bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaeal Hydroxylated Isoprenoid GDGTs in Asian Lake Sediments: A New Tool for Terrestrial Paleotemperature Reconstructions
Authors: Wu Jie , Yang Huan , Shen Caiming , Zhu Liping , Yang Yi , Xie Shucheng 
Published: March 2024

AbstractHydroxylated isoprenoid GDGTs (OH‐GDGTs) have emerged as a novel tool for reconstructing sea surface temperatures. However, when using marine OH‐GDGT calibration in lacustrine settings, it leads to a significant overestimation of temperatures, emphasizing the necessity for a thorough examination of OH‐GDGTs in lakes. Here, we investigated OH‐GDGT distributions in surface sediments from 65 lakes in West China and compiled published Asian lake and global marine OH‐GDGT data sets. Among all GDGT‐based indices, RI‐OH showed the strongest correlation with temperature across Asian lakes. The RI‐OH value was higher in lakes than in marine sediments, likely due to differences in the composition of Group 1.1a thaumarchaeotal species between the two settings. The first RI‐OH temperature calibration for lakes was developed and it addressed the issue of temperature overestimation when applied to both water column and sediment core, highlighting the potential of OH‐GDGTs as a new terrestrial paleothermometer.
Kinematics of the Reykjanes Ridge: Influence of the Iceland Hotspot on Plate Boundary Evolution
Authors: Thorhallsson Daniel , Martinez Fernando , Hey Richard , Höskuldsson Ármann 
Published: March 2024

AbstractThe slow spreading Reykjanes Ridge overlies the Iceland hotspot and has undergone well ordered changes in crustal segmentation. Previous studies have attributed these changes to varying mantle plume thermal effects, rendering the lithosphere ductile or brittle. Here we use seafloor spreading magnetic anomalies to show that crustal accretion has been focused throughout its spreading history and to determine the detailed evolution of Reykjanes Ridge segments. By ∼53 Ma, organized spreading had developed on an orthogonally spreading linear axis following continental breakup. After a plate motion change at ∼38 Ma, orthogonally spreading offset ridge segments formed by ridge propagation forming varying length fracture zones. From then to the present, the offset segments diachronously migrated back to the original linear geometry from north to south replacing orthogonal with oblique spreading as the axis became linear again. Fracture zones were not terminated, however, simply by reducing segment offsets even to zero. Their termination involved the axial propagation of buoyant upwelling instabilities across the discontinuities, correspondingly extending V‐shaped crustal ridges southward. This evolution was guided by a persistent linear deep damp mantle melting interval maintained by the episodic propagation of buoyant upwelling instabilities. Our study indicates that at slow spreading ridges, where buoyant upwelling instabilities govern crustal segmentation, spatial gradients in mantle melting properties may direct the behavior of the instabilities. Where ridges overlie regional hotspot gradients in mantle melting, buoyant instabilities may propagate systematically, and plate boundary evolution may follow an organized pattern.
Mixing of the Connecticut River Plume During Ambient Flood Tides: Spatial Heterogeneity and Contributions of Bottom‐Generated and Interfacial Mixing
Authors: Whitney Michael M. , Spicer Preston , MacDonald Daniel G. , Huguenard Kimberly D. , Cole Kelly L. , Jia Yan , Delatolas Nikiforos 
Published: March 2024

AbstractThe Connecticut River plume is influenced by energetic ambient tides in the Long Island Sound receiving waters. The objectives of this modeling study are (a) characterizing the spatial heterogeneity of turbulent buoyancy fluxes, (b) partitioning turbulent buoyancy fluxes into bottom‐generated and interfacial shear contributions, and (c) quantifying contributions to plume‐integrated mixing within the tidal plume. The plume formed during ambient flood tides under low river discharge, spring tides, and no winds is analyzed. Turbulent buoyancy fluxes (B) and depth‐integrated B through the plume (Bd) are characterized by pronounced spatial heterogeneity. Strong mixing (Bd ∼ 10−5‐10−4 m3/s3) occurs near the mouth, in the nearfield plume turning region, over shoals, and nearshore shallow areas. Low to moderate mixing (Bd ∼ 10−8‐10−6 m3/s3) occupies half the plume. Buoyancy fluxes are first partitioned based on the depth of the shear stress minimum between plume‐generated and bottom‐generated shear maxima. Four other tested partitioning methods are based on open channel flow and stratified shear flow parameterizations. Interfacial and bottom‐generated shear contribute to different areas of intense and moderate mixing. All methods indicate a significant plume mixing role for bottom‐generated mixing, but interfacial mixing is a bigger contributor. Plume‐integrated total and interfacial mixing peak at max ambient flood and the timing of peak bottom‐generated mixing varies among partitioning methods. Two‐thirds of the mixing occurs in concentrated intense mixing areas. A parameter space with the ambient tidal Froude number and plume thickness to depth ratio as axes indicates many tidally modulated plumes are moderately to dominantly influenced by bottom‐generated tidal mixing.
Regional Inversion Shows Promise in Capturing Extreme‐Event‐Driven CO2 Flux Anomalies but Is Limited by Atmospheric CO2 Observational Coverage
Authors: Byrne B. , Liu J. , Bowman K. W. , Yin Y. , Yun J. , Ferreira G. D. , Ogle S. M. , Baskaran L. , He L. , Li X. , Xiao J. , Davis K. J. 
Published: March 2024

AbstractExtreme climate events are becoming more frequent, with poorly understood implications for carbon sequestration by terrestrial ecosystems. A better understanding will critically depend on accurate and precise quantification of ecosystems responses to these events. Taking the 2019 US Midwest floods as a case study, we investigate current capabilities for tracking regional flux anomalies with “top‐down” inversion analyses that assimilate atmospheric CO2 observations. For this analysis, we develop a regionally nested version of the NASA Carbon Monitoring System‐Flux system for North America (CMS‐Flux‐NA) that allows high resolution atmospheric transport (0.5° × 0.625°). Relative to a 2018 baseline, we find the 2019 US Midwest growing season net carbon uptake is reduced by 11–57 TgC (3%–16%, range across assimilated CO2 data sets). These estimates are found to be consistent with independent “bottom‐up” estimates of carbon uptake based on vegetation remote sensing (15–78 TgC). We then investigate current limitations in tracking regional carbon budgets using “top‐down” methods. In a set of observing system simulation experiments, we show that the ability of atmospheric CO2 inversions to capture regional carbon flux anomalies is still limited by observational coverage gaps for both in situ and satellite observations. Future space‐based missions that allow for daily observational coverage across North America would largely mitigate these observational gaps, allowing for improved top‐down estimates of ecosystem responses to extreme climate events.
Phase-driven progress in nanophotonic biosensing
Authors: Barth Isabel , Lee Hakho 
Published: March 2024

AbstractIn the continuous pursuit of enhancing the sensitivity of nanophotonic biosensors by leveraging phase phenomena, a recent development involved the engineering of an atomically thin Ge2Sb2Te5 layer on a silver nanofilm to generate large Goos–Hänchen-shifts associated with phase singularities. The resulting detection limit reached ~7 × 10−7 RIU.
Multimodal digital assessment of depression with actigraphy and app in Hong Kong Chinese
Authors: Chen Jie , Chan Ngan Yin , Li Chun-Tung , Chan Joey W. Y. , Liu Yaping , Li Shirley Xin , Chau Steven W. H. , Leung Kwong Sak , Heng Pheng-Ann , Lee Tatia M. C. , Li Tim M. H. , Wing Yun-Kwok 
Published: March 2024

AbstractThere is an emerging potential for digital assessment of depression. In this study, Chinese patients with major depressive disorder (MDD) and controls underwent a week of multimodal measurement including actigraphy and app-based measures (D-MOMO) to record rest-activity, facial expression, voice, and mood states. Seven machine-learning models (Random Forest [RF], Logistic regression [LR], Support vector machine [SVM], K-Nearest Neighbors [KNN], Decision tree [DT], Naive Bayes [NB], and Artificial Neural Networks [ANN]) with leave-one-out cross-validation were applied to detect lifetime diagnosis of MDD and non-remission status. Eighty MDD subjects and 76 age- and sex-matched controls completed the actigraphy, while 61 MDD subjects and 47 controls completed the app-based assessment. MDD subjects had lower mobile time (P = 0.006), later sleep midpoint (P = 0.047) and Acrophase (P = 0.024) than controls. For app measurement, MDD subjects had more frequent brow lowering (P = 0.023), less lip corner pulling (P = 0.007), higher pause variability (P = 0.046), more frequent self-reference (P = 0.024) and negative emotion words (P = 0.002), lower articulation rate (P < 0.001) and happiness level (P < 0.001) than controls. With the fusion of all digital modalities, the predictive performance (F1-score) of ANN for a lifetime diagnosis of MDD was 0.81 and 0.70 for non-remission status when combined with the HADS-D item score, respectively. Multimodal digital measurement is a feasible diagnostic tool for depression in Chinese. A combination of multimodal measurement and machine-learning approach has enhanced the performance of digital markers in phenotyping and diagnosis of MDD.
Progression free survival of myeloma patients who become IFE-negative correlates with the detection of residual monoclonal free light chain (FLC) by mass spectrometry
Authors: Giles H. V. , Drayson M. T. , Kishore B. , Pawlyn C. , Kaiser M. , Cook G. , de Tute R. , Owen R. G. , Cairns D. , Menzies T. , Davies F. E. , Morgan G. J. , Pratt G. , Jackson G. H. 
Published: March 2024

AbstractDeeper responses are associated with improved survival in patients being treated for myeloma. However, the sensitivity of the current blood-based assays is limited. Historical studies suggested that normalisation of the serum free light chain (FLC) ratio in patients who were negative by immunofixation electrophoresis (IFE) was associated with improved outcomes. However, recently this has been called into question. Mass spectrometry (MS)-based FLC assessments may offer a superior methodology for the detection of monoclonal FLC due to greater sensitivity. To test this hypothesis, all available samples from patients who were IFE negative after treatment with carfilzomib and lenalidomide-based induction and autologous stem cell transplantation (ASCT) in the Myeloma XI trial underwent FLC-MS testing. FLC-MS response assessments from post-induction, day+100 post-ASCT and six months post-maintenance randomisation were compared to serum FLC assay results. Almost 40% of patients had discordant results and 28.7% of patients with a normal FLC ratio had residual monoclonal FLC detectable by FLC-MS. FLC-MS positivity was associated with reduced progression-free survival (PFS) but an abnormal FLC ratio was not. This study demonstrates that FLC-MS provides a superior methodology for the detection of residual monoclonal FLC with FLC-MS positivity identifying IFE-negative patients who are at higher risk of early progression.
Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes
Authors: Sanchez Ambrocio , Ortega Pedro , Sakhtemani Ramin , Manjunath Lavanya , Oh Sunwoo , Bournique Elodie , Becker Alexandrea , Kim Kyumin , Durfee Cameron , Temiz Nuri Alpay , Chen Xiaojiang S. , Harris Reuben S. , Lawrence Michael S. , Buisson Rémi 
Published: March 2024

AbstractAntiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver
Authors: Plata-Gómez Ana Belén , de Prado-Rivas Lucía , Sanz Alba , Deleyto-Seldas Nerea , García Fernando , de la Calle Arregui Celia , Silva Camila , Caleiras Eduardo , Graña-Castro Osvaldo , Piñeiro-Yáñez Elena , Krebs Joseph , Leiva-Vega Luis , Muñoz Javier , Jain Ajay , Sabio Guadalupe , Efeyan Alejo 
Published: March 2024

AbstractThe metabolic functions of the liver are spatially organized in a phenomenon called zonation, linked to the differential exposure of portal and central hepatocytes to nutrient-rich blood. The mTORC1 signaling pathway controls cellular metabolism in response to nutrients and insulin fluctuations. Here we show that simultaneous genetic activation of nutrient and hormone signaling to mTORC1 in hepatocytes results in impaired establishment of postnatal metabolic and zonal identity of hepatocytes. Mutant hepatocytes fail to upregulate postnatally the expression of Frizzled receptors 1 and 8, and show reduced Wnt/β-catenin activation. This defect, alongside diminished paracrine Wnt2 ligand expression by endothelial cells, underlies impaired postnatal maturation. Impaired zonation is recapitulated in a model of constant supply of nutrients by parenteral nutrition to piglets. Our work shows the role of hepatocyte sensing of fluctuations in nutrients and hormones for triggering a latent metabolic zonation program.
Button shear testing for adhesion measurements of 2D materials
Authors: Schätz Josef , Nayi Navin , Weber Jonas , Metzke Christoph , Lukas Sebastian , Walter Jürgen , Schaffus Tim , Streb Fabian , Reato Eros , Piacentini Agata , Grundmann Annika , Kalisch Holger , Heuken Michael , Vescan Andrei , Pindl Stephan , Lemme Max C. 
Published: March 2024

AbstractTwo-dimensional (2D) materials are considered for numerous applications in microelectronics, although several challenges remain when integrating them into functional devices. Weak adhesion is one of them, caused by their chemical inertness. Quantifying the adhesion of 2D materials on three-dimensional surfaces is, therefore, an essential step toward reliable 2D device integration. To this end, button shear testing is proposed and demonstrated as a method for evaluating the adhesion of 2D materials with the examples of graphene, hexagonal boron nitride (hBN), molybdenum disulfide, and tungsten diselenide on silicon dioxide and silicon nitride substrates. We propose a fabrication process flow for polymer buttons on the 2D materials and establish suitable button dimensions and testing shear speeds. We show with our quantitative data that low substrate roughness and oxygen plasma treatments on the substrates before 2D material transfer result in higher shear strengths. Thermal annealing increases the adhesion of hBN on silicon dioxide and correlates with the thermal interface resistance between these materials. This establishes button shear testing as a reliable and repeatable method for quantifying the adhesion of 2D materials.
Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations
Authors: Butt Yasha , Sakhtemani Ramin , Mohamad-Ramshan Rukshana , Lawrence Michael S. , Bhagwat Ashok S. 
Published: March 2024

AbstractThe APOBEC3 enzymes convert cytosines in single-stranded DNA to uracils to protect against viruses and retrotransposons but can contribute to mutations that diversify tumors. To understand the mechanism of mutagenesis, we map the uracils resulting from expression of APOBEC3B or its catalytic carboxy-terminal domain (CTD) in Escherichia coli. Like APOBEC3A, the uracilomes of A3B and A3B-CTD show a preference to deaminate cytosines near transcription start sites and the lagging-strand replication templates and in hairpin loops. Both biochemical activities of the enzymes and genomic uracil distribution show that A3A prefers 3 nt loops the best, while A3B prefers 4 nt loops. Reanalysis of hairpin loop mutations in human tumors finds intrinsic characteristics of both the enzymes, with a much stronger contribution from A3A. We apply Hairpin Signatures 1 and 2, which define A3A and A3B preferences respectively and are orthogonal to published methods, to evaluate their contribution to human tumor mutations.
The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis
Authors: Ohara Kentaro , Rendeiro André Figueiredo , Bhinder Bhavneet , Eng Kenneth Wha , Ravichandran Hiranmayi , Nguyen Duy , Pisapia David , Vosoughi Aram , Fernandez Evan , Shohdy Kyrillus S. , Manohar Jyothi , Beg Shaham , Wilkes David , Robinson Brian D. , Khani Francesca , Bareja Rohan , Tagawa Scott T. , Ouseph Madhu M. , Sboner Andrea , Elemento Olivier , Faltas Bishoy M. , Mosquera Juan Miguel 
Published: March 2024

AbstractThe molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient.
Evolutionary origin of Hoxc13-dependent skin appendages in amphibians
Authors: Carron Marjolein , Sachslehner Attila Placido , Cicekdal Munevver Burcu , Bruggeman Inge , Demuynck Suzan , Golabi Bahar , De Baere Elfride , Declercq Wim , Tschachler Erwin , Vleminckx Kris , Eckhart Leopold 
Published: March 2024

AbstractCornified skin appendages, such as hair and nails, are major evolutionary innovations of terrestrial vertebrates. Human hair and nails consist largely of special intermediate filament proteins, known as hair keratins, which are expressed under the control of the transcription factor Hoxc13. Here, we show that the cornified claws of Xenopus frogs contain homologs of hair keratins and the genes encoding these keratins are flanked by promoters in which binding sites of Hoxc13 are conserved. Furthermore, these keratins and Hoxc13 are co-expressed in the claw-forming epithelium of frog toe tips. Upon deletion of hoxc13, the expression of hair keratin homologs is abolished and the development of cornified claws is abrogated in X. tropicalis. These results indicate that Hoxc13-dependent expression of hair keratin homologs evolved already in stem tetrapods, presumably as a mechanism for protecting toe tips, and that this ancestral genetic program was coopted to the growth of hair in mammals.
Optimizing quantum gates towards the scale of logical qubits
Authors: Klimov Paul V. , Bengtsson Andreas , Quintana Chris , Bourassa Alexandre , Hong Sabrina , Dunsworth Andrew , Satzinger Kevin J. , Livingston William P. , Sivak Volodymyr , Niu Murphy Yuezhen , Andersen Trond I. , Zhang Yaxing , Chik Desmond , Chen Zijun , Neill Charles , Erickson Catherine , Grajales Dau Alejandro , Megrant Anthony , Roushan Pedram , Korotkov Alexander N. , Kelly Julian , Smelyanskiy Vadim , Chen Yu , Neven Hartmut 
Published: March 2024

AbstractA foundational assumption of quantum error correction theory is that quantum gates can be scaled to large processors without exceeding the error-threshold for fault tolerance. Two major challenges that could become fundamental roadblocks are manufacturing high-performance quantum hardware and engineering a control system that can reach its performance limits. The control challenge of scaling quantum gates from small to large processors without degrading performance often maps to non-convex, high-constraint, and time-dynamic control optimization over an exponentially expanding configuration space. Here we report on a control optimization strategy that can scalably overcome the complexity of such problems. We demonstrate it by choreographing the frequency trajectories of 68 frequency-tunable superconducting qubits to execute single- and two-qubit gates while mitigating computational errors. When combined with a comprehensive model of physical errors across our processor, the strategy suppresses physical error rates by ~3.7× compared with the case of no optimization. Furthermore, it is projected to achieve a similar performance advantage on a distance-23 surface code logical qubit with 1057 physical qubits. Our control optimization strategy solves a generic scaling challenge in a way that can be adapted to a variety of quantum operations, algorithms, and computing architectures.
Fast Human Motion reconstruction from sparse inertial measurement units considering the human shape
Authors: Xiao Xuan , Wang Jianjian , Feng Pingfa , Gong Ao , Zhang Xiangyu , Zhang Jianfu 
Published: March 2024

AbstractInertial Measurement Unit-based methods have great potential in capturing motion in large-scale and complex environments with many people. Sparse Inertial Measurement Unit-based methods have more research value due to their simplicity and flexibility. However, improving the computational efficiency and reducing latency in such methods are challenging. In this paper, we propose Fast Inertial Poser, which is a full body motion estimation deep neural network based on 6 inertial measurement units considering body parameters. We design a network architecture based on recurrent neural networks according to the kinematics tree. This method introduces human body shape information by the causality of observations and eliminates the dependence on future frames. During the estimation of joint positions, the upper body and lower body are estimated using separate network modules independently. Then the joint rotation is obtained through a well-designed single-frame kinematics inverse solver. Experiments show that the method can greatly improve the inference speed and reduce the latency while ensuring the reconstruction accuracy compared with previous methods. Fast Inertial Poser runs at 65 fps with 15 ms latency on an embedded computer, demonstrating the efficiency of the model.