Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the ...analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin's ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We report on nonsequential double ionization of Ar by a laser pulse consisting of two counterrotating circularly polarized fields (390 and 780 nm). The double-ionization probability depends strongly ...on the relative intensity of the two fields and shows a kneelike structure as a function of intensity. We conclude that double ionization is driven by a beam of nearly monoenergetic recolliding electrons, which can be controlled in intensity and energy by the field parameters. The electron momentum distributions show the recolliding electron as well as a second electron which escapes from an intermediate excited state of Ar^{+}.
Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the ...frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100-200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transformation.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with fragment ions, we deduce the ...molecule's orientation and photoelectron emission direction in the laboratory frame. Thereby, we retrieve a fourfold differential PECD clearly beyond 50%. This strong chiral asymmetry is reproduced by ab initio electronic structure calculations. Providing such a pronounced contrast makes PECD of fixed-in-space chiral molecules an even more sensitive tool for chiral recognition in the gas phase.
Depression diagnosis requires five or more symptoms (Diagnostic and Statistical Manual of Mental Disorders-DSM-5). One of them must be either Depressed mood or Anhedonia, named main criteria. ...Although the secondary symptoms can be divided into somatic and non-somatic clusters, the DSM-5 identify depression in all or none fashion. In contrast, depression severity is a continuous variable. Therefore, it is commonly assessed with scales such as the Hamilton Depression Rating Scale (HAMD). Previously, we reported that patients with moderate depression (MD) exhibit greater impairments in cardiac-autonomic modulation than severely depressed (SD) patients. However, clinicians usually do not use scales.
To verify whether the DSM-5 symptoms would be able to discriminate SD from MD and MD from non-depressed (ND) subjects.
Depression was diagnosed based on the Structured Clinical Interview for DSM-5® Disorders. The HAMD evaluated depression severity. In depressed subjects, MD and SD were defined considering the HAMD scores. ND was defined considering both the absence of DSM-5 criteria for depression and the HAMD score. Among 782 outpatients, 46 SD were found. MD and ND subjects were randomly sampled to match the demographic variables of the SD group.
Discriminant analysis showed that Depressed Mood was the most reliable symptom to discriminate ND from MD. Anhedonia discriminated SD from MD. Among the secondary DSM-5 criteria, the somatic cluster discriminated ND from MD and the non-somatic cluster SD from MD patients.
The presence of the somatic cluster in MD may indicate decreased vagal tone and/or increased sympathetic tone, leading to higher cardiovascular risk. As SD is associated with the non-somatic cluster, these patients are at risk of committing suicide. The DSM-5 symptoms exhibited by the patient may help the choice of adequate pharmacological treatment. This would avoid the use of antidepressants that unnecessarily increase cardiac risk in MD. When the symptom cluster suggests SD, the treatment must focus on the prevention of suicide.
Depression severity may be inferred based on the DSM-5 criteria. The presence of the Anhedonia main criterium accompanied by non-somatic criteria indicate SD. The Depressive Mood criterium followed by somatic criteria suggest MD.
Abstract
When a very strong light field is applied to a molecule an electron can be ejected by tunneling. In order to quantify the time-resolved dynamics of this ionization process, the concept of ...the Wigner time delay can be used. The properties of this process can depend on the tunneling direction relative to the molecular axis. Here, we show experimental and theoretical data on the Wigner time delay for tunnel ionization of H
2
molecules and demonstrate its dependence on the emission direction of the electron with respect to the molecular axis. We find, that the observed changes in the Wigner time delay can be quantitatively explained by elongated/shortened travel paths of the emitted electrons, which occur due to spatial shifts of the electrons’ birth positions after tunneling. Our work provides therefore an intuitive perspective towards the Wigner time delay in strong-field ionization.
We report on the nonadiabatic offset of the initial electron momentum distribution in the plane of polarization upon single ionization of argon by strong field tunneling and show how to ...experimentally control the degree of nonadiabaticity. Two-color counter- and corotating fields (390 and 780 nm) are compared to show that the nonadiabatic offset strongly depends on the temporal evolution of the laser electric field. We introduce a simple method for the direct access to the nonadiabatic offset using two-color counter- and corotating fields. Further, for a single-color circularly polarized field at 780 nm, we show that the radius of the experimentally observed donutlike distribution increases for increasing momentum in the light propagation direction. Our observed initial momentum offsets are well reproduced by the strong-field approximation. A mechanistic picture is introduced that links the measured nonadiabatic offset to the magnetic quantum number of virtually populated intermediate states.
This Progress Report highlights recent developments in dye‐sensitized solar cells composed of both liquid electrolytes and solid‐state hole transport materials. The authors discuss and review the ...present understanding of and recent developments in the operational processes, such as charge generation, transport, recombination, and charge collection. Also, the merits and challenges of alternative device approaches are discussed, including extremely thin absorber cells, devices containing inorganic p‐type hole‐transporters and non‐TiO2 mesoporous metal‐oxide electrodes employed in dye‐sensitized solar cells.
Liquid‐electrolyte and solid‐state dye‐sensitized solar cells (DSCs) are an important candidate for future energy solutions. Recent developments in DSC research are highlighted in this Progress Report . Underlying processes, such as charge generation, transport, recombination, and charge collection are discussed. Recently developed alternative device concepts are also described, including extremely thin absorber cells, inorganic p‐type hole‐transporter cells, and a range of non‐TiO2 mesoporous metal‐oxide electrodes employed in DSCs.
BACKGROUND
Across the developed world couples are postponing parenthood. This review assesses the consequences of delayed family formation from a demographic and medical perspective. One main focus ...is on the quantitative importance of pregnancy postponement.
METHODS
Medical and social science databases were searched for publications on relevant subjects such as delayed parenthood, female and male age, fertility, infertility, time to pregnancy (TTP), fetal death, outcome of medically assisted reproduction (MAR) and mental well-being.
RESULTS
Postponement of parenthood is linked to a higher rate of involuntary childlessness and smaller families than desired due to increased infertility and fetal death with higher female and male age. For women, the increased risk of prolonged TTP, infertility, spontaneous abortions, ectopic pregnancies and trisomy 21 starts at around 30 years of age with a more pronounced effects >35 years, whereas the increasing risk of preterm births and stillbirths starts at around 35 years with a more pronounced effect >40 years. Advanced male age has an important but less pronounced effect on infertility and adverse outcomes. MAR treatment cannot overcome the age-related decline in fecundity.
CONCLUSIONS
In general, women have partners who are several years older than themselves and it is important to focus more on the combined effect of higher female and male age on infertility and reproductive outcome. Increasing public awareness of the impact of advanced female and male age on the reproductive outcome is essential for people to make well-informed decisions on when to start family formation.
DNA nanotechnology enables the synthesis of nanometer‐sized objects that can be site‐specifically functionalized with a large variety of materials. For these reasons, DNA‐based devices such as DNA ...origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)–polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost‐effective, and robust route to protect DNA‐based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded.
Polymeric protection: DNA origami nanostructures generally need higher ionic strengths than those of common cell culture buffers to maintain their integrity and are quickly degraded by nucleases. They can, however, be protected from these processes through the formation of polyplex micelles with poly(ethylene glycol)‐b‐polylysine.
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