Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and ...consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.
While conventional random forest regression (RFR) virtual screening models appear to have excellent accuracy on random held-out test sets, they prove lacking in actual practice. Analysis of 18 ...historical virtual screens showed that random test sets are far more similar to their training sets than are the compounds project teams actually order. A new, cluster-based “realistic” training/test set split, which mirrors the chemical novelty of real-life virtual screens, recapitulates the poor predictive power of RFR models in real projects. The original Profile-QSAR (pQSAR) method greatly broadened the domain of applicability over conventional models by using as independent variables a profile of activity predictions from all historical assays in a large protein family. However, the accuracy still fell short of experiment on realistic test sets. The improved “pQSAR 2.0” method replaces probabilities of activity from naïve Bayes categorical models at several thresholds with predicted IC50s from RFR models. Unexpectedly, the high accuracy also requires removing the RFR model for the actual assay of interest from the independent variable profile. With these improvements, pQSAR 2.0 activity predictions are now statistically comparable to medium-throughput four-concentration IC50 measurements even on the realistic test set. Beyond the yes/no activity predictions from a typical high-throughput screen (HTS) or conventional virtual screen, these semiquantitative IC50 predictions allow for predicted potency, ligand efficiency, lipophilic efficiency, and selectivity against antitargets, greatly facilitating hitlist triaging and enabling virtual screening panels such as toxicity panels and overall promiscuity predictions.
Phase Retrieval for Wide Band Signals Jaming, Philippe; Kellay, Karim; Perez, Rolando
The Journal of fourier analysis and applications,
08/2020, Letnik:
26, Številka:
4
Journal Article
Recenzirano
Odprti dostop
This study investigates the phase retrieval problem for wide-band signals. We solve the following problem: given
f
∈
L
2
(
R
)
with Fourier transform in
L
2
(
R
,
e
2
c
|
x
|
d
x
)
, we find all ...functions
g
∈
L
2
(
R
)
with Fourier transform in
L
2
(
R
,
e
2
c
|
x
|
d
x
)
, such that
|
f
(
x
)
|
=
|
g
(
x
)
|
for all
x
∈
R
. To do so, we first translate the problem to functions in the Hardy spaces on the disc via a conformal bijection, and take advantage of the inner-outer factorization. We also consider the same problem with additional constraints involving some transforms of
f
and
g
, and determine if these constraints force uniqueness of the solution.
Summary
Deep‐water access is arguably the most effective, but under‐studied, mechanism that plants employ to survive during drought. Vulnerability to embolism and hydraulic safety margins can predict ...mortality risk at given levels of dehydration, but deep‐water access may delay plant dehydration. Here, we tested the role of deep‐water access in enabling survival within a diverse tropical forest community in Panama using a novel data‐model approach.
We inversely estimated the effective rooting depth (ERD, as the average depth of water extraction), for 29 canopy species by linking diameter growth dynamics (1990–2015) to vapor pressure deficit, water potentials in the whole‐soil column, and leaf hydraulic vulnerability curves. We validated ERD estimates against existing isotopic data of potential water‐access depths.
Across species, deeper ERD was associated with higher maximum stem hydraulic conductivity, greater vulnerability to xylem embolism, narrower safety margins, and lower mortality rates during extreme droughts over 35 years (1981–2015) among evergreen species. Species exposure to water stress declined with deeper ERD indicating that trees compensate for water stress‐related mortality risk through deep‐water access.
The role of deep‐water access in mitigating mortality of hydraulically‐vulnerable trees has important implications for our predictive understanding of forest dynamics under current and future climates.
Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal ...biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation's sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.
Kauffman picture of normal and tumor states as attractors in an abstract state space is used in order to interpret gene expression data for 15 cancer localizations obtained from The Cancer Genome ...Atlas. A principal component analysis of this data unveils the following qualitative aspects about tumors: 1) The state of a tissue in gene expression space can be described by a few variables. In particular, there is a single variable describing the progression from a normal tissue to a tumor. 2) Each cancer localization is characterized by a gene expression profile, in which genes have specific weights in the definition of the cancer state. There are no less than 2500 differentially-expressed genes, which lead to power-like tails in the expression distribution functions. 3) Tumors in different localizations share hundreds or even thousands of differentially expressed genes. There are 6 genes common to the 15 studied tumor localizations. 4) The tumor region is a kind of attractor. Tumors in advanced stages converge to this region independently of patient age or genetic characteristics. 5) There is a landscape of cancer in gene expression space with an approximate border separating normal tissues from tumors.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We prove that if f and g are holomorphic functions on an open connected domain, with the same moduli on two intersecting segments, then
$f=g$
up to the multiplication of a unimodular constant, ...provided the segments make an angle that is an irrational multiple of
$\pi $
. We also prove that if f and g are functions in the Nevanlinna class, and if
$|f|=|g|$
on the unit circle and on a circle inside the unit disc, then
$f=g$
up to the multiplication of a unimodular constant.
Environmental gradients act as potent filters on species distributions driving compositional shifts across communities. Compositional shifts may reflect differences in physiological tolerances to a ...limiting resource that result in broad distributions for tolerant species and restricted distributions for intolerant species (i.e. a nested pattern). Alternatively, trade‐offs in resource use or conflicting species' responses to multiple resources can result in complete turnover of species along gradients.
We combined trait (leaf area, leaf mass per area, wood density and maximum height) and distribution data for 550 tree species to examine taxonomic and functional composition at 72 sites across strong gradients of soil phosphorus (P) and rainfall in central Panama.
We determined whether functional and taxonomic composition was nested or turned over completely and whether community mean traits and species composition were more strongly driven by P or moisture.
Turnover characterized the functional composition of tree communities. Leaf traits responded to both gradients, with species having larger and thinner leaves in drier and more fertile sites than in wetter and less fertile sites. These leaf trait–moisture relationships contradict predictions based on drought responses and suggest a greater role for differences in light availability than in moisture. Shifts in wood density and maximum height were weaker than for leaf traits with taller species dominating wet sites and low wood density species dominating P‐rich sites.
Turnover characterized the taxonomic composition of tree communities. Geographic distances explained a larger fraction of variation for taxonomic composition than for functional composition, and community mean traits were more strongly driven by P than moisture.
Synthesis. Our results offer weak support for the tolerance hypothesis for tree communities in central Panama. Instead, we observe functional and taxonomic turnover reflecting trade‐offs and conflicting species' responses to multiple abiotic factors including moisture, soil phosphorus and potentially other correlated variables (e.g. light).
Our results offer weak support for the tolerance hypothesis for tree communities in central Panama. Instead, we observe functional and taxonomic turnover reflecting trade‐offs and conflicting species' responses to multiple abiotic factors including moisture, soil phosphorus and potentially other correlated variables (e.g. light).
Summary
Tree size shapes forest carbon dynamics and determines how trees interact with their environment, including a changing climate. Here, we conduct the first global analysis of among‐site ...differences in how aboveground biomass stocks and fluxes are distributed with tree size.
We analyzed repeat tree censuses from 25 large‐scale (4–52 ha) forest plots spanning a broad climatic range over five continents to characterize how aboveground biomass, woody productivity, and woody mortality vary with tree diameter. We examined how the median, dispersion, and skewness of these size‐related distributions vary with mean annual temperature and precipitation.
In warmer forests, aboveground biomass, woody productivity, and woody mortality were more broadly distributed with respect to tree size. In warmer and wetter forests, aboveground biomass and woody productivity were more right skewed, with a long tail towards large trees. Small trees (1–10 cm diameter) contributed more to productivity and mortality than to biomass, highlighting the importance of including these trees in analyses of forest dynamics.
Our findings provide an improved characterization of climate‐driven forest differences in the size structure of aboveground biomass and dynamics of that biomass, as well as refined benchmarks for capturing climate influences in vegetation demographic models.
See also the Commentary on this article by Zuidema & van der Sleen, 234: 1544–1546.
The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In ...addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.
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