An international team of over forty stratigraphic experts have helped to build the most up-to-date international stratigraphic framework for the Precambrian and Phanerozoic. This successor to A ...Geologic Time Scale 1989 by W. Brian Harland et al. (CUP 0521 387655) begins with an introduction to the theory and methodology behind the construction of the new time scale. The main part of the book is devoted to the scale itself, systematically presenting the standard subdivisions at all levels using a variety of correlation markers. Extensive use is made of isotope geochronology, geomathematics and orbital tuning to produce a standard geologic scale of unprecedented detail and accuracy with a full error analysis. A wallchart summarising the whole time scale, with paleogeographic reconstructions throughout the Phanerozoic, is included in the back of the book. The time scale will be an invaluable reference source for academic and professional researchers and students.
This study assesses the potential of lung ultrasonography to diagnose acute respiratory failure.
This observational study was conducted in university-affiliated teaching-hospital ICUs. We performed ...ultrasonography on consecutive patients admitted to the ICU with acute respiratory failure, comparing lung ultrasonography results on initial presentation with the final diagnosis by the ICU team. Uncertain diagnoses and rare causes (frequency < 2%) were excluded. We included 260 dyspneic patients with a definite diagnosis. Three items were assessed: artifacts (horizontal A lines or vertical B lines indicating interstitial syndrome), lung sliding, and alveolar consolidation and/or pleural effusion. Combined with venous analysis, these items were grouped to assess ultrasound profiles.
Predominant A lines plus lung sliding indicated asthma (n = 34) or COPD (n = 49) with 89% sensitivity and 97% specificity. Multiple anterior diffuse B lines with lung sliding indicated pulmonary edema (n = 64) with 97% sensitivity and 95% specificity. A normal anterior profile plus deep venous thrombosis indicated pulmonary embolism (n = 21) with 81% sensitivity and 99% specificity. Anterior absent lung sliding plus A lines plus lung point indicated pneumothorax (n = 9) with 81% sensitivity and 100% specificity. Anterior alveolar consolidations, anterior diffuse B lines with abolished lung sliding, anterior asymmetric interstitial patterns, posterior consolidations or effusions without anterior diffuse B lines indicated pneumonia (n = 83) with 89% sensitivity and 94% specificity. The use of these profiles would have provided correct diagnoses in 90.5% of cases.
Lung ultrasound can help the clinician make a rapid diagnosis in patients with acute respiratory failure, thus meeting the priority objective of saving time.
The hidden structure of human enamel Beniash, Elia; Stifler, Cayla A; Sun, Chang-Yu ...
Nature communications,
09/2019, Letnik:
10, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Enamel is the hardest and most resilient tissue in the human body. Enamel includes morphologically aligned, parallel, ∼50 nm wide, microns-long nanocrystals, bundled either into 5-μm-wide rods or ...their space-filling interrod. The orientation of enamel crystals, however, is poorly understood. Here we show that the crystalline c-axes are homogenously oriented in interrod crystals across most of the enamel layer thickness. Within each rod crystals are not co-oriented with one another or with the long axis of the rod, as previously assumed: the c-axes of adjacent nanocrystals are most frequently mis-oriented by 1°-30°, and this orientation within each rod gradually changes, with an overall angle spread that is never zero, but varies between 30°-90° within one rod. Molecular dynamics simulations demonstrate that the observed mis-orientations of adjacent crystals induce crack deflection. This toughening mechanism contributes to the unique resilience of enamel, which lasts a lifetime under extreme physical and chemical challenges.
While the catalog of mammalian transcripts and their expression levels in different cell types and disease states is rapidly expanding, our understanding of transcript function lags behind. We ...present a robust technology enabling systematic investigation of the cellular consequences of repressing or inducing individual transcripts. We identify rules for specific targeting of transcriptional repressors (CRISPRi), typically achieving 90%–99% knockdown with minimal off-target effects, and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9. Together they enable modulation of gene expression over a ∼1,000-fold range. Using these rules, we construct genome-scale CRISPRi and CRISPRa libraries, each of which we validate with two pooled screens. Growth-based screens identify essential genes, tumor suppressors, and regulators of differentiation. Screens for sensitivity to a cholera-diphtheria toxin provide broad insights into the mechanisms of pathogen entry, retrotranslocation and toxicity. Our results establish CRISPRi and CRISPRa as powerful tools that provide rich and complementary information for mapping complex pathways.
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•CRISPRi and CRISPRa provide complementary information for mapping complex pathways•CRISPRi/a expression series (up to ∼1,000-fold) reveal how gene dose controls function•CRISPRi provides strong (typically 90%–99%) knockdown with minimal off-target effects•Genome-scale screens elucidate pathways controlling cholera/diphtheria toxicity
Genome-scale-specific targeting of transcriptional repressors (CRISPRi) and activators (CRISPRa) to endogenous genes via endonuclease-deficient Cas9 have been applied to growth and toxin-resistance screens, establishing CRISPRi and CRISPRa as powerful tools that provide rich and complementary information.
Highlights • Conditionally rare taxa (CRTs) contribute to microbial community changes but their ecological roles are largely unknown. • CRTs are difficult to observe due to their inherent rarity, ...technological limitations with sequencing, and modest time series data. • Conceptualizing microbial taxa as dynamic components along species occurrence and species abundance distributions will improve understanding of CRTs and their transitions into and out of the rare biosphere. • As CRTs are better documented, we can better pose and test hypotheses about their contributions to community resilience after perturbation and ecoevolutionary dynamics.
The spatiotemporal organization and dynamics of chromatin play critical roles in regulating genome function. However, visualizing specific, endogenous genomic loci remains challenging in living ...cells. Here, we demonstrate such an imaging technique by repurposing the bacterial CRISPR/Cas system. Using an EGFP-tagged endonuclease-deficient Cas9 protein and a structurally optimized small guide (sg) RNA, we show robust imaging of repetitive elements in telomeres and coding genes in living cells. Furthermore, an array of sgRNAs tiling along the target locus enables the visualization of nonrepetitive genomic sequences. Using this method, we have studied telomere dynamics during elongation or disruption, the subnuclear localization of the MUC4 loci, the cohesion of replicated MUC4 loci on sister chromatids, and their dynamic behaviors during mitosis. This CRISPR imaging tool has potential to significantly improve the capacity to study the conformation and dynamics of native chromosomes in living human cells.
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•An optimized CRISPR enables live imaging and better gene regulation in human cells•CRISPR imaging visualizes either repetitive or nonrepetitive genomic sequences•CRISPR imaging reports telomere length change and telomere movements•CRISPR imaging monitors the dynamics of gene loci throughout the cell cycle
A new CRISPR-based technology allows precise visualization of individual gene loci in living cells.
Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally ...important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.
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•Salinity elevation decreased both the activity and abundance of denitrifiers.•The nitrifiers (AOB) were most abundant under the intermediate salinity conditions.•Salinity significantly shaped the nitrifying and denitrifying community structures.•These findings may increase concern regarding threats of salinity intrusion.
Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based ...on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale.
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► Inactive CRISPR associated 9 protein (dCas9) is repurposed for genome engineering ► dCas9 and a complementary short guide RNA can target specific genomic sites ► CRISPR interference (CRISPRi) can regulate multiple genes without off-target effects ► CRISPRi is compact and can be ported to bacterial and mammalian cells
The authors have developed a CRISPR interference system in which a catalytically dead Cas9 protein can be targeted to a specific genomic site through a complementary small guide RNA, allowing systematic perturbation of gene transcription in bacteria and mammalian cells.
The rapid improvement of camera traps in recent decades has revolutionized biodiversity monitoring. Despite clear applications in conservation science, camera traps have seldom been used to model the ...abundance of unmarked animal populations. We sought to summarize the challenges facing abundance estimation of unmarked animals, compile an overview of existing analytical frameworks, and provide guidance for practitioners seeking a suitable method. When a camera records multiple detections of an unmarked animal, one cannot determine whether the images represent multiple mobile individuals or a single individual repeatedly entering the camera viewshed. Furthermore, animal movement obfuscates a clear definition of the sampling area and, as a result, the area to which an abundance estimate corresponds. Recognizing these challenges, we identified 6 analytical approaches and reviewed 927 camera‐trap studies published from 2014 to 2019 to assess the use and prevalence of each method. Only about 5% of the studies used any of the abundance‐estimation methods we identified. Most of these studies estimated local abundance or covariate relationships rather than predicting abundance or density over broader areas. Next, for each analytical approach, we compiled the data requirements, assumptions, advantages, and disadvantages to help practitioners navigate the landscape of abundance estimation methods. When seeking an appropriate method, practitioners should evaluate the life history of the focal taxa, carefully define the area of the sampling frame, and consider what types of data collection are possible. The challenge of estimating abundance of unmarked animal populations persists; although multiple methods exist, no one method is optimal for camera‐trap data under all circumstances. As analytical frameworks continue to evolve and abundance estimation of unmarked animals becomes increasingly common, camera traps will become even more important for informing conservation decision‐making.
Estimación de la Abundancia de Animales No Marcados con Base en Datos de Cámaras Trampa
Resumen
La rápida mejoría de las cámaras trampa en las décadas recientes ha revolucionado el monitoreo de la biodiversidad. A pesar de su clara aplicación en las ciencias de la conservación, las cámaras trampa han sido utilizadas pocas veces para modelar la abundancia de las poblaciones de animales no marcados. Buscamos resumir los retos que enfrenta la estimación de la abundancia de animales no marcados, compilar una perspectiva general de los marcos analíticos de trabajo existentes y proporcionar una guía para aquellos practicantes que buscan un método adecuado. Cuando una cámara registra múltiples detecciones de animales no marcados, no se puede determinar si las imágenes representan a diferentes individuos en movimiento o a un solo individuo que entra repetidamente a la zona de visión de la cámara. Sumado a esto, el movimiento animal ofusca una definición clara del área de muestreo y, como resultado, del área a la cual corresponde un estimado de abundancia. Después de reconocer estos retos, identificamos seis estrategias analíticas y revisamos 927 estudios con cámaras trampa publicados entre 2014 y 2019 para evaluar el uso y la prevalencia de cada método. Solamente en el 5% de los estudios se usó cualquiera de los métodos de estimación de abundancia que identificamos. La mayoría de estos estudios estimaron la abundancia local o las relaciones de covarianza en lugar de predecir la abundancia o la densidad a lo largo de áreas más amplias. Después, para cada estrategia analítica, recopilamos los requerimientos de datos, suposiciones, ventajas y desventajas para ayudar a los practicantes a navegar el paisaje de los métodos de estimación de abundancia. Cuando los practicantes busquen un método apropiado deberán evaluar la historia de vida del taxón focal, definir cuidadosamente el área del marco de muestreo y considerar cuáles tipos de recolección de datos son posibles. El reto de estimar la abundancia de poblaciones de animales no marcados persiste; aunque existan muchos métodos, no hay método único óptimo para los datos de las cámaras trampa que cumpla con todas las circunstancias. Mientras los marcos analíticos de trabajo sigan evolucionando y la estimación de la abundancia de animales no marcados sea cada vez más común, las cámaras trampa serán todavía más importantes para informar la toma de decisiones de conservación.
摘要
近几十年来红外相机陷阱技术的快速发展已经彻底改变了生物多样性监测的现状。尽管红外相机陷阱法在动物保护科学中有明确的应用, 但它很少被用来模拟无标记动物的种群数量。本研究旨在总结无标记动物的丰度估计所面临的挑战, 总结现有的分析框架并为寻求合适方法的实践者提供指导意见。当红外相机多次记录到无标记的动物时, 人们无法确定这些图像代表的是多个个体还是一个重复进入相机拍摄范围的个体。此外, 动物的运动导致不能清晰地划定采样区域, 因此也模糊了所对应区域的丰度估计。面对这些挑战, 我们确定了六种分析方法, 并综述了 2014 年至 2019 年发表的 927 项红外相机陷阱研究, 以评估每种方法的使用情况和流行程度。结果发现, 只有约 5% 的研究使用了至少一种我们确定的丰度估计方法。这些研究大多是估计局部丰度或协变量关系, 而不是预测更大范围内的动物丰度或密度。接下来, 我们总结了每种分析方法的数据需求、假设、优点和缺点, 以帮助实践者了解丰度估计方法的总体情况。实践者在寻找合适的方法时, 应评估研究所关注类群的生活史, 谨慎地确定采样范围, 并考虑可能收集到的数据类型。无标记动物的种群数量估计仍面临挑战, 虽然已存在多种方法, 但没有一种方法对于所有红外相机陷阱数据都是最优的。随着分析框架的不断发展和对无标记动物数量估计变得越来越普遍, 红外相机陷阱法在为指导保护决策中也将更加重要。【翻译: 胡怡思; 审校: 聂永刚】
Article impact statement: Camera traps have yet to meet their potential to model abundance of unmarked animals, but methods are emerging to meet the need.
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