bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical Regression Analysis of Breakages in Cold Rolling
Authors: Belskiy S M , Shopin I I
Published: November 2020

The maximum probability of strip’s breakage during the cold rolling is observed when the values of edge wedge are greater than 150 microns and the saddle coefficient is less than -0.075 and greater than 0.050. It is also shown that there is a pronounced synergistic effect of influence of combination of the saddle coefficient and the edge wedge on the breakage of the strip. When the edge wedge is reduced below 50 microns, the saddle coefficient ceases to affect the breakage of the strip during the cold rolling. At the same time, when the edge wedge is higher than 160 microns, the breakage is minimal with the saddle coefficient in the range from 0 to 0.025.
Improvement of the Device for Continuous Pressing of Non-Ferrous Metals and Alloys and Computer Simulation of the Deformation Process in This Device
Authors: Lezhnev S , Naizabekov A , Panin E
Published: November 2020

A new design of the device for continuous pressing is proposed, which combines the principles of the ECAP and Linex processes. To assess the possibility of the process and the efficiency of metal processing, computer modeling was performed. It is found that the greatest load is received by the mobile segments that ensure the movement of metal through the matrix. The distribution of stress-strain state parameters in the longitudinal section of the workpiece is extremely uneven, which is due to the transverse action of the pulling force. In the first two channels, due to a backpressure the compressive stresses occur. In the output channel, the metal experiences tensile stresses.
The Model for Predicting the Radius of Curvature of the Neck Forming on Cylindrical Specimens during Tensile Testing
Authors: Erpalov M V , Pavlov D A
Published: November 2020

The article is devoted to the testing of cylindrical specimens for tension. The main tendency of tensile tests is the improvement of methods for determining equivalent stresses acting in specimens while deformation localizes in the neck, i.e. methods for determining the hardening curves of materials up to the fracture. The most reliable way to study the rheological properties of materials is the direct measurement of the neck profile, namely the determination of the specimen diameter in the minimum cross-section of the neck and the radius of its curvature. However, direct measurements of the neck are associated with certain difficulties. They include a small number of measurements corresponding to different instants of the test, as well as inaccurate determination of the radius of the neck curvature due to the subjective approach to the measurement process. The measurements become more accurate if you use some equation for the analytical description of the neck profile and perform the measurements using optical methods during the test. However, such processing algorithms are often inaccessible to researchers. In this regard, this work proposes a model for predicting the radius of the neck curvature that is formed during tensile testing the cylindrical specimens. This model relies on the volume conservation law and the analytical description of the neck profile using the one-parameter equation. To calculate the radius of the neck curvature at each instant of the test it is necessary to know only the current values of elongation and the minimum specimen diameter. The effectiveness of the proposed mathematical model is evaluated using the computer simulation. The simulation results show that the use of predicted radius of the neck curvature allows calculating the equivalent stresses close to proper ones without the need of the direct neck profile measurement.
Graphene@attapulgite nanohybrid silicone Sol-gel coating toward good corrosion resistance
Authors: Wang Jiancheng , Yan Han , Tian Shu , Pu Jibin , Lu Guangming , Ren Lichun , Liu Zhixiong , Fan Xiaoqiang , Wang Liping
Published: November 2020

Graphene with shielding effect can improve the corrosion resistance of organic coatings, but its high electrical conductivity intensifies the corrosion of metal substrate due to micro-galvanic effect on the interface of coating and substrate. The regulation of graphene’s conductivity can inhibit the corrosion-promotion effect. Hence, graphene supported attapulgite (GNS-ATP) nanosheets with lower conductivity were successfully prepared by using TEOS as coupling agent, then were introduced into Sol-gel coatings via using gamma methacryloxypropyltrimethoxysilane (MPS) and tetraethyl orthosilicate (TEOS) as precursors. The characterization on corrosion resistance of the hybrid coatings illustrates that a small amount of well-dispersed GNS-ATP nanosheets can significantly enhance the corrosion resistance, mainly depending on the structure and performance characteristics of GNS-ATP nanosheets. Such advantages on reducing porosity and conductivity of hybrid coatings offer a better corrosion resistance.
Magnetic order and competition with superconductivity in (Ho-Er)Ni2B2C
Authors: Gundogdu Suleyman , Clancy J Patrick , Xu Guangyong , Zhao Yang , Dube Paul A , Karalar Tufan C , Cho Beong Ki , Lynn Jeffrey W , Ramazanoglu M
Published: November 2020

The rare earth magnetic order in pure and doped Ho(1−x)Er
x
Ni2B2C (x = 0, 0.25, 0.50, 0.75, 1) single crystal samples was investigated using magnetization and neutron diffraction measurements. Superconducting quaternary borocarbides, RNi2B2C where R = Ho, Er , are magnetic intermetallic superconductors with the transition temperatures ∼10 K in which long range magnetic order develops in the same temperature range and competes with superconductivity. Depending on the rare earth composition the coupling between superconductivity and magnetism creates several phases, ranging from a near reentrant superconductor with a mixture of commensurate and incommensurate antiferromagnetism to an incommensurate antiferromagnetic spin modulation with a weak ferromagnetic component. All of these phases coexist with superconductivity. RKKY magnetic interactions are used to describe the magnetic orders in the pure compounds. However, the doping of Er on Ho sites which have two strong magnetic moments with two different easy directions creates new and complicated magnetic modulations with possible local disorder effects. One fascinating effect is the development of an induced magnetic state resembling the pure and doped R
2CuO4 cuprate with R = Nd and Pr.
Modeling process–structure–property relationships in metal additive manufacturing: a review on physics-driven versus data-driven approaches
Authors: Kouraytem Nadia , Li Xuxiao , Tan Wenda , Kappes Branden , Spear Ashley D
Published: November 2020

Metal additive manufacturing (AM) presents advantages such as increased complexity for a lower part cost and part consolidation compared to traditional manufacturing. The multiscale, multiphase AM processes have been shown to produce parts with non-homogeneous microstructures, leading to variability in the mechanical properties based on complex process–structure–property (p-s-p) relationships. However, the wide range of processing parameters in additive machines presents a challenge in solely experimentally understanding these relationships and calls for the use of digital twins that allow to survey a larger set of parameters using physics-driven methods. Even though physics-driven methods advance the understanding of the p-s-p relationships, they still face challenges of high computing cost and the need for calibration of input parameters. Therefore, data-driven methods have emerged as a new paradigm in the exploration of the p-s-p relationships in metal AM. Data-driven methods are capable of predicting complex phenomena without the need for traditional calibration but also present drawbacks of lack of interpretability and complicated validation. This review article presents a collection of physics- and data-driven methods and examples of their application for understanding the linkages in the p-s-p relationships (in any of the links) in widely used metal AM techniques. The review also contains a discussion of the advantages and disadvantages of the use of each type of model, as well as a vision for the future role of both physics-driven and data-driven models in metal AM.
Challenges in laser-assisted milling of titanium alloys
Authors: Dargusch Matthew S , Sivarupan Tharmalingam , Bermingham Michael , Rashid Rizwan Abdul Rahman , Palanisamy Suresh , Sun Shoujin
Published: November 2020

Several detailed studies have comprehensively investigated the benefits and limitations of laser-assisted machining (LAM) of titanium alloys. These studies have highlighted the positive impact of the application of laser preheating on reducing cutting forces and improving productivity but have also identified the detrimental effect of LAM on tool life. This paper seeks to evaluate a series of the most common cutting tools with different coating types used in the machining of titanium alloys to identify whether coating type has a dramatic effect on the dominant tool wear mechanisms active during the process. The findings provide a clear illustration that the challenges facing the application of LAM are associated with the development of new types of cutting tools which are not subjected to the diffusion-controlled wear processes that dominate the performance of current cutting tools.
Topological analysis of traffic pace via persistent homology*
Authors: Carmody Daniel R , Sowers Richard B
Published: November 2020

We develop a topological analysis of robust traffic pace patterns using persistent homology. We develop Rips filtrations, parametrized by pace, for a symmetrization of traffic pace along the (naturally) directed edges in a road network. Our symmetrization is inspired by recent work of Turner (2019 Algebr. Geom. Topol.
19 1135–1170). Our goal is to construct barcodes which help identify meaningful pace structures, namely connected components or ‘rings’. We develop a case study of our methods using datasets of Manhattan and Chengdu traffic speeds. In order to cope with the computational complexity of these large datasets, we develop an auxiliary application of the directed Louvain neighborhood-finding algorithm. We implement this as a preprocessing step prior to our main persistent homology analysis in order to coarse-grain small topological structures. We finally compute persistence barcodes on these neighborhoods. The persistence barcodes have a metric structure which allows us to both qualitatively and quantitatively compare traffic networks. As an example of the results, we find robust connected pace structures near Midtown bridges connecting Manhattan to the mainland.
Bio inspired synthesis of silver nanoparticles and its applications to spin – orbit interactions of light
Authors: Prajapati Chandravati , Jolly Anju , Ravulapalli Sathyavathi
Published: November 2020

Spin–orbit interaction of light serves as an important property of light, which deals with the study of polarization and phase modulations in the light beam. These studies are essential and principal characeristics of light beam that have been used for most of the nanophotonics applications. Silver nanoparticles (Ag NPs) prepared via biosynthesis are used for one of such nanophotonics application in scattering via studying the light scattered through these nanoparticles. The silver nanoparticles Ag NPs were synthesized using green method, where reduction of silver ions to silver nanoparticles happen during the reaction of aqueous solution of Ag NO3 with the biomolecules present in fresh leaf extract of Coleus amboinicus plant. The nanoparticles were characterized using UV-visible (UV–vis) spectroscopy, Transmission electron microscopy (TEM) and Fourier Transform Infrared (FTIR) spectroscopy. TEM analysis shows the wide size distribution of spherical shape nanoparticles with 80 nm average size. The study of polarization and phase changes in the scattered light field has been carried out using Stokes polarimetry in forward direction scattering. Under the preliminary measurements of Polarimetry, the modification in the polarization components was studied by demonstrating changes in the Stokes S2, S3 parameters, polarization orientation (ψ) and ellipticity angle (χ) using transverse magnetic (TM) polarized Gaussian light beam.
Carbon-supported Pd-Ir nanoalloys as cathodic catalyst for oxygen reduction reaction
Authors: Zhang Yuchen , Xiao Xingyue , Geng Dejia , Dai Yu , Xia Fan
Published: November 2020

Pd as cathodic catalyst exhibits relatively low current density in mixing kinetic/diffusion controlled region. To improve catalytic activity of Pd, alloying Pd with another transition metal is an effective approach. Here, we prepared carbon-supported Pd-Ir nanoalloys (Pd-Ir/C) through impregnation method. Four types of Pd-Ir/C were designed and referred as Pd19Ir/C, Pd9Ir/C, Pd3Ir/C, and PdIr/C using nominal Pd/Ir atomic ratios of 19:1, 9:1, 3:1, and 1:1, respectively. The results showed that Pd and Ir formed the nanoalloy structures and Pd-Ir/C exhibited significantly improved catalytic activity for oxygen reduction reaction than Pd/C, indicating that Ir had important effect on Pd-Ir nanoalloys.
The rachis cannot hold, plants fall apart. A commentary on: ‘The unique disarticulation layer formed in the rachis of Aegilops longissima likely results from the spatial co-expression of Btr1 and Btr2’
Authors: Kellogg Elizabeth A
Published: November 2020

This article comments on:

Xiaoxue Zeng, Gang Chen, Lei Wang, Akemi Tagiri, Shinji Kikuchi, Hidenori Sassa and Takao Komatsuda, The unique disarticulation layer formed in the rachis of Aegilops longissima probably results from the spatial co-expression of Btr1 and Btr2, Annals of Botany, Volume 127, Issue 3, 16 February 2021, Pages 297–304, https://doi.org/10.1093/aob/mcaa147
Effect of Platelet-Derived Concentrated Growth Factor on Single-Layer, Multi-Layer, and Crushed Onlay Cartilage Grafts
Authors: Gürsoy Koray , Teymur Hakan , Göktaş Demircan Fethiye Berna , Tanas Işikçi Özlem , Gümüş Murat , Koçer Uğur
Published: November 2020

Background

The main concern with utilizing cartilage grafts to achieve structural integrity and volume restoration is the loss of volume over time and their unpredictable viability. Preservation of the volume of cartilage grafts is necessary to ensure their long-term success.

Objectives

The main aim of this study was to investigate the effect of concentrated growth factor (CGF) sheet on single-layer, multi-layer, and crushed block cartilage grafts.

Methods

Cartilage grafts obtained from the ears of rabbits were prepared in 3 different forms: single-layer, triple-layer, and crushed. After measuring the weight and thickness of the cartilage grafts, the grafts in the experimental group were wrapped with the prepared autologous CGF. These cartilage grafts were placed in subcutaneous pouches created on the backs of the rabbits. After 4 months, the rabbits were killed. The weight and thickness of the cartilage grafts were measured and the cartilage viability and peripheral changes were examined microscopically.

Results

The percentage changes in the weights and thicknesses of the single-layer, multi-layer, and crushed cartilage grafts wrapped with CGF were found to be statistically significantly lower than in the control group. When the cartilage viability and changes in peripheral tissue were evaluated, CGF-wrapped cartilage groups did not achieve statistically significantly better scores than the untreated control groups.

Conclusions

In cases planned to receive a block cartilage graft, especially if graft resorption is not desired or should be minimized, wrapping the graft with autologous CGF is a feasible option.
John D Barrow (1952–2020)
Authors: Maguelio João , Webb John
Published: November 2020

João Magueijo and John Webb remember the athlete, wide-ranging cosmologist, prolific author and walking encyclopedia.
Emerging roles of RNA modifications in genome integrity
Authors: Lee Seo Yun , Kim Jae Jin , Miller Kyle M
Published: November 2020

Post-translational modifications of proteins are well-established participants in DNA damage response (DDR) pathways, which function in the maintenance of genome integrity. Emerging evidence is starting to reveal the involvement of modifications on RNA in the DDR. RNA modifications are known regulators of gene expression but how and if they participate in DNA repair and genome maintenance has been poorly understood. Here, we review several studies that have now established RNA modifications as key components of DNA damage responses. RNA modifying enzymes and the binding proteins that recognize these modifications localize to and participate in the repair of UV-induced and DNA double-strand break lesions. RNA modifications have a profound effect on DNA–RNA hybrids (R-loops) at DNA damage sites, a structure known to be involved in DNA repair and genome stability. Given the importance of the DDR in suppressing mutations and human diseases such as neurodegeneration, immunodeficiencies, cancer and aging, RNA modification pathways may be involved in human diseases not solely through their roles in gene expression but also by their ability to impact DNA repair and genome stability.
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations
Authors: Tripathi Swarnendu , Dsouza Nikita R , Urrutia Raul , Zimmermann Michael T
Published: November 2020

Motivation

Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated.

Results

Here, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance.

Availability and implementation

All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data.

Supplementary information

Supplementary data are available at Bioinformatics online.
Quantification of aneuploidy in targeted sequencing data using ASCETS
Authors: Spurr Liam F , Touat Mehdi , Taylor Alison M , Dubuc Adrian M , Shih Juliann , Meredith David M , Pisano William V , Meyerson Matthew L , Ligon Keith L , Cherniack Andrew D , Li Yvonne Y , Beroukhim Rameen
Published: November 2020

The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data.

Availability and implementation

ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation.

Supplementary information

Supplementary data are available at Bioinformatics online.
Robustifying genomic classifiers to batch effects via ensemble learning
Authors: Zhang Yuqing , Patil Prasad , Johnson W. Evan , Parmigiani Giovanni
Published: November 2020

Motivation

Genomic data are often produced in batches due to practical restrictions, which may lead to unwanted variation in data caused by discrepancies across batches. Such ‘batch effects’ often have negative impact on downstream biological analysis and need careful consideration. In practice, batch effects are usually addressed by specifically designed software, which merge the data from different batches, then estimate batch effects and remove them from the data. Here, we focus on classification and prediction problems, and propose a different strategy based on ensemble learning. We first develop prediction models within each batch, then integrate them through ensemble weighting methods.

Results

We provide a systematic comparison between these two strategies using studies targeting diverse populations infected with tuberculosis. In one study, we simulated increasing levels of heterogeneity across random subsets of the study, which we treat as simulated batches. We then use the two methods to develop a genomic classifier for the binary indicator of disease status. We evaluate the accuracy of prediction in another independent study targeting a different population cohort. We observed that in independent validation, while merging followed by batch adjustment provides better discrimination at low level of heterogeneity, our ensemble learning strategy achieves more robust performance, especially at high severity of batch effects. These observations provide practical guidelines for handling batch effects in the development and evaluation of genomic classifiers.

Availability and implementation

The data underlying this article are available in the article and in its online supplementary material. Processed data is available in the Github repository with implementation code, at https://github.com/zhangyuqing/bea_ensemble.

Supplementary information

Supplementary data are available at Bioinformatics online.
Climatic control of mat vegetation communities on inselberg archipelagos in south-eastern Brazil
Authors: De Paula Luiza F A , Forzza Rafaela Campostrini , Azevedo Luísa O , Bueno Marcelo L , Solar Ricardo R C , Vanschoenwinkel Bram , Porembski Stefan
Published: November 2020

Granite and/or gneiss inselbergs are excellent examples of geomorphologically stable island habitats, considered as old, climatically buffered, infertile landscapes (OCBILs). However, unlike oceanic islands, their underlying drivers of diversity patterns remain to be investigated. Here, we studied 24 inselbergs in south-eastern Brazil, aiming to understand the role of landscape variables and environmental conditions in the assembly of the characteristic extremophilic mat vegetation communities. We found that beta diversity was largely explained by climatic variables, whereas species richness did not vary among inselbergs. Classic determinants of the diversity of island communities do not generally seem to apply to these plant assemblages. Overall, these communities change along a coast-to-inland gradient that captures increased seasonality with a replacement of more hydrophilic taxa by more drought-tolerant taxa. Changes in species composition in space involved strong species replacement, with several widespread genera locally represented on distinct inselbergs by different narrowly distributed species. Despite the deterministic sorting of taxa based on climatic conditions, a substantial fraction of the beta diversity remained unexplained. This underlines the importance of historical processes, which are easier to notice in stable OCBIL regions, such as range expansion, local extinction, dispersal constraints and allopatric speciation.
Male hybrid sterility in the cattle-yak and other bovines: a review
Authors: Niayale Robert , Cui Yan , Adzitey Fredrick
Published: November 2020

Hybridization is important for both animal breeders attempting to fix new phenotypic traits and researchers trying to unravel the mechanism of reproductive barriers in hybrid species and the process of speciation. In interspecies animal hybrids, gains made in terms of adaptation to environmental conditions and hybrid vigor may be offset by reduced fertility or sterility. Bovine hybrids exhibit remarkable hybrid vigor compared to their parents. However, the F1 male hybrid exhibits sterility, whereas the female is fertile. This male-biased sterility is consistent with the Haldane rule where heterogametic sex is preferentially rare, absent, or sterile in the progeny of two different species. The obstacle of fixing favorable traits and passing them to subsequent generations due to the male sterility is a major setback in improving the reproductive potential of bovines through hybridization. Multiperspective approaches such as molecular genetics, proteomics, transcriptomics, physiology, and endocrinology have been used by several researchers over the past decade in an attempt to unravel the potential mechanisms underlying male hybrid sterility. However, the mechanism of sterility in the hybrid male is still not completely unravelled. This review seeks to provide an update of the mechanisms of the sterility in the cattle-yak and other bovines.
PET-MRI nanoparticles imaging of blood–brain barrier damage and modulation after stroke reperfusion
Authors: Debatisse Justine , Eker Omer Faruk , Wateau Océane , Cho Tae-Hee , Wiart Marlène , Ramonet David , Costes Nicolas , Mérida Inés , Léon Christelle , Dia Maya , Paillard Mélanie , Confais Joachim , Rossetti Fabien , Langlois Jean-Baptiste , Troalen Thomas , Iecker Thibaut , Le Bars Didier , Lancelot Sophie , Bouchier Baptiste , Lukasziewicz Anne-Claire , Oudotte Adrien , Nighoghossian Norbert , Ovize Michel , Contamin Hugues , Lux François , Tillement Olivier , Canet-Soulas Emmanuelle
Published: November 2020

In an acute ischaemic stroke, understanding the dynamics of blood–brain barrier injury is of particular importance for the prevention of symptomatic haemorrhagic transformation. However, the available techniques assessing blood–brain barrier permeability are not quantitative and are little used in the context of acute reperfusion therapy. Nanoparticles cross the healthy or impaired blood–brain barrier through combined passive and active processes. Imaging and quantifying their transfer rate could better characterize blood–brain barrier damage and refine the delivery of neuroprotective agents. We previously developed an original endovascular stroke model of acute ischaemic stroke treated by mechanical thrombectomy followed by positron emission tomography-magnetic resonance imaging. Cerebral capillary permeability was quantified for two molecule sizes: small clinical gadolinium Gd-DOTA (<1 nm) and AGuIX® nanoparticles (∼5 nm) used for brain theranostics. On dynamic contrast-enhanced magnetic resonance imaging, the baseline transfer constant Ktrans was 0.94 [0.48, 1.72] and 0.16 [0.08, 0.33] ×10−3 min−1, respectively, in the normal brain parenchyma, consistent with their respective sizes, and 1.90 [1.23, 3.95] and 2.86 [1.39, 4.52] ×10−3 min−1 in choroid plexus, confirming higher permeability than brain parenchyma. At early reperfusion, Ktrans for both Gd-DOTA and AGuIX® nanoparticles was significantly higher within the ischaemic area compared to the contralateral hemisphere; 2.23 [1.17, 4.13] and 0.82 [0.46, 1.87] ×10−3 min−1 for Gd-DOTA and AGuIX® nanoparticles, respectively. With AGuIX® nanoparticles, Ktrans also increased within the ischaemic growth areas, suggesting added value for AGuIX®. Finally, Ktrans was significantly lower in both the lesion and the choroid plexus in a drug-treated group (ciclosporin A, n = 7) compared to placebo (n = 5). Ktrans quantification with AGuIX® nanoparticles can monitor early blood–brain barrier damage and treatment effect in ischaemic stroke after reperfusion.
Pterostilbene accelerates wound healing by modulating diabetes-induced estrogen receptor β suppression in hematopoietic stem cells
Authors: Xie Weiguo , Zhou Xueqing , Hu Weigang , Chu Zhigang , Ruan Qiongfang , Zhang Haimou , Li Min , Zhang Hongyu , Huang Xiaodong , Yao Paul
Published: November 2020

Background

Delayed wound healing is one of the major complications of diabetes mellitus and is characterized by prolonged inflammation, delayed re-epithelialization and consistent oxidative stress, although the detailed mechanism remains unknown. In this study, we aimed to investigate the potential role and effect of pterostilbene (PTE) and hematopoietic stem cells (HSCs) on diabetic wound healing.

Methods

Diabetic rats were used to measure the epigenetic changes in both HSCs and peripheral blood mononuclear cells (PBMCs). A cutaneous burn injury was induced in the rats and PTE-treated diabetic HSCs were transplanted for evaluation of wound healing. In addition, several biomedical parameters, including gene expression, oxidative stress, mitochondrial function and inflammation in macrophages, were also measured.

Results

Our data showed that PTE had a much stronger effect than resveratrol on accelerating diabetic wound healing, likely because PTE can ameliorate diabetes-induced epigenetic changes to estrogen receptor β promoter in HSCs, while resveratrol cannot. Further investigation showed that bone marrow transplantation of PTE-treated diabetic HSCs restores diabetes-induced suppression of estrogen receptor β and its target genes, including nuclear respiratory factor-1 and superoxide dismutase 2, and protects against diabetes-induced oxidative stress, mitochondrial dysfunction and elevated pro-inflammatory cytokines in both PBMCs and macrophages, subsequently accelerating cutaneous wound healing.

Conclusions

HSC may play an important role in wound healing through transferring epigenetic modifications to subsequent PBMCs and macrophages by differentiation, while PTE accelerates diabetic wound healing by modulating diabetes-induced epigenetic changes in HSCs. Thus, PTE may be a novel therapeutic strategy for diabetic wound healing.
Evaluating mucus exudation dynamics through isotopic enrichment and turnover of skin mucus fractions in a marine fish model
Authors: Ordóñez-Grande Borja , Fernández-Alacid Laura , Sanahuja Ignasi , Sánchez-Nuño Sergio , Fernández-Borràs Jaume , Blasco Josefina , Ibarz Antoni
Published: November 2020

Fish skin mucus is composed of insoluble components, which form the physical barrier, and soluble components, which are key for interrelationship functions. Mucus is continuously secreted, but rates of production and exudation are still unknown, as are the underlying mechanisms. Using stable isotope analysis, here, we evaluate skin mucus turnover and renewal in gilthead sea bream, separating raw mucus and its soluble and insoluble fractions. Isotopic abundance analysis reveals no differences between mucus and white muscle, thus confirming mucus samples as reliable non-invasive biomarkers. Mucus production was evaluated using a single labelled meal packaged in a gelatine capsule, with both 13C and 15N, via a time-course trial. 13C was gradually allocated to skin mucus fractions over the first 12 h and was significantly (4-fold) higher in the soluble fraction, indicating a higher turnover of soluble mucus components that are continuously produced and supplied. 15N was also gradually allocated to mucus, indicating incorporation of new proteins containing the labelled dietary amino acids, but with no differences between fractions. When existent mucus was removed, dietary stable isotopes revealed stimulated mucus neoformation dependent on the components. All this is novel knowledge concerning skin mucus dynamics and turnover in fish and could offer interesting non-invasive approaches to the use of skin mucus production in ecological or applied biological studies such as climate change effects, human impact, alterations in trophic networks or habitat degradation, especially of wild-captured species or protected species.
“Daughterlands”: Personal and Political Mappings in Scottish Women’s Poetry
Authors: Norquay Glenda
Published: November 2020

Scottish women’s poetry in recent years has evinced an interest in mapping daughterhood, frequently through linguistic negatives that challenge binary thinking. This essay argues that such “daughterlands” offer an imaginative alternative to the more familiar “motherland”: encompassing past, present, and future and positioning women in multiple roles, they have played a transformative role in the poetic imagining of “Scotland” in the new millennium. The essay considers the deployment of daughterly spaces by influential writers such as Carol Ann Duffy, Liz Lochhead, Jackie Kay, and Kathleen Jamie and then traces more recent instantiations by a younger generation of poets such as Claire Askew, Theresa Muñoz, and Em Strang. In conclusion, it demonstrates the experiential and metaphoric potential of daughterhood for shaping broad political thinking in an explicitly public poem by Kay.
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
Authors: Sousa Diana , Lamurias Andre , Couto Francisco M
Published: November 2020

Biomedical relation extraction (RE) datasets are vital in the construction of knowledge bases and to potentiate the discovery of new interactions. There are several ways to create biomedical RE datasets, some more reliable than others, such as resorting to domain expert annotations. However, the emerging use of crowdsourcing platforms, such as Amazon Mechanical Turk (MTurk), can potentially reduce the cost of RE dataset construction, even if the same level of quality cannot be guaranteed. There is a lack of power of the researcher to control who, how and in what context workers engage in crowdsourcing platforms. Hence, allying distant supervision with crowdsourcing can be a more reliable alternative. The crowdsourcing workers would be asked only to rectify or discard already existing annotations, which would make the process less dependent on their ability to interpret complex biomedical sentences. In this work, we use a previously created distantly supervised human phenotype–gene relations (PGR) dataset to perform crowdsourcing validation. We divided the original dataset into two annotation tasks: Task 1, 70% of the dataset annotated by one worker, and Task 2, 30% of the dataset annotated by seven workers. Also, for Task 2, we added an extra rater on-site and a domain expert to further assess the crowdsourcing validation quality. Here, we describe a detailed pipeline for RE crowdsourcing validation, creating a new release of the PGR dataset with partial domain expert revision, and assess the quality of the MTurk platform. We applied the new dataset to two state-of-the-art deep learning systems (BiOnt and BioBERT) and compared its performance with the original PGR dataset, as well as combinations between the two, achieving a 0.3494 increase in average F-measure. The code supporting our work and the new release of the PGR dataset is available at https://github.com/lasigeBioTM/PGR-crowd.
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls
Authors: Biggs Harry , Parthasarathy Padmini , Gavryushkina Alexandra , Gardner Paul P
Published: November 2020

Variants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature. The database consists of 721 non-coding variants linked to the published literature describing the evidence of functional consequences. We have also sampled 7228 covariate-matched benign controls, that have a population frequency of over 5%, from the single nucleotide polymorphism database (dbSNP151) database. These were sampled controlling for potential confounding factors such as linkage with pathogenic variants, annotation type (untranslated region, intron, intergenic, etc.) and variant type (substitution or indel). The dataset presented here represents a curated repository, with a potential use for the training or evaluation of algorithms used in the prediction of non-coding variant functionality.

Database URL: https://github.com/Gardner-BinfLab/ncVarDB.
Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea)
Authors: Ettahi Khaoula , Lhee Duckhyun , Sung Ji Yeon , Simpson Alastair G B , Park Jong Soo , Yoon Hwan Su
Published: November 2020

Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), because this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829-bp-long circular molecule, including 40 coding sequences (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and Naegleria fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).
Ambient noise correlation analysis of S-net records: extracting surface wave signals below instrument noise levels
Authors: Takagi Ryota , Toyokuni Genti , Chikasada Naotaka
Published: November 2020

We applied ambient noise cross-correlation analysis to the cabled ocean bottom seismic network offshore northeast Japan (Seafloor observation network for earthquakes and tsunamis along the Japan Trench: S-net) to extract surface waves propagating in the ocean area of the forearc region. We found two types of peculiar pulses in the cross-correlation functions (CCFs) of ambient seismic noise records: periodic pulses mainly every minute and sharp pulses around the lag time zero. These pulses strongly contaminate the surface wave signals in the CCFs at frequencies below ∼0.1 Hz. The periodic pulses originate from periodic instrument noises, while the zero-lag pulses originate from random instrument noises which are coherent within station pairs. By developing solutions to remove the periodic and zero-lag pulses based on the characteristics of the pulses, we succeeded in extracting Rayleigh and Love wave signals from the S-net records at 0.03–0.3 Hz, while the surface wave signals at 0.03–0.1 Hz were not visible without the application of these solutions. These solutions widen the frequency range of analysis, and may be applicable to other seismic networks, particularly to recent dense but non-broad-band networks. We identified the fundamental and first higher modes of Rayleigh waves and the fundamental mode of the Love wave. The extracted surface wave signals can constrain the shear wave velocity structure from the sediment to seismogenic zone around the megathrust plate boundary in the forearc region.
Intruders in a Balancing Act: Black Economic Empowerment, Transitional Justice and Investment Arbitration Tribunals
Authors: Le Moli Ginevra
Published: November 2020

This article examines the role of ad hoc investment arbitration tribunals in arbitrating highly sensitive matters in transitional justice contexts, focusing on disputes arising from black economic empowerment (BEE) policies in countries formerly under racially discriminatory regimes. After an overview of the investment protection system, the article introduces the historical context of BEE policies. It subsequently analyses three main disputes, one against South Africa and two against Zimbabwe, where white concession holders and landowners relied on Bilateral Investment Treaties to claim compensation for the consequences of BEE mining and land redistribution policies. These disputes provide a testing ground to shed light on the role of investment arbitration in the context of transitional justice. The article concludes that such a role essentially amounts to an intrusion in the perilous ‘balancing act’ of managing a transitional justice process.
Comorbid patterns of anaemia and diarrhoea among children aged under 5 years in Ghana: a multivariate complex sample logistic regression analysis and spatial mapping visualisation
Authors: Duah Henry Ofori , Amankwa Charles Enyaah , Adomako Isaac , Owusu Benson , Agbadi Pascal
Published: November 2020

Background

Anaemia and diarrhoea are known independent causes of under-five morbidity and mortality. This study sought to investigate predictors of comorbid patterns of anaemia and diarrhoea using the 2014 Ghana Demographic and Health Survey (GDHS).

Methods

The study employed analysis of secondary data from the 2014 GDHS. We performed a multivariate complex sample logistic regression and spatial analysis.

Results

The weighted prevalence of comorbid anaemia and diarrhoea was 9.28% with the highest burden (16.45%) found in the Upper West region. Independent predictors (risk factors) of comorbid patterns of anaemia and diarrhoea were children aged 6–23 mo (OR=2.17, 95% CI 1.42 to 3.33), male gender (OR=1.50, 95% C1 1.04 to 2.16), history of fever (OR=4.37, 95% CI 2.94 to 6.50) and living in a household with two children aged <5 y (OR=1.80, 95% CI 1.14 to 2.84). Protective factors were having a father with secondary or higher education (OR=0.57, 95% CI 0.33 to 0.97), living in a household with ≥6 members (OR=0.46, 95% CI 0.28 to 0.75) and living in a richer household (OR=0.38, 95% CI 0.16 to 0.89). Surface maps revealed inter-regional and subregional variations.

Conclusion

The study shows that the independent predictors of comorbid patterns of anaemia and diarrhoea among children aged <5 y in Ghana are age, gender, history of fever, the number of children aged <5 y in the household, parental education, household size and household wealth. The study identified zones to be targeted for cost-effective policy interventions.
Impact of the COVID-19 pandemic on community antibiotic prescribing in Scotland
Authors: Malcolm William , Seaton Ronald A , Haddock Gail , Baxter Linsey , Thirlwell Sarah , Russell Polly , Cooper Lesley , Thomson Anne , Sneddon Jacqueline
Published: November 2020

Background

Following concerns about increased antibiotic use during the COVID-19 pandemic, trends in community antibiotic prescriptions in Scotland were evaluated.

Methods

The primary care prescription electronic messaging system used in GP practices with NHS contracts provided near real-time data analysis of national data. The main outcome measures were the weekly number of prescriptions for antibiotics generated by prescribers in GP practices in 2020 compared with 2019.

Results

At end of Week 12 2020 (22 March), after a sharp increase, the number of prescriptions commonly used for respiratory infections was 44% higher than the corresponding week in 2019. The number of prescriptions for respiratory antibiotics reduced through April and May 2020, with 34% fewer prescriptions issued by end of Week 22 (31 May) than in the corresponding week in 2019. Reductions were pronounced in all age groups but particularly apparent for prescriptions for children aged 0–4 years. These data were compared with weekly prescriptions for a selection of non-respiratory antibiotics and no difference was seen between 2020 and 2019.

Conclusions

Trends in antibiotic prescription data show that after an initial surge, and following ‘lockdown’ in Scotland, the total number of prescriptions for antibiotics commonly used for respiratory infections fell. We believe this is the first published national evaluation of the impact of COVID-19 on community use of antibiotics. Further analysis of national data is planned to provide a greater understanding of the reasons behind these trends.
Deconstructing Dud Disarmament Disputes
Authors: Fry James D , Nair Saroj
Published: November 2020

This Article explores the limits of judicial settlement of nuclear-weapon disputes through a case study of the Marshall Islands’ cases against India, Pakistan and the UK before the International Court of Justice in 2016. It posits that judicial settlement is limited mainly by the quality of the arguments and evidence submitted by the disputants, not by any limitations inherent in judicial settlement with such politically sensitive disputes. The lawyers in the Marshall Islands’ cases should have taken greater care in crafting their arguments and in tying them explicitly to Article VI of the Nuclear Non-Proliferation Treaty and its customary equivalent.
Knockout of Transient Receptor Potential Melastatin 4 Channel Mitigates Cerebral Edema and Neuronal Injury After Status Epilepticus in Mice
Authors: Chen Xing , Liu Kewei , Lin Zhenzhou , Huang Kaibin , Pan Suyue
Published: November 2020

This study aimed to evaluate whether the knockout of transient receptor potential melastatin 4 (TRPM4) could reduce cerebral edema and improve neurologic outcome in a mouse model of status epilepticus (SE). Wild-type (WT) (n = 61) and Trpm4–/– mice (n = 61) with behavioral seizures induced by lithium (10 mEq/kg) and pilocarpine (30–40 mg/kg) were terminated 2.5 hours after the onset of SE. After SE, 28 WT-SE and 27 Trpm4–/–-SE mice were observed for 28 days and assessed for survival and cognitive function; the others were killed after 24 hours, 72 hours, or 7 days, and evaluated for cerebral edema and histological injury. In comparison to WT-SE mice, the mortality and cognitive deficit for Trpm4–/–-SE mice following SE after 28 days were significantly ameliorated. Trpm4–/–-SE mice also showed less water content and cerebral edema assessed by magnetic resonance imaging, and decreased blood-brain barrier breakdown after SE. Moreover, Trpm4 deficiency significantly mitigated neuronal loss, cellular necrosis and apoptosis in the hippocampus and piriform cortex and mitigated astrocytosis and microgliosis. In conclusion, this study suggests that Trmp4 may represent a new target for improving outcomes after SE.
The “Strings Attached” to Community Difference and Potential Pathways to Fire Adaptiveness in the Wildland Urban Interface
Authors: Billings Mark C , Carroll Matthew S , Paveglio Travis B
Published: November 2020

This article identifies specific social characteristics in two wildland urban interface communities that may have significant impacts on the ability of those communities to adapt to wildfire. Researchers used a mixed-methods approach to triangulate results to identify potential views and motives surrounding three important behaviors and values related to crafting potential strategies to mitigate wildfire risk. The analysis of quantitative data in the form of responses to Likert-type questions and qualitative data in the form of responses to questions asked during focus group sessions yielded a deeper understanding of the way the terms independence and trust are conceptualized from one community to another. Understanding what these concepts mean in the context of a given community is essential to understanding how to move forward with strategies to reduce risk and eliminate potential barriers to doing so.