bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaginal microbiota and human papillomavirus infection among young Swedish women
Authors: Cheng Liqin , Norenhag Johanna , Hu Yue O. O. , Brusselaers Nele , Fransson Emma , Ährlund-Richter Andreas , Guðnadóttir Unnur , Angelidou Pia , Zha Yinghua , Hamsten Marica , Schuppe-Koistinen Ina , Olovsson Matts , Engstrand Lars , Du Juan 
Published: October 2020

AbstractHuman papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. To define the HPV-associated microbial community among a high vaccination coverage population, we carried out a cross-sectional study with 345 young Swedish women. The microbial composition and its association with HPV infection, including 27 HPV types, were analyzed. Microbial alpha-diversity was found significantly higher in the HPV-infected group (especially with oncogenic HPV types and multiple HPV types), compared with the HPV negative group. The vaginal microbiota among HPV-infected women was characterized by a larger number of bacterial vaginosis-associated bacteria (BVAB), Sneathia, Prevotella, and Megasphaera. In addition, the correlation analysis demonstrated that twice as many women with non-Lactobacillus-dominant vaginal microbiota were infected with oncogenic HPV types, compared with L. crispatus-dominated vaginal microbiota. The data suggest that HPV infection, especially oncogenic HPV types, is strongly associated with a non-Lactobacillus-dominant vaginal microbiota, regardless of age and vaccination status.
Seasonal variations in PM10 inorganic composition in the Andean city
Authors: Zalakeviciute Rasa , Alexandrino Katiuska , Rybarczyk Yves , Debut Alexis , Vizuete Karla , Diaz Maria 
Published: October 2020

AbstractParticulate matter (PM) is one of the key pollutants causing health risks worldwide. While the preoccupation for increased concentrations of these particles mainly depends on their sources and thus chemical composition, some regions are yet not well investigated. In this work the composition of chemical elements of atmospheric PM10 (particles with aerodynamic diameters ≤ 10 µm), collected at the urban and suburban sites in high elevation tropical city, were chemically analysed during the dry and wet seasons of 2017–2018. A large fraction (~ 68%) of PM10 composition in Quito, Ecuador is accounted for by water-soluble ions and 16 elements analysed using UV/VIS spectrophotometer and Inductively Coupled Plasma—Optical Emission Spectroscopy (ICP-OES). Hierarchical clustering analysis was performed to study a correlation between the chemical composition of urban pollution and meteorological parameters. The suburban area displays an increase in PM10 concentrations and natural elemental markers during the dry (increased wind intensity, resuspension of soil dust) season. Meanwhile, densely urbanized area shows increased total PM10 concentrations and anthropogenic elemental markers during the wet season, which may point to the worsened combustion and traffic conditions. This might indicate the prevalence of cardiovascular and respiratory problems in motorized areas of the cities in the developing world.
Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding
Authors: Wang Yuanxin , Liu Yanhong , Wang Xingchun , Jia Dong , Hu Jun , Gao Ling-Ling , Ma Ruiyan 
Published: October 2020

AbstractHerbivorous insects use plant volatile compounds to find their host plants for feeding and egg deposition. The monophagous beetle Agasicles hygrophila uses a volatile (E)-4,8-dimethyl-1,3,7-nonanetriene (DMNT) to recognize its host plant Alternanthera philoxeroides. Alternanthera philoxeroides releases DMNT in response to A. hygrophila attack and nerolidol synthase (NES) is a key enzyme in DMNT biosynthesis; however, the effect of A. hygrophila on NES expression remains unclear. In this study, the A. philoxeroides transcriptome was sequenced and six putative NES genes belonging to the terpene synthase-g family were characterized. The expression of these NES genes was assayed at different times following A. hygrophila contact, feeding or mechanical wounding. Results showed that A. hygrophila contact and feeding induced NES expression more rapidly and more intensely than mechanical wounding alone. This may account for a large release of DMNT following A. hygrophila feeding in a previous study and subsequently facilitate A. hygrophila to find host plants. Our research provides a powerful genetic platform for studying invasive plants and lays the foundation for further elucidating the molecular mechanisms of the interaction between A. philoxeroides and its specialist A. hygrophila.
Defect-assisted synthesis of magneto-plasmonic silver-spinel ferrite heterostructures in a flower-like architecture
Authors: Sanna Angotzi Marco , Mameli Valentina , Cara Claudio , Grillo Vincenzo , Enzo Stefano , Musinu Anna , Cannas Carla 
Published: October 2020

AbstractArtificial nano-heterostructures (NHs) with controlled morphology, obtained by combining two or more components in several possible architectures, make them suitable for a wide range of applications. Here, we propose an oleate-based solvothermal approach to design silver-spinel ferrite flower-like NHs. Small oleate-coated silver nanoparticles were used as seeds for the growth of magnetic spinel ferrite (cobalt ferrite and spinel iron oxide) nanodomains on their surface. With the aim of producing homogeneous flower-like heterostructures, a careful study of the effect of the concentration of precursors, the reaction temperature, the presence of water, and the chemical nature of the spinel ferrite was carried out. The magnetic and optical properties of the NHs were also investigated. A heterogeneous growth of the spinel ferrite phase on the silver nanoparticles, through a possible defect-assisted mechanism, was suggested in the light of the high concentration of stacking faults (intrinsic and twins) in the silver seeds, revealed by Rietveld refinement of powder X-ray diffraction patterns and High-Resolution electron microscopy.
OSERR: an open-source standalone electrophysiology recording system for rodents
Authors: Cheng Ning , Murari Kartikeya 
Published: October 2020

AbstractBehavioral assessment of rodents is critical for investigation of brain function in health and disease. In vivo neurophysiological recordings are powerful tools to mechanistically dissect neural pathways that underlie behavioral changes, and serve as markers for dynamics, efficacy and safety of potential therapeutic approaches. However, most in vivo recording systems require tethers or telemetry receivers, limiting their compatibility with some behavioral tests. Here, we developed an open-source standalone electrophysiology recording system for rodents (OSERR). It is a tether-free, standalone recording device with two channels, a reference and a ground, that acquires, amplifies, filters and stores data all in itself. Thus, it does not require any cable or receiver. It is also compact and light-weight, and compatible with juvenile mice, as well as multiple recording modalities and standard electrode implantation methods. In addition, we provide the complete design of hardware, and software for operation. As an example, we demonstrated that this standalone system, when configured with a bandwidth of 1–120 Hz and gain of 1000, successfully collected EEG signals during induced seizure, extended recording, anesthesia, and social interactions in mice. The design of this system is practical, economical, and freely available. Thus, this system could enable recording of brain activity during diverse behavioral assays in a variety of arenas and settings, and allow simultaneous recordings from multiple subjects to examine social behaviors. Importantly, with the open-source documentation, researchers could customize the design of the system to their specific needs.
Machine learning identifies abnormal Ca2+ transients in human induced pluripotent stem cell-derived cardiomyocytes
Authors: Hwang Hyun , Liu Rui , Maxwell Joshua T. , Yang Jingjing , Xu Chunhui 
Published: October 2020

AbstractHuman-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide an excellent platform for potential clinical and research applications. Identifying abnormal Ca2+ transients is crucial for evaluating cardiomyocyte function that requires labor-intensive manual effort. Therefore, we develop an analytical pipeline for automatic assessment of Ca2+ transient abnormality, by employing advanced machine learning methods together with an Analytical Algorithm. First, we adapt an existing Analytical Algorithm to identify Ca2+ transient peaks and determine peak abnormality based on quantified peak characteristics. Second, we train a peak-level Support Vector Machine (SVM) classifier by using human-expert assessment of peak abnormality as outcome and profiled peak variables as predictive features. Third, we train another cell-level SVM classifier by using human-expert assessment of cell abnormality as outcome and quantified cell-level variables as predictive features. This cell-level SVM classifier can be used to assess additional Ca2+ transient signals. By applying this pipeline to our Ca2+ transient data, we trained a cell-level SVM classifier using 200 cells as training data, then tested its accuracy in an independent dataset of 54 cells. As a result, we obtained 88% training accuracy and 87% test accuracy. Further, we provide a free R package to implement our pipeline for high-throughput CM Ca2+ analysis.
The role of selection in the evolution of marine turtles mitogenomes
Authors: Ramos Elisa Karen da Silva , Freitas Lucas , Nery Mariana F. 
Published: October 2020

AbstractSea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.
After the lockdown: simulating mobility, public health and economic recovery scenarios
Authors: Spelta Alessandro , Flori Andrea , Pierri Francesco , Bonaccorsi Giovanni , Pammolli Fabio 
Published: October 2020

AbstractThe spread of SARS-COV-2 has affected many economic and social systems. This paper aims at estimating the impact on regional productive systems in Italy of the interplay between the epidemic and the mobility restriction measures put in place to contain the contagion. We focus then on the economic consequences of alternative lockdown lifting schemes. We leverage a massive dataset of human mobility which describes daily movements of over four million individuals in Italy and we model the epidemic spreading through a metapopulation SIR model, which provides the fraction of infected individuals in each Italian district. To quantify economic backslashes this information is combined with socio-economic data. We then carry out a scenario analysis to model the transition to a post-lockdown phase and analyze the economic outcomes derived from the interplay between (a) the timing and intensity of the release of mobility restrictions and (b) the corresponding scenarios on the severity of virus transmission rates. Using a simple model for the spreading disease and parsimonious assumptions on the relationship between the infection and the associated economic backlashes, we show how different policy schemes tend to induce heterogeneous distributions of losses at the regional level depending on mobility restrictions. Our work shed lights on how recovery policies need to balance the interplay between mobility flows of disposable workers and the diffusion of contagion.
Genetic regulation of gene expression of MIF family members in lung tissue
Authors: Florez-Sampedro Laura , Brandsma Corry-Anke , de Vries Maaike , Timens Wim , Bults Rene , Vermeulen Cornelis J. , van den Berge Maarten , Obeidat Ma’en , Joubert Philippe , Nickle David C. , Poelarends Gerrit J. , Faiz Alen , Melgert Barbro N. 
Published: October 2020

AbstractMacrophage migration inhibitory factor (MIF) is a cytokine found to be associated with chronic obstructive pulmonary disease (COPD). However, there is no consensus on how MIF levels differ in COPD compared to control conditions and there are no reports on MIF expression in lung tissue. Here we studied gene expression of members of the MIF family MIF, D-Dopachrome Tautomerase (DDT) and DDT-like (DDTL) in a lung tissue dataset with 1087 subjects and identified single nucleotide polymorphisms (SNPs) regulating their gene expression. We found higher MIF and DDT expression in COPD patients compared to non-COPD subjects and found 71 SNPs significantly influencing gene expression of MIF and DDTL. Furthermore, the platform used to measure MIF (microarray or RNAseq) was found to influence the splice variants detected and subsequently the direction of the SNP effects on MIF expression. Among the SNPs found to regulate MIF expression, the major LD block identified was linked to rs5844572, a SNP previously found to be associated with lower diffusion capacity in COPD. This suggests that MIF may be contributing to the pathogenesis of COPD, as SNPs that influence MIF expression are also associated with symptoms of COPD. Our study shows that MIF levels are affected not only by disease but also by genetic diversity (i.e. SNPs). Since none of our significant eSNPs for MIF or DDTL have been described in GWAS for COPD or lung function, MIF expression in COPD patients is more likely a consequence of disease-related factors rather than a cause of the disease.
Smart filtering of phase residues in noisy wrapped holograms
Authors: Tayebi Behnam , Sharif Farnaz , Han Jae-Ho 
Published: October 2020

AbstractPhase unwrapping is one of the major challenges in multiple branches of science that extract three-dimensional information of objects from wrapped signals. In several applications, it is important to extract the unwrapped information with minimal signal resolution degradation. However, most of the denoising techniques for unwrapping are designed to operate on the entire phase map to remove a limited number of phase residues, and therefore they significantly degrade critical information contained in the image. In this paper, we present a novel, smart, and automatic filtering technique for locally minimizing the number of phase residues in noisy wrapped holograms, based on the phasor average filtering (PAF) of patches around each residue point. Both patch sizes and PAF filters are increased in an iterative algorithm to minimize the number of residues and locally restrict the artifacts caused by filtering to the pixels around the residue pixels. Then, the improved wrapped phase can be unwrapped using a simple phase unwrapping technique. The feasibility of our method is confirmed by filtering, unwrapping, and enhancing the quality of a noisy hologram of neurons; the intensity distribution of the spatial frequencies demonstrates a 40-fold improvement, with respect to previous techniques, in preserving the higher frequencies.
A scoping review of research funding for small-scale farmers in water scarce regions
Authors: Ricciardi Vincent , Wane Abdrahmane , Sidhu Balsher Singh , Godde Cecile , Solomon Divya , McCullough Ellen , Diekmann Florian , Porciello Jaron , Jain Meha , Randall Nicola , Mehrabi Zia 
Published: October 2020

AbstractWater scarcity is a global issue that disproportionately affects small-scale farmers in low- and middle-income countries (LMICs). Through geospatial analysis, we estimated that less than 37% of small-scale farms probably have irrigation in water scarce regions across LMICs, compared with 42% of non-small-scale farms. Through a literature synthesis assisted by machine learning, we then systematically mapped the existing research for on-farm interventions that improve the incomes or yields of small-scale farmers in water scarce regions. We mapped over 888 on-farm interventions used to combat water scarcity from 560 publications and showed a research bias towards yields rather than livelihoods. We found gaps in evidence for many commonly proposed solutions, including livestock management, digital technology and solutions to protect natural resources at the farm-level, such as buffer strips. Our findings can be used to set a funding agenda for research on the geographies that are most at risk of water scarcity and the interventions that most lack evidence.
Probing of breast cancer using a combination of plasma and urinary circulating cell-free DNA
Authors: Zuo Zhigang , Tang Jiying , Cai Xiaojun , Ke Feng , Shi Zhenzong 
Published: October 2020

Abstract
Monitoring of early-stage breast cancer is critical in promptly addressing disease relapse. Circulating cell-free DNA provides a minimally invasive and sensitive means to probing the disease. In a longitudinal analysis of 250 patients with early breast cancer, we compared the circulating cell-free DNA recovered from both plasma and urine specimens. For comparison, 50 healthy controls were also recruited. Specific mutations associated with the disease were profiled to determine the clinical sensitivity and specificity. Correlations of recovered concentrations of cell-free DNA with outcomes were examined to address early prognostication. PIK3CA mutation profiling in both plasma and urinary cell-free DNA showed an agreement of 97.2% compared with the results obtained for tumor tissues. The analysis of healthy controls revealed that cell-free DNA measurements were stable and consistent over time. Over the short 6-month period of monitoring, our analyses showed declines in recovered cell-free DNA; these findings may aid physicians in stratifying patients at higher risk for relapse. Similar results were observed in both plasma and urine specimens (hazard ratios: 2.16 and 2.48, respectively). Cell-free DNA presents a novel and sensitive method for the monitoring of early-stage breast cancer. In the present study, serial measurements of both plasma and urine specimens were useful in probing the disease.
Differential rotation of the solar corona: A new data-adaptive multiwavelength approach
Authors: Mancuso S. , Giordano S. , Barghini D. , Telloni D. 
Published: October 2020

Context. The characterization of the differential rotation of the extended corona is still lacking conclusive results about the actual rotation rate profiles, and it is also expected to vary along the solar cycle. While some studies supported the quasi-rigidity of coronal rotation, others have found evidence of differential rotation to occur.
Aims. For the purpose of investigating the differential rotation of the solar corona, we analyzed ultraviolet (UV) spectral line observations acquired on both the east and west limbs at 1.7 R⊙ by the Ultraviolet Coronagraph Spectrometer (UVCS) on-board the Solar and Heliospheric Observatory during the solar minimum preceding solar cycle 23. To obtain a reliable and statistically robust picture of the rotational profile, we used a set of simultaneous 400 day long spectral line intensities of five different spectral lines: O VI 1032 Å, O VI 1037 Å, Si XII 499 Å, Si XII 521 Å, and H I Lyα 1216 Å, which are routinely observed by UVCS.
Methods. The data were analyzed by means of two different techniques: the generalized Lomb-Scargle periodogram and a multivariate data-adaptive technique called multichannel singular spectrum analysis. Among many other positive outcomes, this latter method is unique in its ability to recognize common oscillatory modes between the five time series observed at both limbs.
Results. The latitudinal rotation profile obtained in this work emphasizes that the low-latitude region of the UV corona (about ±20° from the solar equator) exhibits differential rotation, while the higher-latitude structures do rotate quasi-rigidly. Moreover, in contrast to previous results obtained using only O VI 1032 Å data over a 365 day time interval during solar minimum activity, the alleged north-south rotational asymmetry of the UV corona, if existent, is much less pronounced.
Conclusions. The differential rotation rate of the solar corona as evinced at low-latitudes is consistent with the rotational profile of the near-surface convective zone of the Sun, suggesting that the rotation of the corona at 1.7 R⊙ is linked to intermediate-scale magnetic bipole structures anchored near 0.99 R⊙. The quasi-rigid rotation rate found at mid and high latitudes is instead attributed to the influence of large-scale coronal structures linked to the rigidly rotating coronal holes. We further suggest that the methodology presented in this paper could represent a milestone for future investigations on differential rotation rates when dealing with simultaneous multiwavelength data.
Opportunities and Challenges for the Industrial Titanium Market
Authors: Henson Hershel Robert 
Published: October 2020

The industrial titanium market is the second largest segment of the titanium industry and currently comprises less than 20 % of the overall titanium market. In spite of a more than 50 year history of successful application in corrosive environments myths about availability, fabrication, pricing and corrosion resistance are still part of the conversation and culture with many potential customers. The author will discuss these issues and present comparisons with other common materials of construction to demonstrate the business case for titanium.
With seawater/brackish water being the most common corrosive environment where titanium is applied examples of current applications will be presented. By highlighting the characteristics of titanium that led to the material choice in these examples potential new applications can be identified. These examples will come from application on offshore platforms, LNG liquefaction plants, power generation, desalination and petroleum refining operations.
Against the backdrop of the application analysis the author will also explore regulatory, market influences and new technology impacting the industrial titanium market segment. Drawing on statistics from the Titanium Association and other resources a projection for industrial growth will be presented for the next decade.