bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of photocatalyst dosage and air loading in photocatalytic degradation of metamifop
Authors: Nik Yusoff N R , Lim P W , Azmi N A B , Yusoff M , Muhammad M 
Published: September 2021

Abstract
Excessive used of agrochemical product such as metamifop herbicide, besides having high crop yield production, it has resulted in runoff which later affected groundwater and give negative impact on the environment. Photocatalytic degradation is one of the Advanced Oxidation Process where it creates hydroxyl radicals (·OH) in the presence of UV light. Performance of TiO2/Al2O3/carbon nanotube (CNT) (10 mg and 20 mg) which was produced through a hydrothermal process was applied to degrading 5 ppm and 10 ppm of metamifop. The performance of TiO2/Al2O3/CNT to degrade metamifop was evaluated statistically via a two-way analysis of variance (ANOVA) followed by a post-hoc Turkey’s test. The average performance of photocatalytic degradation gave a significant result at confident level of 0.05 hence the null hypothesis (Ho) was rejected. The best performance was occurred in degrading 5 ppm of metamifop using 20 mg of TiO2/Al2O3/CNT photocatalyst in the presence of air (2L/min) which resulted in 95.26% of percentage degradation. The addition of air assisted the photocatalytic degradation process from 84.54% to 92.44% and 83.62% to 91.47% when 10 mg of photocatalyst was used to degrade 5 ppm and 10 ppm of metamifop, respectively. When 20 mg of TiO2/Al2O3/CNT photocatalyst was applied in degrading 5 ppm and 10 ppm metamifop, the percentage degradation increased from 86.94% to 95.26% and 85.88% to 94.62%, respectively when photocatalytic degradation was conducted in the absence of air to the presence of air. The inferential results show a significant difference in average performance of TiO2/Al2O3/CNT photocatalyst and concentration of metamifop solution. However, there is no interaction effect between dosages of photocatalyst used with consumption of air in degrading metamifop. The study also proved that the produced photocatalyst was performed very well and suitable to be used in degrading metamifop herbicide.
Recovery of Au, Ag and Cu from printed circuit board leachate using activated carbon derived from foxtail fruit
Authors: Nik Yusoff N R , Maizatul N N 
Published: September 2021

Abstract
Printed circuit boards (PCBs) are the e-waste generated from the end-of-life electronic equipment such as laptops and mobile phone. PCBs contain various metals including precious metals (gold, silver, copper) and detrimental heavy metals as well (arsenic, mercury) [9]. Recycling of e-waste is potentially to be one of the best mechanisms to overcome the human and environmental health threat hence, the valuable metals can be recovered and could avoid the depletion of our ore resources. In this paper, hydrometallurgical process on PCBs was carrying out to recover the precious metals. The PCBs were immersed into aqua regia leaching solution and later the targeted metals were leached out and extracted using activated carbon through adsorption process. The precious metals were then recovered by desorbing the spent activated carbon using hydrochloric acid (HCl) as desorbing agent. In this study, foxtail palm fruit was used to produce activated carbon for metals recovery process. Therefore, the objective of this study was to evaluate the efficiency of the prepared activated carbon derived from foxtail fruit for the recovery of Au, Ag and Cu contain in the PCB leachate. The effect of adsorbent dosage (1, 2, 3, 4, 5g), contact time (20, 40, 60, 80, 100 min) and desorption process of spent activated were investigated. The characterization of the prepared activated carbon was determined using field emission scanning electron microscope (FESEM) whereas the PCBs leachate solution before and after metal recovery process were quantified using flame atomic absorption spectrophotometer (FAAS). The obtained result showed that, the adsorption percentage of Au, Ag and Cu at high adsorbent dosage (5g) with longer contact time (100 min) were 65.51%, 30.30% and 62.51% respectively. However, the attained result for desorption percentage of the metals recovery for Au, Ag and Cu were recorded to be higher at shorter contact time (20 min) as the spent activated carbon could deteriorate at longer contact time with concentrated HCl. The percentage recovery values for 20 minutes desorption process were 99.77% (Au) when 5g of activated carbon was used, whilst 97.41% (Ag) and 98.83% (Cu) were obtained when 2g of activated carbon were applied, respectively. Thus, it can be concluded that the adsorption of Au, Ag and Cu were greater when higher dosage of activated carbon and longer contact time were applied. Meanwhile, shorter contact time were needed to recover the metals. Therefore, this study could be one of the finding in safeguarding our environment by minimizing the e-waste pollution as well as practicing metal recycling in community.
Mechanical behavior and corrosion properties of Ti-7Mo-8Nb alloy for biomedical applications
Authors: Saood Modar , Ibrahim Khaled M , El-kashif Emad , Shoeib Madiha , Elshalakany Abobakr , Mohamed Mamdouh S 
Published: September 2021

Abstract
The present study investigates the microstructural, mechanical and corrosion properties of Ti-7Mo-8Nb alloy manufactured through powder metallurgy. The performance of the developed alloy is benchmarked against cast Ti-6Al-4V. Microstructure examination of Ti-7Mo-8Nb revealed a Widmanstätten structure containing equiaxed β grains along with acicular α phase. In regards to the mechanical properties, Ti-7Mo-8Nb possessed higher compressive yield strength, higher hardness but lower elastic modulus than Ti-6Al-4V. The elastic modulus of Ti-7Mo-8Nb was almost 44.9 GPa, approaching the usually desired value of 30 GPa for cortical bone. Wear test revealed also a lower wear rate for Ti-7Mo-8Nb. Potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) experiments were carried out for both Ti-7Mo-8Nb and Ti-6Al-4V immersed in Hank’s solution as a simulated body fluid at a temperature of 37 °C. Both experiments revealed higher corrosion resistance for Ti-7Mo-8Nb manifested by lower corrosion and passivation current densities, higher negative phase angle, higher impedance modulus and larger Nyquist semicircle diameter as compared to Ti-6Al-4V alloy. The superior corrosion properties of Ti-7Mo-8Nb are indicative of the development of a more stable passive layer on the surface. The fitting of EIS data into an equivalent circuit suggested the formation of a double oxide layer consisting of an inner compact base passive film along with an external porous layer. The presented combination of high strength, high corrosion resistance along with low elastic modulus puts forward the Ti-7Mo-8Nb alloy as a good candidate for orthopedic biomedical applications.
Electronic transport calculations showing electron-phonon separation in directions transverse to high current
Authors: Patitsas S N 
Published: September 2021

Abstract
An electron-phonon Boltzmann transport equation is formulated which accounts for second order collisions with an electron-phonon vertex and a three-phonon vertex. This approach for electronic transport at second order reveals the existence of two forces perpendicular to the primary direction of electrical current, acting on the electrons and phonons. The force on electrons is equal and opposite to that on the phonons. Solutions for stationary states confirm that charge and thermal energy become separated. The force terms include both conservative and dissipative components, which for the phonons, lead to a modified Guyer-Krumhansl equation. The conservative components exist only when there exist explicit transverse gradients in the dissipated energy, and these terms may be incorporated into a Poisson kinematics. The dissipative force terms can cause threshold induced spontaneous symmetry breaking.
Fast 3D particle reconstruction using a convolutional neural network: application to dusty plasmas
Authors: Himpel Michael , Melzer André 
Published: September 2021

Abstract
We present an algorithm to reconstruct the three-dimensional positions of particles in a dense cloud of particles in a dusty plasma using a convolutional neural network. The approach is found to be very fast and yields a relatively high accuracy. In this paper, we describe and examine the approach regarding the particle number and the reconstruction accuracy using synthetic data and experimental data. To show the applicability of the approach the 3D positions of particles in a dense dust cloud in a dusty plasma under weightlessness are reconstructed from stereoscopic camera images using the prescribed neural network.
Psychological Response to the Diagnosis of Advanced Cancer: A Systematic Review
Authors: Bai Mei 
Published: September 2021

Abstract

Background
Despite major efforts to address psychological distress and quality of life (QOL) in people with cancer, only none to small intervention effect has been observed. There is reason to question whether psychosocial needs of patients have already been met under the usual oncology care.

Purpose
The purpose of this systematic review was to examine changes in depression, anxiety and QOL during the existential plight in advanced cancer.

Methods
A literature search was performed in the PubMed and APA PsycINFO databases from year 1976 up to May 31, 2021. Longitudinal observational or experimental research targeting depression, anxiety or QOL in advanced cancer (stage III or IV), with baseline time since cancer diagnosis within 100 days, follow-up within 16 weeks post-baseline were eligible. Quality rating was based on the GRADE guidelines.

Results
Overall QOL did not reveal clinically relevant changes for the majority of studies as evaluated by effect size and raw score changes (median effect size 0.01, interquartile range −0.10–0.15). Nonetheless, modest to moderate improvement was found for depression (median effect size 0.28, interquartile range 0.03–0.38) and anxiety (median effect size 0.57, interquartile range 0.32–0.79).

Conclusion
Transient distress symptoms and temporarily reduced functioning in the oncology setting may be considered normal, whereas impaired overall QOL needs to be addressed. Developing innovative interventions that enhance QOL for patients newly diagnosed with advanced cancer without interfering with patients’ natural adaptation process is imperative.
TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T-cell receptor α and β chains
Authors: Mösch Anja , Frishman Dmitrij 
Published: September 2021

Abstract

Summary
The ability of a T cell to recognize foreign peptides is defined by a single α and a single β hypervariable complementarity determining region (CDR3), which together form the T-cell receptor (TCR) heterodimer. In ∼30–35% of T cells, two α chains are expressed at the mRNA level but only one α chain is part of the functional TCR. This effect can also be observed for β chains, although it is less common. The identification of functional α/β chain pairs is instrumental in high-throughput characterization of therapeutic TCRs. TCRpair is the first method that predicts whether an α and β chain pair forms a functional, HLA-A*02:01 specific TCR without requiring the sequence of a recognized peptide. By taking additional amino acids flanking the CDR3 regions into account, TCRpair achieves an AUC of 0.71.

Availability and implementation
TCRpair is implemented in Python using TensorFlow 2.0 and is freely available at https://www.github.com/amoesch/TCRpair.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data
Authors: Lee Simon , Nguyen Loan T , Hayes Ben J , Ross Elizabeth M 
Published: September 2021

Abstract

Motivation
Trimming and filtering tools are useful in DNA sequencing analysis because they increase the accuracy of sequence alignments and thus the reliability of results. Oxford nanopore technologies (ONT) trimming and filtering tools are currently rudimentary, generally only filtering reads based on whole read average quality. This results in discarding reads that contain regions of high-quality sequence. Here, we propose Prowler, a trimmer that uses a window-based approach inspired by algorithms used to trim short read data. Importantly, we retain the phase and read length information by optionally replacing trimmed sections with Ns.

Results
Prowler was applied to mammalian and bacterial datasets, to assess its effect on alignment and assembly, respectively. Compared to data filtered with Nanofilt, alignments of data trimmed with Prowler had lower error rates and more mapped reads. Assemblies of Prowler trimmed data had a lower error rate than those filtered with Nanofilt; however, this came at some cost to assembly contiguity.

Availability and implementation
Prowler is implemented in Python and is available at https://github.com/ProwlerForNanopore/ProwlerTrimmer.

Supplementary information
Supplementary data are available at Bioinformatics online.
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning
Authors: Katuwawala Akila , Zhao Bi , Kurgan Lukasz 
Published: September 2021

AbstractMotivationIntrinsically disordered protein regions interact with proteins, nucleic acids and lipids. Regions that bind lipids are implicated in a wide spectrum of cellular functions and several human diseases. Motivated by the growing amount of experimental data for these interactions and lack of tools that can predict them from the protein sequence, we develop DisoLipPred, the first predictor of the disordered lipid-binding residues (DLBRs).ResultsDisoLipPred relies on a deep bidirectional recurrent network that implements three innovative features: transfer learning, bypass module that sidesteps predictions for putative structured residues, and expanded inputs that cover physiochemical properties associated with the protein–lipid interactions. Ablation analysis shows that these features drive predictive quality of DisoLipPred. Tests on an independent test dataset and the yeast proteome reveal that DisoLipPred generates accurate results and that none of the related existing tools can be used to indirectly identify DLBR. We also show that DisoLipPred’s predictions complement the results generated by predictors of the transmembrane regions. Altogether, we conclude that DisoLipPred provides high-quality predictions of DLBRs that complement the currently available methods.Availability and implementationDisoLipPred’s webserver is available at http://biomine.cs.vcu.edu/servers/DisoLipPred/.Supplementary informationSupplementary data are available at Bioinformatics online.
Amyloid-driven disruption of default mode network connectivity in cognitively healthy individuals
Authors: Ingala Silvia , Tomassen Jori , Collij Lyduine E , Prent Naomi , van ‘t Ent Dennis , ten Kate Mara , Konijnenberg Elles , Yaqub Maqsood , Scheltens Philip , de Geus Eco J C , Teunissen Charlotte E , Tijms Betty , Wink Alle Meije , Barkhof Frederik , van Berckel Bart N M , Visser Pieter Jelle , den Braber Anouk 
Published: September 2021

AbstractCortical accumulation of amyloid beta is one of the first events of Alzheimer’s disease pathophysiology, and has been suggested to follow a consistent spatiotemporal ordering, starting in the posterior cingulate cortex, precuneus and medio-orbitofrontal cortex. These regions overlap with those of the default mode network, a brain network also involved in memory functions. Aberrant default mode network functional connectivity and higher network sparsity have been reported in prodromal and clinical Alzheimer’s disease. We investigated the association between amyloid burden and default mode network connectivity in the preclinical stage of Alzheimer’s disease and its association with longitudinal memory decline. We included 173 participants, in which amyloid burden was assessed both in CSF by the amyloid beta 42/40 ratio, capturing the soluble part of amyloid pathology, and in dynamic PET scans calculating the non-displaceable binding potential in early-stage regions. The default mode network was identified with resting-state functional MRI. Then, we calculated functional connectivity in the default mode network, derived from independent component analysis, and eigenvector centrality, a graph measure recursively defining important nodes on the base of their connection with other important nodes. Memory was tested at baseline, 2- and 4-year follow-up. We demonstrated that higher amyloid burden as measured by both CSF amyloid beta 42/40 ratio and non-displaceable binding potential in the posterior cingulate cortex was associated with lower functional connectivity in the default mode network. The association between amyloid burden (CSF and non-displaceable binding potential in the posterior cingulate cortex) and aberrant default mode network connectivity was confirmed at the voxel level with both functional connectivity and eigenvector centrality measures, and it was driven by voxel clusters localized in the precuneus, cingulate, angular and left middle temporal gyri. Moreover, we demonstrated that functional connectivity in the default mode network predicts longitudinal memory decline synergistically with regional amyloid burden, as measured by non-displaceable binding potential in the posterior cingulate cortex. Taken together, these results suggest that early amyloid beta deposition is associated with aberrant default mode network connectivity in cognitively healthy individuals and that default mode network connectivity markers can be used to identify subjects at risk of memory decline.
An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing
Authors: Esteves Eden , Whyte Paul , Mills John , Brightwell Gale , Gupta Tanushree B , Bolton Declan 
Published: September 2021

ABSTRACT
The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored in this study. A total of 120 carcass and 120 rump steak swabs were collected immediately after slaughtering and boning, respectively from five meat plants, anaerobically incubated and enriched at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeq, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). The microbiota recovered from both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5 to 20% and 0.1 to 29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0 to 0.8% on carcass and 0 to 1.8% on rump steak swabs, respectively. Alpha and beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. This study highlights the presence of potential spoilage bacteria, mainly anaerobic genera on and between carcass and rump steaks, as an indication of contamination on and between these samples.
Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Zidi Marwa , Denis Françoise , Klai Khouloud , Chénais Benoît , Caruso Aurore , Djebbi Salma , Mezghani Maha , Casse Nathalie 
Published: September 2021

Abstract
The whitefly, Bemisia tabaci is a hemipteran pest of vegetable crops vectoring a broad category of viruses. Currently, this insect pest showed a high adaptability and resistance to almost all the chemical compounds commonly used for its control. In many cases, transposable elements (TEs) contributed to the evolution of host genomic plasticity. This study focuses on the annotation of Mariner-like elements (MLEs) and their derived Miniature Inverted repeat Transposable Elements (MITEs) in the genome of B. tabaci. Two full-length MLEs belonging to mauritiana and irritans subfamilies were detected and named Btmar1.1 and Btmar2.1, respectively. Additionally, 548 defective MLE sequences clustering mainly into 19 different Mariner lineages of mauritiana and irritans subfamilies were identified. Each subfamily showed a significant variation in MLE copy number and size. Furthermore, 71 MITEs were identified as MLEs derivatives that could be mobilized via the potentially active transposases encoded by Btmar 1.1 and Btmar2.1. The vast majority of sequences detected in the whitefly genome present unusual terminal inverted repeats (TIRs) of up to 400 bp in length. However, some exceptions are sequences without TIRs. This feature of the MLEs and their derived MITEs in B. tabaci genome that distinguishes them from all the other MLEs so far described in insects, which have TIRs size ranging from 20 to 40 bp. Overall, our study provides an overview of MLEs, especially those with large TIRs, and their related MITEs, as well as diversity of their families, which will provide a better understanding of the evolution and adaptation of the whitefly genome.
Understanding population structure in an evolutionary context: population-specificFST and pairwiseFST
Authors: Kitada Shuichi , Nakamichi Reiichiro , Kishino Hirohisa 
Published: September 2021

AbstractPopulations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.