bluuebunny/crossref_metadata_2025_split huggingface dataset:
CASPI: collaborative photon processing for active single-photon imaging
Authors: Lee Jongho , Ingle Atul , Chacko Jenu V. , Eliceiri Kevin W. , Gupta Mohit 
Published: May 2023

AbstractImage sensors capable of capturing individual photons have made tremendous progress in recent years. However, this technology faces a major limitation. Because they capture scene information at the individual photon level, the raw data is sparse and noisy. Here we propose CASPI: Collaborative Photon Processing for Active Single-Photon Imaging, a technology-agnostic, application-agnostic, and training-free photon processing pipeline for emerging high-resolution single-photon cameras. By collaboratively exploiting both local and non-local correlations in the spatio-temporal photon data cubes, CASPI estimates scene properties reliably even under very challenging lighting conditions. We demonstrate the versatility of CASPI with two applications: LiDAR imaging over a wide range of photon flux levels, from a sub-photon to high ambient regimes, and live-cell autofluorescence FLIM in low photon count regimes. We envision CASPI as a basic building block of general-purpose photon processing units that will be implemented on-chip in future single-photon cameras.
Curvature-controlled band alignment transition in 1D van der Waals heterostructures
Authors: Zhao Shu , Yang Chunxia , Zhu Ziye , Yao Xiaoping , Li Wenbin 
Published: May 2023

AbstractThe effect of curvature on the band alignment of one-dimensional (1D) van der Waals (vdW) transition metal dichalcogenide (TMDC) heterostructures is studied by comprehensive first-principles calculations. We find that, as the diameter of a TMDC nanotube decreases, the combined effect of curvature-induced flexoelectricity and circumferential tensile strain causes a rapid lowering of the conduction band minimum, whereas the valence band maximum exhibits an initial lowering before rising. As individual TMDC nanotubes form coaxial heterostructures, the concerted effect of diameter-dependent band-edge levels and intertube coupling via flexovoltage can result in a transition of intertube band alignment from Type II to Type I in multiple heterostructural systems, including large-diameter MoSe2@WS2, MoTe2@MoSe2, and MoTe2@WS2 heterostructures. These results lay down a foundation for the rational design of 1D vdW heterostructures.
Identification of PLOD3 and LRRN3 as potential biomarkers for Parkinson’s disease based on integrative analysis
Authors: Guo Xing , Hu Wenjun , Gao Zijie , Fan Yang , Wu Qianqian , Li Weiguo 
Published: May 2023

AbstractParkinson’s disease (PD) is one of the most prevalent movement disorders and its diagnosis relies heavily on the typical clinical manifestations in the late stages. This study aims to screen and identify biomarkers of PD for earlier intervention. We performed a differential analysis of postmortem brain transcriptome studies. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify biomarkers related to Braak stage. We found 58 genes with significantly different expression in both PD brain tissue and blood samples. PD gene signature and risk score model consisting of nine genes were constructed using least absolute shrinkage and selection operator regression (LASSO) and logistic regression. PLOD3 and LRRN3 in gene signature were identified to serve as key genes as well as potential risk factors in PD. Gene function enrichment analysis and evaluation of immune cell infiltration revealed that PLOD3 was implicated in suppression of cellular metabolic function and inflammatory cell infiltration, whereas LRRN3 exhibited an inverse trend. The cellular subpopulation expression of the PLOD3 and LRRN3 has significant distributional variability. The expression of PLOD3 was more enriched in inflammatory cell subpopulations, such as microglia, whereas LRRN3 was more enriched in neurons and oligodendrocyte progenitor cells clusters (OPC). Additionally, the expression of PLOD3 and LRRN3 in Qilu cohort was verified to be consistent with previous results. Collectively, we screened and identified the functions of PLOD3 and LRRN3 based the integrated study. The combined detection of PLOD3 and LRRN3 expression in blood samples can improve the early detection of PD.
Hole-type superconducting gatemon qubit based on Ge/Si core/shell nanowires
Authors: Zhuo Enna , Lyu Zhaozheng , Sun Xiaopei , Li Ang , Li Bing , Ji Zhongqing , Fan Jie , Bakkers E.P.A.M. , Han Xiaodong , Song Xiaohui , Qu Fanming , Liu Guangtong , Shen Jie , Lu Li 
Published: May 2023

AbstractWe demonstrate that superconducting gatemon qubits based on superconductor-semiconductor-superconductor Josephson junctions can be constructed on hole-type Ge/Si core/shell nanowires. The frequency of the qubit can be set firstly by controlling the diffusion of Al in the nanowire via thermal annealing, which yields a suitable critical supercurrent allowing the qubit frequency to be within the experimentally accessible range, and then by fine tuning of a gate voltage, by which an accurate adjustment of the frequency can be realized. On the resulted qubit, Rabi oscillation with an energy relaxation time $${T}_{1} \sim 180\,{\rm{ns}}$$

T

1

~
180

ns

was observed in the time domain, an average decoherence time $${T}_{2}^{* } \sim 15\,{\rm{ns}}$$

T

2

*

~
15

ns

was obtained, and the gate voltage dependence of both $${T}_{1}$$

T

1

and $${T}_{2}^{* }$$

T

2

*

was investigated. Such a hole-type superconducting gatemon qubit, based on materials with strong spin-orbit coupling and potentially the absence of hyperfine interaction after isotope purification, could be used for exploring the quantum coherence phenomena of hole-gas and even Majorana physics in Ge-based quantum devices.
Realization of practical eightfold fermions and fourfold van Hove singularity in TaCo2Te2
Authors: Rong Hongtao , Huang Zhenqiao , Zhang Xin , Kumar Shiv , Zhang Fayuang , Zhang Chengcheng , Wang Yuan , Hao Zhanyang , Cai Yongqing , Wang Le , Liu Cai , Ma Xiaoming , Guo Shu , Shen Bing , Liu Yi , Cui Shengtao , Shimada Kenya , Wu Quansheng , Lin Junhao , Yao Yugui , Wang Zhiwei , Xu Hu , Chen Chaoyu 
Published: May 2023

AbstractSpace groups describing the symmetry of lattice structure allow the emergence of fermionic quasiparticles with various degeneracy in the band structure. Theoretical efforts have predicted many materials hosting fermions with the highest degeneracy, i.e., eightfold fermions, yet lacking experimental realization. Here, we explore the band degeneracies in TaCo2Te2 crystals. Through systematic experimental and theoretical analyses, we establish TaCo2Te2 as a nonsymmorphic crystal with negligible spin–orbit coupling (SOC) and long-range magnetic order. These critical properties guarantee the realization of practical eightfold fermions and fourfold van Hove singularity, as directly observed by photoemission spectroscopy. TaCo2Te2 serves as a topological quantum critical platform, which can be tuned into various magnetic, topologically trivial, and nontrivial phases by adding strain, magnetic field, or SOC. The latter is demonstrated by our first-principles calculations, which show that enhancing SOC in TaCo2Te2 will promote the experimental observation of bulk hourglass fermions. Our results establish TaCo2Te2 as a platform to explore the interplay between symmetry and band topology.
ASP-2/Trans-sialidase chimeric protein induces robust protective immunity in experimental models of Chagas’ disease
Authors: Castro Julia T. , Brito Rory , Hojo-Souza Natalia S. , Azevedo Bárbara , Salazar Natalia , Ferreira Camila P. , Junqueira Caroline , Fernandes Ana Paula , Vasconcellos Ronnie , Cardoso Jamille M. , Aguiar-Soares Rodrigo D. O. , Vieira Paula M. A. , Carneiro Cláudia M. , Valiate Bruno , Toledo Cristiane , Salazar Andres M. , Caballero Otávia , Lannes-Vieira Joseli , Teixeira Santuza R. , Reis Alexandre B. , Gazzinelli Ricardo T. 
Published: May 2023

AbstractImmunization with the Amastigote Surface Protein-2 (ASP-2) and Trans-sialidase (TS) antigens either in the form of recombinant protein, encoded in plasmids or human adenovirus 5 (hAd5) confers robust protection against various lineages of Trypanosoma cruzi. Herein we generated a chimeric protein containing the most immunogenic regions for T and B cells from TS and ASP-2 (TRASP) and evaluated its immunogenicity in comparison with our standard protocol of heterologous prime-boost using plasmids and hAd5. Mice immunized with TRASP protein associated to Poly-ICLC (Hiltonol) were highly resistant to challenge with T. cruzi, showing a large decrease in tissue parasitism, parasitemia and no lethality. This protection lasted for at least 3 months after the last boost of immunization, being equivalent to the protection induced by DNA/hAd5 protocol. TRASP induced high levels of T. cruzi-specific antibodies and IFNγ-producing T cells and protection was primarily mediated by CD8+ T cells and IFN-γ. We also evaluated the toxicity, immunogenicity, and efficacy of TRASP and DNA/hAd5 formulations in dogs. Mild collateral effects were detected at the site of vaccine inoculation. While the chimeric protein associated with Poly-ICLC induced high levels of antibodies and CD4+ T cell responses, the DNA/hAd5 induced no antibodies, but a strong CD8+ T cell response. Immunization with either vaccine protected dogs against challenge with T. cruzi. Despite the similar efficacy, we conclude that moving ahead with TRASP together with Hiltonol is advantageous over the DNA/hAd5 vaccine due to pre-existing immunity to the adenovirus vector, as well as the cost-benefit for development and large-scale production.
Establishment of isotype-switched, antigen-specific B cells in multiple mucosal tissues using non-mucosal immunization
Authors: Prior John T. , Limbert Vanessa M. , Horowitz Rebecca M. , D’Souza Shaina J. , Bachnak Louay , Godwin Matthew S. , Bauer David L. , Harrell Jaikin E. , Morici Lisa A. , Taylor Justin J. , McLachlan James B. 
Published: May 2023

AbstractAlthough most pathogens infect the human body via mucosal surfaces, very few injectable vaccines can specifically target immune cells to these tissues where their effector functions would be most desirable. We have previously shown that certain adjuvants can program vaccine-specific helper T cells to migrate to the gut, even when the vaccine is delivered non-mucosally. It is not known whether this is true for antigen-specific B cell responses. Here we show that a single intradermal vaccination with the adjuvant double mutant heat-labile toxin (dmLT) induces a robust endogenous, vaccine-specific, isotype-switched B cell response. When the vaccine was intradermally boosted, we detected non-circulating vaccine-specific B cell responses in the lamina propria of the large intestines, Peyer’s patches, and lungs. When compared to the TLR9 ligand adjuvant CpG, only dmLT was able to drive the establishment of isotype-switched resident B cells in these mucosal tissues, even when the dmLT-adjuvanted vaccine was administered non-mucosally. Further, we found that the transcription factor Batf3 was important for the full germinal center reaction, isotype switching, and Peyer’s patch migration of these B cells. Collectively, these data indicate that specific adjuvants can promote mucosal homing and the establishment of activated, antigen-specific B cells in mucosal tissues, even when these adjuvants are delivered by a non-mucosal route. These findings could fundamentally change the way future vaccines are formulated and delivered.
Strong and ductile titanium–oxygen–iron alloys by additive manufacturing
Authors: Song Tingting , Chen Zibin , Cui Xiangyuan , Lu Shenglu , Chen Hansheng , Wang Hao , Dong Tony , Qin Bailiang , Chan Kang Cheung , Brandt Milan , Liao Xiaozhou , Ringer Simon P. , Qian Ma 
Published: May 2023

AbstractTitanium alloys are advanced lightweight materials, indispensable for many critical applications1,2. The mainstay of the titanium industry is the α–β titanium alloys, which are formulated through alloying additions that stabilize the α and β phases3–5. Our work focuses on harnessing two of the most powerful stabilizing elements and strengtheners for α–β titanium alloys, oxygen and iron1–5, which are readily abundant. However, the embrittling effect of oxygen6,7, described colloquially as ‘the kryptonite to titanium’8, and the microsegregation of iron9 have hindered their combination for the development of strong and ductile α–β titanium–oxygen–iron alloys. Here we integrate alloy design with additive manufacturing (AM) process design to demonstrate a series of titanium–oxygen–iron compositions that exhibit outstanding tensile properties. We explain the atomic-scale origins of these properties using various characterization techniques. The abundance of oxygen and iron and the process simplicity for net-shape or near-net-shape manufacturing by AM make these α–β titanium–oxygen–iron alloys attractive for a diverse range of applications. Furthermore, they offer promise for industrial-scale use of off-grade sponge titanium or sponge titanium–oxygen–iron10,11, an industrial waste product at present. The economic and environmental potential to reduce the carbon footprint of the energy-intensive sponge titanium production12 is substantial.
Deterministic evolution and stringent selection during preneoplasia
Authors: Karlsson Kasper , Przybilla Moritz J. , Kotler Eran , Khan Aziz , Xu Hang , Karagyozova Kremena , Sockell Alexandra , Wong Wing H. , Liu Katherine , Mah Amanda , Lo Yuan-Hung , Lu Bingxin , Houlahan Kathleen E. , Ma Zhicheng , Suarez Carlos J. , Barnes Chris P. , Kuo Calvin J. , Curtis Christina 
Published: May 2023

AbstractThe earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours.
Engineered tRNAs suppress nonsense mutations in cells and in vivo
Authors: Albers Suki , Allen Elizabeth C. , Bharti Nikhil , Davyt Marcos , Joshi Disha , Perez-Garcia Carlos G. , Santos Leonardo , Mukthavaram Rajesh , Delgado-Toscano Miguel Angel , Molina Brandon , Kuakini Kristen , Alayyoubi Maher , Park Kyoung-Joo Jenny , Acharya Grishma , Gonzalez Jose A. , Sagi Amit , Birket Susan E. , Tearney Guillermo J. , Rowe Steven M. , Manfredi Candela , Hong Jeong S. , Tachikawa Kiyoshi , Karmali Priya , Matsuda Daiki , Sorscher Eric J. , Chivukula Pad , Ignatova Zoya 
Published: May 2023

AbstractNonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2–7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP–sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
A pan-influenza antibody inhibiting neuraminidase via receptor mimicry
Authors: Momont Corey , Dang Ha V. , Zatta Fabrizia , Hauser Kevin , Wang Caihong , di Iulio Julia , Minola Andrea , Czudnochowski Nadine , De Marco Anna , Branch Kaitlin , Donermeyer David , Vyas Siddhant , Chen Alex , Ferri Elena , Guarino Barbara , Powell Abigail E. , Spreafico Roberto , Yim Samantha S. , Balce Dale R. , Bartha Istvan , Meury Marcel , Croll Tristan I. , Belnap David M. , Schmid Michael A. , Schaiff William Timothy , Miller Jessica L. , Cameroni Elisabetta , Telenti Amalio , Virgin Herbert W. , Rosen Laura E. , Purcell Lisa A. , Lanzavecchia Antonio , Snell Gyorgy , Corti Davide , Pizzuto Matteo Samuele 
Published: May 2023

AbstractRapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
Chimera: An atlas of regular vines on up to 8 nodes
Authors: Morales-Nápoles Oswaldo , Rajabi-Bahaabadi Mojtaba , Torres-Alves Gina Alexandra , ’t Hart Cornelis Marcel Pieter 
Published: May 2023

AbstractVine copulas have become the standard tool for modelling complex probabilistic dependence. It has been shown that the number of regular vines grows extremely quickly with the number of nodes. Chimera is the first attempt to map the vast space of regular vines. Software for operating with regular vines is available for R, matlab and Python. However, no dataset containing all regular vines is available. Our atlas of regular vines, Chimera, comprises all 24 4 × 4 matrices representing regular vines on 4 nodes, 480 5 × 5 matrices representing regular vines on 5 nodes, 23,040 6 × 6 matrices representing regular vines on 6 nodes, 2,580,480 7 × 7 matrices representing regular vines on 7 nodes and 660,602,880 8 × 8 matrices representing regular vines on 8 nodes. Regular vines in Chimera are classified according to their tree-equivalence class. We fit all regular vines to synthetic data to demonstrate the potential of Chimera. Chimera provides thus a tool for researchers to navigate this vast space in an orderly fashion.
Mitochondrial DNA and local ecological knowledge reveal two lineages of leatherback turtle on the beaches of Oaxaca, Mexico
Authors: Castillo-Morales Carlos Abraham , Sáenz-Arroyo Andrea , Castellanos-Morales Gabriela , Ruíz-Montoya Lorena 
Published: May 2023

AbstractDespite multiple conservation efforts of the Mexican government, the leatherback turtle is at serious risk of extinction. In this study, we investigated the possible presence of a genetic bottleneck that could prevent the recovery of this species and compared these findings with those of the olive ridley turtle, which is in true recovery. Our results confirmed that a demographic change occurred in the past and the presence of two different leatherback turtle lineages that diverged approximately 13.5 million years ago. Local ecological knowledge (LEK) also described the presence of these two lineages and warned that one is at higher risk of extinction than the other. Genetic analysis confirmed 124 mutations between the two lineages, and much lower genetic diversity in one lineage than the other. Our study highlights and substantiates the power of mixing LEK, environmental history, and genetics to better understand conservation challenges of highly threatened species such as the leatherback turtle. Moreover, we report a new lineage of the leatherback turtle which may represent a distinct species. Future studies should focus on morphological, ecological, biogeographical, evolutionary and conservation perspectives for the analysis of the new lineage.
Face masks influence emotion judgments of facial expressions: a drift–diffusion model
Authors: Williams W. Craig , Haque Eisha , Mai Becky , Venkatraman Vinod 
Published: May 2023

AbstractFace masks slow the spread of SARS-CoV-2, but it has been unknown how masks might reshape social interaction. One important possibility is that masks may influence how individuals communicate emotion through facial expressions. Here, we clarify to what extent—and how—masks influence facial emotion communication, through drift–diffusion modeling (DDM). Over two independent pre-registered studies, conducted three and 6 months into the COVID-19 pandemic, online participants judged expressions of 6 emotions (anger, disgust, fear, happiness, sadness, surprise) with the lower or upper face “masked” or unmasked. Participants in Study 1 (N = 228) correctly identified expressions above chance with lower face masks. However, they were less likely—and slower—to correctly identify these expressions relative to without masks, and they accumulated evidence for emotion more slowly—via decreased drift rate in DDM. This pattern replicated and intensified 3 months later in Study 2 (N = 264). These findings highlight how effectively individuals still communicate with masks, but also explain why they can experience difficulties communicating when masked. By revealing evidence accumulation as the underlying mechanism, this work suggests that time-sensitive situations may risk miscommunication with masks. This research could inform critical interventions to promote continued mask wearing as needed.