Identifying predictors of translocation success in rare plant species.

The fundamental goal of a rare plant translocation is to create self-sustaining populations with the evolutionary resilience to persist in the long term. Yet, most plant translocation syntheses focus on a few factors influencing short-term benchmarks of success (e.g., survival and reproduction). Short-term benchmarks can be misleading when trying to infer future growth and viability because the factors that promote establishment may differ from those required for long-term persistence. We assembled a large (n = 275) and broadly representative data set of well-documented and monitored (7.9 years on average) at-risk plant translocations to identify the most important site attributes, management techniques, and species' traits for six life-cycle benchmarks and population metrics of translocation success. We used the random forest algorithm to quantify the relative importance of 29 predictor variables for each metric of success. Drivers of translocation outcomes varied across time frames and success metrics. Management techniques had the greatest relative influence on the attainment of life-cycle benchmarks and short-term population trends, whereas site attributes and species' traits were more important for population persistence and long-term trends. Specifically, large founder sizes increased the potential for reproduction and recruitment into the next generation, whereas declining habitat quality and the outplanting of species with low seed production led to increased extinction risks and a reduction in potential reproductive output in the long-term, respectively. We also detected novel interactions between some of the most important drivers, such as an increased probability of next-generation recruitment in species with greater seed production rates, but only when coupled with large founder sizes. Because most significant barriers to plant translocation success can be overcome by improving techniques or resolving site-level issues through early intervention and management, we suggest that by combining long-term monitoring with adaptive management, translocation programs can enhance the prospects of achieving long-term success.

Identificación de pronosticadores del éxito de reubicación en especies raras de plantas Resumen El objetivo fundamental de la reubicación de plantas raras es la creación de poblaciones autosuficientes con resiliencia evolutiva que persistan a la larga. De todas maneras, la mayoría de las síntesis de estas reubicaciones se enfocan en unos cuantos factores que influyen sobre los parámetros a corto plazo del éxito (supervivencia y reproducción). Los parámetros a corto plazo pueden ser engañosos si se intenta inferir el crecimiento y la viabilidad en el futuro ya que los factores que promueven el establecimiento pueden diferir de aquellos requeridos para la persistencia a largo plazo. Ensamblamos un conjunto grande de datos representativos en general (n = 275) de las reubicaciones de plantas en riesgo bien documentadas y monitoreadas (7.9 años en promedio) para identificar los atributos de sitio más importantes, las técnicas de manejo y los rasgos de las especies para seis parámetros de ciclos de vida y medidas poblacionales del éxito de reubicación. Usamos el algoritmo de bosque aleatorio para cuantificar la importancia relativa de las 29 variables de pronosticadores para cada medida del éxito. Los factores en los resultados de las reubicaciones variaron con los marcos temporales y las medidas de éxito. Las técnicas de manejo tuvieron la mayor influencia relativa sobre la obtención de parámetros de ciclos de vida y tendencias poblacionales a corto plazo, mientras que los atributos de sitio y los rasgos de la especie fueron más importantes para la persistencia poblacional y las tendencias a largo plazo. En específico, las grandes cantidades de fundadores incrementaron el potencial de reproducción y reclutamiento de la siguiente generación, mientras que la declinación de la calidad del hábitat incrementó el riesgo de extinción y el trasplante de especies con baja producción de semillas redujo el rendimiento del potencial reproductivo a la larga. También detectamos interacciones novedosas entre algunos de los factores más importantes, como el aumento en la probabilidad del reclutamiento en la siguiente generación en especies con tasas mayores de producción de semillas, pero sólo cuando se emparejó con grandes cantidades de fundadores. Ya que las barreras más significativas para el éxito de la reubicación de plantas pueden superarse al mejorar las técnicas o resolver los temas a nivel de sitio por medio de un manejo y una intervención temprana, sugerimos que con la combinación del monitoreo a largo plazo con el manejo adaptativo los programas de reubicación pueden aumentar el prospecto de lograr el éxito a largo plazo.

Patient and dermatologists' perspectives on augmented intelligence for melanoma screening: A prospective study.

BACKGROUND: Artificial intelligence (AI) shows promising potential to enhance human decision-making as synergistic augmented intelligence (AuI), but requires critical evaluation for skin cancer screening in a real-world setting. OBJECTIVES: To investigate the perspectives of patients and dermatologists after skin cancer screening by human, artificial and augmented intelligence. METHODS: A prospective comparative cohort study conducted at the University Hospital Basel included 205 patients (at high-risk of developing melanoma, with resected or advanced disease) and 8 dermatologists. Patients underwent skin cancer screening by a dermatologist with subsequent 2D and 3D total-body photography (TBP). Any suspicious and all melanocytic skin lesions ≥3 mm were imaged with digital dermoscopes and classified by corresponding convolutional neural networks (CNNs). Excisions were performed based on dermatologist's melanoma suspicion, study-defined elevated CNN risk-scores and/or melanoma suspicion by AuI. Subsequently, all patients and dermatologists were surveyed about their experience using questionnaires, including quantification of patient's safety sense following different examinations (subjective safety score (SSS): 0-10). RESULTS: Most patients believed AI could improve diagnostic performance (95.5%, n = 192/201). In total, 83.4% preferred AuI-based skin cancer screening compared to examination by AI or dermatologist alone (3D-TBP: 61.3%; 2D-TBP: 22.1%, n = 199). Regarding SSS, AuI induced a significantly higher feeling of safety than AI (mean-SSS (mSSS): 9.5 vs. 7.7, p < 0.0001) or dermatologist screening alone (mSSS: 9.5 vs. 9.1, p = 0.001). Most dermatologists expressed high trust in AI examination results (3D-TBP: 90.2%; 2D-TBP: 96.1%, n = 205). In 68.3% of the examinations, dermatologists felt that diagnostic accuracy improved through additional AI-assessment (n = 140/205). Especially beginners (<2 years' dermoscopic experience; 61.8%, n = 94/152) felt AI facilitated their clinical work compared to experts (>5 years' dermoscopic experience; 20.9%, n = 9/43). Contrarily, in divergent risk assessments, only 1.5% of dermatologists trusted a benign CNN-classification more than personal malignancy suspicion (n = 3/205). CONCLUSIONS: While patients already prefer AuI with 3D-TBP for melanoma recognition, dermatologists continue to rely largely on their own decision-making despite high confidence in AI-results. TRIAL REGISTRATION: ClinicalTrials.gov (NCT04605822).

Objective hand eczema severity assessment with automated lesion anatomical stratification.

Hand eczema (HE) is one of the most frequent dermatoses, known to be both relapsing and remitting. Regular and precise evaluation of the disease severity is key for treatment management. Current scoring systems such as the hand eczema severity index (HECSI) suffer from intra- and inter-observer variance. We propose an automated system based on deep learning models (DLM) to quantify HE lesions' surface and determine their anatomical stratification. In this retrospective study, a team of 11 experienced dermatologists annotated eczema lesions in 312 HE pictures, and a medical student created anatomical maps of 215 hands pictures based on 37 anatomical subregions. Each data set was split into training and test pictures and used to train and evaluate two DLMs, one for anatomical mapping, the other for HE lesions segmentation. On the respective test sets, the anatomy DLM achieved average precision and sensitivity of 83% (95% confidence interval [CI] 80-85) and 85% (CI 82-88), while the HE DLM achieved precision and sensitivity of 75% (CI 64-82) and 69% (CI 55-81). The intraclass correlation of the predicted HE surface with dermatologists' estimated surface was 0.94 (CI 0.90-0.96). The proposed method automatically predicts the anatomical stratification of HE lesions' surface and can serve as support to evaluate hand eczema severity, improving reliability, precision and efficiency over manual assessment. Furthermore, the anatomical DLM is not limited to HE and can be applied to any other skin disease occurring on the hands such as lentigo or psoriasis.

Human epidermis organotypic cultures, a reproducible system recapitulating the epidermis in vitro.

The translatability of research is highly dependent on models that recapitulate human tissues and organs. Here, we describe a procedure for the generation of human epidermis organotypic cultures (HEOCs) from primary keratinocytes isolated from foreskin and adult skin as well as from an immortalized keratinocyte cell line (KerTr). We tested several media conditions to develop a defined HEOC growing and expansion media. We characterized the HEOCs and show that in optimal culture conditions they express the proliferation marker Ki67, the basement membrane protein collagen 17 (col17) and the epidermal differentiation markers keratin 15 (K15), keratin 14 (K14), keratin 5 (K5), keratin 10 (K10), keratin 1 (K1), transglutaminase 1 (TGM1), transglutaminase 3 (TGM3) and filaggrin (FLG). Thus, they recapitulate the human epidermis and are stratified from the basal layer to the stratum corneum. These HEOC can be generated reproducibly on a large scale, making it an invaluable model for screening therapeutic compounds and also for the study of pathologies affecting the epidermis.

Closing the gap - development of an analytical methodology using volumetric absorptive microsampling of finger prick blood followed by LC-HRMS/MS for adherence monitoring of antihypertensive drugs.

Volumetric absorptive microsampling (VAMS), an emerging microsampling technique, is a promising tool for adherence monitoring. This study focused on development of an analytical methodology to improve VAMS-based strategies for adherence assessment by analyzing angiotensin-converting-enzyme (ACE) inhibitors, loop diuretics, a potassium-sparing diuretic, and a thiazide diuretic. Development included sample preparation, chromatographic conditions, mass spectrometry settings, validation, and demonstrating proof of concept. Quantification of analytes, by name furosemide, hydrochlorothiazide, lisinopril, torasemide, and the active metabolites, canrenone, enalaprilat, and ramiprilat in finger prick blood (FPB), was validated based on international guidelines. Selectivity, carryover, and within/between-run accuracy and precision were in accordance with the recommendations. The matrix effect was evaluated at three different hematocrit levels (HT: 20%, 40%, 60%) and the coefficients of variation did not exceed 15%. Dilution integrity (1:10 and 1:20) was given for all analytes except lisinopril, yet for lisinopril, the therapeutic range was already covered by the calibration range. Long-term stability in VAMS tips was tested for 2 weeks at 24 °C in the dark and revealed no degradation of analytes. The proof of concept was performed by analyzing 35 intakes of ACE-inhibitors and diuretics in 18 VAMS and matched plasma samples. Hereby, determined concentration in FPB and plasma cannot be used interchangeably, and thus specific reference ranges for whole blood must be established. Nevertheless, the VAMS-based strategy was shown to be suitable for assessing adherence of all classes of antihypertensive drugs used in the guidelines to manage hypertension.

Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography.

Desmosomes are cell-cell junctions that link tissue cells experiencing intense mechanical stress. Although the structure of the desmosomal cadherins is known, the desmosome architecture-which is essential for mediating numerous functions-remains elusive. Here, we recorded cryo-electron tomograms (cryo-ET) in which individual cadherins can be discerned; they appear variable in shape, spacing, and tilt with respect to the membrane. The resulting sub-tomogram average reaches a resolution of ∼26 Å, limited by the inherent flexibility of desmosomes. To address this challenge typical of dynamic biological assemblies, we combine sub-tomogram averaging with atomistic molecular dynamics (MD) simulations. We generate models of possible cadherin arrangements and perform an in silico screening according to biophysical and structural properties extracted from MD simulation trajectories. We find a truss-like arrangement of cadherins that resembles the characteristic footprint seen in the electron micrograph. The resulting model of the desmosomal architecture explains their unique biophysical properties and strength.

Structure of RNA polymerase I transcribing ribosomal DNA genes.

RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.

Cardio-renal interaction - Clinical trials update 2022.

AIMS: Chronic kidney disease is a common cardiovascular risk indicator and strongly associated with increased morbidity and mortality. The heart and kidneys are pathophysiologically closely connected, which becomes particularly obvious in patients with cardiorenal syndrome. This review summarizes clinically relevant studies on the cardio-renal interaction published in 2021 and 2022. DATA SYNTHESIS: Selected trials published in high-impact journals were chosen from the database Pubmed and included in this review. New evidence about the selective mineralocorticoid receptor antagonist finerenone and the renoprotective sodium-glucose co-transporter-2-inhibitors (SGLT2-Inhibitors) are discussed and we update on novel insights about the treatment of arterial hypertension in patients with severe chronic kidney disease with the thiazide-like diuretic chlorthalidone. Finally, data on infective endocarditis in patients on chronic hemodialysis and the treatment of secondary hyperparathyroidism with the calcimimetic drug etelcalcetide in patients with end stage kidney disease are critically reviewed. CONCLUSION: Several important studies investigating cardio-renal interactions were recently published may affect clinical practice. The graphical abstract (Fig. 1) depicts the most relevant clinical studies investigating cardio-renal interactions.

Statistical analysis of in vivo alkaline comet assay data - Comparison of median and geometric mean as centrality measures.

The comet assay is one of the standard tests for evaluating the genotoxic potential of a test item able to detect DNA strand breaks in cells or isolated nuclei from various tissues. The in vivo alkaline comet assay is part of the standard test battery, given in option 2 of the ICH guidance S2 (R1) and a follow-up test in the EFSA framework on genotoxicity testing. The current OECD guideline for the testing of chemicals No. 489 directly affects the statistical analysis of comet data as it suggests using the median per slide and the mean of all medians per animal. However, alternative approaches can be used if scientifically justified. In this work, we demonstrated that the selection of different centrality measures to describe an average value per slide may lead to fundamentally different statistical test results and contradicting interpretations. Our focus was on geometric means and medians per slide for the primary endpoint "tail intensity". We compared both strategies using original and simulated data in different experimental settings incl. a varying number of animals, slides and cells per slide. In general, it turned out that the chosen centrality measure has an immense impact on the final statistical test result.

Effects of life history and reproduction on recruitment time lags in reintroductions of rare plants.

Reintroductions are important components of conservation and recovery programs for rare plant species, but their long-term success rates are poorly understood. Previous reviews of plant reintroductions focused on short-term (e.g., ≤3 years) survival and flowering of founder individuals rather than on benchmarks of intergenerational persistence, such as seedling recruitment. However, short-term metrics may obscure outcomes because the unique demographic properties of reintroductions, including small size and unstable stage structure, could create lags in population growth. We used time-to-event analysis on a database of unusually well-monitored and long-term (4-28 years) reintroductions of 27 rare plant species to test whether life-history traits and population characteristics of reintroductions create time-lagged responses in seedling recruitment (i.e., recruitment time lags [RTLs]), an important benchmark of success and indicator of persistence in reintroduced populations. Recruitment time lags were highly variable among reintroductions, ranging from <1 to 17 years after installation. Recruitment patterns matched predictions from life-history theory with short-lived species (fast species) exhibiting consistently shorter and less variable RTLs than long-lived species (slow species). Long RTLs occurred in long-lived herbs, especially in grasslands, whereas short RTLs occurred in short-lived subtropical woody plants and annual herbs. Across plant life histories, as reproductive adult abundance increased, RTLs decreased. Highly variable RTLs were observed in species with multiple reintroduction events, suggesting local processes are just as important as life-history strategy in determining reintroduction outcomes. Time lags in restoration outcomes highlight the need to scale success benchmarks in reintroduction monitoring programs with plant life-history strategies and the unique demographic properties of restored populations. Drawing conclusions on the long-term success of plant reintroduction programs is premature given that demographic processes in species with slow life-histories take decades to unfold.

Efectos de la Historia de Vida y la Reproducción sobre las Demoras en el Tiempo de Reclutamiento en la Reintroducción de Plantas Raras Resumen Las reintroducciones son componentes importantes de los programas de conservación y recuperación de especies raras de plantas, pero las tasas de éxito a largo plazo cuentan con muy poco entendimiento. Las revisiones previas de las reintroducciones de plantas se han enfocado en la supervivencia a corto plazo (p. ej.: ≤ 3 años) y en el florecimiento de individuos fundadores en lugar de enfocarse en puntos de referencia para la persistencia inter-generacional, como el reclutamiento de plántulas. Sin embargo, las medidas a corto plazo pueden ocultar los resultados ya que las propiedades demográficas únicas de las reintroducciones, incluyendo el menor tamaño y la estructura inestable de estadio, podrían crear demoras en el crecimiento poblacional. Usamos un análisis de tiempo-para-evento en una base de datos de reintroducciones inusualmente bien monitoreadas y de largo plazo (4-28 años) de 27 especies raras de plantas para probar si los atributos de la historia de vida y las características poblacionales de la reintroducción crean respuestas con demoras temporales en el reclutamiento de plántulas (es decir, demoras temporales en el reclutamiento), un punto de referencia importante para el éxito y un indicador de la persistencia en poblaciones reintroducidas. Las demoras temporales de reclutamiento (RTLs, en inglés) fueron muy variables entre las reintroducciones, abarcando desde <1 hasta 17 años después de la instalación. Los patrones de reclutamiento se acoplaron a las predicciones de la teoría de historias de vida, donde las especies de vida corta (especies rápidas) exhibieron RTLs consistentemente más cortas y menos variables que las especies de vida larga (especies lentas). Las RTLs largas ocurrieron en hierbas de vida larga, especialmente en los pastizales, mientras que las RTLs cortas ocurrieron en plantas leñosas subtropicales de vida corta y en hierbas anuales. En todas las historias de vida de las plantas, conforme incrementó la abundancia de adultos reproductivos, las RTLs disminuyeron. Se observaron RTLs altamente variables en las especies con eventos de reintroducción múltiples, lo que sugiere que los procesos locales son igual de importantes que la estrategia de historia de vida para determinar los resultados de las reintroducciones. Las demoras temporales en los resultados de restauración resaltan la necesidad de poner a escala los puntos de referencia de éxito en los programas de monitoreo de reintroducciones que tengan estrategias de historia de vida de las plantas y las propiedades demográficas únicas de las poblaciones restauradas. La obtención de conclusiones sobre el éxito a largo plazo de los programas de reintroducción de plantas es algo prematuro ya que los procesos demográficos de especies con historias de vida lentas tardan décadas en desarrollarse.

Optical coherence tomography imaging of melanoma skin cancer.

No consensus guidelines exist on the use of optical coherence tomography (OCT) for diagnosis of cutaneous melanoma. The objectives of this review are to provide a descriptive review of the literature on characteristics of cutaneous melanomas seen on high-definition OCT (HD-OCT), speckle variance OCT (SV-OCT), and conventional OCT and to compare their diagnostic ability with that of histopathology. A review of PubMed and Google Scholar identified all available literature on OCT in melanoma skin cancer that included all in vivo and ex vivo studies on human or human tissues and excluded all studies on non-human subjects or animal studies. Two hundred nine abstracts were considered for evaluation, 31 abstracts were selected for manuscript review, and 14 abstracts were included that met all criteria. Diagnoses of MIS and MM using HD-OCT and SV-OCT were consistently reported to correlate with histopathology. However, accuracy of diagnosis using conventional OCT varied. Most authors agreed that it was difficult to differentiate MM from benign nevi using conventional OCT. HD-OCT, SV-OCT, and conventional OCT show promise for visualizing cutaneous melanoma. The use of OCT in diagnosis of melanoma is rarely reported in the literature. There is a need to increase and standardize reporting of OCT for diagnosis of cutaneous melanoma.

Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium.

Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry. Each NAP has two pairs of globular lobes (named α and ß lobes), arranged as a dimer of heterodimers with each lobe connected by a stalk to the cell membrane. The ß lobes are larger than the α lobes by 20%. Classification of NAPs showed that the complex can tilt with respect to the cell membrane. A protein complex containing exclusively the proteins P140 and P110, was purified from M. genitalium and was structurally characterized by negative-stain single particle EM reconstruction. The close structural similarity found between intact NAPs and the isolated P140/P110 complexes, shows that dimers of P140/P110 heterodimers are the only components of the extracellular region of intact NAPs in M. genitalium.

Venus Flytrap Rarely Traps Its Pollinators.

Because carnivorous plants rely on arthropods as pollinators and prey, they risk consuming would-be mutualists. We examined this potential conflict in the Venus flytrap (Dionaea muscipula), whose pollinators were previously unknown. Diverse arthropods from two classes and nine orders visited flowers; 56% of visitors carried D. muscipula pollen, often mixed with pollen of coflowering species. Within this diverse, generalized community, certain bee and beetle species appear to be the most important pollinators, on the basis of their abundance, pollen load size, and pollen fidelity. Dionaea muscipula prey spanned four invertebrate classes and 11 orders; spiders, beetles, and ants were most common. At the family and species levels, few taxa were shared between traps and flowers, yielding a near-zero value of niche overlap for these potentially competing structures. Spatial separation of traps and flowers may contribute to partitioning the invertebrate community between nutritional and reproductive functions in D. muscipula.

Short- and long-term effects of two emollients on itching and skin restoration in xerotic eczema.

Pruritus is associated with various skin diseases, dry skin, and with it an impaired skin barrier function. The study objective was to investigate short-term and long-term effects of two emollients on symptoms and skin barrier functions in xerotic eczema. Randomized, double-blind, study enrolling females/males, with bilateral itching. Two emollients, containing lactic acid and refined almond oil with/without polidocanol were administered on left versus right body sides. Itching severity, skin moisture, lipid content, and pH were assessed on Day 1, within 30-120 min after first administration, and on Days 7 and 14, and compared with baseline assessments. Severity of itching decreased 30 min after first administration of both emollients compared with baseline (p < .0001) and reached a maximum reduction of 63% (p < .0001) and 69% (p < .0001) on Day 14. Skin moisture and lipid content increased after first application, and further ameliorated within 14 days of treatment (p < .0001). Both emollients were tolerated well, and only a few adverse events were reported. This study confirmed the clinical efficacy of the two study emollients to substantially reduce itching already after first administration, and restore skin barrier integrity and thus should be considered as therapeutic approach for xerotic eczema.

Life and extinction of megafauna in the ice-age Arctic.

Understanding the population dynamics of megafauna that inhabited the mammoth steppe provides insights into the causes of extinctions during both the terminal Pleistocene and today. Our study area is Alaska's North Slope, a place where humans were rare when these extinctions occurred. After developing a statistical approach to remove the age artifacts caused by radiocarbon calibration from a large series of dated megafaunal bones, we compare the temporal patterns of bone abundance with climate records. Megafaunal abundance tracked ice age climate, peaking during transitions from cold to warm periods. These results suggest that a defining characteristic of the mammoth steppe was its temporal instability and imply that regional extinctions followed by population reestablishment from distant refugia were characteristic features of ice-age biogeography at high latitudes. It follows that long-distance dispersal was crucial for the long-term persistence of megafaunal species living in the Arctic. Such dispersal was only possible when their rapidly shifting range lands were geographically interconnected. The end of the last ice age was fatally unique because the geographic ranges of arctic megafauna became permanently fragmented after stable, interglacial climate engendered the spread of peatlands at the same time that rising sea level severed former dispersal routes.

Three-dimensional CTF correction improves the resolution of electron tomograms.

Correction of the contrast transfer function (CTF) of the microscope is a necessary step, in order to achieve high resolution from averaged electron microscopic images. Thereby, the CTF is first estimated and subsequently the electron micrograph is corrected, so that the negative oscillations of the CTF are equalized. Typically, the CTF correction is performed in 2D and the tilt-induced focus gradient is taken into account. Most often, the sample-thickness-induced focus gradient is ignored. Theoretical considerations, as well as implementation suggestions, for a 3D CTF correction that considers both gradients have been proposed before, although an implementation achieving a resolution improvement has been lacking, primarily due to computational reasons. Here, we present a comprehensive solution for a 3D CTF correction based on the Jensen-Kornberg scheme, which performs a slice-by-slice correction of the CTF within the tomographic reconstruction. We show that the computational requirements are comparable to those of 2D CTF correction. Using the examples of mitochondrial ribosomes and tobacco mosaic virus we demonstrate the improvement of the reconstruction quality with the 3D CTF correction, and the resolution gain on sub-tomogram averaging. More interestingly, for tomographic applications, the quality of the individual sub-tomograms before averaging increases significantly. We find that 3D CTF correction always produces equal or better results than 2D CTF correction.

Upconversion-enabled array spectrometer for the mid-infrared, featuring kilohertz spectra acquisition rates.

Mid-infrared spectroscopy is an essential analytical method in science and industry. Unlike in the near-infrared range, grating spectrometers for the mid-infrared are rarely employed, mostly due to the limited availability and performance of suitable line array detectors. In this work, continuous-wave nonlinear-optical upconversion is used to enable mid-infrared spectroscopy. A broad spectral window between 3.7 and 4.7 µm is upconverted to 825 - 867 nm for detection on a silicon-camera-based near-infrared grating spectrometer with a high sensitivity down to sub-picowatt of input power. A theoretical model is presented that accurately describes the upconversion process and the total system behavior. Spectroscopic flame emission measurements demonstrate the applicability towards the analysis of highly dynamic processes.

American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change.

Existing radiocarbon ((14)C) dates on American mastodon (Mammut americanum) fossils from eastern Beringia (Alaska and Yukon) have been interpreted as evidence they inhabited the Arctic and Subarctic during Pleistocene full-glacial times (∼ 18,000 (14)C years B.P.). However, this chronology is inconsistent with inferred habitat preferences of mastodons and correlative paleoecological evidence. To establish a last appearance date (LAD) for M. americanum regionally, we obtained 53 new (14)C dates on 36 fossils, including specimens with previously published dates. Using collagen ultrafiltration and single amino acid (hydroxyproline) methods, these specimens consistently date to beyond or near the ∼ 50,000 y B.P. limit of (14)C dating. Some erroneously "young" (14)C dates are due to contamination by exogenous carbon from natural sources and conservation treatments used in museums. We suggest mastodons inhabited the high latitudes only during warm intervals, particularly the Last Interglacial [Marine Isotope Stage (MIS) 5] when boreal forests existed regionally. Our (14)C dataset suggests that mastodons were extirpated from eastern Beringia during the MIS 4 glacial interval (∼ 75,000 y ago), following the ecological shift from boreal forest to steppe tundra. Mastodons thereafter became restricted to areas south of the continental ice sheets, where they suffered complete extinction ∼ 10,000 (14)C years B.P. Mastodons were already absent from eastern Beringia several tens of millennia before the first humans crossed the Bering Isthmus or the onset of climate changes during the terminal Pleistocene. Local extirpations of mastodons and other megafaunal populations in eastern Beringia were asynchrononous and independent of their final extinction south of the continental ice sheets.