Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT ...reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.
Whole-body attenuation correction (AC) is still challenging in combined PET/MR scanners. We describe Dixon-VIBE Deep Learning (DIVIDE), a deep-learning network that allows synthesizing pelvis ...pseudo-CT maps based only on the standard Dixon volumetric interpolated breath-hold examination (Dixon-VIBE) images currently acquired for AC in some commercial scanners.
We propose a network that maps between the four 2-dimensional (2D) Dixon MR images (water, fat, in-phase, and out-of-phase) and their corresponding 2D CT image. In contrast to previous methods, we used transposed convolutions to learn the up-sampling parameters, we used whole 2D slices to provide context information, and we pretrained the network with brain images. Twenty-eight datasets obtained from 19 patients who underwent PET/CT and PET/MR examinations were used to evaluate the proposed method. We assessed the accuracy of the μ-maps and reconstructed PET images by performing voxel- and region-based analysis comparing the SUVs (in g/mL) obtained after AC using the Dixon-VIBE (PET
), DIVIDE (PET
), and CT-based (PET
) methods. Additionally, the bias in quantification was estimated in synthetic lesions defined in the prostate, rectum, pelvis, and spine.
Absolute mean relative change values relative to CT AC were lower than 2% on average for the DIVIDE method in every region of interest except for bone tissue, where it was lower than 4% and 6.75 times smaller than the relative change of the Dixon method. There was an excellent voxel-by-voxel correlation between PET
and PET
(
= 0.9998,
< 0.01). The Bland-Altman plot between PET
and PET
showed that the average of the differences and the variability were lower (mean PET
-PET
SUV, 0.0003; PET
-PET
SD, 0.0094; 95% confidence interval, -0.0180,0.0188) than the average of differences between PET
and PET
(mean PET
-PET
SUV, 0.0006; PET
-PET
SD, 0.0264; 95% confidence interval, -0.0510,0.0524). Statistically significant changes in PET data quantification were observed between the 2 methods in the synthetic lesions, with the largest improvement in femur and spine lesions.
The DIVIDE method can accurately synthesize a pelvis pseudo-CT scan from standard Dixon-VIBE images, allowing for accurate AC in combined PET/MR scanners. Additionally, our implementation allows rapid pseudo-CT synthesis, making it suitable for routine applications and even allowing retrospective processing of Dixon-VIBE data.
MRI has emerged as the most comprehensive non-invasive diagnostic tool for liver diseases. In recent years, the value of MRI in hepatology has been significantly enhanced by a wide range of contrast ...agents, both clinically available and under development, that add functional information to anatomically detailed morphological images, or increase the distinction between normal and pathological tissues by targeting molecular and cellular events. Several classes of contrast agents are available for contrast-enhanced hepatic MRI, including i) conventional non-specific extracellular fluid contrast agents for assessing tissue perfusion; ii) hepatobiliary-specific contrast agents that are taken up by functioning hepatocytes and excreted through the biliary system for evaluating hepatobiliary function; iii) superparamagnetic iron oxide particles that accumulate in Kupffer cells; and iv) novel molecular contrast agents that are biochemically targeted to specific molecular/cellular processes for staging liver diseases or detecting treatment responses. The use of different functional and molecular MRI methods enables the non-invasive assessment of disease burden, progression, and treatment response in a variety of liver diseases. A high diagnostic performance can be achieved with MRI by combining imaging biomarkers.
We analyze the propagation of excitons in a d-dimensional lattice with power-law hopping ∝1/rα in the presence of dephasing, described by a generalized Haken-Strobl-Reineker model. We show that in ...the strong dephasing (quantum Zeno) regime the dynamics is described by a classical master equation for an exclusion process with long jumps. In this limit, we analytically compute the spatial distribution, whose shape changes at a critical value of the decay exponent αcr=(d+2)/2. The exciton always diffuses anomalously: a superdiffusive motion is associated to a Lévy stable distribution with long-range algebraic tails for α≤αcr, while for α>αcr the distribution corresponds to a surprising mixed Gaussian profile with long-range algebraic tails, leading to the coexistence of short-range diffusion and long-range Lévy flights. In the many-exciton case, we demonstrate that, starting from a domain-wall exciton profile, algebraic tails appear in the distributions for any α, which affects thermalization: the longer the hopping range, the faster equilibrium is reached. Our results are directly relevant to experiments with cold trapped ions, Rydberg atoms, and supramolecular dye aggregates. They provide a way to realize an exclusion process with long jumps experimentally.
Hepatobiliary-specific contrast agents are one of several classes of contrast agents available for magnetic resonance (MR) imaging of the liver. These agents are taken up by functioning hepatocytes ...and excreted in the bile, and their paramagnetic properties cause shortening of the longitudinal relaxation time (T1) of the liver and biliary tree. The three contrast agents that have been developed are mangafodipir trisodium (Mn-DPDP), gadobenate dimeglumine (Gd-BOPTA), and gadoxetic acid (Gd-EOB-DTPA). These three MR contrast agents vary in mode of administration and dose, mechanism of cellular uptake, degree of excretion through the biliary pathway, and imaging characteristics. In the liver, hepatobiliary-specific agents can be used to improve lesion detection, to characterize lesions as hepatocellular or nonhepatocellular, and to specifically characterize some hepatocellular lesions, notably focal nodular hyperplasia. Biliary excretion of these agents can be used to evaluate the anatomic structure and function of the biliary tree. In the future, hepatobiliary-specific contrast agents may have wider applications, such as grading of cirrhosis and quantification of liver function.
Premise of research. Phylogenetic relationships of Araucariaceae (Coniferophyta, Araucariales) are revised on the basis of the first combined data matrix for the family.
Methodology. Taxon sampling ...includes 39 ingroup species (31 extant, 8 fossils) and outgroup species of all the remaining conifer families. Five fossilAraucariaspecies, one species of the genusAraucarites, and two species of the extinct generaWairarapaiaandEmwadeawere included in the analyses. Character sampling includes 23 genomic regions (19 plastid, 2 nuclear, and 2 mitochondrial) and 62 morphological characters (52 discrete and 10 continuous). The phylogenetic analyses were conducted with equally weighted parsimony. Additionally, several analyses under different taxon- and gene-sampling regimes were analyzed for identifying the causes of the long-lasting controversies in the interrelationships of the three extant genera of Araucariaceeae.
Pivotal results. Monophyletic Araucariaceae is the sister group of Podocarpaceae, forming the order Araucariales. Monophyly ofAraucariaandAgathisis also strongly supported by the data. The results of both molecular and combined analyses indicate thatWollemiaandAgathisform a clade (=agathioid clade) sister toAraucaria. WithinAraucaria, the analyses support the monophyly of the four currently recognized sections:Araucaria,Bunya,Intermedia, andEutacta. Results support the monophyly of living and fossilAraucaria(includingAraucarites), whereas the remaining extinct genera are placed as the stem of the agathioid clade. In terms of the sensitivity analyses performed, results suggest that inconsistencies among previous results would be related to ingroup sampling.
Conclusions. By means of a combined phylogenetic analysis, we have been able to obtain a strongly supported and well-resolved phylogeny of Araucariaceae that includes both living species and fossil species for the group. This study shows the feasibility and usefulness of phylogenetic analyses that incorporate multiple sources of evidence (molecules/morphology, living/fossil species, discrete/continuous characters).
Robust evidence from phylogenomic analyses of 997 nuclear genes has recently shown, beyond doubt, that the genus
is polyphyletic with three separate lineages, each with affinities to other genera of ...mimosoids: (i)
is an isolated lineage placed in the grade of
,
and
that subtends the core mimosoid clade; (ii) the remaining Old World species of
form a clade that is sister to the Indo-Nepalese monospecific genus
and (iii) New World
has the Namibian / Namaqualand monospecific endemic genus
nested within it. This means that it is now clear that maintaining the unity of the genus
sensu Burkart (1976) is no longer tenable. These three distinct lineages of
species correspond directly to Burkart's (1976) sectional classification of the genus, to previously recognised genera and to the differences in types of armature that underpin Burkart's sections. Here, we address this non-monophyly by resurrecting three segregate genera -
,
and
and provide 57 new name combinations where necessary, while maintaining the morphologically distinctive and geographically isolated genera
and
. The genus
itself is reduced to just three species and an emended description is presented. The impacts of these name changes for a genus of such high ecological and human use importance are discussed. These impacts are mitigated by clear differences in armature which facilitate identification and by potential benefits from the deeper biological understanding brought about by recognition of these divergent lineages at generic rank. We provide an identification key to genera and present a map showing the distributions of the segregate genera, as well as drawings and photos illustrating variation in armature and fruits.
Individuals with type 2 diabetes mellitus (T2DM) have an increased risk of bone fragility fractures compared to nondiabetic subjects. This increased fracture risk may occur despite normal or even ...increased values of bone mineral density (BMD), and poor bone quality is suggested to contribute to skeletal fragility in this population. These concepts explain why the only evaluation of BMD could not be considered an adequate tool for evaluating the risk of fracture in the individual T2DM patient. Unfortunately, nowadays, the bone quality could not be reliably evaluated in the routine clinical practice. On the other hand, getting further insight on the pathogenesis of T2DM-related bone fragility could consent to ameliorate both the detection of the patients at risk for fracture and their appropriate treatment. The pathophysiological mechanisms underlying the increased risk of fragility fractures in a T2DM population are complex. Indeed, in T2DM, bone health is negatively affected by several factors, such as inflammatory cytokines, muscle-derived hormones, incretins, hydrogen sulfide (H2S) production and cortisol secretion, peripheral activation, and sensitivity. All these factors may alter bone formation and resorption, collagen formation, and bone marrow adiposity, ultimately leading to reduced bone strength. Additional factors such as hypoglycemia and the consequent increased propensity for falls and the direct effects on bone and mineral metabolism of certain antidiabetic medications may contribute to the increased fracture risk in this population. The purpose of this review is to summarize the literature evidence that faces the pathophysiological mechanisms underlying bone fragility in T2DM patients.
BACKGROUND: Literature describing temporal variation in the secondary sex ratio among humans reports an association between population stressors and declines in the odds of male birth. Explanations ...of this phenomenon draw on reports that stressed females spontaneously abort male more than female fetuses, and that stressed males exhibit reduced sperm motility. This work has led to the argument that population stress induced by a declining economy reduces the human sex ratio. No direct test of this hypothesis appears in the literature. Here, a test is offered based on a comparison of the sex ratio in East and West Germany for the years 1946 to 1999. The theory suggests that the East German sex ratio should be lower in 1991, when East Germany’s economy collapsed, than expected from its own history and from the sex ratio in West Germany. METHODS: The hypothesis is tested using time‐series modelling methods. RESULTS: The data support the hypothesis. The sex ratio in East Germany was at its lowest in 1991. CONCLUSION: This first direct test supports the hypothesis that economic decline reduces the human sex ratio.
The sizes of life Tekwa, Eden W; Catalano, Katrina A; Bazzicalupo, Anna L ...
PloS one,
03/2023, Letnik:
18, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Recent research has revealed the diversity and biomass of life across ecosystems, but how that biomass is distributed across body sizes of all living things remains unclear. We compile the ...present-day global body size-biomass spectra for the terrestrial, marine, and subterranean realms. To achieve this compilation, we pair existing and updated biomass estimates with previously uncatalogued body size ranges across all free-living biological groups. These data show that many biological groups share similar ranges of body sizes, and no single group dominates size ranges where cumulative biomass is highest. We then propagate biomass and size uncertainties and provide statistical descriptions of body size-biomass spectra across and within major habitat realms. Power laws show exponentially decreasing abundance (exponent -0.9±0.02 S.D., R2 = 0.97) and nearly equal biomass (exponent 0.09±0.01, R2 = 0.56) across log size bins, which resemble previous aquatic size spectra results but with greater organismal inclusivity and global coverage. In contrast, a bimodal Gaussian mixture model describes the biomass pattern better (R2 = 0.86) and suggests small (~10-15 g) and large (~107 g) organisms outweigh other sizes by one order magnitude (15 and 65 Gt versus ~1 Gt per log size). The results suggest that the global body size-biomass relationships is bimodal, but substantial one-to-two orders-of-magnitude uncertainty mean that additional data will be needed to clarify whether global-scale universal constraints or local forces shape these patterns.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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