Generation of entanglement using a short-wavelength seeded free-electron laser.

Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser. The observed generation of entanglement is interpreted using the time-dependent von Neumann entropy. Our results unveil the potential for using short-wavelength coherent light pulses from free-electron lasers to generate entangled photoelectron and ion systems for studying spooky action at a distance.

Draft genome assemblies for two species of Escallonia (Escalloniales).

OBJECTIVES: Escallonia (Escalloniaceae) belongs to the Escalloniales, a diverse clade of flowering plants with unclear placement in the tree of life. Escallonia species show impressive morphological and ecological diversity and are widely distributed across three hotspots of biodiversity in the Neotropics. To shed light on the genomic substrate of this radiation and the phylogenetic placement of Escalloniales as well as to generate useful data for comparative evolutionary genomics across flowering plants, we produced and annotated draft genomes for two species of Escallonia. DATA DESCRIPTION: Genomic DNA from E. rubra and E. herrerae was sequenced with Oxford Nanopore sequencing chemistry, generating 3.4 and 12 million sequence reads with an average read length of 9.4 and 9.1 Kb (approximately 31 and 111 Gb of sequence data), respectively. In addition, we generated Illumina 100-bp paired-end short read data for E. rubra (approximately 75 Gb of sequence data). The Escallonia rubra genome was 566 Mb, with 3,233 contigs and an N50 of 285 Kb. The assembled genome for E. herrerae was 994 Mp, with 5,760 contigs and an N50 of 317 Kb. The genome sequences were annotated with 31,038 (E. rubra) and 47,905 (E. herrerea) protein-coding gene models supported by transcriptome/protein evidence and/or Pfam domain content. BUSCO assessments indicated completeness levels of approximately 98% for the genome assemblies and 88% for the genome annotations.

Cholec80-CVS: An open dataset with an evaluation of Strasberg's critical view of safety for AI.

Strasberg's criteria to detect a critical view of safety is a widely known strategy to reduce bile duct injuries during laparoscopic cholecystectomy. In spite of its popularity and efficiency, recent studies have shown that human miss-identification errors have led to important bile duct injuries occurrence rates. Developing tools based on artificial intelligence that facilitate the identification of a critical view of safety in cholecystectomy surgeries can potentially minimize the risk of such injuries. With this goal in mind, we present Cholec80-CVS, the first open dataset with video annotations of Strasberg's Critical View of Safety (CVS) criteria. Our dataset contains CVS criteria annotations provided by skilled surgeons for all videos in the well-known Cholec80 open video dataset. We consider that Cholec80-CVS is the first step towards the creation of intelligent systems that can assist humans during laparoscopic cholecystectomy.

Photoionization and core resonances from range-separated time-dependent density-functional theory for open-shell states: Example of the lithium atom.

We consider the calculations of photoionization spectra and core resonances of open-shell systems using range-separated time-dependent density-functional theory. Specifically, we use the time-dependent range-separated hybrid (TDRSH) scheme, combining a long-range Hartree-Fock exchange potential and kernel with a short-range potential and kernel from a local density-functional approximation, and the time-dependent locally range-separated hybrid (TDLRSH) scheme, which uses a local range-separation parameter. To efficiently perform the calculations, we formulate a spin-unrestricted linear-response Sternheimer approach in a non-orthogonal B-spline basis set using appropriate frequency-dependent boundary conditions. We illustrate this approach on the Li atom, which suggests that TDRSH and TDLRSH are adequate simple methods for estimating the single-electron photoionization spectra of open-shell systems.

Sars-CoV-2 infection rate in employees of a medium and high complexity hospital / Velocidad de la infección con Sars-CoV-2, en funcionarios en un hospital de mediana y alta complejidad

Introduction: The coronavirus disease 2019 (COVID-19) was originally identified in the city of Wuhan, China, in December 2019. Current evidence indicates that the COVID-19-causing virus is transmitted person-to-person through direct contact and droplets. Objective: To estimate Sars-CoV-2 virus infection rate in hospital employees according to their job responsibilities. Materials and methods: Retrospective cohort study to detect Sars-CoV-2 infection in hospital employees, carried out between February 2020 and October 2021. The Kaplan Meier procedure was carried out to estimate the virus infection rate based on variables such as gender, age and job description. Results: There was a difference in infection rate between young and older adult age groups (Log Rank=18.6 gl=1 p=<0.0001). A significant difference was also found between young adult and older adult groups (Log Rank=10.6 gl=1 p=0.0011). Conclusions: The older adult group showed a higher infection rate than that observed in younger age groups. These findings highlight the occupational risk of Sars-CoV-2 infection in health workers, especially in older employees. Therefore, it is necessary to maintain safety measures in order to reduce infection risks.

Introducción: La enfermedad por coronavirus 2019 se identificó originalmente en la ciudad de Wuhan, China, en diciembre de 2019. La evidencia actual indica que el virus que causa la COVID-19 se transmite de persona a persona a través del contacto directo y gotitas. Objetivo: Estimar la tasa de infección por el virus Sars-CoV-2 en empleados de hospitales según sus responsabilidades laborales. Materiales y métodos: Estudio de cohorte retrospectivo para detectar infección por Sars-CoV-2 en empleados de hospitales, realizado entre febrero 2020 y octubre 2021. Se realizó el procedimiento de Kaplan Meier para estimar la tasa de infección del virus según género, edad y descripción del trabajo. Resultados: Hubo una diferencia en la tasa de infección entre los grupos de edad de adultos jóvenes y mayores (Log Rank=18,6 gl=1 p=<0,0001). Se encontró una diferencia significativa entre grupos de adultos jóvenes y adultos mayores (Log Rank=10.6 gl=1 p=0.0011). Conclusiones: Los adultos mayores presentaron una tasa de infección superior a la observada en grupos de edades más jóvenes. Se resalta el riesgo ocupacional de infección por Sars-CoV-2 en los trabajadores de la salud, especialmente en los empleados de mayor edad. Es necesario mantener las medidas de seguridad para reducir los riesgos de infección.

Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae.

Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.

Attosecond dynamics of multi-channel single photon ionization.

Photoionization of atoms and molecules is one of the fastest processes in nature. The understanding of the ultrafast temporal dynamics of this process often requires the characterization of the different angular momentum channels over a broad energy range. Using a two-photon interferometry technique based on extreme ultraviolet and infrared ultrashort pulses, we measure the phase and amplitude of the individual angular momentum channels as a function of kinetic energy in the outer-shell photoionization of neon. This allows us to unravel the influence of channel interference as well as the effect of the short-range, Coulomb and centrifugal potentials, on the dynamics of the photoionization process.

Observation of Rabi dynamics with a short-wavelength free-electron laser.

Rabi oscillations are periodic modulations of populations in two-level systems interacting with a time-varying field1. They are ubiquitous in physics with applications in different areas such as photonics2, nano-electronics3, electron microscopy4 and quantum information5. While the theory developed by Rabi was intended for fermions in gyrating magnetic fields, Autler and Townes realized that it could also be used to describe coherent light-matter interactions within the rotating-wave approximation6. Although intense nanometre-wavelength light sources have been available for more than a decade7-9, Rabi dynamics at such short wavelengths has not been directly observed. Here we show that femtosecond extreme-ultraviolet pulses from a seeded free-electron laser10 can drive Rabi dynamics between the ground state and an excited state in helium atoms. The measured photoelectron signal reveals an Autler-Townes doublet and an avoided crossing, phenomena that are both fundamental to coherent atom-field interactions11. Using an analytical model derived from perturbation theory on top of the Rabi model, we find that the ultrafast build-up of the doublet structure carries the signature of a quantum interference effect between resonant and non-resonant photoionization pathways. Given the recent availability of intense attosecond12 and few-femtosecond13 extreme-ultraviolet pulses, our results unfold opportunities to carry out ultrafast manipulation of coherent processes at short wavelengths using free-electron lasers.

Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop "Inclusivity in the Plant Sciences".

A future in which scientific discoveries are valued and trusted by the general public cannot be achieved without greater inclusion and participation of diverse communities. To envision a path towards this future, in January 2019 a diverse group of researchers, educators, students, and administrators gathered to hear and share personal perspectives on equity, diversity, and inclusion (EDI) in the plant sciences. From these broad perspectives, the group developed strategies and identified tactics to facilitate and support EDI within and beyond the plant science community. The workshop leveraged scenario planning and the richness of its participants to develop recommendations aimed at promoting systemic change at the institutional level through the actions of scientific societies, universities, and individuals and through new funding models to support research and training. While these initiatives were formulated specifically for the plant science community, they can also serve as a model to advance EDI in other disciplines. The proposed actions are thematically broad, integrating into discovery, applied and translational science, requiring and embracing multidisciplinarity, and giving voice to previously unheard perspectives. We offer a vision of barrier-free access to participation in science, and a plant science community that reflects the diversity of our rapidly changing nation, and supports and invests in the training and well-being of all its members. The relevance and robustness of our recommendations has been tested by dramatic and global events since the workshop. The time to act upon them is now.

Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom.

We explore the merits of linear-response range-separated time-dependent density-functional theory (TDDFT) for the calculation of photoionization spectra. We consider two variants of range-separated TDDFT, namely, the time-dependent range-separated hybrid (TDRSH) scheme, which uses a global range-separation parameter, and the time-dependent locally range-separated hybrid (TDLRSH), which uses a local range-separation parameter, and compare with standard time-dependent local-density approximation (TDLDA) and time-dependent Hartree-Fock (TDHF). We show how to calculate photoionization spectra with these methods using the Sternheimer approach formulated in a non-orthogonal B-spline basis set with appropriate frequency-dependent boundary conditions. We illustrate these methods on the photoionization spectrum of the Be atom, focusing, in particular, on the core resonances. Both the TDRSH and TDLRSH photoionization spectra are found to constitute a large improvement over the TDLDA photoionization spectrum and a more modest improvement over the TDHF photoionization spectrum.

Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits.

Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.].

Phylogenetic inference of where species spread or split across barriers.

SignificanceGeography molds how species evolve in space. Strong geographical barriers to movement, for instance, both inhibit dispersal between regions and allow isolated populations to diverge as new species. Weak barriers, by contrast, permit species range expansion and persistence. These factors present a conundrum: How strong must a barrier be before between-region speciation outpaces dispersal? We designed a phylogenetic model of dispersal, extinction, and speciation that allows regional features to influence rates of biogeographic change and applied it to the neotropical radiation of Anolis lizards. Separation by water induces a threefold steeper barrier to movement than equivalent distances over land. Our model will help biologists detect relationships between evolutionary processes and the spatial contexts in which they operate.

Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora.

Siphonophores are complex colonial animals, consisting of asexually produced bodies (zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. We examine gene expression within species, conduct classical analyses examining expression patterns between species, and introduce species branch filtering, which allows us to examine the evolution of expression across species in a phylogenetic framework. Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. Traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile.

The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.

An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae).

What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species ([Formula: see text]) and that phenomic and genomic data seldom delimit congruent entities ([Formula: see text]). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different 'types of species'. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.

Relict inland mangrove ecosystem reveals Last Interglacial sea levels.

Climatic oscillations during the Pleistocene played a major role in shaping the spatial distribution and demographic dynamics of Earth's biota, including our own species. The Last Interglacial (LIG) or Eemian Period (ca. 130 to 115 thousand years B.P.) was particularly influential because this period of peak warmth led to the retreat of all ice sheets with concomitant changes in global sea level. The impact of these strong environmental changes on the spatial distribution of marine and terrestrial ecosystems was severe as revealed by fossil data and paleogeographic modeling. Here, we report the occurrence of an extant, inland mangrove ecosystem and demonstrate that it is a relict of the LIG. This ecosystem is currently confined to the banks of the freshwater San Pedro Mártir River in the interior of the Mexico-Guatemala El Petén rainforests, 170 km away from the nearest ocean coast but showing the plant composition and physiognomy typical of a coastal lagoon ecosystem. Integrating genomic, geologic, and floristic data with sea level modeling, we present evidence that this inland ecosystem reached its current location during the LIG and has persisted there in isolation ever since the oceans receded during the Wisconsin glaciation. Our study provides a snapshot of the Pleistocene peak warmth and reveals biotic evidence that sea levels substantially influenced landscapes and species ranges in the tropics during this period.

Thermal and Mechanochemical Tuning of the Porphyrin Singlet-Triplet Gap for Selective Energy Transfer Processes: A Molecular Dynamics Approach.

Molecular dynamics simulations provide fundamental knowledge on the reaction mechanism of a given simulated molecular process. Nevertheless, other methodologies based on the "static" exploration of potential energy surfaces are usually employed to firmly provide the reaction coordinate directly related to the reaction mechanism, as is the case in intrinsic reaction coordinates for thermally activated reactions. Photoinduced processes in molecular systems can also be studied with these two strategies, as is the case in the triplet energy transfer process. Triplet energy transfer is a fundamental photophysical process in photochemistry and photobiology, being for instance involved in photodynamic therapy, when generating the highly reactive singlet oxygen species. Here, we study the triplet energy transfer process between porphyrin, a prototypical energy transfer donor, and different biologically relevant acceptors, including molecular oxygen, carotenoids, and rhodopsin. The results obtained by means of nanosecond time-scale molecular dynamics simulations are compared to the "static" determination of the reaction coordinate for such a thermal process, leading to the distortions determining an effective energy transfer. This knowledge was finally applied to propose porphyrin derivatives for producing the required structural modifications in order to tune their singlet-triplet energy gap, thus introducing a mechanochemical description of the mechanism.

Factores asociados al síndrome de desgaste laboral en auxiliares de enfermería / Factors associated with burnout syndrome in nursing assistants

Introducción: El Síndrome de Desgaste Laboral o Burnout, es entendido como una baja resiliencia para afrontar el estrés laboral. Objetivo: Identificar factores asociados al Burnout y la prevalencia global y de cada uno de sus constructos, entre auxiliares de enfermería en un hospital de referencia de mediana y alta complejidad, en Colombia. Materiales y métodos: Estudio de casos y controles, con 183 auxiliares registradas en un hospital. Se utilizó el instrumento de Maslach y se identificaron los factores asociados utilizando la regresión Log-Binomial determinando los Odds Ratio (OR). Resultados: Los factores encontrados asociados con Burnout que aumentan la probabilidad de ocurrencia son: trabajar más de 48 horas por semana, OR=1,02 (1,01-1.05) al 90% de confianza; sentirse mal con el trabajo que se realiza OR=3,87 (1,18-10,71); el dormir siete horas o más al día OR=0,70 (0,53-0,91), disminuye la probabilidad. La prevalencia total de Burnout fue 44,7%, siendo 11,8% para agotamiento personal, 14,9% despersonalización y 47,81% pobre realización personal. Conclusiones: Los factores asociados: no dormir suficiente y sentirse mal con la tarea que se realiza, aumentan la probabilidad de desarrollar Burnout, mientras que dormir 7 o más horas diarias la disminuye. Estos hallazgos facilitarán la aplicación de medidas de control institucional.

Introduction: The Burnout syndrome is understood as a low resilience to face work stress. Objective: To identify factors and constructs associated with Burnout and its overall prevalence in nursing assistants in a reference hospital of medium and high complexity level from Colombia. Materials and methods: A case-control study was conducted on 183 nursing assistants from a hospital. The Maslach instrument and Log-Binomial regression were used to identify associated factors, determining their Odds Ratio (OR). Results: The factors found associated with Burnout that increase its probability of occurrence are: working more than 48 hours a week (OR=1.02 (1.01-1.05) 90% CI) and feeling negatively about the work being done (OR=3.87 (1.18-10.71)). However, sleeping 7 or more hours a day reduces such probability (OR=0.70 (0.53-0.91)). The total Burnout prevalence was 44.7%, the main causes being personal fatigue (11.8%), depersonalization (14.9%), and poor personal fulfillment (47.81%). Conclusions: Associated factors, such as not getting enough sleep and feeling negatively about the work being done, increase the probability to develop Burnout, while this probability decreases by sleeping 7 or more hours a day. These findings will facilitate the implementation of institutional control measures.

Revising transcriptome assemblies with phylogenetic information.

A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.

Diversification, disparification and hybridization in the desert shrubs Encelia.

There are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. Using a nearly complete species-level phylogeny based on double-digest restriction-aided sequencing along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity and assess phenotypic divergence across environmental gradients. We show that Encelia originated and diversified recently (mid-Pleistocene) and rapidly, with rates comparable to notable adaptive radiations in plants. Encelia probably originated in the hot deserts of North America, with subsequent diversification across steep environmental gradients. We uncover multiple instances of gene flow between species. The radiation of Encelia is characterized by fast rates of phenotypic evolution, trait lability and extreme disparity across environments and between species pairs with overlapping geographic ranges. Encelia exemplifies how interspecific gene flow in combination with high trait lability can enable exceptionally fast diversification and disparification across steep environmental gradients.