 1200 °C for 60 minutes in inert condition (N2 atmosphere). Testing methods performed are Optical microscope (OM), X-Ray diffraction (XRD), Field-Emission Scanning Electron Microscopy (FE-SEM), and Energy Dispersive X-ray spectroscopy (EDX), calculating of the average particle size, and metal recovery. The results showed that the active additive used was sodium sulfate compared to sulfur. At the addition of 4.5 wt.% sodium sulfate, it was obtained phases of titanium suboxide, Ti6O11 and Ti3O5, with very high intensity. Recovery and grades of the reduced sample with 4.5 wt.% sodium sulfate are reached 70.91% and 94.20% Fe, respectively. Moreover, the average particle size of metallic iron increased from 11.96 μm to 38.36 μm with the addition of 4.5wt.% sodium sulfate.
The Fabrication of Zn-Zr Alloy through Centrifugal Casting and Box Furnace Method for Implant Application
Authors: Trinanda Achmad Fauzi , Ghani Fahmi Moh Waqyan , Pratiwi Rizki Yuni , Zakiyuddin Ahmad , Astutiningsih Sotya
Published: July 2020

Recently, zinc (Zn) is extensively observed as biomaterial or biodegradable implant for medical application. A biomaterial is any substance that has been engineered to interact with biological systems for a medical purpose. Zn is chosen because it has moderate degradation compared to Mg and Fe. Unfortunately, Zn has limitation on its mechanical properties that still low. The Alloying element is needed to improve the mechanical properties of Zn. Alloying element, such as zirconium (Zr) can improve the mechanical properties of Zn. In this study the addition of Zr with the composition variations of 0%, 0.5%, 1%, and 2% were used. Two kinds of alloying method used are centrifugal casting and box furnace with a temperature of 550°C. The aims of this study are to know the effect of each fabrication method to the mechanical properties and the result of Zn-Zr alloy microstructures. The results show that the microstructure of the alloy from centrifugal casting is more homogenous than the box furnace method. The mechanical properties of centrifugal casting are also higher than the box furnace method. The hardness value obtained from centrifugal casting of 0, 0.5, 1, 1.5 and 2% of Zr are 35.162 HV, 41.988 HV, 42.324 HV, 57.112 HV, respectively.
Ibuprofen Adsorption Study by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich Models Using Nano Zinc Oxide from Mild Hydrothermal Condition
Authors: Ulfa Maria , Iswanti Yuli
Published: July 2020

Ibuprofen in the aquatic area as inflammatory drug residue is dangerous for environmental sustainability. The removal of ibuprofen at the aquatic area is carried out on nano zinc oxide (NZO) as an adsorbent. The NZO adsorbent was synthesized by gelatin self-assembly as a green method and characterized by FT-IR and XRD techniques. The residual ibuprofen model was prepared by dissolution of ibuprofen in water-hexane at ratio 10:0; 1:9; 5:5, 9:1 and 0:10. The optimized batch of experimental parameters were 100 ppm for 55 min at room temperature. Adsorption data was investigated by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich models. The result shows that Temkin model is the best model for describing the adsorption mechanism between ibuprofen as adsorbate and zinc oxide as an adsorbent. The adsorption capacity of 9:1 is the highest on that ibuprofen adsorption indicated that the composition of both solvents is favorable for ibuprofen dissolution due to polar-nonpolar interaction which is reaching 92% removal of ibuprofen. In the future, zinc oxide as adsorbent may be used for the removal of ibuprofen from any aquatic core area due to the economic and environmental reason.
Intracellular delivery of nanoparticles fabricated from monoclonal and polyclonal antibodies against influenza A and hepatitis B virus antigens
Authors: Morozova O.V. , Pavlova E.R. , Isaeva E.I. , Sokolova A.I. , Obraztsova E.A. , Ivleva E.A. , Klinov D.V.
Published: July 2020

Specific antibodies (AB) may serve as molecular tools for both targeted, etiotropic and immunomodulation therapy of the infectious and oncological diseases. Despite their ability to bind with extracellular virions and isolated viral antigens AB may not pass through host cell membranes to inhibit intracellular infectious agents. Nanoparticles (NP) were fabricated from polyclonal and monoclonal AB against the influenza A structural and non-structural proteins as well as against the hepatitis B virus surface antigen (HBsAg). ELISA and immunofluorescent analysis revealed the ligand-binding activity of the AB NP comparable with the properties of the original AB. Fluorescent microscopy and quantitation showed efficient cellular uptake of the labeled AB NP and their degradation in 5 days posttreatment. Intracellular AB NP induced interferon (IFN) gene expression but not interleukin (IL) 4 and IL10 transcription. The cytokines mediated immunomodulation potential of the protein NP.
Analysis of different microcracks shapes and the effect of each shape on performance of PV modules
Authors: Bdour Mathhar , Al-Sadi Aseel
Published: July 2020

Photovoltaic solar panels became the world’s largest distributed Renewable technology through its easy manufacturing and installation, moreover, the cost of photovoltaic panels falls continuously which provided a safe environment to investors to invest in such systems. The Photovoltaic solar panel made from different layers starting from anti reflected coated glass layer, encapsulation material, solar cells matrix another encapsulant layer and back sheet. This structure does not provide the needed protection to the solar cells encapsulated inside and there will be a possibility of microcracks happen at different stages of the project life cycle starting from the production, transportation, installation, cleaning and operation, and maintenance stage. Through this research, modules from different projects were tested to see the microcracks and their effect. Results show that those cracks can cause a power drop up to 3.21% depending on the type of the module. Furthermore, microcracks are classified as minor and major ones based on their shape, dendritic and vertical shapes are resulted to be the most severe ones.
Study of printed polymeric flexible energy harvesting elements – impact of the electrode materials and patterns
Authors: Aleksandrova M , Aepuru R , Dobrikov G
Published: July 2020

In this paper is presented study of flexible pressure piezoelectric energy harvesting developed with an screen-printing of polyvinylidene fluoride-trifluoroethylene (P(VDF-TrFE)) ink on three different metal electrodes (silver, gold and aluminium) with three different topologies – rectangular, meander and side comb. The influence of the electrode type and pattern is studied in terms of polymer coating distribution and morphology, piezoelectric voltage generation and stability at multiple bending, as well as piezoelectric coefficient. The elements are studied at low mass loading of up to 100 g and frequency up to 50 Hz. They produce voltage between 916 and 362 mV from active area of 1 cm2 and piezoelectric polymer film of 3 μm, according to the electrode metal nature and shape. It was found that the silver electrode with meander shape is the optimal for electrical performance and mechanical stability giving superior piezoelectric coefficient of 0.332 V.m/N to the reported values and only 8.6 % decrease of the piezoelectric voltage at 1500 repeating bending cycles.
Laser induced resistivity of chiral single wall carbon nanotubes
Authors: Twum Anthony , Mensah Samuel Yeboah , Edziah Raymond , Arthur Augustine
Published: July 2020

Using the Boltzmann transport equation within the semi-classical approximation with constant relaxation time, we theoretically studied the dynamics of electrons in chiral single wall nanotubes (SWNTs) subjected to a temperature gradient (∇T) in the presence of a combined direct current and high frequency alternating fields. We obtained an expression for the resistivity (ρ

c
) of the SWNTs which varies with temperature and depends among others on material’s chiral angle (θ
h), dc field strength (Eo) and ac field amplitude (Es). Our results show that chiral SWNTs exhibit metallic behavior with resistivity increasing approximately linearly with temperature over a wide temperature range well above 100 K. Based on the low chiral resistivity obtained for the SWNTs at room temperatures, we propose these materials as good candidates for possible optoelectronic applications.
Social Distancing as a Health Behavior: County-Level Movement in the United States During the COVID-19 Pandemic Is Associated with Conventional Health Behaviors
Authors: Bourassa Kyle J , Sbarra David A , Caspi Avshalom , Moffitt Terrie E
Published: July 2020

Background

Social distancing—when people limit close contact with others outside their household—is a primary intervention available to combat the COVID-19 pandemic. The importance of social distancing is unlikely to change until effective treatments or vaccines become widely available. However, relatively little is known about how best to promote social distancing. Applying knowledge from social and behavioral research on conventional health behaviors (e.g., smoking, physical activity) to support public health efforts and research on social distancing is promising, but empirical evidence supporting this approach is needed.

Purpose

We examined whether one type of social distancing behavior—reduced movement outside the home—was associated with conventional health behaviors.

Method

We examined the association between GPS-derived movement behavior in 2,858 counties in USA from March 1 to April 7, 2020 and the prevalence of county-level indicators influenced by residents’ conventional health behaviors.

Results

Changes in movement were associated with conventional health behaviors, and the magnitude of these associations were similar to the associations among the conventional health behaviors. Counties with healthier behaviors—particularly less obesity and greater physical activity—evidenced greater reduction in movement outside the home during the initial phases of the pandemic in the USA.

Conclusions

Social distancing, in the form of reduced movement outside the home, is associated with conventional health behaviors. Existing scientific literature on health behavior and health behavior change can be more confidently used to promote social distancing behaviors during the COVID-19 pandemic.
Bayesian Pathway Analysis for Complex Interactions
Authors: Baurley James W , Kjærsgaard Anders , Zwick Michael E , Cronin-Fenton Deirdre P , Collin Lindsay J , Damkier Per , Hamilton-Dutoit Stephen , Lash Timothy L , Ahern Thomas P
Published: July 2020

Modern epidemiologic studies permit investigation of the complex pathways that mediate effects of social, behavioral, and molecular factors on health outcomes. Conventional analytical approaches struggle with high-dimensional data, leading to high likelihoods of both false-positive and false-negative inferences. Herein, we describe a novel Bayesian pathway analysis approach, the algorithm for learning pathway structure (ALPS), which addresses key limitations in existing approaches to complex data analysis. ALPS uses prior information about pathways in concert with empirical data to identify and quantify complex interactions within networks of factors that mediate an association between an exposure and an outcome. We illustrate ALPS through application to a complex gene-drug interaction analysis in the Predictors of Breast Cancer Recurrence (ProBe CaRe) Study, a Danish cohort study of premenopausal breast cancer patients (2002–2011), for which conventional analyses severely limit the quality of inference.
How to Write About Superheroes
Authors: Burt Stephanie
Published: July 2020

Eighty years after the first Superman comic, scholars are catching up to the importance, and to the popularity, of superheroes in comics and in other media. Recent monographs and edited collections examine racial politics, disabilities, other identities, and reception history across a range of decades and of superhero characters. Most of these worthy works remain within the limits of critique, judging the comics on how well they handle one or another theme; the result is a picture of superhero comics that cannot do justice to the genre. To them and to their like, the academic critics of the future might add—what vernacular comics critics already contribute—additional attention to what one or another character does best, to the transformative potential of even minor superhero work, and to how commercially produced superhero comics at their best handle narrative form.

One superhero symbol can work many ways, as Neal Curtis’s examination of Truth and other Captain America stories shows: Cap has repeatedly fought off right-wing doubles, alternatively costumed versions of himself who aspired to make America white again.
Philosophical proofs against common sense
Authors: Frances Bryan
Published: July 2020

Many philosophers are sceptical about the power of philosophy to refute commonsensical claims. They look at the famous attempts and judge them inconclusive. I prove that, even if those famous attempts are failures, there are alternative successful philosophical proofs against commonsensical claims. After presenting the proofs I briefly comment on their significance .
DNA Features Viewer: a sequence annotation formatting and plotting library for Python
Authors: Zulkower Valentin , Rosser Susan
Published: July 2020

Motivation

Although the Python programming language counts many Bioinformatics and Computational Biology libraries; none offers customizable sequence annotation visualizations with layout optimization.

Results

DNA Features Viewer is a sequence annotation plotting library which optimizes plot readability while letting users tailor other visual aspects (colors, labels, highlights etc.) to their particular use case.

Availability and implementation

Open-source code and documentation are available on Github under the MIT license (https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer).

Supplementary information

Supplementary data are available at Bioinformatics online.
EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM
Authors: Lim Dongjoon , Blanchette Mathieu
Published: July 2020

Motivation

Accurate probabilistic models of sequence evolution are essential for a wide variety of bioinformatics tasks, including sequence alignment and phylogenetic inference. The ability to realistically simulate sequence evolution is also at the core of many benchmarking strategies. Yet, mutational processes have complex context dependencies that remain poorly modeled and understood.

Results

We introduce EvoLSTM, a recurrent neural network-based evolution simulator that captures mutational context dependencies. EvoLSTM uses a sequence-to-sequence long short-term memory model trained to predict mutation probabilities at each position of a given sequence, taking into consideration the 14 flanking nucleotides. EvoLSTM can realistically simulate mammalian and plant DNA sequence evolution and reveals unexpectedly strong long-range context dependencies in mutation probabilities. EvoLSTM brings modern machine-learning approaches to bear on sequence evolution. It will serve as a useful tool to study and simulate complex mutational processes.

Availability and implementation

Code and dataset are available at https://github.com/DongjoonLim/EvoLSTM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions
Authors: Yan Zichao , Hamilton William L , Blanchette Mathieu
Published: July 2020

Motivation

RNA-protein interactions are key effectors of post-transcriptional regulation. Significant experimental and bioinformatics efforts have been expended on characterizing protein binding mechanisms on the molecular level, and on highlighting the sequence and structural traits of RNA that impact the binding specificity for different proteins. Yet our ability to predict these interactions in silico remains relatively poor.

Results

In this study, we introduce RPI-Net, a graph neural network approach for RNA-protein interaction prediction. RPI-Net learns and exploits a graph representation of RNA molecules, yielding significant performance gains over existing state-of-the-art approaches. We also introduce an approach to rectify an important type of sequence bias caused by the RNase T1 enzyme used in many CLIP-Seq experiments, and we show that correcting this bias is essential in order to learn meaningful predictors and properly evaluate their accuracy. Finally, we provide new approaches to interpret the trained models and extract simple, biologically interpretable representations of the learned sequence and structural motifs.

Availability and implementation

Source code can be accessed at https://www.github.com/HarveyYan/RNAonGraph.

Supplementary information

Supplementary data are available at Bioinformatics online.
Artificial-cell-type aware cell-type classification in CITE-seq
Authors: Lian Qiuyu , Xin Hongyi , Ma Jianzhu , Konnikova Liza , Chen Wei , Gu Jin , Chen Kong
Published: July 2020

Motivation

Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), couples the measurement of surface marker proteins with simultaneous sequencing of mRNA at single cell level, which brings accurate cell surface phenotyping to single-cell transcriptomics. Unfortunately, multiplets in CITE-seq datasets create artificial cell types (ACT) and complicate the automation of cell surface phenotyping.

Results

We propose CITE-sort, an artificial-cell-type aware surface marker clustering method for CITE-seq. CITE-sort is aware of and is robust to multiplet-induced ACT. We benchmarked CITE-sort with real and simulated CITE-seq datasets and compared CITE-sort against canonical clustering methods. We show that CITE-sort produces the best clustering performance across the board. CITE-sort not only accurately identifies real biological cell types (BCT) but also consistently and reliably separates multiplet-induced artificial-cell-type droplet clusters from real BCT droplet clusters. In addition, CITE-sort organizes its clustering process with a binary tree, which facilitates easy interpretation and verification of its clustering result and simplifies cell-type annotation with domain knowledge in CITE-seq.

Availability and implementation

http://github.com/QiuyuLian/CITE-sort.

Supplementary information

Supplementary data is available at Bioinformatics online.
Copy number evolution with weighted aberrations in cancer
Authors: Zeira Ron , Raphael Benjamin J
Published: July 2020

Motivation

Copy number aberrations (CNAs), which delete or amplify large contiguous segments of the genome, are a common type of somatic mutation in cancer. Copy number profiles, representing the number of copies of each region of a genome, are readily obtained from whole-genome sequencing or microarrays. However, modeling copy number evolution is a substantial challenge, because different CNAs may overlap with one another on the genome. A recent popular model for copy number evolution is the copy number distance (CND), defined as the length of a shortest sequence of deletions and amplifications of contiguous segments that transforms one profile into the other. In the CND, all events contribute equally; however, it is well known that rates of CNAs vary by length, genomic position and type (amplification versus deletion).

Results

We introduce a weighted CND that allows events to have varying weights, or probabilities, based on their length, position and type. We derive an efficient algorithm to compute the weighted CND as well as the associated transformation. This algorithm is based on the observation that the constraint matrix of the underlying optimization problem is totally unimodular. We show that the weighted CND improves phylogenetic reconstruction on simulated data where CNAs occur with varying probabilities, aids in the derivation of phylogenies from ultra-low-coverage single-cell DNA sequencing data and helps estimate CNA rates in a large pan-cancer dataset.

Availability and implementation

Code is available at https://github.com/raphael-group/WCND.

Supplementary information

Supplementary data are available at Bioinformatics online.
DNA Chisel, a versatile sequence optimizer
Authors: Zulkower Valentin , Rosser Susan
Published: July 2020

Motivation

Accounting for biological and practical requirements in DNA sequence design often results in challenging optimization problems. Current software solutions are problem-specific and hard to combine.

Results

DNA Chisel is an easy-to-use, easy-to-extend sequence optimization framework allowing to freely define and combine optimization specifications via Python scripts or Genbank annotations.

Availability and implementation

The framework is available as a web application (https://cuba.genomefoundry.org/sculpt_a_sequence) or open-source Python library (see at https://github.com/Edinburgh-Genome-Foundry/DNAChisel for code and documentation).

Supplementary information

Supplementary data are available at Bioinformatics online.
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
Authors: Morgan-Lang Connor , McLaughlin Ryan , Armstrong Zachary , Zhang Grace , Chan Kevin , Hallam Steven J
Published: July 2020

Motivation

Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate.

Results

We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.

Availability and implementation

TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https://github.com/hallamlab/TreeSAPP.

Supplementary information

Supplementary data are available at Bioinformatics online.
ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant
Authors: Gallant James Luke , Heunis Tiaan , Sampson Samantha Leigh , Bitter Wilbert
Published: July 2020

Proteomics is a powerful tool for protein expression analysis and is becoming more readily available to researchers through core facilities or specialized collaborations. However, one major bottleneck for routine implementation and accessibility of this technology to the wider scientific community is the complexity of data analysis. To this end, we have created ProVision, a free open-source web-based analytics platform that allows users to analyze data from two common proteomics relative quantification workflows, namely label-free and tandem mass tag-based experiments. Furthermore, ProVision allows the freedom to interface with the data analysis pipeline while maintaining a user-friendly environment and providing default parameters for fast statistical and exploratory data analysis. Finally, multiple customizable quality control, differential expression plots as well as enrichments and protein–protein interaction prediction can be generated online in one platform.

Availability and implementation

Quick start and step-by-step tutorials as well as tutorial data are fully incorporated in the web application. This application is available online at https://provision.shinyapps.io/provision/ for free use. The source code is available at https://github.com/JamesGallant/ProVision under the GPL version 3.0 license.
Naked mole rat (HETEROCEPHALUS GLABER)
Authors: Wicks Ian
Published: July 2020

Enriching BioScience's role as a Forum for Integrating the Life Sciences, Arts in Science provides an occasional venue for poems, visual art, and other forms of artistic expression that explore and enliven our understanding of life. Through the contributions in this section, we hope to share with our readers the passion for nature that science inspires.

This contribution is from Ian Wicks, Head of the Inflammation Division at the Walter and Eliza Hall Institute of Medical Research and Professor/Director of the Rheumatology Unit at the Royal Melbourne Hospital and University of Melbourne.
Oral microbial dysbiosis and its performance in predicting oral cancer
Authors: Su Shih-Chi , Chang Lun-Ching , Huang Hsien-Da , Peng Chih-Yu , Chuang Chun-Yi , Chen Yi-Tzu , Lu Ming-Yi , Chiu Yu-Wei , Chen Pei-Yin , Yang Shun-Fa
Published: July 2020

Dysbiosis of oral microbiome may dictate the progression of oral squamous cell carcinoma (OSCC). Yet, the composition of oral microbiome fluctuates by saliva and distinct sites of oral cavity and is affected by risky behaviors (smoking, drinking and betel quid chewing) and individuals’ oral health condition. To characterize the disturbances in the oral microbial population mainly due to oral tumorigenicity, we profiled the bacteria within the surface of OSCC lesion and its contralateral normal tissue from discovery (n = 74) and validation (n = 42) cohorts of male patients with cancers of the buccal mucosa. Significant alterations in the bacterial diversity and relative abundance of specific oral microbiota (most profoundly, an enrichment for genus Fusobacterium and the loss of genus Streptococcus in the tumor sites) were identified. Functional prediction of oral microbiome shown that microbial genes related to the metabolism of terpenoids and polyketides were differentially enriched between the control and tumor groups, indicating a functional role of oral microbiome in formulating a tumor microenvironment via attenuated biosynthesis of secondary metabolites with anti-cancer effects. Furthermore, the vast majority of microbial signatures detected in the discovery cohort was generalized well to the independent validation cohort, and the clinical validity of these OSCC-associated microbes was observed and successfully replicated. Overall, our analyses reveal signatures (a profusion of Fusobacterium nucleatum CTI-2 and a decrease in Streptococcus pneumoniae) and functions (decreased production of tumor-suppressive metabolites) of oral microbiota related to oral cancer.
Increased Arginase1 expression in tumor microenvironment promotes mammary carcinogenesis via multiple mechanisms
Authors: Croce Michela , Damonte Patrizia , Morini Monica , Pigozzi Simona , Chiossone Laura , Vacca Paola , Bronte Vincenzo , Barbieri Ottavia , Astigiano Simonetta
Published: July 2020

Arginine metabolism plays a significant role in regulating cell function, affecting tumor growth and metastatization. To study the effect of the arginine-catabolizing enzyme Arginase1 (ARG1) on tumor microenvironment, we generated a mouse model of mammary carcinogenesis by crossbreeding a transgenic mouse line overexpressing ARG1 in macrophages (FVBArg+/+) with the MMTV-Neu mouse line (FVBNeu+/+). This double transgenic line (FVBArg+/−;Neu+/+) showed a significant shortening in mammary tumor latency, and an increase in the number of mammary nodules. Transfer of tumor cells from FVBNeu+/+ into either FVB wild type or FVBArg+/+ mice resulted in increase regulatory T cells in the tumor infiltrate, suggestive of an impaired antitumor immune response. However, we also found increased frequency of tumor stem cells in tumors from FVBArg+/−;Neu+/+ transgenic compared with FVBNeu+/+ mice, suggesting that increased arginine metabolism in mammary tumor microenvironment may supports the cancer stem cells niche. We provide in vivo evidence of a novel, yet unexploited, mechanism through which ARG1 may contribute to tumor development.
NF-κB-miR-155 axis activation mediates ovulation-induced oncogenic effects in fallopian tube epithelium
Authors: Brand Hadar , Barnabas Georgina D , Sapoznik Stav , Bahar-Shany Keren , Pozniak Yair , Yung Yuval , Hourvitz Ariel , Geiger Tamar , Jacob-Hirsch Jasmine , Levanon Keren
Published: July 2020

The fallopian tube secretory epithelial cells (FTSECs) are the cell-of-origin of most high-grade serous ovarian carcinomas (HGSOC). FTSECs are repeatedly exposed to inflammation induced by follicular fluid (FF) that is released with every ovulation cycle throughout a woman’s reproductive years. Uninterrupted ovulation cycles are an established risk factor for HGSOC. Stimuli present in the FF induce an inflammatory environment which may cause DNA damage eventually leading to serous tumorigenesis. With the aim of elucidating possible mechanistic pathways, we established an ‘ex vivo persistent ovulation model’ mimicking the repeated exposure of human benign fallopian tube epithelium (FTE) to FF. We performed mass spectrometry analysis of the secretome of the ex vivo cultures as well as confirmatory targeted expressional and functional analyses. We demonstrated activation of the NF-κB pathway and upregulation of miR-155 following short-term exposure of FTE to human FF. Increased expression of miR-155 was also detected in primary HGSOC tumors compared with benign primary human FTE and corresponded with changes in the expression of miR-155 target genes. The phenotype of miR-155 overexpression in FTSEC cell line is of increased migratory and altered adhesion capacities. Overall, activation of the NF-κB-miR-155 axis in FTE may represent a possible link between ovulation-induced inflammation, DNA damage, and transcriptional changes that may eventually lead to serious carcinogenesis.
Parietal Oscillatory Dynamics Mediate Developmental Improvement in Motor Performance
Authors: Heinrichs-Graham Elizabeth , Taylor Brittany K , Wang Yu-Ping , Stephen Julia M , Calhoun Vince D , Wilson Tony W
Published: July 2020

Numerous recent studies have sought to determine the developmental trajectories of motor-related oscillatory responses from youth to adulthood. However, most of this work has relied on simple movements, and rarely have these studies linked developmental neural changes with maturational improvements in motor performance. In this study, we recorded magnetoencephalography during a complex finger-tapping task in a large sample of 107 healthy youth aged 9–15 years old. The relationships between region-specific neural activity, age, and performance metrics were examined using structural equation modeling. We found strong developmental effects on behavior and beta oscillatory activity during movement planning, as well as associations between planning-related beta activity and activity within the same region during the movement execution period. However, when all factors were tested, we found that only right parietal cortex beta dynamics mediated the relationship between age and performance on the task. These data suggest that strong, sustained beta activity within the right parietal cortex enhances motor performance, and that these sustained oscillations develop through childhood into early adolescence. In sum, these are the first data to link developmental trajectories in beta oscillatory dynamics with distinct motor performance metrics and implicate the right parietal cortex as a crucial hub in movement execution.
A Rapid and Sensitive HPLC Method for Simultaneous Determination of Irinotecan Hydrochloride and Curcumin in Co-delivered Polymeric Nanoparticles
Authors: Xiao Haijun , Sedlařík Vladimír
Published: July 2020

In recent years, a great deal of attention has been paid to the combined use of multiple antitumor drugs for better cancer treatment. The aims of the study are to construct a nanoparticle drug delivery system for the co-delivery of irinotecan hydrochloride and curcumin and to develop an analytical method for simultaneously quantifying these molecules, which is essential for further studies of the co-delivered nano system. The irinotecan hydrochloride and curcumin co-delivered nanoparticle (ICN) were prepared by combinatorially entrapping them into polyethylene glycol–poly lactic acid-co-glycolic acid (PEG–PLGA) polymeric nanoparticles. A simple, sensitive and rapid high-performance liquid chromatography method was developed and validated to simultaneously quantify the compounds in the co-delivered nanoparticle system. Acetonitrile and ultrapure water containing sodium dodecyl sulfate (0.08 mol/L), disodium phosphate (Na2HPO4, 0.002 mol/L) and acetic acid (4%, v/v) were used as the mobile phase and their ratio was set at 50:50. The flow rate was set to 1.0 mL/min, and the temperature in the column oven was maintained at 40°C. The analysis was carried out at 256 and 424 nm to assess irinotecan hydrochloride and curcumin, respectively. Detectors with only one channel can also visualize both analytes in one chromatogram at 379 nm and still demonstrate acceptable sensitivity. The retention times for irinotecan hydrochloride and curium were 3.317 and 5.560 min, respectively. The method developed was confirmed to be sensitive, accurate (recovery, 100 ± 2%), precise (relative standard deviation, RSD ≤ 1%), robust and linear (R2 ≥ 0.9996) in the range from 2.05 to 1050 μg/mL. The presented method has been used to quantify irinotecan hydrochloride and curcumin in the co-delivered ICN nano system to assess the drug delivery quality of the nanoparticles and can also be used for routine analysis because of its simplicity and accuracy.
Piping Plover population increase after Hurricane Sandy mediated by immigration and reproductive output
Authors: Robinson Samantha G , Gibson Daniel , Riecke Thomas V , Fraser James D , Bellman Henrietta A , DeRose-Wilson Audrey , Karpanty Sarah M , Walker Katie M , Catlin Daniel H
Published: July 2020

Evaluating population-level responses to conservation action following large-scale disturbance can improve the efficacy of future habitat conservation measures. In October 2012, Hurricane Sandy storm surges cleared vegetation and opened inlets through the barrier islands, Fire Island and Westhampton Island, New York, creating Piping Plover (Charadrius melodus) habitat. Storm effects prompted an island-wide stabilization project, which had the potential to negatively affect novel Piping Plover habitat. Certain sections of Fire Island were designed to create and/or improve habitat (hereafter, restoration areas) to mitigate possible habitat loss or degradation. Since Piping Plovers in New York appear to be habitat-limited, we anticipated positive population growth following habitat creation. From 2013 to 2018, we captured and banded 152 adults and 353 chicks, and monitored 279 nests and 160 broods. We developed an integrated population model to assess demographic processes in response to hurricane created-habitat (2013–2018) and the creation of restoration areas (2015–2018). We observed positive population growth in 3 of 5 yr, and overall growth throughout the period (λ¯ = 1.13). Immigration and reproductive output were correlated with population growth (r = 0.92 [95% CI: 0.22 to 0.98] and 0.84 [95% CI: –0.47 to 0.95], respectively). Compared with the rest of the study area, restoration areas had higher chick survival, and lower nest survival and after second-year site fidelity. The result was population growth in restoration areas (λ¯= 1.14) similar to the whole study area. In the short term, restoration areas seemed to mimic natural Piping Plover habitat. Vegetation removal, an important process in renewing natural Piping Plover habitat, likely will be necessary to maintain habitat suitability. Efforts to increase immigration of new breeding adults into the system, and to improve reproductive output, primarily by habitat creation or maintenance, are likely to have the greatest local effect on population growth.