bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning derived retinal pigment score from ophthalmic imaging shows ethnicity is not biology
Authors: Rajesh Anand E. , Olvera-Barrios Abraham , Warwick Alasdair N. , Wu Yue , Stuart Kelsey V. , Biradar Mahantesh I. , Ung Chuin Ying , Khawaja Anthony P. , Luben Robert , Foster Paul J. , Cleland Charles R. , Makupa William U. , Denniston Alastair K. , Burton Matthew J. , Bastawrous Andrew , Keane Pearse A. , Chia Mark A. , Turner Angus W. , Lee Cecilia S. , Tufail Adnan , Lee Aaron Y. , Egan Catherine ,   UK Biobank Eye and Vision Consortium, Allen Naomi , Aslam Tariq , Atan Denize , Balaskas Konstantinos , Barman Sarah , Barrett Jenny , Bishop Paul , Black Graeme , Braithwaite Tasanee , Carare Roxana , Chakravarthy Usha , Chan Michelle , Chua Sharon , Day Alexander , Desai Parul , Dhillon Baljean , Dick Andrew , Doney Alexander , Ennis Sarah , Gallacher John , Garway-Heath David Ted , Gibson Jane , Guggenheim Jeremy , Hammond Chris , Hardcastle Alison , Harding Simon , Hogg Ruth , Hysi Pirro , Lascaratos Gerassimos , Littlejohns Thomas , Lotery Andrew , Luthert Phil , MacGillivray Tom , Mackie Sarah , Madhusudhan Savita , McGuinness Bernadette , McKay Gareth , McKibbin Martin , Moore Tony , Morgan James , O’Sullivan Eoin , Oram Richard , Owen Chris , Patel Praveen , Paterson Euan , Peto Tunde , Petzold Axel , Pontikos Nikolas , Rahi Jugnoo , Rudnicka Alicja , Sattar Naveed , Self Jay , Sergouniotis Panagiotis , Sivaprasad Sobha , Steel David , Stratton Irene , Strouthidis Nicholas , Sudlow Cathie , Sun Zihan , Tapp Robyn , Thomas Dhanes , Trucco Emanuele , Viswanathan Ananth , Vitart Veronique , Weedon Mike , Williams Katie , Williams Cathy , Woodside Jayne , Yates Max , Zheng Yalin 
Published: January 2025

AbstractFew metrics exist to describe phenotypic diversity within ophthalmic imaging datasets, with researchers often using ethnicity as a surrogate marker for biological variability. We derived a continuous, measured metric, the retinal pigment score (RPS), that quantifies the degree of pigmentation from a colour fundus photograph of the eye. RPS was validated using two large epidemiological studies with demographic and genetic data (UK Biobank and EPIC-Norfolk Study) and reproduced in a Tanzanian, an Australian, and a Chinese dataset. A genome-wide association study (GWAS) of RPS from UK Biobank identified 20 loci with known associations with skin, iris and hair pigmentation, of which eight were replicated in the EPIC-Norfolk cohort. There was a strong association between RPS and ethnicity, however, there was substantial overlap between each ethnicity and the respective distributions of RPS scores. RPS decouples traditional demographic variables from clinical imaging characteristics. RPS may serve as a useful metric to quantify the diversity of the training, validation, and testing datasets used in the development of AI algorithms to ensure adequate inclusion and explainability of the model performance, critical in evaluating all currently deployed AI models. The code to derive RPS is publicly available at: https://github.com/uw-biomedical-ml/retinal-pigmentation-score.
STAT1 regulates immune-mediated intestinal stem cell proliferation and epithelial regeneration
Authors: Takashima Shuichiro , Sharma Roshan , Chang Winston , Calafiore Marco , Fu Ya-Yuan , Jansen Suze A. , Ito Takahiro , Egorova Anastasiya , Kuttiyara Jason , Arnhold Viktor , Sharrock Jessica , Santosa Endi , Chaudhary Ojasvi , Geiger Heather , Iwasaki Hiromi , Liu Chen , Sun Joseph , Robine Nicolas , Mazutis Linas , Lindemans Caroline A. , Hanash Alan M. 
Published: January 2025

AbstractThe role of the immune system in regulating tissue stem cells remains poorly understood, as does the relationship between immune-mediated tissue damage and regeneration. Graft vs. host disease (GVHD) occurring after allogeneic bone marrow transplantation (allo-BMT) involves immune-mediated damage to the intestinal epithelium and its stem cell compartment. To assess impacts of T-cell-driven injury on distinct epithelial constituents, we have performed single cell RNA sequencing on intestinal crypts following experimental BMT. Intestinal stem cells (ISCs) from GVHD mice have exhibited global transcriptomic changes associated with a substantial Interferon-γ response and upregulation of STAT1. To determine its role in crypt function, STAT1 has been deleted within murine intestinal epithelium. Following allo-BMT, STAT1 deficiency has resulted in reduced epithelial proliferation and impaired ISC recovery. Similarly, epithelial Interferon-γ receptor deletion has also attenuated proliferation and ISC recovery post-transplant. Investigating the mechanistic basis underlying this epithelial response, ISC STAT1 expression in GVHD has been found to correlate with upregulation of ISC c-Myc. Furthermore, activated T cells have stimulated Interferon-γ-dependent epithelial regeneration in co-cultured organoids, and Interferon-γ has directly induced STAT1-dependent c-Myc expression and ISC proliferation. These findings illustrate immunologic regulation of a core tissue stem cell program after damage and support a role for Interferon-γ as a direct contributor to epithelial regeneration.
Structural and electronic features enabling delocalized charge-carriers in CuSbSe2
Authors: Fu Yuchen , Lohan Hugh , Righetto Marcello , Huang Yi-Teng , Kavanagh Seán R. , Cho Chang-Woo , Zelewski Szymon J. , Woo Young Won , Demetriou Harry , McLachlan Martyn A. , Heutz Sandrine , Piot Benjamin A. , Scanlon David O. , Rao Akshay , Herz Laura M. , Walsh Aron , Hoye Robert L. Z. 
Published: January 2025

AbstractInorganic semiconductors based on heavy pnictogen cations (Sb3+ and Bi3+) have gained significant attention as potential nontoxic and stable alternatives to lead-halide perovskites for solar cell applications. A limitation of these novel materials, which is being increasingly commonly found, is carrier localization, which substantially reduces mobilities and diffusion lengths. Herein, CuSbSe2 is investigated and discovered to have delocalized free carriers, as shown through optical pump terahertz probe spectroscopy and temperature-dependent mobility measurements. Using a combination of theory and experiment, the critical enabling factors are found to be: 1) having a layered structure, which allows distortions to the unit cell during the propagation of an acoustic wave to be relaxed in the interlayer gaps, with minimal changes in bond length, thus limiting deformation potentials; 2) favourable quasi-bonding interactions across the interlayer gap giving rise to higher electronic dimensionality; 3) Born effective charges not being anomalously high, which, combined with the small bandgap ($$\le$$
≤
1.2 eV), result in a low ionic contribution to the dielectric constant compared to the electronic contribution, thus reducing the strength of Fröhlich coupling. These insights can drive forward the rational discovery of perovskite-inspired materials that can avoid carrier localization.
Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy
Authors: Guo Min , Wu Yicong , Hobson Chad M. , Su Yijun , Qian Shuhao , Krueger Eric , Christensen Ryan , Kroeschell Grant , Bui Johnny , Chaw Matthew , Zhang Lixia , Liu Jiamin , Hou Xuekai , Han Xiaofei , Lu Zhiye , Ma Xuefei , Zhovmer Alexander , Combs Christian , Moyle Mark , Yemini Eviatar , Liu Huafeng , Liu Zhiyi , Benedetto Alexandre , La Riviere Patrick , Colón-Ramos Daniel , Shroff Hari 
Published: January 2025

AbstractOptical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained ‘de-aberration’ networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.
SOX2+ sustentacular cells are stem cells of the postnatal adrenal medulla
Authors: Santambrogio Alice , Kemkem Yasmine , Willis Thea L. , Berger Ilona , Kastriti Maria Eleni , Faure Louis , Russell John P. , Lodge Emily J. , Yianni Val , Kövér Bence , Oakey Rebecca J. , Altieri Barbara , Bornstein Stefan R. , Steenblock Charlotte , Adameyko Igor , Andoniadou Cynthia L. 
Published: January 2025

AbstractRenewal of the catecholamine-secreting chromaffin cell population of the adrenal medulla is necessary for physiological homeostasis throughout life. Definitive evidence for the presence or absence of an adrenomedullary stem cell has been enigmatic. In this work, we demonstrate that a subset of sustentacular cells endowed with a support role, are in fact adrenomedullary stem cells. Through genetic tracing and comprehensive transcriptomic data of the mouse adrenal medulla, we show that cells expressing Sox2/SOX2 specialise as a unique postnatal population from embryonic Schwann Cell Precursors and are also present in the normal adult human adrenal medulla. Postnatal SOX2+ cells give rise to chromaffin cells of both the adrenaline and noradrenaline lineages in vivo and in vitro. We reveal that SOX2+ stem cells have a second, paracrine role in maintaining adrenal chromaffin cell homeostasis, where they promote proliferation through paracrine secretion of WNT6. This work identifies SOX2+ cells as a true stem cell for catecholamine-secreting chromaffin cells.
Verifiable measurement-based quantum random sampling with trapped ions
Authors: Ringbauer Martin , Hinsche Marcel , Feldker Thomas , Faehrmann Paul K. , Bermejo-Vega Juani , Edmunds Claire L. , Postler Lukas , Stricker Roman , Marciniak Christian D. , Meth Michael , Pogorelov Ivan , Blatt Rainer , Schindler Philipp , Eisert Jens , Monz Thomas , Hangleiter Dominik 
Published: January 2025

AbstractQuantum computers are now on the brink of outperforming their classical counterparts. One way to demonstrate the advantage of quantum computation is through quantum random sampling performed on quantum computing devices. However, existing tools for verifying that a quantum device indeed performed the classically intractable sampling task are either impractical or not scalable to the quantum advantage regime. The verification problem thus remains an outstanding challenge. Here, we experimentally demonstrate efficiently verifiable quantum random sampling in the measurement-based model of quantum computation on a trapped-ion quantum processor. We create and sample from random cluster states, which are at the heart of measurement-based computing, up to a size of 4 × 4 qubits. By exploiting the structure of these states, we are able to recycle qubits during the computation to sample from entangled cluster states that are larger than the qubit register. We then efficiently estimate the fidelity to verify the prepared states—in single instances and on average—and compare our results to cross-entropy benchmarking. Finally, we study the effect of experimental noise on the certificates. Our results and techniques provide a feasible path toward a verified demonstration of a quantum advantage.
An integrated photonic engine for programmable atomic control
Authors: Christen Ian , Propson Thomas , Sutula Madison , Sattari Hamed , Choong Gregory , Panuski Christopher , Melville Alexander , Mallek Justin , Brabec Cole , Hamilton Scott , Dixon P. Benjamin , Menssen Adrian J. , Braje Danielle , Ghadimi Amir H. , Englund Dirk 
Published: January 2025

AbstractSolutions for scalable, high-performance optical control are important for the development of scaled atom-based quantum technologies. Modulation of many individual optical beams is central to applying arbitrary gate and control sequences on arrays of atoms or atom-like systems. At telecom wavelengths, miniaturization of optical components via photonic integration has pushed the scale and performance of classical and quantum optics far beyond the limitations of bulk devices. However, material platforms for high-speed telecom integrated photonics lack transparency at the short wavelengths required by leading atomic systems. Here, we propose and implement a scalable and reconfigurable photonic control architecture using integrated, visible-light modulators based on thin-film lithium niobate. We combine this system with techniques in free-space optics and holography to demonstrate multi-channel, gigahertz-rate visible beamshaping. When applied to silicon-vacancy artificial atoms, our system enables the spatial and spectral addressing of a dynamically-selectable set of these stochastically-positioned point emitters.
Banning new gas boilers as a no-regret mitigation option
Authors: Escribe Célia , Vivier Lucas 
Published: January 2025

AbstractThe low uptake of low-carbon heating systems across Europe has prompted authorities to consider more ambitious measures, including a complete ban on the installation of new fossil fuel boilers. In this analysis, we simulate the impacts of introducing this ban in France under 11,664 scenarios covering major uncertainties. We find that the ban induces major changes in the energy system, leading to efficiency gains. Additionally, we find that the ban increases the likelihood of reaching carbon neutrality while reducing total system cost in over 75% of scenarios. Finally, we show that the implementation of the ban, when coupled with the existing subsidy framework, mitigates inequalities among owner-occupied households but generates adverse effects for those in privately rented homes.
Engineering ultra-strong electron-phonon coupling and nonclassical electron transport in crystalline gold with nanoscale interfaces
Authors: Kumbhakar Shreya , Maji Tuhin Kumar , Tongbram Binita , Mandal Shinjan , Soundararaj Shri Hari , Debnath Banashree , T Phanindra Sai , Jain Manish , Krishnamurthy H. R. , Pandey Anshu , Ghosh Arindam 
Published: January 2025

AbstractElectrical resistivity in good metals, particularly noble metals such as gold (Au), silver (Ag), or copper, increases linearly with temperature (T) for T > ΘD, where ΘD is the Debye temperature. This is because the coupling (λ) between the electrons and the lattice vibrations, or phonons, in these metals is weak, with λ ~ 0.1−0.2. In this work, we outline a nanostructuring strategy of crystalline Au where this concept of metallic transport breaks down. We show that by embedding a distributed network of ultra-small Ag nanoparticles (AgNPs) of radius ~ 1–2 nm inside a crystalline Au shell, the electron-phonon interaction can be enhanced, with an effective λ as high as ≈ 20. With increasing AgNP density, the electrical resistivity deviates from T-linearity and approaches a saturation to the Mott-Ioffe-Regel scale ρMIR ~ ha/e2 for both disorder (T → 0) and phonon (T ≫ ΘD)-dependent components of resistivity (here, a = 0.3 nm, is the lattice constant of Au).
Harnessing orbital Hall effect in spin-orbit torque MRAM
Authors: Gupta Rahul , Bouard Chloé , Kammerbauer Fabian , Ledesma-Martin J. Omar , Bose Arnab , Kononenko Iryna , Martin Sylvain , Usé Perrine , Jakob Gerhard , Drouard Marc , Kläui Mathias 
Published: January 2025

AbstractSpin-Orbit Torque (SOT) Magnetic Random-Access Memory (MRAM) devices offer improved power efficiency, nonvolatility, and performance compared to static RAM, making them ideal, for instance, for cache memory applications. Efficient magnetization switching, long data retention, and high-density integration in SOT MRAM require ferromagnets (FM) with perpendicular magnetic anisotropy (PMA) combined with large torques enhanced by Orbital Hall Effect (OHE). We have engineered a PMA [Co/Ni]3 FM on selected OHE layers (Ru, Nb, Cr) and investigated the potential of theoretically predicted larger orbital Hall conductivity (OHC) to quantify the torque and switching current in OHE/[Co/Ni]3 stacks. Our results demonstrate a ~30% enhancement in damping-like torque efficiency with a positive sign for the Ru OHE layer compared to a pure Pt layer, accompanied by a ~20% reduction in switching current for Ru compared to pure Pt across more than 250 devices, leading to more than a 60% reduction in switching power. These findings validate the application of Ru in devices relevant to industrial contexts, supporting theoretical predictions regarding its superior OHC. This investigation highlights the potential of enhanced orbital torques to improve the performance of orbital-assisted SOT-MRAM, paving the way for next-generation memory technology.
Fam102a translocates Runx2 and Rbpjl to facilitate Osterix expression and bone formation
Authors: Yamashita Yu , Hayashi Mikihito , Liu Anhao , Sasaki Fumiyuki , Tsuchiya Yosuke , Takayanagi Hiroshi , Saito Mitsuru , Nakashima Tomoki 
Published: January 2025

AbstractBone remodeling maintains the robustness of the bone tissue by balancing bone resorption by osteoclasts and bone formation by osteoblasts. Although these cells together play a crucial role in bone remodeling, only a few reports are available on the common factors involved in the differentiation of the two types of cells. Here, we show family with sequence similarity 102 member A (Fam102a) as a bone-remodeling factor that positively regulates both osteoclast and osteoblast differentiation. Fam102a regulates osteoblast differentiation by controlling recombination signal binding protein for immunoglobulin κ J region-like (Rbpjl). The Fam102a-Rbpjl axis promotes the nuclear translocation of transcription factors and enhances the expression of Osterix, a transcription factor essential for osteoblast differentiation. The deletion of Fam102a or a functional mutation in Rbpjl leads to osteopenia accompanied by reduced osteoblastic bone formation. Thus, the Fam102a-Rbpjl axis plays an important role in osteoblasts and this finding provides insights into bone remodeling.
Universal, untargeted detection of bacteria in tissues using metabolomics workflows
Authors: Chen Wei , Qiu Min , Paizs Petra , Sadowski Miriam , Ramonaite Toma , Zborovsky Lieby , Mejias-Luque Raquel , Janßen Klaus-Peter , Kinross James , Goldin Robert D. , Rebec Monica , Liebeke Manuel , Takats Zoltan , McKenzie James S. , Strittmatter Nicole 
Published: January 2025

AbstractFast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS). A spectral metabolic library of 233 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 359 so-called taxon-specific markers (TSMs). We apply these TSMs to the in situ detection of bacteria using healthy and cancerous gastrointestinal tissues as well as faecal samples. To demonstrate the MS method-agnostic nature, samples are analysed using spatial metabolomics and traditional bulk-based metabolomics approaches. In this work, TSMs are found in >90% of samples, suggesting the general applicability of this workflow to detect bacterial presence with standard MS-based analytical methods.
Generic residue numbering of the GAIN domain of adhesion GPCRs
Authors: Seufert Florian , Pérez-Hernández Guillermo , Pándy-Szekeres Gáspár , Guixà-González Ramon , Langenhan Tobias , Gloriam David E. , Hildebrand Peter W. 
Published: January 2025

AbstractThe GPCR autoproteolysis inducing (GAIN) domain is an ancient protein fold ubiquitous in adhesion G protein-coupled receptors (aGPCR). It contains a tethered agonist necessary and sufficient for receptor activation. The GAIN domain is a hotspot for pathological mutations. However, the low primary sequence conservation of GAIN domains has thus far hindered the knowledge transfer across different GAIN domains in human receptors as well as species orthologs. Here, we present a scheme for generic residue numbering of GAIN domains, based on structural alignments of over 14,000 modeled GAIN domain structures. This scheme is implemented in the GPCR database (GPCRdb) and elucidates the domain topology across different aGPCRs and their homologs in a large panel of species. We identify conservation hotspots and statistically cancer-enriched positions in human aGPCRs and show the transferability of positional and structural information between GAIN domain homologs. The GAIN-GRN scheme provides a robust strategy to allocate structural homologies at the primary and secondary levels also to GAIN domains of polycystic kidney disease 1/PKD1-like proteins, which now renders positions in both GAIN domain types comparable to one another. In summary, our work enables researchers to generate hypothesis and rationalize experiments related to GAIN domain function and pathology.
Multipocket synergy towards high thermoelectric performance in topological semimetal TaAs2
Authors: Hu Haihua , Feng Xiaolong , Pan Yu , Hasse Vicky , Wang Honghui , He Bin , Felser Claudia 
Published: January 2025

AbstractCharge-carrier compensation in topological semimetals amplifies the Nernst signal and simultaneously degrades the Seebeck coefficient. In this study, we report the simultaneous achievement of both a large Nernst signal and an unsaturating magneto-Seebeck coefficient in a topological nodal-line semimetal TaAs2 single crystal. The unique dual-high transverse and longitudinal thermopowers are attributed to multipocket synergy effects: the combination of a strong phonon-drag effect and the two overlapping highly dispersive conduction and valence bands with electron–hole compensation and high mobility, promising a large Nernst effect; the third Dirac band causes a large magneto-Seebeck effect. High transverse and longitudinal power factors of ~3100 and ~50 μW cm−1 K−2, respectively, are achieved, surpassing those of other topological semimetals and mainstream semiconductors. Our study presents a feasible approach for optimizing the longitudinal and transverse thermopowers in topological semimetals simultaneously and demonstrates the potential of TaAs2 for low temperature solid-state cooling.