bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allocation and validation of the second revision of the International Staging System in the ICARIA-MM and IKEMA studies
Authors: Richardson Paul G. , Perrot Aurore , Mikhael Joseph , Martin Thomas , Beksac Meral , Spicka Ivan , Capra Marcelo , D’Agostino Mattia , Sonneveld Pieter , Bisht Kamlesh , Fukao Taro , Zhang Rick , Tada Keisuke , Tekle Christina , Macé Sandrine , Klippel Zandra , van de Velde Helgi , Moreau Philippe 
Published: November 2024

AbstractThe International Staging System for multiple myeloma recently underwent a second revision (R2-ISS) to include gain/amplification of 1q21 and account for the additive prognostic significance of multiple high-risk features. The phase 3 ICARIA-MM (isatuximab–pomalidomide–dexamethasone vs. pomalidomide–dexamethasone) and IKEMA (isatuximab–carfilzomib–dexamethasone vs. carfilzomib–dexamethasone) studies provide large datasets for retrospectively validating the prognostic value of the R2-ISS in relapsed/refractory multiple myeloma. Of 609 pooled patients, 68 (11.2%) were reclassified as R2-ISS stage I, 136 (22.3%) as R2-ISS stage II, 204 (33.5%) as R2-ISS stage III, 55 (9.0%) as stage IV, and 146 (24.0%) “Not classified”. Median progression-free survival was shorter among those reclassified as R2-ISS stage II (HR 1.52, 95% CI 0.979–2.358), stage III (HR 2.59, 95% CI 1.709–3.923), and stage IV (HR 3.51, 95% CI 2.124–5.784) versus stage I. Adding isatuximab led to longer progression-free survival versus doublet therapy (adjusted HR 0.544 [95% CI 0.436–0.680]), with a consistent treatment effect observed across all R2-ISS stages. This is the first study to validate the R2-ISS with novel agents, including anti-CD38 monoclonal antibodies, and to show that R2-ISS, as a prognostic scoring system, can be applied to patients with relapsed/refractory multiple myeloma.
Outcomes with loncastuximab tesirine following CAR T-cell therapy in patients with relapsed or refractory diffuse large B-cell lymphoma
Authors: Epperla Narendranath , Lucero Melanie , Bailey Tom , Mirams Laura , Cheung Jolenta , Amet Mona , Milligan Gary , Chen Lei 
Published: November 2024

AbstractThe efficacy of loncastuximab tesirine (lonca) following chimeric antigen receptor T-cell therapy (CAR-T) progression/failure is unknown. Hence, we sought to examine real-world use and outcomes of lonca following CAR-T in patients with relapsed or refractory (R/R) diffuse large B-cell lymphoma (DLBCL) in the USA. In this retrospective study, we included adults (age ≥ 18 years) with R/R DLBCL who received lonca monotherapy as third- (3 L) or fourth line (4 L) treatment after progressing on second line (2 L) or 3 L CAR-T, respectively. Post-CAR-T lonca outcomes included response rates (overall response rate [ORR] and complete response [CR] rate), duration of response (DOR), progression-free survival (PFS), and overall survival (OS). A total of 118 patients were included in the analysis with 95 receiving lonca following 2 L CAR-T (median age:66 years; 61% male) and 23 following 3 L CAR-T (median age:57 years; 43% male). Patients with 2 L CAR-T/3 L lonca had an ORR of 73% (CR rate of 34%). With a median follow-up of 8.5 months following lonca initiation, median DOR, PFS, and OS were not reached. The DOR, PFS, and OS at 12 months were 68%, 77%, and 84%, respectively. Patients with 3 L CAR-T/4 L lonca had an ORR of 78% (CR rate of 17%). With a median follow-up of 13 months following lonca initiation, the median DOR and PFS were 7.6 and 12.0 months, while median OS was not reached. OS at 12 months was 95%. In this study, we found that lonca monotherapy was an effective treatment option in R/R DLBCL in 3 L and 4 L settings including those who were resistant to or progressed after CAR-T.
Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program
Authors: Skovbjerg Cathrine Kiel , Sarup Pernille , Wahlström Ellen , Jensen Jens Due , Orabi Jihad , Olesen Lotte , Jensen Just , Jahoor Ahmed , Ramstein Guillaume 
Published: November 2024

Abstract
Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem. In this study we performed single- and multi-population GWAS on heading date and lodging in four barley breeding populations with varying combinations of row-type and growth habit. Focusing on a recently established 6-rowed winter (6RW) barley population, single-population GWAS hardly resulted in any significant associations. Nevertheless, the combination of the 6RW target population with other populations in multi-population GWAS detected four and five robust candidate quantitative trait loci for heading date and lodging, respectively. Of these, three remained undetected when analysing the combined populations individually. Further, multi-population GWAS detected markers capturing a larger proportion of genetic variance in 6RW. For multi-population GWAS, we compared the findings of a univariate model (MP1) with a multivariate model (MP2). While both models surpassed single-population GWAS in power, MP2 offered a significant advantage by having more realistic assumptions while pointing towards robust marker-trait associations across populations. Additionally, comparisons of GWAS findings for MP2 and single-population GWAS allowed identification of population-specific loci. In conclusion, our study presents a promising approach to kick-start genomics-based breeding in newly established breeding populations.
Enhanced light absorption for solid-state brown carbon from wildfires due to organic and water coatings
Authors: Cheng Zezhen , Shrivastava Manish , Ijaz Amna , Veghte Daniel , Vandergrift Gregory W. , Tseng Kuo-Pin , Lata Nurun Nahar , Kew Will , Suski Kaitlyn , Weis Johannes , Kulkarni Gourihar , Berg Larry K. , Fast Jerome D. , Kovarik Libor , Mazzoleni Lynn R. , Zelenyuk Alla , China Swarup 
Published: November 2024

AbstractWildfires emit solid-state strongly absorptive brown carbon (solid S-BrC, commonly known as tar ball), critical to Earth’s radiation budget and climate, but their highly variable light absorption properties are typically not accounted for in climate models. Here, we show that from a Pacific Northwest wildfire, over 90% of particles are solid S-BrC with a mean refractive index of 1.49 + 0.056i at 550 nm. Model sensitivity studies show refractive index variation can cause a ~200% difference in regional absorption aerosol optical depth. We show that ~50% of solid S-BrC particles from this sample uptake water above 97% relative humidity. We hypothesize these results from a hygroscopic organic coating, potentially facilitating solid S-BrC as nuclei for cloud droplets. This water uptake doubles absorption at 550 nm and the organic coating on solid S-BrC can lead to even higher absorption enhancements than water. Incorporating solid S-BrC and water interactions should improve Earth’s radiation budget predictions.
Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: insights from a perturbative, DFT-based analysis
Authors: Woodgate Christopher D. , Marchant George A. , Pártay Livia B. , Staunton Julie B. 
Published: November 2024

AbstractWe study the phase behaviour of the AlxCrFeCoNi high-entropy alloy. Our approach is based on a perturbative analysis of the internal energy of the paramagnetic solid solution as evaluated within the Korringa-Kohn-Rostoker formulation of density functional theory, using the coherent potential approximation to average over disorder. Via application of a Landau-type linear response theory, we infer preferential chemical orderings directly. In addition, we recover a pairwise form of the alloy internal energy suitable for study via atomistic simulations, which in this work are performed using the nested sampling algorithm, which is well-suited for studying complex potential energy surfaces. When the underlying lattice is fcc, at low concentrations of Al, depending on the value of x, we predict either an L12 or D022 ordering emerging below approximately 1000 K. On the other hand, when the underlying lattice is bcc, consistent with experimental observations, we predict B2 ordering temperatures higher than the melting temperature of the alloy, confirming that this ordered phase forms directly from the melt. For both fcc and bcc systems, chemical orderings are dominated by Al moving to one sublattice, Ni and Co the other, while Cr and Fe remain comparatively disordered. On the bcc lattice, our atomistic modelling suggests eventual decomposition into B2 NiAl and Cr-rich phases. These results shed light on the fundamental physical origins of atomic ordering tendencies in these intriguing materials.
Bayesian assessment of commonly used equivalent circuit models for corrosion analysis in electrochemical impedance spectroscopy
Authors: Zhang Runze , Sur Debashish , Li Kangming , Witt Julia , Black Robert , Whittingham Alexander , Scully John R. , Hattrick-Simpers Jason 
Published: November 2024

AbstractElectrochemical Impedance Spectroscopy (EIS) is a crucial technique for assessing corrosion of metallic materials. The analysis of EIS hinges on the selection of an appropriate equivalent circuit model (ECM) that accurately characterizes the system under study. In this work, we systematically examined the applicability of three commonly used ECMs across several typical material degradation scenarios. By applying Bayesian Inference to simulated corrosion EIS data, we assessed the suitability of these ECMs under different corrosion conditions and identified regions where the EIS data lacks sufficient information to statistically substantiate the ECM structure. Additionally, we posit that the traditional approach to EIS analysis, which often requires measurements to very low frequencies, might not be always necessary to correctly model the appropriate ECM. Our study assesses the impact of omitting data from low to medium-frequency ranges on inference results and reveals that a significant portion of low-frequency measurements can be excluded without substantially compromising the accuracy of extracting system parameters. Further, we propose simple checks to the posterior distributions of the ECM components and posterior predictions, which can be used to quantitatively evaluate the suitability of a particular ECM and the minimum frequency required to be measured. This framework points to a pathway for expediting EIS acquisition by intelligently reducing low-frequency data collection and permitting on-the-fly EIS measurements.
Cast vote records: A database of ballots from the 2020 U.S. Election
Authors: Kuriwaki Shiro , Reece Mason , Baltz Samuel , Conevska Aleksandra , Loffredo Joseph R. , Mutlu Can , Samarth Taran , Acevedo Jetter Kevin E. , Djanogly Garai Zachary , Murray Kate , Hirano Shigeo , Lewis Jeffrey B. , Snyder James M. , Stewart Charles 
Published: November 2024

AbstractBallots are the core records of elections. Electronic records of actual ballots cast (cast vote records) are available to the public in some jurisdictions. However, they have been released in a variety of formats and have not been independently evaluated. Here we introduce a database of cast vote records from the 2020 U.S. general election. We downloaded publicly available unstandardized cast vote records, standardized them into a multi-state database, and extensively compared their totals to certified election results. Our release includes vote records for President, Governor, U.S. Senate and House, and state upper and lower chambers, covering 42.7 million voters in 20 states who voted for more than 2,200 candidates. This database serves as a uniquely granular administrative dataset for studying voting behavior and election administration. Using this data, we show that in battleground states, 1.9 percent of solid Republicans (as defined by their congressional and state legislative voting) in our database split their ticket for Joe Biden, while 1.2 percent of solid Democrats split their ticket for Donald Trump.
mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics
Authors: Mirarchi Antonio , Giorgino Toni , De Fabritiis Gianni 
Published: November 2024

AbstractRecent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive datasets that focus on the dynamics of proteins, which are crucial for understanding protein function, folding, and interactions. To address this critical gap, we introduce mdCATH, a dataset generated through an extensive set of all-atom molecular dynamics simulations of a diverse and representative collection of protein domains. This dataset comprises all-atom systems for 5,398 domains, modeled with a state-of-the-art classical force field, and simulated in five replicates each at five temperatures from 320 K to 450 K. The mdCATH dataset records coordinates and forces every 1 ns, for over 62 ms of accumulated simulation time, effectively capturing the dynamics of the various classes of domains and providing a unique resource for proteome-wide statistical analyses of protein unfolding thermodynamics and kinetics. We outline the dataset structure and showcase its potential through four easily reproducible case studies, highlighting its capabilities in advancing protein science.
Towards construction of embankment on soft soil: a comparative study of lightweight materials and deep replacement techniques
Authors: Abdrabbo Fathi M. , Gaaver Khaled E. , Elwakil Amr Z. , Khalifa Shahinaz A. 
Published: November 2024

AbstractPlanning embankments demands comprehensive studies to select suitable materials, enhance soil stability, ensure optimal performance, and comply with building code requirements and sustainability standards. This study offers an evaluation of various alternatives and their effectiveness for constructing embankments on weak soil using the 2D finite element software Plaxis 8. It highlights the convergence of different techniques, offering flexibility in selecting the optimal strategy for projects. The behaviour of multilayer clayey soil under an embankment of lightweight filling materials such as mixed sawdust or geo-foam and that carrying an embankment of traditional fill material improved by deep replacement techniques like concrete piles (CP), deep-mixing columns (DMC), stone columns (SC), and sand piles (SP) were compared considering factors like stress distribution, pore water pressure, and settlement of the soil. The results demonstrate that lightweight materials reduced settlement by 11–98% and stress by 5–89%, while deep replacement techniques reduced settlement by 8.5–75% and stress by 44–88%. Notably, the study underscores the effectiveness of DMC in promoting soil reuse compared to CP.
Adjuvants to the S1-subunit of the SARS-CoV-2 spike protein vaccine improve antibody and T cell responses and surrogate neutralization in mice
Authors: Becker William , Rebbani Khadija , Duan Zhijian , Valkov Eugene , Bryant Shawn , Ho Mitchell , Berzofsky Jay A. , Olkhanud Purevdorj B. 
Published: November 2024

AbstractVarious public health measures have contained outbreaks of SARS-CoV-2, but concerns remain over the possibility of future surges. Improvements in broadening the vaccine response can stifle new and nascent infections. In this study, we tested the effects of different adjuvant combinations on the immunization of mice with the receptor-binding domain (RBD)-containing the S1-subunit of the spike protein (S1 protein) from SARS-CoV-2 to induce a robust humoral and cellular immune response. We showed that subcutaneous immunization of S1 protein co-delivered with IL-15 and TLR-ligands (MALP-2, poly I: C, and CpG) or with IL-12 and GM-CSF in DOTAP, or Alum induced significantly high titers of durable antibodies, predominantly IgG1, IgG2a, and IgG2b, that could bind to RBD, S1-subunit, and the full-length ectodomain of SARS-CoV-2 spike protein in sera compared to the immunization with S1 protein alone in both B6 wild-type (WT) and the K18-hACE2 transgenic mice. In addition, immunization with S1 protein co-delivered with IL-15 and TLR-ligands induced antibody responses against S1 protein in aged mice, and sera from younger mice reduced plaque formation of live SARS-CoV-2, and had effective binding to S1 protein from ten different variants of SARS-CoV-2, including Omicron (B.1.1.529), and greater neutralization activity as early as day 21 post-immunization measured by inhibition of RBD binding to hACE2 than sera from mice immunized with S1 protein alone or co-delivered with Alum. We also identified antibody-binding epitopes using 18-mer peptides with 9-residue overlaps from the S1 protein. CD8+ T-cell responses specific to RBD and S1 protein peptide pools were observed up to day 200 post-immunization by tetramer staining. These data show the efficacy of specific immunologically targeted adjuvants for increasing S1 protein immunogenicity in mice and can contribute to more effective vaccines.
Precision parameter estimation in Proton Exchange Membrane Fuel Cells using depth information enhanced Differential Evolution
Authors: Jangir Pradeep , Ezugwu Absalom E. , Arpita  , Agrawal Sunilkumar P. , Pandya Sundaram B. , Parmar Anil , Gulothungan G. , Abualigah Laith 
Published: November 2024

AbstractProton Exchange Membrane Fuel Cell (PEMFC) models require parameter tuning for their design and performance improvement. In this study, Depth Information-Based Differential Evolution (Di-DE) algorithm, a novel and efficient metaheuristic approach, is applied to the complex, nonlinear optimization problem of PEMFC parameter estimation. The Di-DE algorithm was tested on twelve PEMFCs (BCS 500 W PEMFC, Nedstack 600 W PS6 PEMFC, SR-12 500 W PEMFC, H-12 PEMFC, STD 250 W PEMFC, HORIZON 500 W PEMFC and four 250W PEMFC and two H-12 12W PEMFC) and showed excellent accuracy. The Di-DE algorithm is was compared with other advanced evolutionary algorithms like iwPSO, CLPSO, DNLPSO, SLPSO, SaDE, SHADE, JADE, QUATRE, LSA, QUATRE-EMS and C-QUATRE, which obtained a minimum objective function value of 0.0255 and an average runtime improvement of 98.8%. The optimized parameters of the proposed method yielded the Sum of Squared Errors (SSE) as low as 0.00002 in some cases, which indicates better precision and stability. Moreover, the voltage–current (V–I) and power–voltage (P–V) characteristics predicted by Di-DE were within 1% error relative to the experimental data for all tested PEMFCs. The results of this work highlight the potential of the Di-DE algorithm to enable more sophisticated modelling and optimization of PEMFCs, which in turn will help to broaden the use of PEMFCs in clean energy applications.
Effects of foot–ground friction and age-related gait changes on falls during walking: a computational study using a neuromusculoskeletal model
Authors: Izumi Naoto , Yoshida Takashi , Nishi Toshiaki , Masani Kei , Yamaguchi Takeshi 
Published: November 2024

AbstractWe used a neuromusculoskeletal model of bipedal walking to examine the effects of foot–ground friction conditions and gait patterns on slip- and trip-induced falls. We developed three two-dimensional neuro-musculoskeletal models in a self-organized manner representing young adults, elderly non-fallers, and elderly fallers. We simulated walking under different foot-ground friction conditions. The static friction coefficient between the foot and the ground was varied from 0.05 to 2.0. Under low friction conditions, the three gait models demonstrated slip-induced falls. The elderly faller model experienced the most slip. This is because the RCOF was higher in the elderly faller model due to its short stride length but much smaller foot clearance. Under high friction conditions, only the elderly faller model demonstrated trip-induced falls. Based on the analysis using the margin of stability, the forward postural stability of the model gradually decreased under high-friction conditions, with the toe of the swing foot contacting the ground and subsequently falling forward. These results imply that there is an optimal coefficient of friction for the ground to prevent slip- and trip-induced falls by people with less stable gaits, which may provide new insights into the design of shoes and floor surfaces for the elderly.
Evolutionary genomics of Leishmania braziliensis across the neotropical realm
Authors: Heeren Senne , Sanders Mandy , Shaw Jeffrey Jon , Pinto Brandão-Filho Sinval , Côrtes Boité Mariana , Motta Cantanhêde Lilian , Chourabi Khaled , Maes Ilse , Llanos-Cuentas Alejandro , Arevalo Jorge , Marco Jorge D. , Lemey Philippe , Cotton James A. , Dujardin Jean-Claude , Cupolillo Elisa , Van den Broeck Frederik 
Published: November 2024

AbstractThe Neotropical realm, one of the most biodiverse regions on Earth, houses a broad range of zoonoses that pose serious public health threats. Protozoan parasites of the Leishmania (Viannia) braziliensis clade cause zoonotic leishmaniasis in Latin America with clinical symptoms ranging from simple cutaneous to destructive, disfiguring mucosal lesions. We present the first comprehensive genome-wide continental study including 257 cultivated isolates representing most of the geographical distribution of this major human pathogen. The L. braziliensis clade is genetically highly heterogeneous, consisting of divergent parasite groups that are associated with different environments and vary greatly in diversity. Apart from several small ecologically isolated groups with little diversity, our sampling identifies two major parasite groups, one associated with the Amazon and the other with the Atlantic Forest biomes. These groups show different recombination histories, as suggested by high levels of heterozygosity and effective population sizes in the Amazonian group in contrast to high levels of linkage and clonality in the Atlantic group. We argue that these differences are linked to strong eco-epidemiological differences between the two regions. In contrast to geographically focused studies, our study provides a broad understanding of the molecular epidemiology of zoonotic parasites circulating in tropical America.
Impurity flat band states in the diamond chain
Authors: Marques A. M. , Viedma D. , Ahufinger V. , Dias R. G. 
Published: November 2024

AbstractFlat band (FB) systems, featuring dispersionless energy bands, have garnered significant interest due to their compact localized states (CLSs). However, a detailed account on how local impurities affect the physical properties of overlapping CLSs is still missing. Here we study a diamond chain with a finite magnetic flux per plaquette that exhibits a gapped midspectrum FB with non-orthogonal CLSs, and develop a framework for projecting operators onto such non-orthogonal bases. This framework is applied to the case of an open diamond chain with small local impurities in the midchain plaquette, and analytical expressions are derived for FB states influenced by these impurities. For equal impurities in top and bottom sites under diagonal disorder, we show how the impurity states experience an averaged disorder dependent on their spatial extension, leading to enhanced robustness against disorder. For a single impurity, an exotic topological phase with a half-integer winding number is discovered, which is linked to a single in-gap edge state under open boundary conditions. Numerical simulations validate the analytical predictions.