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1.
Nature ; 629(8010): 136-145, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38570684

RESUMEN

Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.


Asunto(s)
Centrómero , Evolución Molecular , Variación Genética , Animales , Humanos , Centrómero/genética , Centrómero/metabolismo , Proteína A Centromérica/metabolismo , Metilación de ADN/genética , ADN Satélite/genética , Cinetocoros/metabolismo , Macaca/genética , Pan troglodytes/genética , Polimorfismo de Nucleótido Simple/genética , Pongo/genética , Masculino , Femenino , Estándares de Referencia , Inmunoprecipitación de Cromatina , Haplotipos , Mutación , Amplificación de Genes , Alineación de Secuencia , Cromatina/genética , Cromatina/metabolismo , Especificidad de la Especie
2.
Annu Rev Genet ; 55: 583-602, 2021 11 23.
Artículo en Inglés | MEDLINE | ID: mdl-34813350

RESUMEN

We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.


Asunto(s)
Centrómero , Genoma , Centrómero/genética , Inestabilidad Genómica/genética , Genómica , Humanos
3.
Nature ; 615(7954): 848-853, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36813960

RESUMEN

Global net land carbon uptake or net biome production (NBP) has increased during recent decades1. Whether its temporal variability and autocorrelation have changed during this period, however, remains elusive, even though an increase in both could indicate an increased potential for a destabilized carbon sink2,3. Here, we investigate the trends and controls of net terrestrial carbon uptake and its temporal variability and autocorrelation from 1981 to 2018 using two atmospheric-inversion models, the amplitude of the seasonal cycle of atmospheric CO2 concentration derived from nine monitoring stations distributed across the Pacific Ocean and dynamic global vegetation models. We find that annual NBP and its interdecadal variability increased globally whereas temporal autocorrelation decreased. We observe a separation of regions characterized by increasingly variable NBP, associated with warm regions and increasingly variable temperatures, lower and weaker positive trends in NBP and regions where NBP became stronger and less variable. Plant species richness presented a concave-down parabolic spatial relationship with NBP and its variability at the global scale whereas nitrogen deposition generally increased NBP. Increasing temperature and its increasing variability appear as the most important drivers of declining and increasingly variable NBP. Our results show increasing variability of NBP regionally that can be mostly attributed to climate change and that may point to destabilization of the coupled carbon-climate system.


Asunto(s)
Secuestro de Carbono , Carbono , Cambio Climático , Ecosistema , Mapeo Geográfico , Plantas , Carbono/análisis , Carbono/metabolismo , Dióxido de Carbono/análisis , Dióxido de Carbono/metabolismo , Secuestro de Carbono/fisiología , Estaciones del Año , Atmósfera/química , Océano Pacífico , Temperatura , Nitrógeno/metabolismo , Plantas/clasificación , Plantas/metabolismo , Medición de Riesgo
4.
Nature ; 621(7978): 344-354, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37612512

RESUMEN

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.


Asunto(s)
Cromosomas Humanos Y , Genómica , Análisis de Secuencia de ADN , Humanos , Secuencia de Bases , Cromosomas Humanos Y/genética , ADN Satélite/genética , Variación Genética/genética , Genética de Población , Genómica/métodos , Genómica/normas , Heterocromatina/genética , Familia de Multigenes/genética , Estándares de Referencia , Duplicaciones Segmentarias en el Genoma/genética , Análisis de Secuencia de ADN/normas , Secuencias Repetidas en Tándem/genética , Telómero/genética
5.
Nature ; 609(7926): 299-306, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36071193

RESUMEN

The potential of mitigation actions to limit global warming within 2 °C (ref. 1) might rely on the abundant supply of biomass for large-scale bioenergy with carbon capture and storage (BECCS) that is assumed to scale up markedly in the future2-5. However, the detrimental effects of climate change on crop yields may reduce the capacity of BECCS and threaten food security6-8, thus creating an unrecognized positive feedback loop on global warming. We quantified the strength of this feedback by implementing the responses of crop yields to increases in growing-season temperature, atmospheric CO2 concentration and intensity of nitrogen (N) fertilization in a compact Earth system model9. Exceeding a threshold of climate change would cause transformative changes in social-ecological systems by jeopardizing climate stability and threatening food security. If global mitigation alongside large-scale BECCS is delayed to 2060 when global warming exceeds about 2.5 °C, then the yields of agricultural residues for BECCS would be too low to meet the Paris goal of 2 °C by 2200. This risk of failure is amplified by the sustained demand for food, leading to an expansion of cropland or intensification of N fertilization to compensate for climate-induced yield losses. Our findings thereby reinforce the urgency of early mitigation, preferably by 2040, to avoid irreversible climate change and serious food crises unless other negative-emission technologies become available in the near future to compensate for the reduced capacity of BECCS.


Asunto(s)
Agricultura , Productos Agrícolas , Seguridad Alimentaria , Calentamiento Global , Agricultura/métodos , Agricultura/tendencias , Atmósfera/química , Dióxido de Carbono/análisis , Secuestro de Carbono , Productos Agrícolas/crecimiento & desarrollo , Ecosistema , Retroalimentación , Seguridad Alimentaria/métodos , Calentamiento Global/prevención & control , Calentamiento Global/estadística & datos numéricos , Objetivos , Humanos , Nitrógeno/análisis , Estaciones del Año , Temperatura , Factores de Tiempo
6.
Development ; 151(2)2024 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-38276966

RESUMEN

Cell shape is a powerful readout of cell state, fate and function. We describe a custom workflow to perform semi-automated, 3D cell and nucleus segmentation, and spherical harmonics and principal components analysis to distill cell and nuclear shape variation into discrete biologically meaningful parameters. We apply these methods to analyze shape in the neuromast cells of the zebrafish lateral line system, finding that shapes vary with cell location and identity. The distinction between hair cells and support cells accounted for much of the variation, which allowed us to train classifiers to predict cell identity from shape features. Using transgenic markers for support cell subpopulations, we found that subtypes had different shapes from each other. To investigate how loss of a neuromast cell type altered cell shape distributions, we examined atoh1a mutants that lack hair cells. We found that mutant neuromasts lacked the cell shape phenotype associated with hair cells, but did not exhibit a mutant-specific cell shape. Our results demonstrate the utility of using 3D cell shape features to characterize, compare and classify cells in a living developing organism.


Asunto(s)
Sistema de la Línea Lateral , Pez Cebra , Animales , Pez Cebra/genética , Forma de la Célula , Animales Modificados Genéticamente , Células Ciliadas Auditivas/fisiología
7.
Nature ; 592(7856): 784-788, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33883741

RESUMEN

It has recently been shown that in anaerobic microorganisms the tricarboxylic acid (TCA) cycle, including the seemingly irreversible citrate synthase reaction, can be reversed and used for autotrophic fixation of carbon1,2. This reversed oxidative TCA cycle requires ferredoxin-dependent 2-oxoglutarate synthase instead of the NAD-dependent dehydrogenase as well as extremely high levels of citrate synthase (more than 7% of the proteins in the cell). In this pathway, citrate synthase replaces ATP-citrate lyase of the reductive TCA cycle, which leads to the spending of one ATP-equivalent less per one turn of the cycle. Here we show, using the thermophilic sulfur-reducing deltaproteobacterium Hippea maritima, that this route is driven by high partial pressures of CO2. These high partial pressures are especially important for the removal of the product acetyl coenzyme A (acetyl-CoA) through reductive carboxylation to pyruvate, which is catalysed by pyruvate synthase. The reversed oxidative TCA cycle may have been functioning in autotrophic CO2 fixation in a primordial atmosphere that is assumed to have been rich in CO2.


Asunto(s)
Procesos Autotróficos , Dióxido de Carbono/química , Ciclo del Ácido Cítrico , Deltaproteobacteria/enzimología , ATP Citrato (pro-S)-Liasa/metabolismo , Acetilcoenzima A/metabolismo , Proteínas Bacterianas/metabolismo , Carbono/metabolismo , Deltaproteobacteria/crecimiento & desarrollo , Presión Parcial , Ácido Pirúvico/metabolismo
8.
Nature ; 598(7881): 468-472, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34552242

RESUMEN

The leaf economics spectrum1,2 and the global spectrum of plant forms and functions3 revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species2. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities4. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability4,5. Here we derive a set of ecosystem functions6 from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems7,8.


Asunto(s)
Ciclo del Carbono , Ecosistema , Plantas/metabolismo , Ciclo Hidrológico , Dióxido de Carbono/metabolismo , Clima , Conjuntos de Datos como Asunto , Humedad , Plantas/clasificación , Análisis de Componente Principal
9.
Nature ; 583(7815): 242-248, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32641817

RESUMEN

Enhanced silicate rock weathering (ERW), deployable with croplands, has potential use for atmospheric carbon dioxide (CO2) removal (CDR), which is now necessary to mitigate anthropogenic climate change1. ERW also has possible co-benefits for improved food and soil security, and reduced ocean acidification2-4. Here we use an integrated performance modelling approach to make an initial techno-economic assessment for 2050, quantifying how CDR potential and costs vary among nations in relation to business-as-usual energy policies and policies consistent with limiting future warming to 2 degrees Celsius5. China, India, the USA and Brazil have great potential to help achieve average global CDR goals of 0.5 to 2 gigatonnes of carbon dioxide (CO2) per year with extraction costs of approximately US$80-180 per tonne of CO2. These goals and costs are robust, regardless of future energy policies. Deployment within existing croplands offers opportunities to align agriculture and climate policy. However, success will depend upon overcoming political and social inertia to develop regulatory and incentive frameworks. We discuss the challenges and opportunities of ERW deployment, including the potential for excess industrial silicate materials (basalt mine overburden, concrete, and iron and steel slag) to obviate the need for new mining, as well as uncertainties in soil weathering rates and land-ocean transfer of weathered products.


Asunto(s)
Agricultura , Dióxido de Carbono/aislamiento & purificación , Productos Agrícolas , Sedimentos Geológicos/química , Calentamiento Global/prevención & control , Objetivos , Silicatos/química , Atmósfera/química , Brasil , China , Política Ambiental/economía , Política Ambiental/legislación & jurisprudencia , Calentamiento Global/economía , India , Hierro/aislamiento & purificación , Minería , Política , Probabilidad , Silicatos/aislamiento & purificación , Acero/aislamiento & purificación , Temperatura , Factores de Tiempo , Estados Unidos
10.
Genome Res ; 32(6): 1137-1151, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35545449

RESUMEN

Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats [HORs]). Although there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we show that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.


Asunto(s)
Algoritmos , Centrómero , Centrómero/genética , Humanos
11.
Nano Lett ; 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38855978

RESUMEN

Integration of 2D semiconductors with photonic crystal slabs provides an attractive approach to achieving strong light-matter coupling and exciton-polariton formation in a chip-compatible geometry. However, for the development of practical devices, it is crucial that polariton excitations are easily tunable and exhibit a strong nonlinear response. Here we study neutral and charged exciton-polaritons in an electrostatically gated photonic crystal slab with an embedded monolayer semiconductor MoSe2 and experimentally demonstrate a novel approach to optical control based on polariton nonlinearity. We show that spatial modulation of the dielectric environment within the photonic crystal unit cell results in the formation of two distinct excitonic species with significantly different nonlinear responses of the corresponding charged exciton-polaritons under optical pumping. This behavior enables optical switching with ultrashort laser pulses and can be sensitively controlled via an electrostatic gate voltage. Our results open new avenues toward the development of active polaritonic devices in a compact chip-compatible implementation.

12.
J Am Chem Soc ; 2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38597585

RESUMEN

Noble metal oxides such as ruthenium dioxide are highly active electrocatalysts for anodic reactions in acidic electrolytes, but dissolution during electrochemical operation impedes wide-scale applications in renewable energy technologies. Improving the fundamental understanding of the dissolution dynamics of application-relevant morphologies such as nanocrystals is critical for the grid-scale implementation of these materials. Herein, we report the nanoscale heterogeneity observed via liquid-phase transmission electron microscopy during ruthenium dioxide nanocrystal dissolution under oxidizing conditions. Single-crystalline ruthenium dioxide nanocrystals enabled the direct observation of dissolution along different crystallographic facets, allowing an unprecedented direct comparison of crystal facet stability. The nanoscale observations revealed substantial heterogeneity in the relative stability of crystallographic facets across different nanocrystals, attributed to the nanoscale strains present in these crystals. These findings highlight the importance of nanoscale heterogeneity in determining macroscale properties such as electrocatalyst stability and provide a characterization methodology that can be integrated into next-generation electrocatalyst discovery efforts.

13.
J Am Chem Soc ; 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39051969

RESUMEN

The synthesis and solution and solid-state characterization of [Pu4+(NPC)4], 1-Pu, (NPC = [NPtBu(pyrr)2]-; tBu = C(CH3)3; pyrr = pyrrolidinyl) and [Pu3+(NPC)4][K(2.2.2.-cryptand)], 2-Pu, is described. Cyclic voltammetry studies of 1-Pu reveal a quasi-reversible Pu4+/3+ couple, an irreversible Pu5+/4+ couple, and a third couple evincing a rapid proton-coupled electron transfer (PCET) reaction occurring after the electrochemical formation of Pu5+. The chemical identity of the product of the PCET reaction was confirmed by independent chemical synthesis to be [Pu4+(NPC)3(HNPC)][B(ArF5)4], 3-Pu, (B(ArF5)4 = tetrakis(2,3,4,5,6-pentafluourophenyl)borate) via two mechanistically distinct transformations of 1-Pu: protonation and oxidation. The kinetics and thermodynamics of this PCET reaction are determined via electrochemical analysis, simulation, and density functional theory. The computational studies demonstrate a direct correlation between the changing nature of 5f and 6d orbital participation in metal-ligand bonding and the electron density on the Nim atom with the thermodynamics of the PCET reaction from Np to Pu, and an indirect correlation with the roughly 5-orders of magnitude faster Pu PCET compared to Np for the An5+ species.

14.
BMC Plant Biol ; 24(1): 278, 2024 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-38609866

RESUMEN

BACKGROUND: The availability of soil phosphorus (P) often limits the productivities of wet tropical lowland forests. Little is known, however, about the metabolomic profile of different chemical P compounds with potentially different uses and about the cycling of P and their variability across space under different tree species in highly diverse tropical rainforests. RESULTS: We hypothesised that the different strategies of the competing tree species to retranslocate, mineralise, mobilise, and take up P from the soil would promote distinct soil 31P profiles. We tested this hypothesis by performing a metabolomic analysis of the soils in two rainforests in French Guiana using 31P nuclear magnetic resonance (NMR). We analysed 31P NMR chemical shifts in soil solutions of model P compounds, including inorganic phosphates, orthophosphate mono- and diesters, phosphonates, and organic polyphosphates. The identity of the tree species (growing above the soil samples) explained > 53% of the total variance of the 31P NMR metabolomic profiles of the soils, suggesting species-specific ecological niches and/or species-specific interactions with the soil microbiome and soil trophic web structure and functionality determining the use and production of P compounds. Differences at regional and topographic levels also explained some part of the the total variance of the 31P NMR profiles, although less than the influence of the tree species. Multivariate analyses of soil 31P NMR metabolomics data indicated higher soil concentrations of P biomolecules involved in the active use of P (nucleic acids and molecules involved with energy and anabolism) in soils with lower concentrations of total soil P and higher concentrations of P-storing biomolecules in soils with higher concentrations of total P. CONCLUSIONS: The results strongly suggest "niches" of soil P profiles associated with physical gradients, mostly topographic position, and with the specific distribution of species along this gradient, which is associated with species-specific strategies of soil P mineralisation, mobilisation, use, and uptake.


Asunto(s)
Microbiota , Fósforo , Bosque Lluvioso , Árboles , Guyana Francesa , Fosfatos , Suelo
15.
Mod Pathol ; 37(9): 100543, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38897453

RESUMEN

Gastrointestinal (GI) tract involvement by Langerhans cell histiocytosis (LCH) is rare and its clinicopathologic characteristics have only been described in case reports and small series. We reviewed hematoxylin and eosin and CD1a, S100, and Langerin immunohistochemical-stained slides from 47 patients with well-documented demographic and clinical findings. Our cases included 8 children and 39 adults, with a mean follow-up of 63 months. All pediatric patients had concurrent multisystem LCH, presented with GI symptoms, and showed nonpolypoid lesions. Seven (88%) showed multifocal GI disease, including 5 with multiple GI organ involvement. All sampled lesions from children exhibited infiltrative growth. More than half had died of the disease or manifested persistent LCH at last follow-up. Twenty-five of 39 (64%) adults had LCH involving only the GI tract (single system), with the remaining 14 (36%) exhibiting multisystem disease. Adult single-system GI LCH was typically encountered incidentally on screening/surveillance endoscopy (72%). Most exhibited isolated colorectal involvement (88%) as a solitary polyp (92%), with a well-demarcated/noninfiltrative growth pattern (70%), and excellent prognosis (100%). In comparison, adult patients with multisystem LCH more frequently presented with GI symptoms (92%, P < .001), noncolorectal GI site involvement (50%, P = .02), multifocal GI lesions (43%, P = .005), nonpolypoid lesions (71%, P < .001), infiltrative histologic growth pattern (78%, P = .04), and persistent disease (57%, P < .001). Adult patients with multisystem LCH appear to exhibit similar clinicopathologic features to those of pediatric patients. These results demonstrated that adults with single-system LCH involving the GI tract have an excellent prognosis, whereas multisystem LCH occurring at any age carries an unfavorable prognosis. High-risk features of GI LCH include pediatric age, GI symptomatology, noncolorectal GI involvement, multifocal GI disease, nonpolypoid lesions, and infiltrative growth pattern.

16.
Magn Reson Med ; 91(5): 1803-1821, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38115695

RESUMEN

PURPOSE: K trans $$ {K}^{\mathrm{trans}} $$ has often been proposed as a quantitative imaging biomarker for diagnosis, prognosis, and treatment response assessment for various tumors. None of the many software tools for K trans $$ {K}^{\mathrm{trans}} $$ quantification are standardized. The ISMRM Open Science Initiative for Perfusion Imaging-Dynamic Contrast-Enhanced (OSIPI-DCE) challenge was designed to benchmark methods to better help the efforts to standardize K trans $$ {K}^{\mathrm{trans}} $$ measurement. METHODS: A framework was created to evaluate K trans $$ {K}^{\mathrm{trans}} $$ values produced by DCE-MRI analysis pipelines to enable benchmarking. The perfusion MRI community was invited to apply their pipelines for K trans $$ {K}^{\mathrm{trans}} $$ quantification in glioblastoma from clinical and synthetic patients. Submissions were required to include the entrants' K trans $$ {K}^{\mathrm{trans}} $$ values, the applied software, and a standard operating procedure. These were evaluated using the proposed OSIP I gold $$ \mathrm{OSIP}{\mathrm{I}}_{\mathrm{gold}} $$ score defined with accuracy, repeatability, and reproducibility components. RESULTS: Across the 10 received submissions, the OSIP I gold $$ \mathrm{OSIP}{\mathrm{I}}_{\mathrm{gold}} $$ score ranged from 28% to 78% with a 59% median. The accuracy, repeatability, and reproducibility scores ranged from 0.54 to 0.92, 0.64 to 0.86, and 0.65 to 1.00, respectively (0-1 = lowest-highest). Manual arterial input function selection markedly affected the reproducibility and showed greater variability in K trans $$ {K}^{\mathrm{trans}} $$ analysis than automated methods. Furthermore, provision of a detailed standard operating procedure was critical for higher reproducibility. CONCLUSIONS: This study reports results from the OSIPI-DCE challenge and highlights the high inter-software variability within K trans $$ {K}^{\mathrm{trans}} $$ estimation, providing a framework for ongoing benchmarking against the scores presented. Through this challenge, the participating teams were ranked based on the performance of their software tools in the particular setting of this challenge. In a real-world clinical setting, many of these tools may perform differently with different benchmarking methodology.


Asunto(s)
Medios de Contraste , Imagen por Resonancia Magnética , Humanos , Reproducibilidad de los Resultados , Imagen por Resonancia Magnética/métodos , Programas Informáticos , Algoritmos
17.
Opt Express ; 32(10): 18257-18267, 2024 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-38858987

RESUMEN

We present a source of indistinguishable photons at telecom wavelength, synchronized to an external clock, for the use in distributed quantum networks. We characterize the indistinguishability of photons generated in independent parametric down-conversion events using a Hong-Ou-Mandel interferometer, and show non-classical interference with coalescence, C = 0.83(5). We also demonstrate the synchronization to an external clock within sub-picosecond timing jitter, which is significantly shorter than the single-photon wavepacket duration of ≈ 35 ps. Our source enables scalable quantum protocols over multi-node, long-distance optical networks using network-based clock recovery systems.

18.
Opt Express ; 32(9): 15680-15690, 2024 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-38859213

RESUMEN

High-quality-factor optical microresonators have become an appealing object for numerous applications. However, the mid-infrared band experiences a lack of applicable materials for nonlinear photonics. Crystalline germanium demonstrates attractive material properties such as high nonlinear refractive index, large transparency window including the mid-IR band, particularly long wave multiphonon absorption limit. Nevertheless, the reported optical losses in germanium microresonators might not allow the potential of the Ge-based devices to be revealed. In this study, we report the fabrication of germanium microresonators with radii of 1.35 and 1.5 mm, exhibiting exceptional quality factors (Q-factors) exceeding 20 million, approaching the absorption-limited values at a wavelength of 2.68 µm. These Q-factors are a hundred times higher than previously reported, to the best of our knowledge. We measured the two-photon absorption coefficient combined with free-carrier absorption leveraging the high-Q of the resonators (obtained ßTPA = (0.71 ± 0.12) · 10-8 m/W at 2.68 µm). This research underscores the potential of whispering gallery mode microresonators as valuable tools for measuring absorption coefficients at different wavelengths, providing a comprehensive analysis of various loss mechanisms. Furthermore, the exceptional Q-factors observed in germanium microresonators open intriguing opportunities for the advancement of germanium-based photonics within the mid-infrared spectral band.

19.
Glob Chang Biol ; 30(1): e17111, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38273581

RESUMEN

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.


Asunto(s)
Rizosfera , Suelo , Suelo/química , Microbiología del Suelo , Carbono/metabolismo , Nitrógeno/metabolismo
20.
Opt Lett ; 49(2): 282-285, 2024 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-38194548

RESUMEN

This Letter presents the first demonstration, to our knowledge, of a Brillouin optical time domain analysis (BOTDA) system based on a self-sweeping fiber laser. The unique feature of such laser sources is the generation of a narrowband tunable radiation with a small (6 MHz) tuning step and a reasonably large tuning range (3 GHz) making self-sweeping lasers extremely attractive for use in BOTDA systems. Since the wavelength tuning occurs solely due to internal processes occurring in the laser cavity, there is no need to use complex current/temperature control and feedback systems. This makes it possible to completely eliminate microwave devices, such as electro-optic modulators, from the BOTDA design. In this work, distributed temperature measurements with sensing line length of 25 km, spatial resolution of 10 m, and sensitivity of 2°C is demonstrated in a BOTDA system based on an Er-doped self-sweeping laser. The described approaches can reduce the complexity and overall cost of the BOTDA systems.

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