bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Interlaboratory Evaluation of an LC–MS/MS Method for the Quantification of Lysozyme in Wine Across Independent Instrument Platforms
Authors: Downs Melanie L , McClure Beth Anne , Jayasena Shyamali , Ramachandran Bini , Krawitzky Michael , Ribeiro Tony , Wallace Julie , Tallman Steve , Mortola Bill 
Published: September 2021

AbstractBackgroundVarious processing aids and fining agents are used in winemaking to help improve sensory characteristics. Some of these materials may contain or be derived from allergenic foods, such as eggs. In order to ensure food safety and that products meet regulatory compliance, it is essential to have robust and effective analytical methods to verify the removal of allergenic proteins following their use. Current methods include ELISA and MS methods, which can target either whole foods or individual proteins, and provide either quantitative data or qualitative confirmation of proteins. MS methods offer the potential to test for multiple proteins within a single assay to improve cost and efficiency, whereas ELISA methods typically analyze for a single protein per assay.ObjectiveThis study focuses on the development of a LC–tandem MS (MS/MS) quantitative method for lysozyme in white wine and compares performance across two laboratories utilizing two different instrument platforms.MethodsLysozyme target peptides were selected by conducting bottom-up discovery proteomics. Candidate targets were evaluated using parallel reaction monitoring (PRM) or selected reaction monitoring (SRM) LC–MS/MS, depending on the instrument in each laboratory. Quantification of lysozyme was conducted using internal, stable isotope-labeled synthetic peptide standards.ResultsThree of eight candidate target peptides showed performance suitable for the final quantitative method. White wine spiked with 0.1 and 0.5 ppm lysozyme demonstrated quantitative recovery of 70–120%. While the PRM method delivered better repeatability, the SRM method gave higher quantitative recovery values.ConclusionA targeted LC–MS/MS method for quantification of lysozyme in white wine has been developed and deployed on two different MS instrument platforms in two laboratories.HighlightsBoth SRM and PRM targeted LC–MS/MS methodologies can be used for quantification of lysozyme in white wine. This study is among the first to evaluate an MS method for food allergen quantification in multiple laboratories.
Linear temporal justification logics with past and future time modalities
Authors: Ghari Meghdad 
Published: September 2021

AbstractTemporal justification logic is a new family of temporal logics of knowledge in which the knowledge of agents is modelled using a justification logic. In this paper, we present various temporal justification logics involving both past and future time modalities. We combine Artemov’s logic of proofs with linear temporal logic with past, and we also investigate several principles describing the interaction of justification and time. We present two kinds of semantics for our temporal justification logics, one based on interpreted systems and Fitting models and the other based on Mkrtychev models, and further, we establish soundness and completeness. We show that the internalization property holds in some of the temporal justification logics. We further investigate the two well-known epistemic-temporal notions of no forgetting and no learning in the framework of justification logics. Finally, we present temporal justification logics that avoid the logical omniscience problem.
Bringing the Forest Home: Lessons Learned during the COVID-19 Pandemic about E-Planning in Community Forestry Contexts
Authors: Beck Samantha , Coleman Kimberly , Tapper J Ethan 
Published: September 2021

AbstractThis paper examines “e-planning,” or the use of computer-based systems to conduct planning and decision-making, in the context of community forest management. E-planning is growing in the field of environmental planning, as it promises greater equity in terms of public participation. However, a lack of scholarly work exists on the applicability for forest planning. During the COVID-19 pandemic, county foresters and other natural resource professionals in Vermont turned to e-planning when safety restrictions limited their ability to engage in face-to-face efforts. This provided an opportunity to collect empirical data about the potential for e-planning to support the public engagement process in the context of forest planning. We provide an overview of e-planning theory and examine data from Vermont to explore the promise of e-planning for forest management. We make recommendations about the applicability of e-planning in the context of forest planning, and highlight areas for future research to investigate.
How Will COVID-19 Change Forestry Education? A Study of US Forest Operations Instructors
Authors: Dodson Elizabeth M , Blinn Charles R 
Published: September 2021

AbstractThe COVID-19 (COVID) pandemic affected nearly every aspect of higher education. It has been particularly disruptive to forest operations courses that rely heavily on field experiences. Dodson and Blinn (2021) surveyed US forest operations instructors at four-year institutions granting SAF-accredited forestry degrees to understand how they rapidly modified courses during spring 2020 to accommodate a move to fully remote instruction. Through an online survey and interviews, a follow-up study was conducted to understand how courses were modified when instructors had time to prepare and what, if any, of those modifications are likely to be retained upon a return to in-person instruction. Two main themes emerged from the survey and interviews: instructors will expand the range of tools and methods used to convey course content, and they have a renewed respect for the importance of field experience and personal interactions.
Coloration and phenology manifest nutrient variability in senesced leaves of 46 temperate deciduous woody species
Authors: Wang Xingchang , Wang Qi , Chen Yue , Zhao Rui , Zhang Jiahui , Quan Xiankui , Liu Fan , Wang Chuankuan 
Published: September 2021

Abstract
Senesced-leaf nutrient concentrations vary significantly among coexisting plant species reflecting different leaf nutrient use strategies. However, interspecific variation in senesced-leaf nutrients and its driving factors are not well understood. Here, we aimed to determine interspecific variation and its driving factors in senesced-leaf nutrients. We explored interspecific variation in carbon (C), nitrogen (N) and phosphorus (P) concentrations in newly fallen leaves of 46 coexisting temperate deciduous woody species across the Maoershan Forest Ecosystem Research Station, Northeast China. The relative importance of 10 biotic factors (i.e. mycorrhiza type, N-fixing type, growth form, shade tolerance, laminar texture, coloring degree, coloring type, peak leaf-coloration date, peak leaf-fall date and end leaf-fall date) was quantified with the random forest model. N and P concentrations varied 4- and 9-fold among species, respectively. The high mean N (15.38 mg g−1) and P (1.24 mg g−1) concentrations suggested a weak N and P limitation in the studied forest. Functional groups had only significant effects on specific nutrients and their ratios. P concentration and N:P were negatively correlated with peak and end leaf-fall dates for the ectomycorrhiza species group. Brighter-colored leaves (red &gt; brown &gt; yellow &gt; yellow-green &gt; green) tended to have lower N and P concentrations and higher C:N and C:P than darker-colored leaves. The random forest model showed that autumn coloration and leaf-fall phenology contributed 80% to the total explanation of nutrient variability among species. The results increase our understanding of the variability in senesced-leaf nutrients as a strategy of woody plant nutrition in temperate forests.
Radiotherapy inhibits neointimal hyperplasia after artificial vascular replacement through Skp2/P27kip1
Authors: Qiu Jian , Shu Chang , Li Shuang , Xiong Qinggen , Wang Lunchang , Liu Zhongtao , Li Xin , Zhang Weichang 
Published: September 2021

Abstract
We aimed to establish an animal model of abdominal aortic vascular replacement in mongrel dogs to investigate the effect of extracorporeal radiotherapy on the intima. Twenty healthy mongrel dogs were randomly divided into four groups: 5-week control group, 5-week radiotherapy group, 10-week control group and 10-week radiotherapy group. We first performed an artificial vascular replacement of the abdominal aortic segment. The radiotherapy group received external radiotherapy with a dose of 7 Gy for 4 days. The thickness of neointimal hyperplasia, immunoreactivity and expression of proliferation-related factors were detected by hematoxylin and eosin (HE) staining, immunohistochemistry, quantitative real-time polymerase chain reaction (qRT-PCR )and western blotting at 5 and 10 weeks after the reconstruction. The results showed that the intimal thickness of the artificial blood vessel in the 5- and 10-week radiotherapy groups was thinner than that in the control groups by HE staining. The immunoreactivity and expression levels of Skp2, c-Myc and CyclinE1 were significantly decreased in the radiotherapy groups than those in control groups by immunohistochemistry, qRT-PCR and western blotting. On the contrary, immunoreactivity and expression levels of P27kip1 were increased. In conclusion, we discovered that postoperative external radiotherapy significantly decreases the intimal hyperplasia of artificial blood vessels by regulating c-Myc-Skp2-P27-CyclinE1 network.
WAKsing plant immunity, waning diseases
Authors: Stephens Christopher , Hammond-Kosack Kim E , Kanyuka Kostya 
Published: September 2021

AbstractWith the requirement to breed more productive crop plants in order to feed a growing global population, compounded by increasingly widespread resistance to pesticides exhibited by pathogens, plant immunity is becoming an increasingly important area of research. Of the genes that contribute to disease resistance, the wall-associated receptor-like kinases (WAKs) are increasingly shown to play a major role, in addition to their contribution to plant growth and development or tolerance to abiotic stresses. Being transmembrane proteins, WAKs form a central pillar of a plant cell’s ability to monitor and interact with the extracellular environment. Found in both dicots and monocots, WAKs have been implicated in defence against pathogens with diverse lifestyles and contribute to plant immunity in a variety of ways. Whilst some act as cell surface-localized immune receptors recognizing either pathogen- or plant-derived invasion molecules (e.g. effectors or damage-associated molecular patterns, respectively), others promote innate immunity through cell wall modification and strengthening, thus limiting pathogen intrusion. The ability of some WAKs to provide both durable resistance against pathogens and other agronomic benefits makes this gene family important targets in the development of future crop ideotypes and important to a greater understanding of the complexity and robustness of plant immunity.
‘A Word of Song’: Reverberations of the Psalms in Christina Rossetti’s Roundels
Authors: Johnson Stephanie L 
Published: September 2021

Abstract
Christina Rossetti’s Verses (1893) collects poetry published originally in her devotional prose works, and 57 of its 331 lyric poems are roundels. Structured helically, the roundels use refrains to accrue meaning through repetition with a difference. While Rossetti follows Swinburne’s 11-line form, she uses the songs of the Word—the liturgical and wisdom psalms in particular—as the inspiration for her words of song. By recognising the antiphonal dialogue of the roundels modelled on the Psalms, we see more clearly how Rossetti’s lyric poetry emphasises not introspection or a Romantic solipsism but rather an interchange with others that turns its participants toward God. The reverberations of the Psalms in her roundels make audible her commitment to a communal, lyric form that unites its dialogic participants in worship and in an inclusive eschatology; that overlays the temporal with the eternal; and that conveys the priestly act of proclaiming the Kingdom of God in the present.
On the influence of halo mass accretion history on galaxy properties and assembly bias
Authors: Montero-Dorta Antonio D , Chaves-Montero Jonás , Artale M Celeste , Favole Ginevra 
Published: September 2021

ABSTRACT
Halo assembly bias is the secondary dependence of the clustering of dark matter haloes on their assembly histories at fixed halo mass. This established dependence is expected to manifest itself on galaxy clustering, a potential effect commonly known as galaxy assembly bias. Using the IllustrisTNG300 magnetohydrodynamical simulation, we analyse the dependence of the properties and clustering of galaxies on the specific mass accretion history of their hosting haloes (sMAH). We first show that several halo and galaxy properties strongly correlate with the slope of the sMAH (β) at fixed halo mass. Haloes with increasingly steeper β increment their masses faster early on, and their hosted galaxies present larger stellar-to-halo mass ratios, lose their gas faster, reach the peak of their star formation histories at higher redshift, and become quenched earlier. We also demonstrate that β provides a more stable link to these key galaxy formation properties than other broadly employed halo proxies, such as formation time. Finally, we measure the secondary dependence of galaxy clustering on β at fixed halo mass. By tracing back the evolution of individual haloes, we show that the amplitude of the galaxy assembly bias signal for the progenitors of z = 0 galaxies increases with redshift, reaching a factor of 2 at z = 1 for haloes of Mhalo = 1011.5–1012 h−1 M⊙. The measurement of the evolution of assembly bias along the merger tree provides a new theoretical perspective to the study of secondary bias. Our findings have also important implications for the generation of mock catalogues for upcoming cosmological surveys.
Probing the physical properties of the intergalactic medium using blazars
Authors: Dalton Tony , Morris Simon L , Fumagalli Michele , Gatuzz Efrain 
Published: September 2021

ABSTRACT
We use Swift blazar spectra to estimate the key intergalactic medium (IGM) properties of hydrogen column density ($\mathit {N}\small {\rm HXIGM}$), metallicity, and temperature over a redshift range of 0.03 ≤ z ≤ 4.7, using a collisional ionization equilibrium model for the ionized plasma. We adopted a conservative approach to the blazar continuum model given its intrinsic variability and use a range of power-law models. We subjected our results to a number of tests and found that the $\mathit {N}\small {\rm HXIGM}$ parameter was robust with respect to individual exposure data and co-added spectra for each source, and between Swift and XMM–Newton source data. We also found no relation between $\mathit {N}\small {\rm HXIGM}$ and variations in source flux or intrinsic power laws. Though some objects may have a bulk Comptonization component that could mimic absorption, it did not alter our overall results. The $\mathit {N}\small {\rm HXIGM}$ from the combined blazar sample scales as (1 + z)1.8 ± 0.2. The mean hydrogen density at z = 0 is n0 = (3.2 ± 0.5) × 10−7 cm−3. The mean IGM temperature over the full redshift range is log(T/K) =6.1 ± 0.1, and the mean metallicity is [X/H] = −1.62 ± 0.04(Z ∼ 0.02). When combining with the results with a gamma-ray burst (GRB) sample, we find the results are consistent over an extended redshift range of 0.03 ≤ z ≤ 6.3. Using our model for blazars and GRBs, we conclude that the IGM contributes substantially to the total absorption seen in both blazar and GRB spectra.
Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross
Authors: Bredemeyer Kevin R , Seabury Christopher M , Stickney Mark J , McCarrey John R , vonHoldt Bridgett M , Murphy William J 
Published: September 2021

Abstract
The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
Predict long-range enhancer regulation based on protein–protein interactions between transcription factors
Authors: Wang Hao , Huang Binbin , Wang Jianrong 
Published: September 2021

Abstract
Long-range regulation by distal enhancers plays critical roles in cell-type specific transcriptional programs. Computational predictions of genome-wide enhancer–promoter interactions are still challenging due to limited accuracy and the lack of knowledge on the molecular mechanisms. Based on recent biological investigations, the protein–protein interactions (PPIs) between transcription factors (TFs) have been found to participate in the regulation of chromatin loops. Therefore, we developed a novel predictive model for cell-type specific enhancer–promoter interactions by leveraging the information of TF PPI signatures. Evaluated by a series of rigorous performance comparisons, the new model achieves superior performance over other methods. The model also identifies specific TF PPIs that may mediate long-range regulatory interactions, revealing new mechanistic understandings of enhancer regulation. The prioritized TF PPIs are associated with genes in distinct biological pathways, and the predicted enhancer–promoter interactions are strongly enriched with cis-eQTLs. Most interestingly, the model discovers enhancer-mediated trans-regulatory links between TFs and genes, which are significantly enriched with trans-eQTLs. The new predictive model, along with the genome-wide analyses, provides a platform to systematically delineate the complex interplay among TFs, enhancers and genes in long-range regulation. The novel predictions also lead to mechanistic interpretations of eQTLs to decode the genetic associations with gene expression.
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale
Authors: Zhang Wenliang , Zhang Yan , Min Zhuochao , Mo Jing , Ju Zhen , Guan Wen , Zeng Binghui , Liu Yang , Chen Jianliang , Zhang Qianshen , Li Hanguang , Zeng Chunxia , Wei Yanjie , Chan Godfrey Chi-Fung 
Published: September 2021

Abstract
Many open access transcriptomic data of coronavirus disease 2019 (COVID-19) were generated, they have great heterogeneity and are difficult to analyze. To utilize these invaluable data for better understanding of COVID-19, additional software should be developed. Especially for researchers without bioinformatic skills, a user-friendly platform is mandatory. We developed the COVID19db platform (http://hpcc.siat.ac.cn/covid19db & http://www.biomedical-web.com/covid19db) that provides 39 930 drug–target–pathway interactions and 95 COVID-19 related datasets, which include transcriptomes of 4127 human samples across 13 body sites associated with the exposure of 33 microbes and 33 drugs/agents. To facilitate data application, each dataset was standardized and annotated with rich clinical information. The platform further provides 14 different analytical applications to analyze various mechanisms underlying COVID-19. Moreover, the 14 applications enable researchers to customize grouping and setting for different analyses and allow them to perform analyses using their own data. Furthermore, a Drug Discovery tool is designed to identify potential drugs and targets at whole transcriptomic scale. For proof of concept, we used COVID19db and identified multiple potential drugs and targets for COVID-19. In summary, COVID19db provides user-friendly web interfaces to freely analyze, download data, and submit new data for further integration, it can accelerate the identification of effective strategies against COVID-19.
Tobacco Tracker: A New Tool to Support College Smoke and Tobacco Free Policies
Authors: Pulvers Kim , Rice Myra , Stewart Susan LeRoy , Tong Elisa 
Published: September 2021

Abstract

Introduction
University community members are critical to the success of their smoke and tobacco free (STF) policies. The present study evaluates changes in social enforcement-related attitudes and behaviors following introduction of a new online Tobacco Tracker tool in two university settings.

Methods
Campus wide surveys were administered to current students, faculty, and staff at two California public universities with 100% STF policies before (November 2018; N = 5078) and after (December 2019–January 2020; N = 4853) introduction of Tobacco Tracker in February 2019. Prospective surveillance reports over 12 months from Tobacco Tracker, a GIS tool for the campus community to report tobacco use and related litter that displays crowdsourced maps of hotspots, were analyzed. Outcomes included awareness and self-reported use of a tobacco reporting tool, readiness for policy social enforcement, an Intellectual Social Affective (ISA) Engagement scale, and environmental surveillance reports from Tobacco Tracker.

Results
In campus surveys, awareness of a tobacco reporting tool doubled (8.0%–16.9%, p &lt; .0001), use of an online reporting tool tripled (1.1%–3.2%, p &lt; .0001), and readiness to enforce the policy increased (p = .0008). ISA engagement did not change (p = .72). In Tobacco Tracker campus reports (N = 1163), active tobacco use was reported more frequently than tobacco-related litter.

Conclusions
Tobacco Tracker is a promising tool for college communities to support STF policy. Introduction of Tobacco Tracker was associated with an increase in campus awareness and utilization of a reporting tool, readiness to enforce policy, and campus tobacco surveillance. Future research should determine how Tobacco Tracker may improve policy compliance.

Implications
Tobacco Tracker is a promising tool for college communities to support smoke and tobacco free (STF) policy through active surveillance of smoking, vaping, and related litter on campus. Introduction of Tobacco Tracker was associated with changes in social enforcement-related attitudes and behaviors critical to realizing the preventive potential of STF policies. A crowdsourcing-based tool for monitoring tobacco use on college campuses can address a major barrier to social enforcement: discomfort confronting tobacco users. Further, it provides an alternative to punitive enforcement approaches and promises a sustainable solution to an infrastructure issue faced by many universities lacking resources to collect data on campus tobacco use and related litter.