bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of carbon emission in slurry shield tunnel construction based on modified process analysis method
Authors: Li Wuxue , Kou Lei , He Xiaoyu , Wang Yibo , Shi Xiaodong , Liang Huiyuan
Published: June 2023

Underground engineering, including shield tunnel construction, is a significant contributor to carbon dioxide emissions in infrastructure engineering projects. To better predict and control the carbon emissions associated with shield tunnel construction, this paper presents a novel calculation method: the modified process analysis method based on input-output and process analysis methods. To evaluate the effectiveness of the proposed method, a specific shield tunnel construction project was selected as a case study. The modified process analysis method was used to analyze the various factors that influence carbon emissions during the project’s construction phase. In addition, a neural network approach was applied to validate the accuracy of the calculation using the LSTM and BP neural network. The results demonstrate that the proposed method not only combines the strengths of traditional methods but also offers high accuracy and acceptable error rates. Based on these findings, several measures to reduce carbon emissions during shield tunnel construction are suggested, providing valuable insights for reducing CO2 emissions associated with infrastructure engineering projects. This study highlights the importance of adopting innovative approaches to reduce carbon emissions and promotes the implementation of sustainable practices in the construction industry. Through the use of advanced analytical methods, such as the proposed modified process analysis method, we can effectively mitigate the environmental impact of construction activities and make significant contributions to the global effort to combat climate change.
Gender and Policing in Early Modern England
Authors: Miller Jonah
Published: June 2023

This book traces the beginnings of a shift from one model of gendered power to another. Over the course of the seventeenth and early eighteenth centuries, traditional practices of local government by heads of household began to be undermined by new legal ideas about what it meant to hold office. In London, this enabled the emergence of a new kind of officeholding and a new kind of policing, rooted in a fraternal culture of official masculinity. London officers arrested, searched, and sometimes assaulted people on the basis of gendered suspicions, especially poorer women. Gender and Policing in Early Modern England describes how a recognisable form of gendered policing emerged from practices of local government by patriarchs and addresses wider questions about the relationship between gender and the state.
The History of Parliament The House of Commons 1640-1660 [Volume lll]
Authors: Roberts Stephen K.
Published: June 2023

This is volume 3 of a 9-volume set providing the most comprehensive and complete study ever compiled about the turbulent period of the English and British Civil Wars and their aftermath.
Understanding men’s beliefs and concerns about linking health data in the context of precision medicine
Authors: Allen Caitlin G. , Jefferson Melanie , Magwood Gayenell , Melvin Cathy , Babatunde Oluwole Adeyemi , Halbert Chanita Hughes
Published: June 2023

Background/Objective:

Linking data is a critical feature of precision medicine initiatives that involves integrating information from multiple sources to improve researchers’ and clinicians’ ability to deliver care. We have limited understanding of how individuals perceive linking data as it relates to precision medicine. The aim of this study was to identify how sociodemographics, comorbidities, and beliefs about precision medicine influence two outcomes related to linking data: beliefs about linking data and concerns about linking data among men.

Methods:

We recruited 124 adult men from primary care practices at a large clinical research university to complete a cross-sectional survey that included questions about sociodemographic characteristics, comorbidities, beliefs, benefits, and limitations of precision medicine, and two outcomes of interest: beliefs about the value of linking data and concerns about linking data. Descriptive statistics, bivariate associations, and multivariable regression were conducted.

Results:

Participants had positive beliefs about linking data for precision medicine (M = 4.05/5) and average concern about linking data (M = 2.1/5). Final multivariable models revealed that higher levels of loneliness are associated with more positive beliefs about linking data (β = 0.41, p = 0.027). Races other than African American (β = –0.64, p = 0.009) and those with lower perceived limitations of precision medicine were less likely to be concerned about linking data (β = –0.75, p = 0.0006).

Conclusion:

Our results advance the literature about perceptions of linking data for use in clinical and research studies among men. Better understanding of factors associated with more positive perceptions of data linkages could help improve how researchers recruit and engage participants.
Interpreting the subterranean building (the crypt) in the northern courtyard of Hagia Sophia in Constantinople
Authors: Özkan Aygün Çiğdem , Arvanitidou Ioanna P. , Gounari Emmanouela G.
Published: June 2023

This article discusses a subterranean building, situated north of Hagia Sophia in Constantinople, which was investigated during a recent interdisciplinary survey conducted by Çiğdem Özkan Aygün. Although it is generally accepted that the edifice had more than one phase of use, the date of its original construction and utilisation has been problematic since the building is not mentioned in any written sources and was either not included in other archaeological excavations and surveys or not studied intensively. The aim of this paper is to present the underground building in detail and to propose a date for its construction based on the new survey data and on ancient written sources about the church of Hagia Sophia. Archaeological data from previous surveys are also taken into account. The subterranean building’s different phases of use are documented, and it is proposed that it was originally used as a reliquary, then later, after a number of alterations, became a cistern.
Preconception and prenatal maternal stress are associated with broad autism phenotype in young adults: Project Ice Storm
Authors: Li Xinyuan , Laplante David P. , Elgbeili Guillaume , King Suzanne
Published: June 2023

Studies show associations between prenatal maternal stress (PNMS) and child autism, with little attention paid to PNMS and autism in young adulthood. The broad autism phenotype (BAP), encompassing sub-clinical levels of autism, includes aloof personality, pragmatic language impairment and rigid personality. It remains unclear whether different aspects of PNMS explain variance in different BAP domains in young adult offspring. We recruited women who were pregnant during, or within 3 months of, the 1998 Quebec ice storm crisis, and assessed three aspects of their stress (i.e., objective hardship, subjective distress and cognitive appraisal). At age 19, the young adult offspring (n = 33, 22F / 11M) completed a BAP self-report. Linear and logistic regressions were implemented to examine associations between PNMS and BAP traits. Up to 21.4% of the variance in BAP total score and in BAP three domains tended to be explained by at least one aspect of maternal stress, For example, 16.8% of the variance in aloof personality tended to be explained by maternal objective hardship; 15.1% of the variance in pragmatic language impairment tended to be explained by maternal subjective distress; 20.0% of the variance in rigid personality tended to be explained by maternal objective hardship and 14.3% by maternal cognitive appraisal. Given the small sample size, the results should be interpreted with caution. In conclusion, this small prospective study suggests that different aspects of maternal stress could have differential effects on different components of BAP traits in young adults.
Upper Ocean Biogeochemistry of the Oligotrophic North Pacific Subtropical Gyre: From Nutrient Sources to Carbon Export
Authors: Dai Minhan , Luo Ya‐Wei , Achterberg Eric P. , Browning Thomas J. , Cai Yihua , Cao Zhimian , Chai Fei , Chen Bingzhang , Church Matthew J. , Ci Dongjian , Du Chuanjun , Gao Kunshan , Guo Xianghui , Hu Zhendong , Kao Shuh‐Ji , Laws Edward A. , Lee Zhongping , Lin Hongyang , Liu Qian , Liu Xin , Luo Weicheng , Meng Feifei , Shang Shaoling , Shi Dalin , Saito Hiroaki , Song Luping , Wan Xianhui Sean , Wang Yuntao , Wang Wei‐Lei , Wen Zuozhu , Xiu Peng , Zhang Jing , Zhang Ruifeng , Zhou Kuanbo
Published: June 2023

Subtropical gyres cover 26%–29% of the world's surface ocean and are conventionally regarded as ocean deserts due to their permanent stratification, depleted surface nutrients, and low biological productivity. Despite tremendous advances over the past three decades, particularly through the Hawaii Ocean Time‐series and the Bermuda Atlantic Time‐series Study, which have revolutionized our understanding of the biogeochemistry in oligotrophic marine ecosystems, the gyres remain understudied. We review current understanding of upper ocean biogeochemistry in the North Pacific Subtropical Gyre, considering other subtropical gyres for comparison. We focus our synthesis on spatial variability, which shows larger than expected dynamic ranges of properties such as nutrient concentrations, rates of N2 fixation, and biological production. This review provides new insights into how nutrient sources drive community structure and export in upper subtropical gyres. We examine the euphotic zone (EZ) in subtropical gyres as a two‐layered vertically structured system: a nutrient‐depleted layer above the top of the nutricline in the well‐lit upper ocean and a nutrient‐replete layer below in the dimly lit waters. These layers vary in nutrient supply and stoichiometries and physical forcing, promoting differences in community structure and food webs, with direct impacts on the magnitude and composition of export production. We evaluate long‐term variations in key biogeochemical parameters in both of these EZ layers. Finally, we identify major knowledge gaps and research challenges in these vast and unique systems that offer opportunities for future studies.
Quantifying Groundwater's Contribution to Regional Environmental‐Flows in Diverse Hydrologic Landscapes
Authors: Mohan Chinchu , Gleeson Tom , Forstner Tara , Famiglietti James S. , de Graaf Inge
Published: June 2023

Increasing recognition of the importance of ecosystem services in water resources management has accelerated the development and application of environmental‐flows requirements for lotic ecosystems. However, most environmental‐flows management focuses on water infrastructure, such as dams or diversions, without explicitly taking groundwater into account and ignoring the importance of groundwater environmental flow contribution. In this study two methods for estimating groundwater environmental flow contributions are presented: (a) a groundwater‐centric method (based on the Sustainability Boundary Approach), which proposes that high levels of ecological protection are maintained if 90% of groundwater discharge is preserved, and (b) a surface water‐centric method (novel method), which quantifies groundwater environmental flow contributions from streamflow using region‐specific streamflow sensitivity metrics and local environmental‐flows policies. The two methods were tested in British Columbia, Canada, which has a diverse, complex, and highly coupled groundwater‐surface water system. The two methods gave comparable results in various hydro‐geoclimatic settings. Although British Columbia was used as a case study, this framework can be implemented across various spatial and temporal scales for different regions and globally, in data‐scarce, hydrologically complex landscapes. Application of these methods can aid in a robust and holistic assessment of environmental‐flows, taking into account the often‐missing groundwater component.
Irregularities Observed at the Edge of a Mid‐Latitude Ionospheric Depletion Following a Geomagnetic Storm
Authors: Helmboldt J. F.
Published: June 2023

This manuscript presents the analysis of data from multiple ground‐ and space‐based sensors in the North American region before, during, and after the 12 October 2021 geomagnetic storm. Total electron content (TEC) and electron density data show the formation and equatorward propagation of a mid‐latitude trough at ∼50°N followed by the appearance of a wider depletion region (∼15° in latitude) at lower latitudes. During the recovery phase on the 13th, the equatorward edge of this depletion region settled at around 30° latitude and exhibited a steep density gradient. By the 14th, this sharp boundary had disappeared. Near this edge on the 13th, small‐scale irregularities formed. The impact of these was observed within Global Positioning System data as elevated rate of TEC index (ROTI) and presented as strong 35 MHz scintillations of cosmic radio sources as well as spread‐F within ionograms from multiple digisonde systems. GPS and 35‐MHz data demonstrated that the irregularity region was narrowly confined (≲5° wide) near the edge of the depletion region. The 35‐MHz scintillation data also showed that the irregularities were moving relatively slowly at ∼7 m s−1, likely toward the southeast. Density and velocity measurements demonstrated that the conditions near the depletion boundary were highly favorable to the gradient drift instability (GDI) with the one‐dimensional growth rate estimated to be ∼0.01 s−1. Since these conditions persisted for many hours, this growth rate was more than sufficient for the GDI to be considered the primary driver of irregularity formation in this case.
Adult-born neurons in critical period maintain hippocampal seizures via local aberrant excitatory circuits
Authors: Chen Liying , Xu Yingwei , Cheng Heming , Li Zhongxia , Lai Nanxi , Li Menghan , Ruan Yeping , Zheng Yang , Fei Fan , Xu Cenglin , Ma Jiao , Wang Shuang , Gu Yan , Han Feng , Chen Zhong , Wang Yi
Published: June 2023

Temporal lobe epilepsy (TLE), one common type of medically refractory epilepsy, is accompanied with altered adult-born dentate granule cells (abDGCs). However, the causal role of abDGCs in recurrent seizures of TLE is not fully understood. Here, taking advantage of optogenetic and chemogenetic tools to selectively manipulate abDGCs in a reversible manner, combined with Ca2+ fiber photometry, trans-synaptic viral tracing, in vivo/vitro electrophysiology approaches, we aimed to test the role of abDGCs born at different period of epileptogenic insult in later recurrent seizures in mouse TLE models. We found that abDGCs were functionally inhibited during recurrent seizures. Optogenetic activation of abDGCs significantly extended, while inhibition curtailed, the seizure duration. This seizure-modulating effect was attributed to specific abDGCs born at a critical early phase after kindled status, which experienced specific type of circuit re-organization. Further, abDGCs extended seizure duration via local excitatory circuit with early-born granule cells (ebDGCs). Repeated modulation of “abDGC-ebDGC” circuit may easily induce a change of synaptic plasticity, and achieve long-term anti-seizure effects in both kindling and kainic acid-induced TLE models. Together, we demonstrate that abDGCs born at a critical period of epileptogenic insult maintain seizure duration via local aberrant excitatory circuits, and inactivation of these aberrant circuits can long-termly alleviate severity of seizures. This provides a deeper and more comprehensive understanding of the potential pathological changes of abDGCs circuit and may be helpful for the precise treatment in TLE.
Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection
Authors: Chen Peiran , Wu Mandi , He Yaqing , Jiang Binghua , He Ming-Liang
Published: June 2023

The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy
Authors: Ragonnet-Cronin Manon , Nutalai Rungtiwa , Huo Jiandong , Dijokaite-Guraliuc Aiste , Das Raksha , Tuekprakhon Aekkachai , Supasa Piyada , Liu Chang , Selvaraj Muneeswaran , Groves Natalie , Hartman Hassan , Ellaby Nicholas , Mark Sutton J. , Bahar Mohammad W. , Zhou Daming , Fry Elizabeth , Ren Jingshan , Brown Colin , Klenerman Paul , Dunachie Susanna J. , Mongkolsapaya Juthathip , Hopkins Susan , Chand Meera , Stuart David I. , Screaton Gavin R. , Rokadiya Sakib
Published: June 2023

COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.
Brain-optimized deep neural network models of human visual areas learn non-hierarchical representations
Authors: St-Yves Ghislain , Allen Emily J. , Wu Yihan , Kay Kendrick , Naselaris Thomas
Published: June 2023

Deep neural networks (DNNs) optimized for visual tasks learn representations that align layer depth with the hierarchy of visual areas in the primate brain. One interpretation of this finding is that hierarchical representations are necessary to accurately predict brain activity in the primate visual system. To test this interpretation, we optimized DNNs to directly predict brain activity measured with fMRI in human visual areas V1-V4. We trained a single-branch DNN to predict activity in all four visual areas jointly, and a multi-branch DNN to predict each visual area independently. Although it was possible for the multi-branch DNN to learn hierarchical representations, only the single-branch DNN did so. This result shows that hierarchical representations are not necessary to accurately predict human brain activity in V1-V4, and that DNNs that encode brain-like visual representations may differ widely in their architecture, ranging from strict serial hierarchies to multiple independent branches.
Ketone α-alkylation at the more-hindered site
Authors: Li Ming-Ming , Zhang Tianze , Cheng Lei , Xiao Wei-Guo , Ma Jin-Tao , Xiao Li-Jun , Zhou Qi-Lin
Published: June 2023

Control of the regioselectivity of α-alkylation of carbonyl compounds is a longstanding topic of research in organic chemistry. By using stoichiometric bulky strong bases and carefully adjusting the reaction conditions, selective alkylation of unsymmetrical ketones at less-hindered α-sites has been achieved. In contrast, selective alkylation of such ketones at more-hindered α-sites remains a persistent challenge. Here we report a nickel-catalysed alkylation of unsymmetrical ketones at the more-hindered α-sites with allylic alcohols. Our results indicate that the space-constrained nickel catalyst bearing a bulky biphenyl diphosphine ligand enables the preferential alkylation of the more-substituted enolate over the less-substituted enolate and reverses the conventional regioselectivity of ketone α-alkylation. The reactions proceed under neutral conditions in the absence of additives, and water is the only byproduct. The method has a broad substrate scope and permits late-stage modification of ketone-containing natural products and bioactive compounds.
Migratory allylic arylation of 1,n-enols enabled by nickel catalysis
Authors: Zhao Dan , Xu Bing , Zhu Can
Published: June 2023

Transition-metal-catalyzed allylic substitution reactions (Tsuji−Trost reactions) proceeding via a π-allyl metal intermediate have been demonstrated as a powerful tool in synthetic chemistry. Herein, we disclose an unprecedented π-allyl metal species migration, walking on the carbon chain involving 1,4-hydride shift as confirmed by deuterium labeling experiments. This migratory allylic arylation can be realized under dual catalysis of nickel and lanthanide triflate, a Lewis acid. Olefin migration has been observed to preferentially occur with the substrate of 1,n-enols (n ≥ 3). The robust nature of the allylic substitution strategy is reflected by a broad scope of substrates with the control of regio- and stereoselectivity. DFT studies suggest that π-allyl metal species migration consists of the sequential β-H elimination and migratory insertion, with diene not being allowed to release from the metal center before producing a new π-allyl nickel species.
A probiotic bi-functional peptidoglycan hydrolase sheds NOD2 ligands to regulate gut homeostasis in female mice
Authors: Gao Jie , Wang Lei , Jiang Jing , Xu Qian , Zeng Nianyi , Lu Bingyun , Yuan Peibo , Sun Kai , Zhou Hongwei , He Xiaolong
Published: June 2023

Secreted proteins are one of the direct molecular mechanisms by which microbiota influence the host, thus constituting a promising field for drug discovery. Here, through bioinformatics-guided screening of the secretome of clinically established probiotics from Lactobacillus, we identify an uncharacterized secreted protein (named LPH here) that is shared by most of these probiotic strains (8/10) and demonstrate that it protects female mice from colitis in multiple models. Functional studies show that LPH is a bi-functional peptidoglycan hydrolase with both N-Acetyl-β-D-muramidase and DL-endopeptidase activities that can generate muramyl dipeptide (MDP), a NOD2 ligand. Different active site mutants of LPH in combination with Nod2 knockout female mice confirm that LPH exerts anti-colitis effects through MDP-NOD2 signaling. Furthermore, we validate that LPH can also exert protective effects on inflammation-associated colorectal cancer in female mice. Our study reports a probiotic enzyme that enhances NOD2 signaling in vivo in female mice and describes a molecular mechanism that may contribute to the effects of traditional Lactobacillus probiotics.
CrRhAs: a member of a large family of metallic kagome antiferromagnets
Authors: Huang Y. N. , Jeschke Harald O. , Mazin Igor I.
Published: June 2023

Kagome lattice materials are an important platform for highly frustrated magnetism as well as for a plethora of phenomena resulting from flat bands, Dirac cones and van Hove singularities in their electronic structures. We study the little known metallic magnet CrRhAs, which belongs to a vast family of materials that includes 3d, 4f, and 5f magnetic elements, as well as numerous nonmagnetic metals and insulators. Using noncollinear spin density functional calculations (mostly spin spirals), we extract a model magnetic Hamiltonian for CrRhAs. While it is dominated by an antiferromagnetic second nearest neighbor coupling in the kagome plane, the metallic nature of the compound leads to numerous nonzero longer range couplings and to important ring exchange terms. We analyze this Hamiltonian and find unusual ground states which are dominated by nearly isolated antiferromagnetic triangles that adopt 120∘ order either with positive or with negative vector chirality. We discuss the connection to the few known experimental facts about CrRhAs. Finally, we give a brief survey of other interesting magnetic members of this family of kagome compounds.
A comprehensive mechanistic model of adipocyte signaling with layers of confidence
Authors: Lövfors William , Magnusson Rasmus , Jönsson Cecilia , Gustafsson Mika , Olofsson Charlotta S. , Cedersund Gunnar , Nyman Elin
Published: June 2023

Adipocyte signaling, normally and in type 2 diabetes, is far from fully understood. We have earlier developed detailed dynamic mathematical models for several well-studied, partially overlapping, signaling pathways in adipocytes. Still, these models only cover a fraction of the total cellular response. For a broader coverage of the response, large-scale phosphoproteomic data and systems level knowledge on protein interactions are key. However, methods to combine detailed dynamic models with large-scale data, using information about the confidence of included interactions, are lacking. We have developed a method to first establish a core model by connecting existing models of adipocyte cellular signaling for: (1) lipolysis and fatty acid release, (2) glucose uptake, and (3) the release of adiponectin. Next, we use publicly available phosphoproteome data for the insulin response in adipocytes together with prior knowledge on protein interactions, to identify phosphosites downstream of the core model. In a parallel pairwise approach with low computation time, we test whether identified phosphosites can be added to the model. We iteratively collect accepted additions into layers and continue the search for phosphosites downstream of these added layers. For the first 30 layers with the highest confidence (311 added phosphosites), the model predicts independent data well (70–90% correct), and the predictive capability gradually decreases when we add layers of decreasing confidence. In total, 57 layers (3059 phosphosites) can be added to the model with predictive ability kept. Finally, our large-scale, layered model enables dynamic simulations of systems-wide alterations in adipocytes in type 2 diabetes.
The illusion of moral decline
Authors: Mastroianni Adam M. , Gilbert Daniel T.
Published: June 2023

Anecdotal evidence indicates that people believe that morality is declining1,2. In a series of studies using both archival and original data (n = 12,492,983), we show that people in at least 60 nations around the world believe that morality is declining, that they have believed this for at least 70 years and that they attribute this decline both to the decreasing morality of individuals as they age and to the decreasing morality of successive generations. Next, we show that people’s reports of the morality of their contemporaries have not declined over time, suggesting that the perception of moral decline is an illusion. Finally, we show how a simple mechanism based on two well-established psychological phenomena (biased exposure to information and biased memory for information) can produce an illusion of moral decline, and we report studies that confirm two of its predictions about the circumstances under which the perception of moral decline is attenuated, eliminated or reversed (that is, when respondents are asked about the morality of people they know well or people who lived before the respondent was born). Together, our studies show that the perception of moral decline is pervasive, perdurable, unfounded and easily produced. This illusion has implications for research on the misallocation of scarce resources3, the underuse of social support4 and social influence5.
CORE: A Global Aggregation Service for Open Access Papers
Authors: Knoth Petr , Herrmannova Drahomira , Cancellieri Matteo , Anastasiou Lucas , Pontika Nancy , Pearce Samuel , Gyawali Bikash , Pride David
Published: June 2023

This paper introduces CORE, a widely used scholarly service, which provides access to the world’s largest collection of open access research publications, acquired from a global network of repositories and journals. CORE was created with the goal of enabling text and data mining of scientific literature and thus supporting scientific discovery, but it is now used in a wide range of use cases within higher education, industry, not-for-profit organisations, as well as by the general public. Through the provided services, CORE powers innovative use cases, such as plagiarism detection, in market-leading third-party organisations. CORE has played a pivotal role in the global move towards universal open access by making scientific knowledge more easily and freely discoverable. In this paper, we describe CORE’s continuously growing dataset and the motivation behind its creation, present the challenges associated with systematically gathering research papers from thousands of data providers worldwide at scale, and introduce the novel solutions that were developed to overcome these challenges. The paper then provides an in-depth discussion of the services and tools built on top of the aggregated data and finally examines several use cases that have leveraged the CORE dataset and services.
Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence
Authors: Feró Orsolya , Karányi Zsolt , Nagy Éva , Mosolygó-L Ágnes , Szaker Henrik Mihály , Csorba Tibor , Székvölgyi Lóránt
Published: June 2023

Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNA (hetsiRNA) loci/regions whose transcriptional activity was significantly changed in the absence of NDX. In addition, data obtained from inflorescence were compared with seedling transcriptomics data, which revealed development-specific changes in gene expression profiles. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further research on NDX function.
1 km-resolution gridded dataset of phosphorus rate for rice wheat and maize in China over 2004–2016
Authors: Zhang Wenmeng , Zhang Tianyi , Yang Xiaoguang
Published: June 2023

Crop-specific, high-resolution phosphorus rate information is essential for sustainable agricultural fertilizer management in China. However, substantial uncertainties exist in the current phosphorus fertilizer dataset because of only coarse national statistics used in dataset development and no crop-specific information provided. This study harmonized provincial and county-level phosphorus and component fertilizer statistics and crop distribution data to generate 1 km gridded maps of phosphorus rate for rice, wheat and maize in the years of 2004–2016 (CN-P). CN-P provides a comparable estimate on phosphorus rate for each crop over 2004–2016, and demonstrates an improved spatial heterogeneity. Existing dataset developed using national statistics tends to smooth out the variability within country and significantly underestimates actual phosphorus rate. CN-P shows that, during 2004–2016, wheat received the most phosphorus rate (8.7 g P2O5 m−2), while maize showed the rapidest increasing trend (2.36% yr−1). The CN-P dataset has the potential to be widely applied in modeling studies on sustainable agricultural fertilizer management strategies and phosphorus pollution.
An intra-annual 30-m dataset of small lakes of the Qilian Mountains for the period 1987–2020
Authors: Li Chao , Zhang Shiqiang , Zhang Dahong , Zhou Gang
Published: June 2023

Small lakes (areas between 0.01 km2 and 1 km2) on the Qinghai–Tibet Plateau (QTP) are prone to fluctuations in number and area, with serious implications for the surface water storage and water and carbon cycles of this fragile environment. However, there are no detailed long-term datasets of the small lakes of the QTP. Therefore, the intra-annual changes of small lakes in the Qilian Mountains region (QMR) in the northeastern part of the QTP were investigated. The small lake water bodies (SLWB) in the QMR were extracted by improving existing commonly used waterbody extraction algorithms. Using the Google Earth Engine platform and 13,297 Landsat TM/ETM + /OLI images, the SLWB of the QMR were extracted from 1987 to 2020 applying the improved algorithm, cross-validation and manual corrections. The reliability, uncertainty and limitations of the improved algorithm were discussed. An intra-annual small lake dataset for QMR (QMR-SLD) from 1987 to 2020 was released, containing eight attributes: code, perimeter (km), area (km2), latitude and longitude, elevation (m), area error, relative error (%), and subregion.
Identification of immune-related gene signature for predicting prognosis in uterine corpus endometrial carcinoma
Authors: Song Siyuan , Gu Haoqing , Li Jingzhan , Yang Peipei , Qi Xiafei , Liu Jiatong , Zhou Jiayu , Li Ye , Shu Peng
Published: June 2023

The objective of this study is to develop a gene signature related to the immune system that can be used to create personalized immunotherapy for Uterine Corpus Endometrial Carcinoma (UCEC). To classify the UCEC samples into different immune clusters, we utilized consensus clustering analysis. Additionally, immune correlation algorithms were employed to investigate the tumor immune microenvironment (TIME) in diverse clusters. To explore the biological function, we conducted GSEA analysis. Next, we developed a Nomogram by integrating a prognostic model with clinical features. Finally, we performed experimental validation in vitro to verify our prognostic risk model. In our study, we classified UCEC patients into three clusters using consensus clustering. We hypothesized that cluster C1 represents the immune inflammation type, cluster C2 represents the immune rejection type, and cluster C3 represents the immune desert type. The hub genes identified in the training cohort were primarily enriched in the MAPK signaling pathway, as well as the PD-L1 expression and PD-1 checkpoint pathway in cancer, all of which are immune-related pathways. Cluster C1 may be a more suitable for immunotherapy. The prognostic risk model showed a strong predictive ability. Our constructed risk model demonstrated a high level of accuracy in predicting the prognosis of UCEC, while also effectively reflecting the state of TIME.
The GET pathway is a major bottleneck for maintaining proteostasis in Saccharomyces cerevisiae
Authors: Josefson Rebecca , Kumar Navinder , Hao Xinxin , Liu Beidong , Nyström Thomas
Published: June 2023

A hallmark of aging in a variety of organisms is a breakdown of proteostasis and an ensuing accumulation of protein aggregates and inclusions. However, it is not clear if the proteostasis network suffers from a uniform breakdown during aging or if some distinct components act as bottlenecks especially sensitive to functional decline. Here, we report on a genome-wide, unbiased, screen for single genes in young cells of budding yeast required to keep the proteome aggregate-free under non-stress conditions as a means to identify potential proteostasis bottlenecks. We found that the GET pathway, required for the insertion of tail-anchored (TA) membrane proteins in the endoplasmic reticulum, is such a bottleneck as single mutations in either GET3, GET2 or GET1 caused accumulation of cytosolic Hsp104- and mitochondria-associated aggregates in nearly all cells when growing at 30 °C (non-stress condition). Further, results generated by a second screen identifying proteins aggregating in GET mutants and analyzing the behavior of cytosolic reporters of misfolding, suggest that there is a general collapse in proteostasis in GET mutants that affects other proteins than TA proteins.
Correlation versus hybridization gap in CaMn$$_{2}$$Bi$$_{2}$$
Authors: Lane Christopher , Piva M. M. , Rosa P. F. S. , Zhu Jian-Xin
Published: June 2023

We study the interplay between electronic correlations and hybridization in the low-energy electronic structure of CaMn$$_2$$

2

Bi$$_2$$

2

, a candidate hybridization-gap semiconductor. By employing a DFT+U approach we find both the antiferromagnetic Néel order and band gap in good agreement with the corresponding experimental values. Under hydrostatic pressure, we find a crossover from hybridization gap to charge-transfer insulting physics due to the delicate balance of hybridization and correlations. Increasing the pressure above $$P_c=4$$

P
c

=
4

GPa we find a simultaneous pressure-induced volume collapse, plane-to-chain, insulator to metal transition. Finally, we have also analyzed the topology in the antiferromagnetic CaMn$$_2$$

2

Bi$$_2$$

2

for all pressures studied.
Analysis of navigational risk indicators as a function of the ship's domain width for the selected offshore wind farm in the Baltic Sea
Authors: Rutkowski Grzegorz , Kubacka Maria
Published: June 2023

This study concerns the analysis of navigational risk indicators as a function of the ship's domain width estimated for nine selected representative ships sailing under various hydrometeorological conditions (average and deteriorated ones) observed within the Offshore Wind Farm to be constructed within the Polish offshore zone on the Baltic Sea. For this purpose, the authors compare three types of domain parameters according to the guidelines by the PIANC, Coldwell and Rutkowski (3D). The study enabled selection of a group of ships which can be considered safe and can optionally be allowed to navigate and/or fish in the immediate vicinity and within the offshore wind farm. The analyses required the use of hydrometeorological data, mathematical models and operating data obtained with the use of maritime navigation and manoeuvring simulators.
Association of obesity, diabetes, and hypertension with arsenic in drinking water in the Comarca Lagunera province (north-central Mexico)
Authors: Sánchez-Rodríguez B. L. , Castillo-Maldonado I. , Pedroza-Escobar D. , Delgadillo-Guzmán D. , Soto-Jiménez M. F.
Published: June 2023

Chronic endemic regional hydroarsenicism (CERHA) is a global issue that affects over 200 million people exposed to arsenic (As) in drinking water. This includes 1.75 million individuals residing in La Comarca Lagunera, a region in north-central Mexico. Arsenic levels in this region typically exceeds the WHO guideline of 10 µg L−1. Biochemical alterations related to the human As metabolism may increase the risk of overweight and obesity (O&O), type 2 diabetes (T2D), and hypertension (AHT). In our study, we investigated the role of As in drinking water as a risk factor for these metabolic diseases. We focused on populations with historically moderate (San Pedro) and low (Lerdo) drinking water As levels and people with no historical evidence of As water contamination. The exposure assessment to As was based on measurements of the drinking water (medians 67.2, 21.0, 4.3 µg L−1) and urinary As concentrations in women (9.4, 5.3, 0.8 µg L−1) and men (18.1, 4.8, 1.0 µg L−1). A significant correlation between As in drinking water and urine evidenced the As exposure in the population (R2 = 0.72). Adjusted odds ratios with 95% confidence intervals evidenced higher chances of being diagnosed with T2D (1.7, 1.2–2.0) and AHT (1.8, 1.7–1.9) in individuals living in San Pedro than those in Lerdo. Still, there was no significant association with obesity. Individuals living in CERHA towns were found to have a higher risk of obesity (1.3–1.9), T2D (1.5 to 3.3), and AHT (1.4 to 2.4) compared to those residing in non-CERHA towns. Finally, obesity is more probable in women [inverse of OR and 95%CI 0.4 (0.2–0.7)] compared to men, while men is more likely to be diagnosed with T2D [OR = 2.0 (1.4–2.3)] and AHT [OR = 2.0 (1.5–2.3)] than women, independently of the municipality.
Overgrowth of long bone in rabbits by growth stimulation through metaphyseal hole creation
Authors: Lee Kyoung-Mi , Ko Eun Ae , Shah Mudit , Oh Seung Eun , Lee Jin Woo , Park Byoung Kyu , Kim Hyun Woo , Park Kun-Bo
Published: June 2023

Overgrowth of long bones was noted in pediatric patients who underwent anterior cruciate ligament reconstruction. Hyperaemia during creating a metaphyseal hole and the microinstability made by the drill hole may induce overgrowth. This study aimed to determine whether metaphyseal hole creation accelerates growth and increases bone length and compare the effects of growth stimulation between metaphyseal hole creation and periosteal resection. We selected 7- to 8-week-old male New Zealand white rabbits. Periosteal resection (N = 7) and metaphyseal hole creation (N = 7) were performed on the tibiae of skeletally immature rabbits. Seven additional sham controls were included as age-matched controls. In the metaphyseal hole group, the hole was made using a Steinman pin at the same level of periosteal resection, and the cancellous bone beneath the physis was removed by curettage. The vacant space in the metaphysis below the physis was filled with bone wax. Tibiae were collected 6 weeks after surgery. The operated tibia was longer in the metaphyseal hole group (10.43 ± 0.29 cm vs. 10.65 ± 0.35 cm, P = 0.002). Overgrowth was higher in the metaphyseal hole group (3.17 ± 1.16 mm) than in the sham group (− 0.17 ± 0.39 mm, P < 0.001). The overgrowth in the metaphyseal hole group was comparable to that in the periosteal resection group (2.23 ± 1.52 mm, P = 0.287). In rabbits, metaphyseal hole creation and interposition with bone wax can stimulate long bone overgrowth, and the amount of overgrowth is similar to that seen in periosteal resection.
Small RNA sequencing analysis of peptide-affinity isolated plasma extracellular vesicles distinguishes pancreatic cancer patients from non-affected individuals
Authors: Roy Jeremy W. , Wajnberg Gabriel , Ouellette Alexie , Boucher Julie Emilie , Lacroix Jacynthe , Chacko Simi , Ghosh Anirban , Ouellette Rodney J. , Lewis Stephen M.
Published: June 2023

Pancreatic ductal adenocarcinoma (PDAC) has a high fatality rate, mainly due to its asymptomatic nature until late-stage disease and therefore delayed diagnosis that leads to a lack of timely treatment intervention. Consequently, there is a significant need for better methods to screen populations that are at high risk of developing PDAC. Such advances would result in earlier diagnosis, more treatment options, and ultimately better outcomes for patients. Several recent studies have applied the concept of liquid biopsy, which is the sampling of a biofluid (such as blood plasma) for the presence of disease biomarkers, to develop screening approaches for PDAC; several of these studies have focused on analysis of extracellular vesicles (EVs) and their cargoes. While these studies have identified many potential biomarkers for PDAC that are present within EVs, their application to clinical practice is hindered by the lack of a robust, reproducible method for EV isolation and analysis that is amenable to a clinical setting. Our previous research has shown that the Vn96 synthetic peptide is indeed a robust and reproducible method for EV isolation that has the potential to be used in a clinical setting. We have therefore chosen to investigate the utility of the Vn96 synthetic peptide for this isolation of EVs from human plasma and the subsequent detection of small RNA biomarkers of PDAC by Next-generation sequencing (NGS) analysis. We find that analysis of small RNA from Vn96-isolated EVs permits the discrimination of PDAC patients from non-affected individuals. Moreover, analyses of all small RNA species, miRNAs, and lncRNA fragments are most effective at segregating PDAC patients from non-affected individuals. Several of the identified small RNA biomarkers have been previously associated with and/or characterized in PDAC, indicating the validity of our findings, whereas other identified small RNA biomarkers may have novel roles in PDAC or cancer in general. Overall, our results provide a basis for a clinically-amendable detection and/or screening strategy for PDAC using a liquid biopsy approach that relies on Vn96-mediated isolation of EVs from plasma.
Interplay between diffusion and magnon-drag thermopower in pure iron and dilute iron alloy nanowire networks
Authors: Marchal Nicolas , da Câmara Santa Clara Gomes Tristan , Abreu Araujo Flavio , Piraux Luc
Published: June 2023

Results of measurements on the thermoelectric power of 45 nm diameter interconnected nanowire networks consisting of pure Fe, dilute FeCu and FeCr alloys and Fe/Cu multilayers are presented. The thermopower values of Fe nanowires are very close to those found in bulk materials, at all temperatures studied between 70 and 320 K. For pure Fe, the diffusion thermopower at room temperature, estimated to be around − 15 $$\upmu$$
μ
V/K from our data, is largely supplanted by the estimated positive magnon-drag contribution, close to 30 $$\upmu$$
μ
V/K. In dilute FeCu and FeCr alloys, the magnon-drag thermopower is found to decrease with increasing impurity concentration to about 10 $$\upmu$$
μ
V/K at 10$$\%$$
%
impurity content. While the diffusion thermopower is almost unchanged in FeCu nanowire networks compared to pure Fe, it is strongly reduced in FeCr nanowires due to pronounced changes in the density of states of the majority spin electrons. Measurements performed on Fe(7 nm)/Cu(10 nm) multilayer nanowires indicate a dominant contribution of charge carrier diffusion to the thermopower, as previously found in other magnetic multilayers, and a cancellation of the magnon-drag effect. The magneto-resistance and magneto-Seebeck effects measured on Fe/Cu multilayer nanowires allow the estimation of the spin-dependent Seebeck coefficient in Fe, which is about − 7.6 $$\upmu$$
μ
V/K at ambient temperature.
MHD Free convection flows of Jeffrey fluid with Prabhakar-like fractional model subject to generalized thermal transport
Authors: Siddique Imran , Adrees Rubina , Ahmad Hijaz , Askar Sameh
Published: June 2023

This article examines the effects of magnetohydrodynamics and heat absorption on an incompressible Jeffrey fluid’ time-dependent free convection flow over an infinite, vertically heated plate with homogeneous heat flux. The constitutive equation for heat flow utilizes the Prabhakar-like fractional derivative. The Laplace transform technique obtains the precise solution for the momentum and thermal profiles. The typical case and well-known outcomes from the literature are retrieved as restraining cases. The graphical analysis of the impact of the flow and fractionalized parameters on the thermal and momentum profiles is presented. Additionally, a comparison is made between the ordinary model and the Prabhakar-like fractional model, which shows that the latter better captures the retention of the physical features of the problem. It is concluded that the Prabhakar-like fractional model is better suited for describing the memory effect of the thermal and momentum fields.