bluuebunny/crossref_metadata_2025_split huggingface dataset:
Institutional earmarks: the earmark moratorium and federal highway spending
Authors: McLaughlin Peter T. 
Published: January 2023

AbstractIn 2010, the United States Congress placed a moratorium on earmarks – congressionally mandated spending projects. But did the earmark moratorium actually rid public policy of earmarks? I use earmark data and 2010–2020 state-level highway funding metrics to examine the relationship between previously expired transportation earmarks and federal highway funding during the earmark moratorium. Earmarks in the 2005 surface transportation law (SAFETEA-LU) continued to benefit certain states in 2020, even though the projects technically expired in 2009. This is because the funding “formulas” established by all post-2009 surface transportation laws were fully determined by the highway allocation percentage each state received in the preceding year, inclusive of earmarks. Further, I find the relationship between SAFETEA-LU earmarks and state funding disparities strengthened from 2010 to 2020, meaning the expired earmarks increased in policy significance during the moratorium. Highly earmarked states became even more advantaged after the earmarks were institutionalised into the highway funding formula.
Multidisciplinary concurrent optimization framework for multi-phase building design process
Authors: Muthumanickam Naveen Kumar , Duarte Jose Pinto , Simpson Timothy W. 
Published: January 2023

AbstractModern day building design projects require multidisciplinary expertise from architects and engineers across various phases of the design (conceptual, preliminary, and detailed) and construction processes. The Architecture Engineering and Construction (AEC) community has recently shifted gears toward leveraging design optimization techniques to make well-informed decisions in the design of buildings. However, most of the building design optimization efforts are either multidisciplinary optimization confined to just a specific design phase (conceptual/preliminary/detailed) or single disciplinary optimization (structural/thermal/daylighting/energy) spanning across multiple phases. Complexity in changing the optimization setup as the design progresses through subsequent phases, interoperability issues between modeling and physics-based analysis tools used at later stages, and the lack of an appropriate level of design detail to get meaningful results from these sophisticated analysis tools are few challenges that limit multi-phase multidisciplinary design optimization (MDO) in the AEC field. This paper proposes a computational building design platform leveraging concurrent engineering techniques such as interactive problem structuring, simulation-based optimization using meta models for energy and daylighting (machine learning based) and tradespace visualization. The proposed multi-phase concurrent MDO framework is demonstrated by using it to design and optimize a sample office building for energy and daylighting objectives across multiple phases. Furthermore, limitations of the proposed framework and future avenues of research are listed.
How social infrastructure saves lives: a quantitative analysis of Japan's 3/11 disasters
Authors: Aldrich Daniel P. 
Published: January 2023

AbstractObservers have long debated how societies should invest resources to safeguard citizens and property, especially in the face of increasing shocks and crises. This article explores how social infrastructure – the spaces and places that help build and maintain social ties and trust, allowing societies to coordinate behavior – plays an important role in our communities, especially in mitigating and recovering from shocks. An analysis of quantitative data on more than 550 neighborhoods across the three Japanese prefectures most affected by the tsunami of 11 March 2011 shows that, controlling for relevant factors, community centers, libraries, parks, and other social infrastructure measurably and cheaply reduced mortality rates among the most vulnerable population. Investing in social infrastructure projects would, based on this data, save more lives during a natural hazard than putting the same money into standard, gray infrastructure such as seawalls. Decision makers at national, regional, and local levels should expand spending on facilities such as libraries, community centers, social businesses, and public parks to increase resilience to multiple types of shocks and to further enhance the quality of life for residents.
Paleoclimate Changes in the Pacific Northwest Over the Past 36,000 Years From Clumped Isotope Measurements and Model Analysis
Authors: Lopez‐Maldonado Ricardo , Bateman Jesse Bloom , Ellis Andre , Bader Nicholas E. , Ramirez Pedro , Arnold Alexandrea , Ajoku Osinachi , Lee Hung‐I , Jesmok Gregory , Upadhyay Deepshikha , Mitsunaga Bryce , Elliott Ben , Tabor Clay , Tripati Aradhna 
Published: January 2023

AbstractSince the last glacial period, North America has experienced dramatic changes in regional climate, including the collapse of ice sheets and changes in precipitation. We use clumped isotope (∆47) thermometry and carbonate δ18O measurements of glacial and deglacial pedogenic carbonates from the Palouse Loess to provide constraints on hydroclimate changes in the Pacific Northwest. We also employ analysis of climate model simulations to help us further provide constraints on the hydroclimate changes in the Pacific Northwest. The coldest clumped isotope soil temperatures T(47) (13.5 ± 1.9°C to 17.1 ± 1.7°C) occurred ∼34,000–23,000 years ago. Using a soil‐to‐air temperature transfer function, we estimate Last Glacial Maximum (LGM) mean annual air temperatures of ∼−5.5°C and warmest average monthly temperatures (i.e., mean summer air temperatures) of ∼4.4°C. These data indicate a regional warming of 16.4 ± 2.6°C from the LGM to the modern temperatures of 10.9°C, which was about 2.5–3 times the global average. Proxy data provide locality constraints on the boundary of the cooler anticyclone induced by LGM ice sheets, and the warmer cyclone in the Eastern Pacific Ocean. Climate model analysis suggests regional amplification of temperature anomalies is due to the proximal location of the study area to the Laurentide Ice Sheet margin and the impact of the glacial anticyclone on the region, as well as local albedo. Isotope‐enabled model experiments indicate variations in water δ18O largely reflect atmospheric circulation changes and enhanced rainout upstream that brings more depleted vapor to the region during the LGM.
Aurora Detection From Nighttime Lights for Earth and Space Science Applications
Authors: Kalb Virginia , Kosar Burcu , Collado‐Vega Yaireska , Davidson Carol 
Published: January 2023

AbstractThis research leverages data from the Day/Night Band (DNB) of the Visible Infrared Imaging Radiometer (VIIRS) instrument onboard the Suomi National Polar‐orbiting Partnership (S‐NPP) satellite. We demonstrate the value of mining the VIIRS DNB for aurora and describe our use of unsupervised machine learning to create a binary mask for aurora occurrence. This mask can be used to flag aurora‐contaminated observations for NASA's nighttime lights products for Earth science applications. The identification of auroral regions can also be used for Space Weather applications, for example, for comparison with aurora forecast model and with other satellite‐ or ground‐based aurora observations. The DNB is a broadband channel that is sensitive to wavelengths from 500 to 900 nm, which covers most of the visible light spectrum, and as the name implies, captures light even at night with a sensitivity at the nanowatt level. This band is suitable for aurora observations since the light emitted by the aurora tends to be dominated by emissions from atomic oxygen, resulting in a greenish glow at a wavelength of 557.7 nm, especially at an altitude of 110 km. This study compares the global nighttime derived aurora regions for 17 and 18 March with the NOAA Space Weather Prediction Center's (SWPC) probability product for the St. Patrick's Day geomagnetic storm in 2015. VIIRS sensors are slated to be added to the next generation of polar‐orbiting operational satellites. Our novel automated approach to aurora identification opens up an efficient way to leverage this unique data source.
SIGMA: Spectral Interpretation Using Gaussian Mixtures and Autoencoder
Authors: Tung Po‐Yen , Sheikh Hassan A. , Ball Matthew , Nabiei Farhang , Harrison Richard J. 
Published: January 2023

AbstractIdentification of unknown micro‐ and nano‐sized mineral phases is commonly achieved by analyzing chemical maps generated from hyperspectral imaging data sets, particularly scanning electron microscope—energy dispersive X‐ray spectroscopy (SEM‐EDS). However, the accuracy and reliability of mineral identification are often limited by subjective human interpretation, non‐ideal sample preparation, and the presence of mixed chemical signals generated within the electron‐beam interaction volume. Machine learning has emerged as a powerful tool to overcome these problems. Here, we propose a machine‐learning approach to identify unknown phases and unmix their overlapped chemical signals. This approach leverages the guidance of Gaussian mixture modeling clustering fitted on an informative latent space of pixel‐wise elemental data points modeled using a neural network autoencoder, and unmixes the overlapped chemical signals of phases using non‐negative matrix factorization. We evaluate the reliability and the accuracy of the new approach using two SEM‐EDS data sets: a synthetic mixture sample and a real‐world particulate matter sample. In the former, the proposed approach successfully identifies all major phases and extracts background‐subtracted single‐phase chemical signals. The unmixed chemical spectra show an average similarity of 83.0% with the ground truth spectra. In the second case, the approach demonstrates the ability to identify potentially magnetic Fe‐bearing particles and their background‐subtracted chemical signals. We demonstrate a flexible and adaptable approach that brings a significant improvement to mineralogical and chemical analysis in a fully automated manner. The proposed analysis process has been built into a user‐friendly Python code with a graphical user interface for ease of use by general users.
Toward Better Understanding of the Ferrofluid Impregnation Process and Potential Artefacts—A Prerequisite for Reliable Interpretation of Magnetic Pore Fabrics
Authors: Pugnetti M. , Prieto M. , Mäder U. , Biedermann A. R. 
Published: January 2023

AbstractMagnetic pore fabrics (MPFs) serve as efficient proxy for pore alignment and preferential flow directions. Anisotropy of magnetic susceptibility of impregnated samples reflects the shape and arrangement of ferrofluid‐filled pores. Reliable interpretation requires that the entire connected pore space is reached by ferrofluid. This study investigates impregnation efficiencies of various methods (standard vacuum, pressure injection, magnetic flowthrough, and resin impregnation) and ferrofluids (water‐based versus oil‐based) on sandstone and calcarenite with different wettabilities. Mass‐based and susceptibility‐based impregnation efficiencies further evaluate the influence of impregnation time and flow rate. Because directional impregnation may introduce artificial fabrics, mutually perpendicular cores were measured, and subsamples served to capture spatial variability. Impregnation efficiencies vary between <1% and >100%, with resin impregnation and pressure injection using oil‐based ferrofluids being least efficient. Oil‐based ferrofluid generally leads to lower susceptibility‐based compared to mass‐based impregnation efficiencies, suggesting particle filtering. Water‐based ferrofluids show larger ranges of susceptibility‐based compared to mass‐based impregnation efficiencies. In particular, impregnation efficiencies >100% exclusively occur for susceptibility‐based impregnation efficiencies of water‐based ferrofluid, using either standard vacuum or pressure injection methods. MPFs after magnetic flowthrough impregnation reflect the impregnation direction rather than pore fabric. A major challenge is to apply enough force to reach sufficiently high impregnation efficiencies without creating MPFs that do not represent pore fabrics. While we cannot define a best practice for ferrofluid impregnation yet, this study improves our understanding of the impregnation process, and provides experimental procedures to identify artifacts.
Formation of a biofilm matrix network shapes polymicrobial interactions
Authors: Wang Lijun , Wang Hongxia , Zhang Hua , Wu Hui 
Published: January 2023

Abstract
Staphylococcus aureus colonizes the same ecological niche as many commensals. However, little is known about how such commensals modulate staphylococcal fitness and persistence. Here we report a new mechanism that mediates dynamic interactions between a commensal streptococcus and S. aureus. Commensal Streptococcus parasanguinis significantly increased the staphylococcal biofilm formation in vitro and enhanced its colonization in vivo. A streptococcal biofilm-associated protein BapA1, not fimbriae-associated protein Fap1, is essential for dual-species biofilm formation. On the other side, three staphylococcal virulence determinants responsible for the BapA1-dependent dual-species biofilm formation were identified by screening a staphylococcal transposon mutant library. The corresponding staphylococcal mutants lacked binding to recombinant BapA1 (rBapA1) due to lower amounts of eDNA in their culture supernatants and were defective in biofilm formation with streptococcus. The rBapA1 selectively colocalized with eDNA within the dual-species biofilm and bound to eDNA in vitro, highlighting the contributions of the biofilm matrix formed between streptococcal BapA1 and staphylococcal eDNA to dual-species biofilm formation. These findings have revealed an additional new mechanism through which an interspecies biofilm matrix network mediates polymicrobial interactions.
Risk of second primary malignancies in patients with chronic lymphocytic leukemia: a population-based study in the Netherlands, 1989-2019
Authors: van der Straten Lina , Levin Mark-David , Dinnessen Manette A. W. , Visser Otto , Posthuma Eduardus F. M. , Doorduijn Jeanette K. , Langerak Anton W. , Kater Arnon P. , Dinmohamed Avinash G. 
Published: January 2023

AbstractThe longevity of patients with chronic lymphocytic leukemia (CLL) has improved progressively over the past decades, making it essential to understand long-term health outcomes, such as second primary malignancies (SPMs). Therefore, this nationwide, population-based study assessed the risk of SPM development in CLL patients diagnosed during 1989-2019 in the Netherlands compared to the expected number of malignancies in an age-, sex-, and period-matched group from the general Dutch population. In 24,815 CLL patients followed for 162,698.49 person-years, 4369 SPMs were diagnosed with a standardized incidence ratio (SIR) of 1.63 (95% confidence interval [CI] 1.59–1.68). This elevated risk was observed for solid (SIR, 1.67; 95% CI, 1.65–1.75) and hematological SPMs (SIR 1.42; 95% CI, 1.24–1.62). The highest risk for SPMs was noted beyond five years post-diagnosis (SIR, 1.70; 95% CI, 1.62–1.77), for male individuals (SIR, 1.70; 95% CI, 1.64–1.77), and patients aged 18–69 years (SIR, 1.92; 95% CI, 1.79–2.05). The risk of SPMs was higher in CLL patients who received anti-neoplastic therapy (SIR, 2.12; 95% CI, 1.96–2.28), as compared with those who did not (SIR, 1.58; 95% CI, 1.53–1.63). Routine surveillance activities and tailored interventions to counteract the increased morbidity and excess mortality associated with SPMs are essential for improving long-term outcomes in CLL patients.
CircIFNGR2 enhances proliferation and migration of CRC and induces cetuximab resistance by indirectly targeting KRAS via sponging to MiR-30b
Authors: Zhang Qi , Zheng Yifeng , Liu Jiajia , Tang Xiaoxiao , Wang Yuan , Li Xianzheng , Li Huibin , Zhou Xiaoying , Tang Shiru , Tang Yitao , Wang Xiaoyan , He Han , Li Tingting 
Published: January 2023

AbstractCurrently the clinical efficacy of colorectal cancer (CRC) which is the most common malignant tumors over the world has not reached an ideal level. Cetuximab, the monoclonal antibody targeting the extracellular domain of EGFR, has shown its great efficacy in the promotion of apoptosis and the inhibition of tumor cells-like characteristics in numerous cancers. However certain KRAS wild-type CRC patients unexpectedly show cetuximab resistance and the specific mechanism remains unclear. Circular RNAs (circRNAs) as the promising novel type of biomarkers in the cancer diagnosis and therapy, have been reported to be related with the drug resistance. In this study, with wondering the mechanism of cetuximab resistance in KRAS wild-type CRC patients, we evaluate the impact of circIFNGR2 on CRC and detect the association among circIFNGR2, miR-30b and KRAS via various experiments such as RT-qPCR, immunohistochemistry, luciferase assays, cell functional experiments and xenograft model. We conclude that circIFNGR2 induces cetuximab resistance in colorectal cancer cells by indirectly regulating target gene KRAS by sponging miR-30b at the post-transcriptional level. It is thus suggested that inhibition of circIFNGR2 can be a promising therapeutic strategy for malignant CRC patients with cetuximab resistance.
Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase
Authors: Oh Juntaek , Kimoto Michiko , Xu Haoqing , Chong Jenny , Hirao Ichiro , Wang Dong 
Published: January 2023

AbstractBacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds–Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.
The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction
Authors: Luqman-Fatah Ahmad , Watanabe Yuzo , Uno Kazuko , Ishikawa Fuyuki , Moran John V. , Miyoshi Tomoichiro 
Published: January 2023

AbstractSome interferon stimulated genes (ISGs) encode proteins that inhibit LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles. Three ISG proteins that interact with ORF1p inhibit retrotransposition: HECT and RLD domain containing E3 ubiquitin-protein ligase 5 (HERC5); 2′−5′-oligoadenylate synthetase-like (OASL); and helicase with zinc finger 2 (HELZ2). HERC5 destabilizes ORF1p, but does not affect its cellular localization. OASL impairs ORF1p cytoplasmic foci formation. HELZ2 recognizes sequences and/or structures within the L1 5′UTR to reduce L1 RNA, ORF1p, and ORF1p cytoplasmic foci levels. Overexpression of WT or reverse transcriptase-deficient L1s lead to a modest induction of IFN-α expression, which is abrogated upon HELZ2 overexpression. Notably, IFN-α expression is enhanced upon overexpression of an ORF1p RNA binding mutant, suggesting ORF1p binding might protect L1 RNA from “triggering” IFN-α induction. Thus, ISG proteins can inhibit retrotransposition by different mechanisms.
Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation
Authors: Souza Thiago Moreno L. , Pinho Vagner D. , Setim Cristina F. , Sacramento Carolina Q. , Marcon Rodrigo , Fintelman-Rodrigues Natalia , Chaves Otavio A. , Heller Melina , Temerozo Jairo R. , Ferreira André C. , Mattos Mayara , Momo Patrícia B. , Dias Suelen S. G. , Gesto João S. M. , Pereira-Dutra Filipe , Viola João P. B. , Queiroz-Junior Celso Martins , Guimarães Lays Cordeiro , Chaves Ian Meira , Guimarães Pedro Pires Goulart , Costa Vivian Vasconcelos , Teixeira Mauro Martins , Bou-Habib Dumith Chequer , Bozza Patrícia T. , Aguillón Anderson R. , Siqueira-Junior Jarbas , Macedo-Junior Sergio , Andrade Edineia L. , Fadanni Guilherme P. , Tolouei Sara E. L. , Potrich Francine B. , Santos Adara A. , Marques Naiani F. , Calixto João B. , Rabi Jaime A. 
Published: January 2023

AbstractOrally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endowed with both antiviral and anti-inflammatory activity are highly desirable. We identified here that kinetin (MB-905) inhibits the in vitro replication of SARS-CoV-2 in human hepatic and pulmonary cell lines. On infected monocytes, MB-905 reduced virus replication, IL-6 and TNFα levels. MB-905 is converted into its triphosphate nucleotide to inhibit viral RNA synthesis and induce error-prone virus replication. Coinhibition of SARS-CoV-2 exonuclease, a proofreading enzyme that corrects erroneously incorporated nucleotides during viral RNA replication, potentiated the inhibitory effect of MB-905. MB-905 shows good oral absorption, its metabolites are stable, achieving long-lasting plasma and lung concentrations, and this drug is not mutagenic nor cardiotoxic in acute and chronic treatments. SARS-CoV-2-infected hACE-mice and hamsters treated with MB-905 show decreased viral replication, lung necrosis, hemorrhage and inflammation. Because kinetin is clinically investigated for a rare genetic disease at regimens beyond the predicted concentrations of antiviral/anti-inflammatory inhibition, our investigation suggests the opportunity for the rapid clinical development of a new antiviral substance for the treatment of COVID-19.
Efficient quantum information probes of nonequilibrium quantum criticality
Authors: M. Oliveira Miguel , Ribeiro Pedro , Kirchner Stefan 
Published: January 2023

AbstractQuantum information-based approaches, in particular the fidelity, have been flexible probes for phase boundaries of quantum matter. A major hurdle to a more widespread application of fidelity and other quantum information measures to strongly correlated quantum materials is the inaccessibility of the fidelity susceptibility to most state-of-the-art numerical methods. This is particularly apparent away from equilibrium where, at present, no general critical theory is available and many standard techniques fail. Motivated by the usefulness of quantum information-based measures we show that a widely accessible quantity, the single-particle affinity, is able to serve as a versatile instrument to identify phase transitions beyond Landau’s paradigm. We demonstrate that it not only is able to signal previously identified nonequilibrium phase transitions but also has the potential to detect hitherto unknown phases in models of quantum matter far from equilibrium.