bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Integrated Approach for Extraction of Carbonate Rocks Based on Landsat OLI Data: a Case Study around Stone Forest, Southwest China – Upgrading for Land-use Planning Purposes
Authors: He Ping , Cheng Xianfeng , Mao Zifei 
Published: December 2020

Abstract
Geological remote sensing information extraction of the lithology has always been the hotspot and difficulty in remote sensing applications. Carbonate rocks covered more than 3.4 million km2 in China. The study area is located around Stone Forest, which is World Natural Heritage. Sedimentary rocks distributes mainly in the area, and their spectral characteristics are complex and difficult to be recognized by remote sensing. Landsat OLI data was selected as the information source. The false color synthesis, principal component change, band ratio and other processing technologies of OLI data were applied to the lithological enhancement identification of carbonate rocks. Selected information will be used to improve the quality of the land-use planning.
Teeth Model Reconstruction Based on Multiple View Image Capture
Authors: Ali Faten Imad , Tarik Al-dahan Ziad 
Published: December 2020

AbstractVarious dentistry fields such as teeth treatment, dental restoration, and denture production require the application of three-dimensional intraoral scanners to create digital impressions. This study presents a method to reconstruct a three-dimensional teeth crown by utilizing a prototype intraoral custom design with publicly available software. The system consists of custom containing an endoscope camera and two light sources (white LED and blue laser), a personal control computer, and photogrammetric open source software packages (VisualSFM, CMVS/PMVS, and MeshLab). Photogrammetry methods were used to acquire the three-dimensional teeth model with high precision. Multi images have been captured of the interesting teeth using the custom system from different angles. The capturing process was done in two phases using one illumination source each time. The captured images are loading to Photogrammetry software to generate the three-dimensional dense point cloud. A comparison has been made of the resulted dense point cloud at each phase. Finally, the dense point cloud is loading to MeshLab software to generate the three-dimensional mesh that can be utilized in CAD/CAM software. The results have shown the superiority of using blue illumination with the photogrammetry software that shows good accuracy of teeth crown details and measurements that are related to the reconstruction algorithm which yields in more number of 3D points of the object to generate good three-dimensional meshes of the teeth crown. This study helps to offer low cost, simple design, and a user-friendly system to generate a three-dimensional teeth crown.
Interfacial Characteristics of Engineered Pulp Fibre Reinforced Concretes Containing Various Pozzolans
Authors: Booya Emad , Adesina Adeyemi , Gorospe Karla , Das Sreekanta 
Published: December 2020

AbstractIncreasing durability threats on existing structures made with cementitious composites has prompted a need to find ways to improve the durability of new structures. One of the effective ways to improve the durability properties of cementitious composites is by the incorporation of fibres. A type of modified Kraft pulp fibres was employed in this study to improve the durability properties of cementitious composites. A microstructural investigation was also conducted to study the fibre morphology and its effect on the performance of the cementitious composites. Moreover, the durability tests in terms of water absorption and rapid chloride penetration were carried out. Overall results showed higher improvement of the durability of the cementitious composites with composites incorporated metakaolin, silica fume, and slag. This was further confirmed by microstructural analysis showing that these supplementary cementitious materials densified the cementitious matrix.
Preparation and Characterization of Nano silica Prepared by Different Precipitation Methods
Authors: Al-Abboodi Sabah M.Thahab , Al-Shaibani Eman Jabber Abed , Alrubai Enass.A. 
Published: December 2020

Abstract
Agricultural waste Rice husk ash (RHA) is large and massive by the output of rice milling manufacture and contains a high amount of silica. Taking into account this verdant technology is utilized to get SiO2 Nanoparticles from rice shell ash. In this research, studies on the extraction methods of Nano-silica by combustion rice shell for 2 h at 700 °C were carried out and investigated. However, the Rice shell ash was undergoing to precipitation methods and sol gel method to manufacture Nano silica. precipitation methods involve refluxing silica from Rice shell ash in boiled (1.0,2.0 N NaOH). While the sol-gel method involves calcination of RHA was treated with HCl at 700 °C for 2 h followed by chemical treatment. Results of The Infrared spectral (IR) information display the presence of hydrogen-bonded silanol group and the siloxane groups in silica. The Optical properties through UV-visible spectroscopy of the Nano silica samples show a wide bandgap value and absorption peaks located in the UV region. As well as, the particles size analysis with values of (13.02, 16.83 and 23.96 nm) for the samples (1NSiO2, 2NSiO2, and acid leaching) were obtained respectively.
Compressibility Characteristics of Soft Clays Treated by Graphene
Authors: Fattah Mohammed Y. , Al-Haddad Sinan A. , Al-Khafaji Kumail R. 
Published: December 2020

Abstract
It is extremely difficult to obtain a change in soil properties by incorporating graphene directly into the soft soil. Therefore, the stability of the soil or cementitious materials can be improved by treating them with graphene. Graphene is easily manufactured from pure graphite powder. Based on this aggregation, it may alter the final properties of graphene, because it completely depends on the raw chemicals and the method of building this material. The mechanical behavior of a new compound graphene was studied through consistency and compression. The soft clay used in this study is characterized with shear strength of 33.0 kPa. It is stabilized with 0.1 % of graphene with curing periods of 1 day and 7 days. It was observed that the void ratio decreased with addition of graphene under a given consolidation pressure. In addition, each of the swelling potential, the coefficient of volume compressibility and the coefficient of consolidation decrease with increasing the period of curing of graphene.
Tunable morphology and band gap alteration of CuO-ZnO nanostructures based photocathode for solar photoelectrochemical cells
Authors: Albadarin Nusayba A , Takriff Mohd Sobri , Tan Sin Tee , Shahahmadi Seyed Ahmad , Minggu Lorna Jeffery , Kadhum Abdul Amir H , Yin Wong Wai , Salehmin Mohd Nur Ikhmal , Alkhalqi Ensaf M , Hamid Muhammad Azmi Abdul , Amin Nowshad 
Published: December 2020

Abstract
A homogeneous CuO-ZnO nanostructure with tunable morphology and optical band structure is successfully synthesized via a hydrothermal method under the different dopant mole ratios of Cu. The robust correlation between the crystallite size, surface morphology, optical band gap alteration of the synthesized CuO-ZnO and its performance in photoelectrochemical (PEC) activity are investigated and compared to the reference ZnO based photocathode. In this report, it is found that the morphology of hexagonal ZnO nanorod is changed to nanosheet and vertically align CuO-ZnO based nanograss after the Cu incorporation. This result is mainly due to the composition phase change after the excessive incorporation of Cu metal into ZnO lattice. Furthermore, the optical band gap of the sample also presented a bathochromic shifted after the Cu insertion. The measurements on PEC activity of CuO-ZnO nanostructure was performed under the irradiation of a 100 mWcm−2 Xenon light in 0.5M Na2SO4 electrolyte. Among the sample, 0 Zn:1 Cu exhibited a highest photocurrent density which is 5 fold as compared to its reference ZnO samples. This finding could be due to the highest surface active area and lowest optical energy band gap in the 0 Zn:1 Cu nanograss that eventually contributes to a high free electron density that facilitates the charge transport in the photoelectrochemical cells. This novel approach could provide an alternative to the future solar hydrogenation application.
Controllable polarization electro-optic absorption graphene modulator
Authors: He Xiaoying , Su Jiale , Rao Lan 
Published: December 2020

Abstract
Graphene, as two-dimensional material with many properties of the gate-voltage tunable Fermi-level and zero band gap, can be utilized for optical modulators by the integration with other material. In this work, an electro-optic modulator based on the fiber-surface waveguide and graphene capacitance has been proposed with the device length of 50 μm, featuring excellent controllable polarization modulation (polarization extinction ratio over 0.12 dB/μm), large modulation bandwidth of ∼40 GHz @ hBN and ∼25 GHz @ Al2O3, and energy consumption low to 11.5 pJ/bit for hBN and 4 pJ/bit for Al2O3. The polarization can be controlled by tuning the core radius from 130 nm for the TE polarized modulation with modulation efficiency over ∼2.56 dB V−1 (Al2O3) and ∼1.15 dB V−1 (hBN) to 170 nm for the TM polarized modulation efficiency up to ∼3.03 dB V−1 (Al2O3) and ∼1.3 dB/V (hBN). This work not only promotes the development of future polarization modulation technology, but also paves the way toward multifunctional fiber devices and systems.
Stencil growth of metallic nanorod: An atomistic simulation
Authors: Kateb Movaffaq 
Published: December 2020

Abstract
The stencil growth of nanoscale patterns using molecular dynamics simulation has been demonstrated. A comparison has been made to a film grown by identical conditions without the stencil. It is shown that in the case of nanoscale proximity between mask and substrate, patterns of the same dimension as the mask can be obtained. The results also indicate that the obtained nanorod presents a higher surface area than the corresponding thin film. It is demonstrated that nanorod surface roughness decreases by merging adjacent surface irregularity during the deposition.
Mini-review: antibody therapeutics targeting G protein-coupled receptors and ion channels
Authors: Hutchings Catherine J 
Published: December 2020

AbstractAntibodies are now well established as therapeutics with many additional advantages over small molecules and peptides relative to their selectivity, bioavailability, half-life and effector function. Major classes of membrane-associated protein targets include G protein-coupled receptors (GPCRs) and ion channels that are linked to a wide range of disease indications across all therapeutic areas. This mini-review summarizes the antibody target landscape for both GPCRs and ion channels as well as current progress in the respective research and development pipelines with some example case studies highlighted from clinical studies, including those being evaluated for the treatment of symptoms in COVID-19 infection.
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data
Authors: Han Xinyin , Zhang Shuying , Zhou Daniel Cui , Wang Dongliang , He Xiaoyu , Yuan Danyang , Li Ruilin , He Jiayin , Duan Xiaohong , Wendl Michael C , Ding Li , Niu Beifang 
Published: December 2020

AbstractMotivation: Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach. Results: We developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines. Availability: MSIsensor-ct is freely available at https://github.com/niu-lab/MSIsensor-ct. Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data
Authors: Wang Shuai , Jiang Yiqi , Li Shuaicheng 
Published: December 2020

Abstract

Motivation
The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain.

Results
These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B.coprocola in the gut microbiota of CRC.

Availabilityand implementation
https://github.com/wshuai294/PStrain.

Supplementary information
Supplementary data are available at Bioinformatics online.
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
Authors: Eling Nils , Damond Nicolas , Hoch Tobias , Bodenmiller Bernd 
Published: December 2020

Abstract

Summary
Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here, we describe cytomapper, a computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualization of selected cells in corresponding images.

Availability and implementation
The cytomapper package can be installed via https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html. Code for analysis and further instructions can be found at https://github.com/BodenmillerGroup/cytomapper_publication.

Supplementary information
Supplementary data are available at Bioinformatics online.
Transitional Safeguarding: Transforming How Adolescents and Young Adults Are Safeguarded
Authors: Cocker Christine , Cooper Adi , Holmes Dez 
Published: December 2020

Abstract
This article argues for a transformation in the protection and safeguarding needs of young people during their transition between childhood and adulthood. In order to explore with local authorities how they would address some of these challenges, the authors facilitated four national workshops with principal social workers, senior and middle managers (n = 88) from approximately one-third of Local Authorities in England (n = 52) from both Children and Adult social services. Participants discussed enablers and barriers to local and regional approaches to transitional safeguarding at practice, managerial, strategic and multi-agency levels. Findings from the workshops showed many examples of commitment to improvement and change, despite funding constraints and system barriers. No single local authority had a coherent and comprehensive approach to Transitional Safeguarding. Although some partnerships had started to lead innovation, it was still too early to demonstrate any effective impact throughout all systems, including whether outcomes for young people had improved. Participants also emphasised that young people should be involved as key stakeholders in developing appropriate responses. The system changes required to improve Transitional Safeguarding practices are complex and involve a re-configuration of the ‘risk’ versus ‘rights’ paradigms that permeate societal responses to the protection of young people.
High-Performance Liquid Chromatography Method for Simultaneous Determination of Guaifenesin, Salbutamol Sulfate and Guaifenesin Impurity (Guaiacol)
Authors: Naguib Ibrahim A , Farag Shimaa A , Zaazaa Hala E , Abdelaleem Eglal A 
Published: December 2020

Abstract
A simple and reliable HPLC method is developed for isocratic separation of a ternary mixture of Salbutamol Sulfate (SAL), Guaifenesin (GUI) and its impurity Guaiacol (GUA) either in pure powder or in pharmaceutical formulation. Chromatographic separation was applied on a Hypersil GOLD CN column with a mobile phase consisting of 0.05 M KH2PO4 (containing 0.1% triethylamine, pH adjusted to 3.7 by phosphoric acid): methanol (60: 40 by volume) using 0.6 mL min−1 flow rate and detection of peaks at 275 nm at 25°C with run time around 6 min. The calibration plots were linear over the concentration ranges of 0.5–20, 0.5–30 and 0.1–10 μg mL−1 for SAL, GUI and GUA, respectively. ICH guidelines were used for the validation of presented method. The obtained results were compared with the results obtained from the reported HPLC method and no significant difference was found regarding accuracy and precision.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Seroprevalence and Risk Factors Among Oligo/Asymptomatic Healthcare Workers: Estimating the Impact of Community Transmission
Authors: Costa Silvia Figueiredo , Giavina-Bianchi Pedro , Buss Lewis , Mesquita Peres Carlos Henrique , Rafael Mayra Matias , dos Santos Lanuse Garcia Neves , Bedin Anderson Aparecido , Francisco Maria Cristina Peres Braido , Satakie Fatima Mitie , Jesus Menezes Maria Aparecida , Dal Secco Ligia Maria , Rodrigues Caron Deyse Mayara , de Oliveira Allan Brum , de Faria Matheus Finardi Lima , de Aurélio Penteado Angelica Sauiuri , de Souza Izabel Oliva Marcilio , de Fatima Pereira Grazielly , Pereira Rafael , Matos Porto Ana Paula , Sanchez Espinoza Evelyn Patrícia , Mendes-Correa Maria Cassia , dos Santos Lazari Carolina , Kalil Jorge , de Moliterno Perondi Maria Beatriz , de Oliveira Bonfa Eloisa Silva Dutra , Perreira Antonio Jose , Sabino Ester , da Silva Duarte Alberto José , Segurado Aluísio Cotrim , dos Santos Vera Aparecida , Levin Anna S 
Published: December 2020

Abstract
We evaluated the seroprevalence of SARS-CoV-2 and risk factors among 4987 oligo/asymptomatic healthcare workers; seroprevalence was 14% and factors associated with SARS-CoV-2 infection were lower educational level (aOR, 1.93; 95% CI, 1.03–3.60), using public transport to work (aOR, 1.65; 95% CI, 1.07–2.62), and working in cleaning or security (aOR, 2.05; 95% CI, 1.04–4.03).
Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection of a Healthcare Worker in a Belgian Nosocomial Outbreak Despite Primary Neutralizing Antibody Response
Authors: Selhorst Philippe , van Ierssel Sabrina H , Michiels Jo , Mariën Joachim , Bartholomeeusen Koen , Dirinck Eveline , Vandamme Sarah , Jansens Hilde , Ariën Kevin K 
Published: December 2020

Abstract

Background
It is currently unclear whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection will remain a rare event, only occurring in individuals who fail to mount an effective immune response, or whether it will occur more frequently when humoral immunity wanes following primary infection.

Methods
A case of reinfection was observed in a Belgian nosocomial outbreak involving 3 patients and 2 healthcare workers. To distinguish reinfection from persistent infection and detect potential transmission clusters, whole genome sequencing was performed on nasopharyngeal swabs of all individuals including the reinfection case’s first episode. Immunoglobulin A, immunoglobulin M, and immunoglobulin G (IgG) and neutralizing antibody responses were quantified in serum of all individuals, and viral infectiousness was measured in the swabs of the reinfection case.

Results
Reinfection was confirmed in a young, immunocompetent healthcare worker as viral genomes derived from the first and second episode belonged to different SARS-CoV-2 clades. The symptomatic reinfection occurred after an interval of 185 days, despite the development of an effective humoral immune response following symptomatic primary infection. The second episode, however, was milder and characterized by a fast rise in serum IgG and neutralizing antibodies. Although contact tracing and viral culture remained inconclusive, the healthcare worker formed a transmission cluster with 3 patients and showed evidence of virus replication but not of neutralizing antibodies in her nasopharyngeal swabs.

Conclusions
If this case is representative of most patients with coronavirus disease 2019, long-lived protective immunity against SARS-CoV-2 after primary infection might not be likely.
Remdesivir Use in the Setting of Severe Renal Impairment: A Theoretical Concern or Real Risk?
Authors: Pettit Natasha N , Pisano Jennifer , Nguyen Cynthia T , Lew Alison K , Hazra Aniruddha , Sherer Renslow , Mullane Kathleen M 
Published: December 2020

AbstractBackgroundRemdesivir (RDV) is US FDA approved for coronavirus disease 2019 (COVID-19) but not recommended in severe renal impairment (SRI, Creatinine clearance &lt;30mL/min or requiring renal replacement therapy). Few studies have evaluated RDV in patients with SRI.MethodsHospitalized patients who received RDV between 1 May 2020 and 31 October 2020 were analyzed in a retrospective chart review. We compared incident adverse events (AEs) in patients with and without SRI, including hepatotoxicity, nephrotoxicity, any reported AE, mortality, and length of stay.ResultsOf a total of 135 patients, 20 had SRI. Patients with SRI were significantly older (70 vs 54 years, P = .0001). The incidence of possible AEs was 30% among those with SRI vs 11% without (P = .06). Liver function test (LFT) elevations occurred in 10% vs 4% (P = .28), and serum creatinine (SCr) elevations in 27% vs 6% (P = .02) of patients with SRI vs without, respectively. LFT and SCr elevations were not attributed to RDV in either group.Mortality and length of stay were consistent with historical controls.ConclusionsRDV AEs occurred infrequently and overall were not significantly different between those with and without SRI. While more of patients with SRI experienced SCr elevations, 3 (75%) patients had acute kidney injury prior to RDV. The use of RDV in this small series of patients with SRI appeared to be relatively safe, and the potential benefit outweighed the theoretical risk of liver or renal toxicity. Additional studies are needed to confirm this finding.