bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana
Authors: Scheid Ray , Dowell James A. , Sanders Dean , Jiang Jianjun , Denu John M. , Zhong Xuehua 
Published: August 2022

AbstractHistone post‐translational modifications (PTMs) play important roles in many biological processes, including gene regulation and chromatin dynamics, and are thus of high interest across many fields of biological research. Chromatin immunoprecipitation coupled with sequencing (ChIP‐seq) is a powerful tool to profile histone PTMs in vivo. This method, however, is largely dependent on the specificity and availability of suitable commercial antibodies. While mass spectrometry (MS)–based proteomic approaches to quantitatively measure histone PTMs have been developed in mammals and several other model organisms, such methods are currently not readily available in plants. One major challenge for the implementation of such methods in plants has been the difficulty in isolating sufficient amounts of pure, high‐quality histones, a step rendered difficult by the presence of the cell wall. Here, we developed a high‐yielding histone extraction and purification method optimized for Arabidopsis thaliana that can be used to obtain high‐quality histones for MS. In contrast to other methods used in plants, this approach is relatively simple, and does not require membranes or additional specialized steps, such as gel excision or chromatography, to extract highly purified histones. We also describe methods for producing MS‐ready histone peptides through chemical labeling and digestion. Finally, we describe an optimized method to quantify and analyze the resulting histone PTM data using a modified version of EpiProfile 2.0 for Arabidopsis. In all, the workflow described here can be used to measure changes to histone PTMs resulting from various treatments, stresses, and time courses, as well as in different mutant lines. © 2022 Wiley Periodicals LLC.Basic Protocol 1: Nuclear isolation and histone acid extractionBasic Protocol 2: Peptide labeling, digestion, and desaltingBasic Protocol 3: Histone HPLC‐MS/MS and data analysis
Dual Structure‐Material Design of Separators toward Dendrite‐Free Lithium Metal Anodes
Authors: Su Zhengkang , Wang Biao , Li Linyan , Yang Guang , Yu Aishui , Li Guang , Zhang Jingjing 
Published: August 2022

AbstractThe practical applications of lithium metal anodes have been severely hindered by the Li dendrite issue. Herein, a dual structure‐material design strategy was developed to fabricate a new type of separator using interconnected hollow porous polyacrylonitrile (PAN) nanofibers (HPPANF), which delivered controllable and dendrite‐free Li depositions. The interconnected mesopores on HPPANF bridged the hollow interiors with the outside voids among the fibers, enabling outstanding electrolyte uptake capabilities for high ion conductivity, and nano‐level wetted electrolyte/anode interface for uniform Li plating/stripping. In parallel, the HPPANF separator enriched with polar groups acted as an exceptional polymer‐based solid‐state electrolyte, providing 3D ion channels for the transport of Li ions. Benefiting from the dual structure‐material design, the HPPANF separator induced uniform Li ion flux for dendrite‐free Li depositions, which caused enhanced cycling stability (1300 h, 3 mA cm−2). This work demonstrates a new method to stabilize Li metal anodes through rational separator design.
Melasma hyperpigmentation: An overview of current topical therapeutics
Authors: AlSalem Sultan , Alexis Andrew 
Published: August 2022

AbstractBackgroundMelasma is a common disorder of hyperpigmentation that affects populations globally and can adversely affect quality of life. Topical therapies—including hydroquinone and nonhydroquinone‐containing formulations—play a central role in the management of melasma.MethodsA literature review was conducted using PubMed and Google Scholar. Search keywords included a combination of the following: “melasma,” “chloasma,” and “topical treatment.” We identified and included seminal and high‐quality peer‐reviewed publications, systematic reviews, randomized controlled trials, case series, case reports, consensus statements, and expert opinions.ResultsTopical therapies are widely used for the treatment of melasma. Triple combination cream containing hydroquinone, fluocinolone, and tretinoin is the most studied formulation with the strongest evidence among treatment options. Numerous other prescription‐based and nonprescription topical agents, including a growing list of cosmeceuticals, have been used in the treatment of melasma, albeit in smaller studies.ConclusionA growing range of topical agents is available for the treatment of melasma. While larger, more robust studies are warranted, nonhydroquinone cosmeceuticals may be useful adjuncts or alternatives to the gold standard of triple‐combination hydroquinone cream.
Low resource availability drives feeding niche partitioning between wild bees and honeybees in a European city
Authors: Casanelles‐Abella Joan , Fontana Simone , Fournier Bertrand , Frey David , Moretti Marco 
Published: August 2022

AbstractCities are socioecological systems that filter and select species, therefore establishing unique species assemblages and biotic interactions. Urban ecosystems can host richer wild bee communities than highly intensified agricultural areas, specifically in resource‐rich urban green spaces such as allotments and family gardens. At the same time, urban beekeeping has boomed in many European cities, raising concerns that the fast addition of a large number of managed bees could deplete the existing floral resources, triggering competition between wild bees and honeybees. Here, we studied the interplay between resource availability and the number of honeybees at local and landscape scales and how this relationship influences wild bee diversity. We collected wild bees and honeybees in a pollination experiment using four standardized plant species with distinct floral morphologies. We performed the experiment in 23 urban gardens in the city of Zurich (Switzerland), distributed along gradients of urban and local management intensity, and measured functional traits related to resource use. At each site, we quantified the feeding niche partitioning (calculated as the average distance in the multidimensional trait space) between the wild bee community and the honeybee population. Using multilevel structural equation models (SEM), we tested direct and indirect effects of resource availability, urban beekeeping, and wild bees on the community feeding niche partitioning. We found an increase in feeding niche partitioning with increasing wild bee species richness. Moreover, feeding niche partitioning tended to increase in experimental sites with lower resource availability at the landscape scale, which had lower abundances of honeybees. However, beekeeping intensity at the local and landscape scales did not directly influence community feeding niche partitioning or wild bee species richness. In addition, wild bee species richness was positively influenced by local resource availability, whereas local honeybee abundance was positively affected by landscape resource availability. Overall, these results suggest that direct competition for resources was not a main driver of the wild bee community. Due to the key role of resource availability in maintaining a diverse bee community, our study encourages cities to monitor floral resources to better manage urban beekeeping and help support urban pollinators.
Fine‐tuning the performance of abundance estimation based on environmental DNA (eDNA) focusing on eDNA particle size and marker length
Authors: Jo Toshiaki , Yamanaka Hiroki 
Published: August 2022

AbstractReliable abundance estimation is a primary challenge in environmental DNA (eDNA) analysis, which has been addressed by considering the effects of eDNA transport and degradation. However, these eDNA spatial dynamics depend on the cellular and molecular structure of eDNA, with its persistence state (particle size and DNA fragment length) being essential for improved abundance estimation. To address the issue, we used datasets obtained from two types of aquarium experiments (targeting zebrafish [Danio rerio] and Japanese jack mackerel [Trachurus japonicus]) and compared the relationships between eDNA concentration and species abundance among different eDNA size fractions and target marker lengths. We reared the fish in experimental tanks with different individual numbers or biomass densities, filtered rearing water using different pore size filters, and quantified eDNA concentrations targeting different fragment lengths or genetic regions. Consequently, both experiments showed that the accuracy and sensitivity in abundance estimation were improved (i.e., R2 values and slopes of linear regressions increased) when targeting eDNA at the 3‐ to 10 μm size fraction. On the contrary, targeting eDNA at the >10 μm size fraction yielded a lower R2 value. This result indicates that the relationship between eDNA concentration and species abundance can be worsened when extremely larger size fractions are targeted. Conversely, the target marker length negatively affected the R2 value. This study proposes that the relationship between eDNA concentration and species abundance relies on the complex interactions between the particle size, persistence, and spatial heterogeneity of eDNA in water.
Evaluation of SDS‐coated iron nanostructure on the gene expression of bio surfactant‐producing genes by Pseudomonas aeruginosa
Authors: Ahsani Arani Yaser , Noormohammadi Zahra , Rasekh Behnam , Yazdian Fatemeh , kazemi Hojjat 
Published: August 2022

AbstractBio surfactants are natural surfactants that induce emulsification, displacement, increased solubility, and mobility of hydrophobic organic compounds. In this study, the gene expression of biosurfactant production genes by Pseudomonas aeruginosa in the presence of sodium dodecyl sulfate coated iron nanostructure (Fe/SDS) were evaluated. Emulsification Index and Surface Tension reduction test to check stability and emulsification the rhamnolipid were done. Purification was evaluated using thin layer chromatography (TLC) and expression of rhlA, mvfR, lasR, rhlR genes was determined using q‐PCR technique. Binding of nanoparticles to bio surfactants was confirmed by TEM. The best emulsification index, was by the sample that exposed to 1 mg/L Fe/SDS nanoparticles for 2 days. Rhamnolipid produced in the presence of nanoparticles had an acceptable ability to reduce surface tension. The Rf (retention factor) value obtained was 0.63 by chromatography. q‐PCR results showed that the expression of rhlA, mvfR, lasR, rhlR genes was significantly increased in Fe/SDS treated cells, which indicates the significant positive effect (P < 0.05) of nanoparticles on biosurfactant production of treated cells. While, SDS and Fe alone were not affected significantly (P > 0.05) on the expression of these genes. Our findings indicated the importance of nanoparticles in increasing the expression of genes involved in the bio surfactant production pathway of Pseudomonas aeruginosa.
Novel application of anti‐human Fc nanobody for screening high‐producing CHO cells for monoclonal antibody
Authors: Zhu Di , Wang Zheng , Xu Yunxia , Lin Jing , Qiu Mei , Liu Jianghai , Li Xinlei 
Published: August 2022

AbstractAnimal‐derived anti‐IgG secondary antibodies are currently employed to stain and screen of human monoclonal antibody(mAb)‐producing cells, but using animal‐derived antibodies may raise the concerns of high cost, complicated operations and biological safety issues in biopharmaceutical manufacturing. Nanobodies(VHHs) are attractive forms of antibodies for their straightforward engineering and expression in both eukaryotic and prokaryotic systems. Using phage‐displayed immune llama VHH library, we identified new anti‐Fc VHHs that could bind to human Fc with high affinity. In GFP fusion format, the anti‐Fc VHH‐GFP generated dramatically stronger FACS signals than AF488 conjugated anti‐IgG antibodies when used for staining mAb‐producing CHO cells. Furthermore, preparative sorting of CHO cells based on anti‐Fc VHH‐GFP staining resulted in the enrichment of cell lines capable of synthesizing mAb at high productivity. This safe and cost‐efficient anti‐Fc VHH‐GFP may optimize the process of generating highly productive cell lines for therapeutic mAb production compared to conventional animal‐derived fluorescent antibodies.
A state‐of‐the‐art review of the fate of heavy metals and product properties from pyrolysis of heavy‐metal(loid)‐enriched biomass harvested from phytoextraction
Authors: He Jing , Kumar Ravinder , Kan Tao , Strezov Vladimir 
Published: August 2022

AbstractVegetation has successfully been used for cleaning up metal(loid) polluted water bodies and lands through extracting and accumulating of contaminants in their aboveground biomass (phytoextraction). As this remediation technique is approaching extensive demonstration scale application and potential commercialisation, research efforts have been investigating new ways to achieve valorization of its by‐products, the heavy‐metal‐enriched biomass (HMEB). Biomass pyrolysis as an energy conversion technique represents a key step to numerous valorization options of HMEB. During the pyrolysis of HMEB, understanding the thermal decomposition pathways, and the migration and transformation of metal(loid)s are critical for the production of clean, safe and value‐added end‐products. This work performs a state‐of‐the‐art review of the studies conducted on phytoextraction and biomass pyrolysis of HMEB with emphasis on the properties of pyrolysis products as well as the behavior of heavy metal(loid)s during pyrolysis in relation to HMEB feedstock properties and the variables of the process.
What does the clean energy transition look like for Russian oil exports?
Authors: Sokhanvar Amin , Sohag Kazi 
Published: August 2022

AbstractThe commitment of governments to achieving the goals of the Paris Agreement and the expected decrease in fossil fuel consumption indicate the importance of studying the risks facing the oil exporters and the range of options and responses. This study adopts the Trade Gravity model to examine the effect of clean energy policies on Russian oil exports during the period 1996–2019. Our results based on Cross‐Sectional Autoregressive Distributed Lags modeling suggest that Russian oil exports are negatively affected by the energy transitions. This indicates that investing in cleaner energy technologies as a channel toward reducing fossil fuel demand can reduce the oil trade globally. Policies and strategies to retain and support the financial stability of the Russian government under the current scenario are suggested.
The CoaST‐Fire: A novel methodology to rapidly expose materials to various fire curves
Authors: Dreyer Jochen A. H. , Laxminarayan Tejasvi , Weinell Claus E. , Dam‐Johansen Kim , Kiil Søren 
Published: August 2022

AbstractA new method for testing materials under simulated fire conditions is introduced. The fundamentally new approach relies on the movement of the sample through zones with a spatially increasing temperature. Adjusting the velocity profile with which the sample is moved makes it possible to expose it to practically any temperature–time curve defined in fire safety standards, from extremely rapid hydrocarbon to more gradual cellulosic fire conditions. This manuscript presents a prototype named CoaST‐Fire that capitalises on this concept by combining a vertical tube furnace with a vertical motion system. The methodology to calibrate the furnace temperature profile, as well as to calculate the velocity profiles are discussed. The velocity profiles are then used to replicate a range of temperature–time curves with exceptional accuracy and reproducibility. A numerical model is developed in COMSOL Multiphysics to study heat fluxes towards the steel substrate as a function of time and thermal insulation. Finally, proof‐of‐concept experiments with two commercial intumescent coatings are presented. The experiments are shown to be highly repeatable while images of the coatings during the experiments can provide additional insights into the occurring reaction steps. Furthermore, CoaST‐Fire makes it possible to conduct experiments under various O2 concentrations and could later be extended with a gas outlet analysis system. The study is in line with recent efforts to develop cheaper and more rapid testing methods for early research and development of intumescent coatings and the setup could potentially also be used to test other types of materials.
Investigating howCOVID‐19 has challenged the Eurocentric concept of ‘development’: a case for sustainable food systems in theUK
Authors: Shittu Eniola , Kantamaneni Komali , Campos Luiza C. 
Published: August 2022

AbstractThe COVID‐19 health crisis has imposed extensive shocks to many global systems, particularly the UK food production chains, further challenging Eurocentric development discourses and stereotypes. Thus, this paper investigates how the pandemic has challenged the UK's development status by analysing how the pandemic has impacted the country's food industry. A literature review was conducted and used to identify, select and critically appraise publications between 2000 and 2021 discussing the challenges in the UK food system. The findings reveal that the UK's food industry is unsustainable as there are significant flaws in the system, that is food insecurity and food waste that go unaddressed. The impact of the pandemic has exacerbated the social and economic impacts of operating with such a system. Compounded with the geopolitical adjustments caused by Brexit, the UK is faced with the challenge of restructuring and developing new frameworks such as policies, regulations, schemes and partnerships to support the food industry's sustainability. Lastly, the findings reinforce that ‘developed’ and ‘developing’ nations encounter similar food challenges, which manifest differently in various landscapes and contexts. Therefore, the world (not just the UK) needs to shift away from Eurocentrism, moving towards a universal but equally personalised development outlook. This review provides an outline of the major problem areas in the UK food system and presents potential solutions aimed at helping guide the government's decision‐making process.
β‐catenin cancer–enhancing genomic regions axis is involved in the development of fibrolamellar hepatocellular carcinoma
Authors: Gulati Ruhi , Johnston Michael , Rivas Maria , Cast Ashley , Kumbaji Meenasri , Hanlon Margaret A. , Lee Sanghoon , Zhou Ping , Lake Charissa , Schepers Emily , Min Kyung‐Won , Yoon Je‐Hyun , Karns Rebekah , Reid Lola M. , Lopez‐Terrada Dolores , Timchenko Lubov , Parameswaran Sreeja , Weirauch Matthew T. , Ranganathan Sarangarajan , Bondoc Alexander , Geller James , Tiao Gregory , Shin Soona , Timchenko Nikolai 
Published: August 2022

Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a disease that occurs in children and young adults. The development of FLC is associated with creation of a fusion oncoprotein DNAJB1‐PKAc kinase, which activates multiple cancer‐associated pathways. The aim of this study was to examine the role of human genomic regions, called cancer‐enhancing genomic regions or aggressive liver cancer domains (CEGRs/ALCDs), in the development of FLC. Previous studies revealed that CEGRs/ALCDs are located in multiple oncogenes and cancer‐associated genes, regularly silenced in normal tissues. Using the regulatory element locus intersection (RELI) algorithm, we searched a large compendium of chromatin immunoprecipitation–sequencing (ChIP) data sets and found that CEGRs/ALCDs contain regulatory elements in several human cancers outside of pediatric hepatic neoplasms. The RELI algorithm further identified components of the β‐catenin–TCF7L2/TCF4 pathway, which interacts with CEGRs/ALCDs in several human cancers. Particularly, the RELI algorithm found interactions of transcription factors and chromatin remodelers with many genes that are activated in patients with FLC. We found that these FLC‐specific genes contain CEGRs/ALCDs, and that the driver of FLC, fusion oncoprotein DNAJB1‐PKAc, phosphorylates β‐catenin at Ser675, resulting in an increase of β‐catenin–TCF7L2/TCF4 complexes. These complexes increase a large family of CEGR/ALCD‐dependent collagens and oncogenes. The DNAJB1‐PKAc–β‐catenin–CEGR/ALCD pathway is preserved in lung metastasis. The inhibition of β‐catenin in FLC organoids inhibited the expression of CEGRs/ALCDs‐dependent collagens and oncogenes, preventing the formation of the organoid's structure. Conclusion: This study provides a rationale for the development of β‐catenin‐based therapy for patients with FLC.
Repositioning potentials of smallpox vaccines and antiviral agents in monkeypox outbreak: A rapid review on comparative benefits and risks
Authors: Islam Md. Rabiul , Hossain Md. Jamal , Roy Arpita , Hasan A. H. M. Nazmul , Rahman Md. Ashrafur , Shahriar Mohammad , Bhuiyan Mohiuddin Ahmed 
Published: August 2022

AbstractBackground and aimsThere is a sought for vaccines and antiviral agents as countermeasures for the recent monkeypox outbreak. Here, we aimed to review and discuss the repurposing potentials of smallpox vaccines and drugs in monkeypox outbreaks based on their comparative benefits and risks. Therefore, we conducted this rapid review and discussed the repurposing potentials of smallpox vaccines and drugs in monkeypox infection.MethodsHere, we searched Google Scholar and PubMed for relevant information and data. We found many articles that have suggested the use of smallpox vaccines and antiviral drugs in monkeypox outbreaks according to the study findings. We read the relevant articles to extract information.ResultsAccording to the available documents, we found two replication‐competent and one replication‐deficient vaccinia vaccines were effective against Orthopoxvirus. However, the healthcare authorities have authorized second‐generation live vaccina virus vaccines against Orthopoxvirus in many countries. Smallpox vaccine is almost 85% effective in preventing monkeypox infection as monkeypox virus, variola virus, and vaccinia virus are similar. The United States and Canada have approved a replication‐deficient third‐generation smallpox vaccine for the prevention of monkeypox infection. However, the widely used second‐generation smallpox vaccines contain a live virus and replicate it into the human cell. Therefore, there is a chance to cause virus‐induced complications among the vaccinated subjects. In those circumstances, the available Orthopoxvirus inhibitors might be a good choice for treating monkeypox infections as they showed similar efficacy in monkeypox infection in different animal model clinical trials. Also, the combined use of antiviral drugs and vaccinia immune globulin can enhance significant effectiveness in immunocompromised subjects.ConclusionRepurposing of these smallpox vaccines and antiviral agents might be weapons to fight monkeypox infection. Also, we recommend further investigations of smallpox vaccines and Orthopoxvirus inhibitors in a human model study to explore their exact role in human monkeypox infections.