Many forests of eastern North American are undergoing a species composition shift in which maples (Acer spp.) are increasingly important while oak (Quercus spp.) regeneration and recruitment has ...become increasingly scarce. This dynamic in species composition occurs across a large and geographically complex region. The elimination of fire has been postulated as the driver of this dynamic; however, some assumptions underlying this postulate have not been completely examined, and alternative hypotheses remain underexplored. Through literature review, and a series of new analyses, we examined underlying assumptions of the "oak and fire" hypothesis and explored a series of alternative hypotheses based on well-known ecosystem drivers: climate change, land-use change, the loss of foundation and keystone species, and dynamics in herbivore populations. We found that the oak-maple dynamic began during a shift in climate regime -from a time of frequent, severe, multi-year droughts to a period of increased moisture availability. Anthropogenic disturbance on the landscape changed markedly during this same time, from an era of Native American utilization, to a time characterized by low population densities, to Euro-American settlement and subsequent land transmogrification. During the initiation of the oak-maple dynamic, a foundation species, the American chestnut, was lost as a canopy tree across a broad range. Several important browsers and acorn predators had substantial population dynamics during this period, e.g. white-tailed deer populations grew substantially concurrent with increasing oak recruitment failure. In conclusion, our analyses suggest that oak forests are reacting to marked changes in a suite of interlocking factors. We propose a "multiple interacting ecosystem drivers hypothesis", which provides a more encompassing framework for understanding oak forest dynamics.
Topography exerts strong control on microclimate, resulting in distinctive vegetation patterns in areas of moderate to high relief. Using the Thornthwaite approach to account for hydrologic cycle ...components, a GIS-based Water Balance Toolset is presented as a means to address fine-scale species–site relationships. For each pixel within a study area, the toolset assesses inter-annual variations in moisture demand (governed by temperature and radiation) and availability (precipitation, soil storage). These in turn enable computation of climatic water deficit, the amount by which available moisture fails to meet demand. Summer deficit computed by the model correlates highly with the Standardized Precipitation–Evapotranspiration Index (SPEI) for drought at several sites across the eastern U.S. Yet the strength of the approach is its ability to model fine-scale patterns. For a 25-ha study site in central Indiana, individual tree locations were linked to summer deficit under different historical conditions: using average monthly climatic variables for 1998–2017, and for the drought year of 2012. In addition, future baseline and drought-year projections were modeled based on downscaled GCM data for 2071–2100. Although small deficits are observed under average conditions (historical or future), strong patterns linked to topography emerge during drought years. The modeled moisture patterns capture vegetation distributions described for the region, with beech and maple preferentially occurring in low-deficit settings, and oak and hickory dominating more xeric positions. End-of-century projections suggest severe deficit, which should favor oak and hickory over more mesic species. Pockets of smaller deficit persist on the landscape, but only when a fine-resolution Light Detection and Ranging (LiDAR)-derived Digital Elevation Model (DEM) is used; a coarse-resolution DEM masks fine-scale variability and compresses the range of observed values. Identification of mesic habitat microrefugia has important implications for retreating species under altered climate. Using readily available data to evaluate fine-scale patterns of moisture demand and availability, the Water Balance Toolset provides a useful approach to explore species–environment linkages.
SARS-CoV-2 variants have emerged with enhanced pathogenicity and transmissibility, and escape from pre-existing immunity, suggesting first-generation vaccines and monoclonal antibodies may now be ...less effective. Here we present an approach for preventing clinical sequelae and the spread of SARS-CoV-2 variants. First, we affinity matured an angiotensin-converting enzyme 2 (ACE2) decoy protein, achieving 1000-fold binding improvements that extend across a wide range of SARS-CoV-2 variants and distantly related, ACE2-dependent coronaviruses. Next, we demonstrated the expression of this decoy in proximal airway when delivered via intranasal administration of an AAV vector. This intervention significantly diminished clinical and pathologic consequences of SARS-CoV-2 challenge in a mouse model and achieved therapeutic levels of decoy expression at the surface of proximal airways when delivered intranasally to nonhuman primates. Importantly, this long-lasting, passive protection approach is applicable in vulnerable populations such as the elderly and immune-compromised that do not respond well to traditional vaccination. This approach could be useful in combating COVID-19 surges caused by SARS-CoV-2 variants and should be considered as a countermeasure to future pandemics caused by one of the many pre-emergent, ACE2-dependent CoVs that are poised for zoonosis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In humid, broadleaf-dominated forests where gap dynamics and partial canopy mortality appears to dominate the disturbance regime at local scales, paleoecological evidence shows alteration at ...regional-scales associated with climatic change. Yet, little evidence of these broad-scale events exists in extant forests. To evaluate the potential for the occurrence of large-scale disturbance, we used 76 tree-ring collections spanning ∼840 000 km
2
and 5327 tree recruitment dates spanning ∼1.4 million km
2
across the humid eastern United States. Rotated principal component analysis indicated a common growth pattern of a simultaneous reduction in competition in 22 populations across 61 000 km
2
. Growth-release analysis of these populations reveals an intense and coherent canopy disturbance from 1775 to 1780, peaking in 1776. The resulting time series of canopy disturbance is so poorly described by a Gaussian distribution that it can be described as "heavy tailed," with most of the years from 1775 to 1780 comprising the heavy-tail portion of the distribution. Historical documents provide no evidence that hurricanes or ice storms triggered the 1775-1780 event. Instead, we identify a significant relationship between prior drought and years with elevated rates of disturbance with an intense drought occurring from 1772 to 1775. We further find that years with high rates of canopy disturbance have a propensity to create larger canopy gaps indicating repeated opportunities for rapid change in species composition beyond the landscape scale. Evidence of elevated, regional-scale disturbance reveals how rare events can potentially alter system trajectory: a substantial portion of old-growth forests examined here originated or were substantially altered more than two centuries ago following events lasting just a few years. Our recruitment data, comprised of at least 21 species and several shade-intolerant species, document a pulse of tree recruitment at the subcontinental scale during the late-1600s suggesting that this event was severe enough to open large canopy gaps. These disturbances and their climatic drivers support the hypothesis that punctuated, episodic, climatic events impart a legacy in broadleaf-dominated forests centuries after their occurrence. Given projections of future drought, these results also reveal the potential for abrupt, meso- to large-scale forest change in broadleaf-dominated forests over future decades.
The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for ...both small‐angle X‐ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator containing both Si(111) crystals and Mo/B4C multilayer elements, rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample‐loading robotics, and mail‐in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high‐resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high‐impact results by providing robust cost‐effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.
Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few ...open-source options exist for deploying models in an interactive interface. Experimenting with different deep learning approaches typically requires switching software libraries and reprocessing data, reducing the feasibility and practicality of experimenting with new architectures. We developed a flexible deep learning library for histopathology called Slideflow, a package which supports a broad array of deep learning methods for digital pathology and includes a fast whole-slide interface for deploying trained models. Slideflow includes unique tools for whole-slide image data processing, efficient stain normalization and augmentation, weakly-supervised whole-slide classification, uncertainty quantification, feature generation, feature space analysis, and explainability. Whole-slide image processing is highly optimized, enabling whole-slide tile extraction at 40x magnification in 2.5 s per slide. The framework-agnostic data processing pipeline enables rapid experimentation with new methods built with either Tensorflow or PyTorch, and the graphical user interface supports real-time visualization of slides, predictions, heatmaps, and feature space characteristics on a variety of hardware devices, including ARM-based devices such as the Raspberry Pi.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Genome-wide association studies (GWAS) of chronic lymphocytic leukemia (CLL) have shown that common genetic variation contributes to the heritable risk of CLL. To identify additional CLL ...susceptibility loci, we conducted a GWAS and performed a meta-analysis with a published GWAS totaling 1,739 individuals with CLL (cases) and 5,199 controls with validation in an additional 1,144 cases and 3,151 controls. A combined analysis identified new susceptibility loci mapping to 3q26.2 (rs10936599, P = 1.74 × 10(-9)), 4q26 (rs6858698, P = 3.07 × 10(-9)), 6q25.2 (IPCEF1, rs2236256, P = 1.50 × 10(-10)) and 7q31.33 (POT1, rs17246404, P = 3.40 × 10(-8)). Additionally, we identified a promising association at 5p15.33 (CLPTM1L, rs31490, P = 1.72 × 10(-7)) and validated recently reported putative associations at 5p15.33 (TERT, rs10069690, P = 1.12 × 10(-10)) and 8q22.3 (rs2511714, P = 2.90 × 10(-9)). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CLL.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
PDF
