Search

Abstract Vortex beams are currently drawing a great deal of interest, from fundamental research to several promising applications. While their generation in bulky optical devices limits their use in integrated complex systems, metasurfaces have recently proven successful in creating optical vortices, especially in the linear regime. In the nonlinear domain, of strategic importance for the future of classical and quantum information, to date orbital angular momentum has only been created in qualitative ways, without discussing discrepancies between design and experimental results. Here, we demonstrate and analyze the generation of high-purity second harmonic (SH) optical vortices via dielectric meta-holograms. Through full-wave simulations and a proper fabrication protocol, we achieve efficient frequency doubling of an unstructured pump beam into SH vortices with topological charges from 1 to 10. Interferometric and modal-purity measurements confirm the generation of high-quality SH vortices with minimal deviations from the intended design thanks to a quasi-local control over the SH phase. Through systematic comparisons between experimental data and semi-analytical calculations, we also provide a clear insight into the occurrence of ghost vortices in the metasurface-generated harmonic beams, highlighting the importance of simple designs that can be readily transposed into fabricated devices with high fidelity. Our findings underscore the potential of nonlinear dielectric metasurfaces for versatile structured-light generation and manipulation, paving the way for future developments in integrated photonic systems.

Abstract Switching of light polarization on the sub-picosecond timescale is a crucial functionality for applications in a variety of contexts, including telecommunications, biology and chemistry. The ability to control polarization at ultrafast speed would pave the way for the development of unprecedented free-space optical links and of novel techniques for probing dynamical processes in complex systems, as chiral molecules. Such high switching speeds can only be reached with an all-optical paradigm, i.e., engineering active platforms capable of controlling light polarization via ultrashort laser pulses. Here we demonstrate giant modulation of dichroism and birefringence in an all-dielectric metasurface, achieved at low fluences of the optical control beam. This performance, which leverages the many degrees of freedom offered by all-dielectric active metasurfaces, is obtained by combining a high-quality factor nonlocal resonance with the giant third-order optical nonlinearity dictated by photogenerated hot carriers at the semiconductor band edge.

Abstract Mutually entangled multi-photon states are at the heart of all-optical quantum technologies. While impressive progresses have been reported in the generation of such quantum light states using free space apparatus, high-fidelity high-rate on-chip entanglement generation is crucial for future scalability. In this work, we use a bright quantum-dot based single-photon source to demonstrate the high fidelity generation of 4-photon Greenberg-Horne-Zeilinger (GHZ) states with a low-loss reconfigurable glass photonic circuit. We reconstruct the density matrix of the generated states using full quantum-state tomography reaching an experimental fidelity to the target state of $${{{{\mathcal{F}}}}}_{{{{{\rm{GHZ}}}}}_{4}}=(86.0\pm 0.4)\, \%$$ F GHZ 4 = ( 86.0 ± 0.4 ) % , and a purity of $${{{{\mathcal{P}}}}}_{{{{{\rm{GHZ}}}}}_{4}}=(76.3\pm 0.6)\, \%$$ P GHZ 4 = ( 76.3 ± 0.6 ) % . The entanglement of the generated states is certified with a semi device-independent approach through the violation of a Bell-like inequality by more than 39 standard deviations. Finally, we carry out a four-partite quantum secret sharing protocol on-chip where a regulator shares with three interlocutors a sifted key with up to 1978 bits, achieving a qubit-error rate of 10.87%. These results establish that the quantum-dot technology combined with glass photonic circuitry offers a viable path for entanglement generation and distribution.

Glucose isomerase (GI) is an enzyme with high potential applications. Characterization of GI producing bacteria with interesting properties from an industrial point of view is essential. Bacillus sp., Paenarthrobacter sp., Chryseobacterium sp., Hymenobacter sp., Mycobacterium sp., and Stenotrophomonas sp. were isolated from soil samples. Optimization of enzyme production yield was investigated in various fermentation conditions using response surface methodology. All isolates exhibited maximum GI activity at 40 °C, pH 6–8 after 4 days of incubation. A mixture of peptone/yeast extract or tryptone/peptone enhanced higher enzyme production. The same trend was observed in fermentation medium containing 1% xylose or 2%–2.5% wheat straw. This study advanced the knowledge of these bacterial isolates in promoting wheat straw as feedstock for the bio-based industry.

Objective: Annexin A5 is a phosphatidylserine binding protein with anti-inflammatory, anticoagulant and anti-apoptotic properties. Preclinical studies have shown that annexin A5 inhibits pro-inflammatory responses and improves organ function and survival in rodent models of sepsis. This clinical trial aimed to evaluate the pharmacokinetic (PK) properties of the recombinant human annexin A5 (SY-005) in severe COVID-19.Methods: This was a pilot randomized, double-blind, placebo-controlled trial. Severe COVID-19 patients were randomly assigned to receive intravenous 50 μg/kg (low dose, n = 3), 100 μg/kg (high dose, n = 5) of SY-005 or placebo (n = 5) every 12 h for 7 days. Plasma SY-005 levels were assessed using enzyme-linked immunosorbent assay (ELISA) and the PK parameters were determined using non-compartmental analysis.Results: All patients treated with SY-005 had a normal baseline estimated glomerular filtration rate (eGFR, 104–125 mL/min/1.73 m2). Both low and high doses of SY-005 were cleared within 6 h after intravenous administration. Plasma maximum concentrations (Cmax), half-life, clearance and volume distribution of low and high doses of SY-005 were 402.4 and 848.9 ng/mL, 0.92 and 0.96 h, 7.52 and 15.19 L/h, and 9.98 and 20.79 L, respectively. Daily pre-dose circulating annexin A5 levels were not significantly different when SY-005 was administered at the low or the high dose 12-h intervals. There was no significant effect on activated partial thromboplastin time (aPTT) or INR (international normalized ratio of prothrombin time) during 7 days of SY-005 treatment.Conclusion: SY-005 doses of 50 and 100 μg/kg were detectable and subsequently cleared from the plasma in severe COVID-19 patients with normal baseline renal function. There was no significant plasma SY-005 accumulation 6 h after drug administration and coagulation was not altered during 7 days of treatment.Clinical trials Registration: This study was registered with ClinicalTrials.gov (NCT04748757, first posted on 10 February 2021).

Understanding the behaviors of droplets at nanoscales is crucial to many applications, yet it remains experimentally challenging to track them in real time. Here, Sbarra et al. use a miniature optomechanical resonator to probe the evaporation dynamics of attoliter droplets with millisecond resolution.

High fructose corn syrup has been industrially produced by converting glucose to fructose by glucose isomerases, tetrameric metalloenzymes widely used in industrial biocatalysis. Advances in enzyme engineering and commercial production of glucose isomerase have paved the way to explore more efficient variants of these enzymes. The 5-hydroxymethylfurfural can be produced from high fructose corn syrup catalytic dehydration, and it can be further converted into various furanic compounds chemically or biologically for various industrial applications as a promising platform chemical. Although the chemical conversion of 5-hydroxymethylfurfural into furanic compounds has been extensively investigated in recent years, bioconversion has shown promise for its mild conditions due to the harsh chemical reaction conditions. This review discusses protein engineering potential for improving glucose isomerase production and recent advancements in bioconversion of 5-hydroxymethylfurfural into value-added furanic derivatives. It suggests biological strategies for the industrial transformation of 5-hydroxymethylfurfural.

The elementary excitations in weakly interacting quantum fluids have a nontrivial nature which is at the basis of defining quantum phenomena such as superfluidity. These excitations and the physics they lead to have been explored in closed quantum systems at thermal equilibrium both theoretically within the celebrated Bogoliubov framework and experimentally in quantum fluids of ultracold atoms. Over the past decade, the relevance of Bogoliubov excitations has become essential to understand quantum fluids of interacting photons. Their driven-dissipative character leads to distinct properties with respect to their equilibrium counterparts. For instance, the condensate coupling to the photonic vacuum environment leads to a nonzero generation rate of elementary excitations with many striking implications. In this work, considering that quantum fluids of light are often hosted in solid-state systems, we show within a joint theory-experiment analysis that the vibrations of the crystal constitute another environment that the condensate is fundamentally coupled to. This coupling leads to a unique heat transfer mechanism, resulting in a large generation rate of elementary excitations in typical experimental conditions, and to a fundamental nonzero contribution at vanishing temperatures. Our work provides a complete framework for solid-embedded quantum fluids of light, which is invaluable in view of achieving a regime dominated by photon-vacuum fluctuations.

The present study identified the pectinase-producing bacterium isolated from the contaminated broth as Bacillus sp. on 16S rDNA sequence analysis. The bacterium illustrated water-like droplets on the colony grown on the Sabouraud dextrose agar plate. It also exhibited multi-enzymes activities, such as pectinase, polygalacturonase, xylanase, and cellulase by using various agro-wastes as low-cost substrates. The orange peel was observed to be the best substrate among the agro-wastes used for maximum multi-enzymes (pectinase, polygalacturonase, xylanase, and cellulase). However, the bacterium demonstrated its capability to produce different enzymes according to the different substrates/agro-wastes used. The Plackett–Burman design was used to determine the essential influencing factors, while the Box Behnken design response surface methodology was for optimizing cultural conditions. At their optimal conditions (40°C incubation temperature, 24 h of incubation period, 1% w/v orange peel, and 2% v/v inoculum volume), the bacterium exhibited the maximum pectinase (9.49 ± 1.25 U/ml) and xylanase (16.27 ± 0.52 U/ml) activities. Furthermore, the study explored the ability of the bacterium to produce bacterial lipids and observed about 25% bacterial lipid content on a dry weight basis. Therefore, the bacterium is a good candidate for producing important multi-enzymes and subsequent agro-waste degradation controlling the environment, and facilitating waste management. Also, the bacterium can be a potential feedstock in producing renewable biofuel.

Abstract Quantum communication networks enable applications ranging from highly secure communication to clock synchronization and distributed quantum computing. Miniaturized, flexible, and cost-efficient resources will be key elements for ensuring the scalability of such networks as they progress towards large-scale deployed infrastructures. Here, we bring these elements together by combining an on-chip, telecom-wavelength, broadband entangled photon source with industry-grade flexible-grid wavelength division multiplexing techniques, to demonstrate reconfigurable entanglement distribution between up to 8 users in a resource-optimized quantum network topology. As a benchmark application we use quantum key distribution, and show low error and high secret key generation rates across several frequency channels, over both symmetric and asymmetric metropolitan-distance optical fibered links and including finite-size effects. By adapting the bandwidth allocation to specific network constraints, we also illustrate the flexible networking capability of our configuration. Together with the potential of our semiconductor source for distributing secret keys over a 60 nm bandwidth with commercial multiplexing technology, these results offer a promising route to the deployment of scalable quantum network architectures.

Owing to its driven-dissipative nature, and its solid-state environment, a resonantly driven polariton condensate can be accompanied by an incoherent reservoir of excitons. Stepanov et al. demonstrate that this situation strongly modifies the spectrum of collective excitations, which determines many quantum hydrodynamic features in a polariton fluid.

We report on a universal method to measure the genuine indistinguishability of n photons—a crucial parameter that determines the accuracy of optical quantum computing. Our approach relies on a low-depth cyclic multiport interferometer with N=2n modes, leading to a quantum interference fringe whose visibility is a direct measurement of the genuine n-photon indistinguishability. We experimentally demonstrate this technique for an eight-mode integrated interferometer fabricated using femtosecond laser micromachining and four photons from a quantum dot single-photon source. We measure a four-photon indistinguishability up to 0.81±0.03. This value decreases as we intentionally alter the photon pairwise indistinguishability. The low-depth and low-loss multiport interferometer design provides an original path to evaluate the genuine indistinguishability of resource states of increasing photon number.

The transient optical response of multiresonant all‐dielectric nanoantennas via a combination of broadband ultrafast reflectivity experiments and nonlinear optics nanoscale modeling is studied. Ultrafast all‐optical control of the reflectivity is demonstrated in variably sized Al.18Ga.82As nanoantennas over four distinct Mie resonances (including Fano‐like resonances), spanning a broad spectral range, from the red to the near‐infrared. A spatially inhomogeneous dynamical model, which accounts for diffusion of the photogenerated carriers inside the semiconductor, is introduced and exploited to isolate the physical phenomena leading to the overall transient response, namely, Drude plasma formation and Pauli blocking following band filling and thermo‐optical effect. The results pave the way to the development of multiwavelength all‐optically reconfigurable filters for next‐generation ultrafast add/drop multiplexing.

Microalgae have the potential to grow in nutrient-rich environments and have the ability to accumulate nutrients from wastewater. The nutrients in malting wastewater are ideal for microalgae cultivation. However, there is limited published work on the growth characteristics of freshwater microalgae grown in malting effluent. This study examined the potential of diluted malting effluent for the growth of freshwater green algae Chlorella sp. and Chlamydomonas sp. isolated from northern Ontario and subsequent biomass and lipid production. Under the 18:6 h light/dark cultivation cycle, the highest cell number counted (540 × 104 cell·mL−1 on day 20) and total chlorophyll content were found in 50% diluted malting effluents for Chlorella sp., whereas the 70% dilution concentration was the most productive for Chlamydomonas (386 × 104 cell·mL−1 on day 16). The total lipid content was higher in the 50% dilution concentration of malting effluent in both Chlorella sp. (maximum 20.5%–minimum 11.5% of dry weight) and Chlamydomonas sp. (max 39.3%–min 25.9% of dry weight). These results emphasize the suitability of using unsterile diluted malting effluent for microalgae cultivation.

Background: Dielectric nanoantennas have recently emerged as an alternative solution to plasmonics for nonlinear light manipulation at the nanoscale, thanks to the magnetic and electric resonances, the strong nonlinearities, and the low ohmic losses characterizing high refractive-index materials in the visible/near-infrared (NIR) region of the spectrum. In this frame, AlGaAs nanoantennas demonstrated to be extremely efficient sources of second harmonic radiation. In particular, the nonlinear polarization of an optical system pumped at the anapole mode can be potentially boosted, due to both the strong dip in the scattering spectrum and the near-field enhancement, which are characteristic of this mode. Plasmonic nanostructures, on the other hand, remain the most promising solution to achieve strong local field confinement, especially in the NIR, where metals such as gold display relatively low losses.Results: We present a nonlinear hybrid antenna based on an AlGaAs nanopillar surrounded by a gold ring, which merges in a single platform the strong field confinement typically produced by plasmonic antennas with the high nonlinearity and low loss characteristics of dielectric nanoantennas. This platform allows enhancing the coupling of light to the nanopillar at coincidence with the anapole mode, hence boosting both second- and third-harmonic generation conversion efficiencies. More than one order of magnitude enhancement factors are measured for both processes with respect to the isolated structure.Conclusion: The present results reveal the possibility to achieve tuneable metamixers and higher resolution in nonlinear sensing and spectroscopy, by means of improved both pump coupling and emission efficiency due to the excitation of the anapole mode enhanced by the plasmonic nanoantenna.

We experimentally demonstrate the possibility to modulate the second harmonic (SH) power emitted by nonlinear AlGaAs metasurfaces embedded in a liquid crystal (LC) matrix. This result is obtained by changing the relative in-plane orientation between the LC director and the linear polarization of the light at the excitation wavelength. According to numerical simulations, second-harmonic is efficiently radiated by the metasurfaces thanks to the sizeable second-order susceptibility of the material and the resonant excitation of either electric or magnetic dipole field distributions inside each meta-atom at the illuminating fundamental wavelength. This resonant behavior strongly depends on the geometric parameters, the crystallographic orientation, and the anisotropy of the metasurface, which can be optimized to modulate the emitted SH power by about one order of magnitude. The devised hybrid platforms are therefore appealing in view of enabling the electrical control of flat nonlinear optical devices.

Pectinases are a group of enzymes with broad application, including in plant fiber processing, pectic wastewater treatment, paper pulping, fruit juice extraction, and clarification. With an increasing industrial demand for these enzymes, it is useful to isolate organisms that produce large amounts of pectinase and possess wide ranges of stability factors like temperature and pH. In this study, 17 out of 29 bacteria (58.62%) from forest soil samples were pectinolytic. However, only four bacteria (S-5, S-10, S-14, and S-17) showed high pectin hydrolysis zones (ranging from 0.2 cm to 1.7 cm). These four bacteria were identified based on colony morphology, microscopic characterization, biochemical characteristics, and 16S rDNA sequencing. They were designated as Streptomyces sp. (S-5, S-14), Cellulomonas sp. (S-10), and Bacillus sp. (S-17). Interestingly, bacteria showed cellulase and xylanase activity in addition to pectinase. The quantitative assay for pectinase activity of the four isolates provided proof that they are pectinase producers and can be considered potential candidates for industrial uses. The crude enzyme extracts of these bacteria are applicable in oil and juice extraction from sesame seeds and apples, respectively.

Aligning the resonances of sets of optical cavities is necessary for advanced photonics and sensing applications. Here, the authors introduce resonant photoelectrochemical etching as a method to collectively and permanently tune the resonant wavelengths of ensembles of resonators on a photonic chip.

Due to adjustable modal birefringence, suspended AlGaAs optical waveguides with submicron transverse sections can support phase-matched frequency mixing in the whole material transparency range, even close to the material bandgap, by tuning the width-to-height ratio. Furthermore, their single-pass conversion efficiency is potentially huge, thanks to the extreme confinement of the interacting modes in the highly nonlinear and high-refractive-index core, with scattering losses lower than in selectively oxidized or quasi-phase-matched AlGaAs waveguides. Here we compare the performances of two types of suspended waveguides made of this material, designed for second-harmonic generation (SHG) in the telecom range: (a) a nanowire suspended in air by lateral tethers and (b) an ultrathin nanorib, made of a strip lying on a suspended membrane of the same material. Both devices have been fabricated from a 123 nm thick AlGaAs epitaxial layer and tested in terms of SHG efficiency, injection and propagation losses. Our results point out that the nanorib waveguide, which benefits from a far better mechanical robustness, performs comparably to the fully suspended nanowire and is well-suited for liquid sensing applications.

The original version of this Article omitted the fourth author, Sara Ducci from Matériaux et Phénomènes Quantiques, Université Paris Diderot, CNRS UMR 7162, Sorbonne Paris-Cité, 10 rue Alice Domon et Léonie Duquet, Paris 75013, France. This mistake has been corrected in both the HTML and PDF versions of the Article.

We study the time coherence of the photoluminescence radiated by spatially indirect excitons confined in a 10 μ m electrostatic trap. Above a critical temperature of about 1 K, we show that the photoluminescence is homogeneously broadened in the dilute regime, with a spectral width around 500 μ eV that weakly varies with the exciton density. By contrast, the spectral width reduces by two-fold below the critical temperature and for experimental parameters at which excitons undergo a gray Bose–Einstein condensation. We find evidence showing that the photoluminescence temporal coherence is limited by interactions between excitons and a low concentration of residual excess charges, leading to a minimum photoluminescence spectral width of around 300 μ eV in the condensed regime.

Objective/Background: Mycobacterial infections including tuberculosis, leprosy, and buruli ulcer are among the most prevalent, debilitating, and deadly tropical diseases, especially in Sub-Saharan Africa. The development of drug resistance to the currently available drugs and the poor compliance emphasize the need for new chemotherapeutic agents. This study was designed to evaluate the in vitro activity of Cleistopholis patens, Annona reticulata, and Greenwayodendron suaveolens against Mycobacterium smegmatis. The safety on normal liver cells was also assessed. Methods: The crude extracts, fractions, and subfractions were tested against M. smegmatis and for cell cytotoxicity on WRL-68, normal human hepatocyte using microdilution resazurin-based assays. The phytochemical screening was performed using standard methods. Results: Most of the extracts, fractions, and subfractions inhibited the growth of M. smegmatis with minimum inhibitory concentration (MIC) values ranging from 6.25 μg/mL to 125 μg/mL. The subfractions P12 and P29 from G. suaveolens twig were more potent with MIC values of 6.25 μg/mL and 25 μg/mL, respectively. Fruit crude extract and root CH2Cl2 fraction from A. reticulata also showed activity with MIC values of 50 μg/mL and 25 μg/mL, respectively. Crude extracts from the twig and stem bark of C. patens displayed inhibition at MIC values of 125 μg/mL and 100 μg/mL, respectively. Majority of active extracts showed no cell cytotoxicity, except the extract from C. patens with IC50 ranging from 41.40 μg/mL to 93.78 μg/mL. The chemical investigation of the promising extracts revealed the presence of phenols, alkaloids, glycosides, triterpenes, and acetogenins. Conclusion: The results achieved from this preliminary antimycobacterial drug discovery study supported the traditional claims of C. patens, A. reticulata, and G. suaveolens in the treatment of mycobacterial infections. Meanwhile, further fractionation is required to characterize the active ingredients.

On-chip generation, manipulation and detection of nonclassical states of light are some of the major issues for quantum information technologies. In this context, the maturity and versatility of semiconductor platforms are important assets towards the realization of ultra-compact devices. In this paper we present our work on the design and study of an electrically injected AlGaAs photon pair source working at room temperature. The device is characterized through its performances as a function of temperature and injected current. Finally we discuss the impact of the device’s properties on the generated quantum state. These results are very promising for the demonstration of electrically injected entangled photon sources at room temperature and let us envision the use of III-V semiconductors for a widespread diffusion of quantum communication technologies.

We experimentally demonstrate the controlled enhancement of the mechanical quality factor Q of gallium arsenide disk optomechanical resonators. Disks vibrating at 1.3 GHz with a mechanical shield integrated in their pedestal show a Q improvement by a factor 10–16. The structure is modeled numerically and different modes of vibration are observed, which shed light on the Q enhancement mechanism. An optimized double-disk geometry is presented that promises Q above the million for a large parameter range.

Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna., (© 2023. The Author(s).)

One of the most important physiological challenges animals had to overcome during terrestrialization (i.e., the transition from sea to land) was water loss, which alters their osmotic and hydric homeostasis. Aquaporins are a superfamily of membrane water transporters heavily involved in osmoregulatory processes. Their diversity and evolutionary dynamics in most animal lineages remain unknown, hampering our understanding of their role in marine-terrestrial transitions. Here, we interrogated aquaporin gene repertoire evolution across the main terrestrial animal lineages. We annotated aquaporin-coding genes in genomic data from 458 species from seven animal phyla where terrestrialization episodes occurred. We then explored aquaporin gene evolutionary dynamics to assess differences between terrestrial and aquatic species through phylogenomics and phylogenetic comparative methods. Our results revealed parallel aquaporin-coding gene duplications during the ecological transition from marine to nonmarine environments (e.g., brackish, freshwater and terrestrial), rather than from aquatic to terrestrial ones, with some notable duplications in ancient lineages. In contrast, we also recovered a significantly lower number of superaquaporin genes in terrestrial arthropods, suggesting that more efficient oxygen homeostasis in land arthropods might be linked to a reduction in this type of aquaporin. Our results thus indicate that aquaporin-coding gene duplication and loss might have been one of the key steps towards the evolution of osmoregulation across animals, facilitating the "out of the sea" transition and ultimately the colonization of land., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic comparative methods seek to disentangle these relationships across the evolutionary history of a group of organisms. Unfortunately, most existing methods fail to accommodate high-dimensional data with dozens or even thousands of observations per taxon. Phylogenetic factor analysis offers a solution to the challenge of dimensionality. However, scientists seeking to employ this modeling framework confront numerous modeling and implementation decisions, the details of which pose computational and replicability challenges.We develop new inference techniques that increase both the computational efficiency and modeling flexibility of phylogenetic factor analysis. To facilitate adoption of these new methods, we present a practical analysis plan that guides researchers through the web of complex modeling decisions. We codify this analysis plan in an automated pipeline that distills the potentially overwhelming array of decisions into a small handful of (typically binary) choices.We demonstrate the utility of these methods and analysis plan in four real-world problems of varying scales. Specifically, we study floral phenotype and pollination in columbines, domestication in industrial yeast, life history in mammals, and brain morphology in New World monkeys.General and impactful community employment of these methods requires a data scientific analysis plan that balances flexibility, speed and ease of use, while minimizing model and algorithm tuning. Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning. These efforts coalesce to create an accessible Bayesian approach to high-dimensional phylogenetic comparative methods on large trees., Competing Interests: Conflict of Interest statement The authors declare no conflicts of interest.

Brain lateralization is a widespread phenomenon although its expression across primates is still controversial due to the reduced number of species analyzed and the disparity of methods used. To gain insight into the diversification of neuroanatomical asymmetries in non-human primates we analyze the endocasts, as a proxy of external brain morphology, of a large sample of New World monkeys and test the effect of brain size, home range and group sizes in the pattern and magnitude of shape asymmetry. Digital endocasts from 26 species were obtained from MicroCT scans and a set of 3D coordinates was digitized on endocast surfaces. Results indicate that Ateles, Brachyteles, Callicebus and Cacajao tend to have a rightward frontal and a leftward occipital lobe asymmetry, whereas Aotus, Callitrichinae and Cebinae have either the opposite pattern or no directional asymmetry. Such differences in the pattern of asymmetry were associated with group and home range sizes. Conversely, its magnitude was significantly associated with brain size, with larger-brained species showing higher inter-hemispheric differences. These findings support the hypothesis that reduction in inter-hemispheric connectivity in larger brains favors the lateralization and increases the structural asymmetries, whereas the patterns of shape asymmetry might be driven by socio-ecological differences among species., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The dissection of the mode and tempo of phenotypic evolution is integral to our understanding of global biodiversity. Our ability to infer patterns of phenotypes across phylogenetic clades is essential to how we infer the macroevolutionary processes governing those patterns. Many methods are already available for fitting models of phenotypic evolution to data. However, there is currently no comprehensive nonparametric framework for characterizing and comparing patterns of phenotypic evolution. Here, we build on a recently introduced approach for using the phylogenetic spectral density profile (SDP) to compare and characterize patterns of phylogenetic diversification, in order to provide a framework for nonparametric analysis of phylogenetic trait data. We show how to construct the SDP of trait data on a phylogenetic tree from the normalized graph Laplacian. We demonstrate on simulated data the utility of the SDP to successfully cluster phylogenetic trait data into meaningful groups and to characterize the phenotypic patterning within those groups. We furthermore demonstrate how the SDP is a powerful tool for visualizing phenotypic space across traits and for assessing whether distinct trait evolution models are distinguishable on a given empirical phylogeny. We illustrate the approach in two empirical data sets: a comprehensive data set of traits involved in song, plumage, and resource-use in tanagers, and a high-dimensional data set of endocranial landmarks in New World monkeys. Considering the proliferation of morphometric and molecular data collected across the tree of life, we expect this approach will benefit big data analyses requiring a comprehensive and intuitive framework., (© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Objectives: Platyrrhines constitute a diverse clade, with the modern Atelidae exhibiting the most variation in cranial and endocast morphology. The processes responsible for this diversification are not well understood. Here, we present a geometric morphometric study describing variation in cranial and endocranial shape of 14 species of Alouatta, Ateles, Brachyteles, and Lagothrix and two extinct taxa, Cartelles and Caipora., Methods: We examined cranial and endocranial shape variation among species using images reconstructed from CT scans and geometric morphometric techniques based on three-dimensional landmarks and semilandmarks. Principal components analyses were used to explore variation, including the Procrustes shape coordinates, summing the logarithm of the Centroid Size, the common allometric component, and residual shape components., Results: Differences in endocranial shape are related to a relative increase or decrease in the volume of the neocortex region with respect to brainstem and cerebellum regions. The relative position of the brainstem varies from a posterior position in Alouatta to a more ventral position in Ateles. The shape of both the cranium and endocast of Caipora is within the observed variation of Brachyteles. Cartelles occupies the most differentiated position relative to the extant taxa, especially in regards to its endocranial shape., Conclusions: The pattern of variation in the extant species in endocranial shape is similar to the variation observed in previous cranial studies, with Alouatta as an outlier. The similarities between Caipora and Brachyteles were unexpected and intriguing given the frugivorous adaptations inferred from the fossil's dentition. Our study shows the importance of considering both extant and fossil species when studying diversification of complex traits., (© 2019 Wiley Periodicals, Inc.)

Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and because some computational complications occur when $p $ exceeds $n$. Alternative phylogenetic comparative methods have recently been proposed to deal with the large $p $ small $n $ scenario but their use and performances are limited. Herein, we develop a penalized likelihood (PL) framework to deal with high-dimensional comparative data sets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian motion (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU), and Pagel's lambda models. We show using simulations that our PL approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when $p$ approaches $n$, and allows for their accurate estimation when $p$ equals or exceeds $n$. In addition, we show that PL models can be efficiently compared using generalized information criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic principal component analysis in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3D data set of brain shape in the New World monkeys. We find a clear support for an EB model suggesting an early diversification of brain morphology during the ecological radiation of the clade. PL offers an efficient way to deal with high-dimensional multivariate comparative data.

Understanding the origin of diversity is a fundamental problem in evolutionary biology. The null expectation for the evolutionary diversification is that all changes in biological diversity are the result of random processes. Adaptive radiations depart from this expectation as ecological factors and natural selection are supposed to play a central role in driving exceptional diversification. However, it is not well understood how large-scale continental radiations, given their characteristics, fit to these opposing theoretical models. Here, we used phylogenetic comparative methods and geometric morphometrics to study the evolutionary process of cranial diversification in the continental radiation of New World monkeys. Particularly, we tested several alternative evolutionary scenarios for morphological evolution in the clade. Results indicated that despite the platyrrhine radiation being old and geographically widespread, the formative patterns arising from the initial stages of diversification probably associated with an adaptive radiation can still be recognized today. We also show that no single explored factor (e.g., ecological or allometric) can be invoked as a complete explanation for the observed phenotypic diversity patterns in the clade and, moreover, that different cranial regions exhibit particular macroevolutionary patterns. Together, our results highlight the evident complexity behind large-scale evolutionary radiations., (© 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.)

Objectives: To assess the feasibility and results of the implementation of systematic HIV screening of pregnant women and antiretroviral (ARV) treatment for those found to be HIV-positive and their newborns at the IHS Gynecology-Obstetrics Department in Dakar, Senegal., Patients and Methods: This cross-sectional prospective study took place in 2014-1016 and examined the results of screening pregnant women for HIV during their prenatal consultations and treating those found to be HIV-positive and their infants with ARV., Results: HIV screening was routinely proposed to the 1616 pregnant women attending antenatal clinics, and 93.9 % accepted. The test was positive for 5 of these women, for an HIV prevalence of 0.3 % of pregnant women. In addition, another 23 HIV-positive pregnant women were referred to the IHS for their prenatal care and delivery, for a total of 28 women with HIV. Their mean age was 30 years, their mean parity 1.6, and all had HIV-1. Triple therapy was initiated for all HIV-positive pregnant women, in line with the WHO guidelines' "B + option", currently adopted by Senegal. During follow-up, only 35.7 % of the women had access to a viral load assay. The outcome of pregnancy was favorable in 91.6 % of cases; 72.2% of the women had vaginal deliveries. All live-born infants were given antiretroviral prophylaxis at birth. The mode of breastfeeding used was mainly exclusive protected breastfeeding (72.2 %). During postnatal follow-up, 2 of the 17 live-born infants were lost to follow-up, and 15 had PCR testing for HIV, which was positive in only 1 case, for a transmission rate of 6.6 %., Conclusion: The systematic offer and performance of HIV testing in all pregnant women is feasible and acceptable. Good organization of care can provide ARV treatment for all HIV-positive pregnant women and their newborns. The accessibility of viral load testing and of PCR screening for neonates still requires improvement.

New World monkeys (order Primates) are an example of a major mammalian evolutionary radiation in the Americas, with a contentious fossil record. There is evidence of an early platyrrhine occupation of this continent by the Eocene-Oligocene transition, evolving in isolation from the Old World primates from then on, and developing extensive morphological and size variation. Previous studies postulated that the platyrrhine clade arose as a local version of the Simpsonian ecospace model, with an early phase involving a rapid increase in morphological and ecological diversity driven by selection and ecological opportunity, followed by a diversification rate that slowed due to niche-filling. Under this model, variation in extant platyrrhines, in particular anatomical complexes, may resemble patterns seen among middle-late Miocene (10-14 Ma) platyrrhines as a result of evolutionary stasis. Here we examine the mandible in this regard, which may be informative about the dietary and phylogenetic history of the New World monkeys. Specifically, we test the hypothesis that the Simpsonian ecospace model applies to the platyrrhine mandible through a geometric morphometric analysis of digital images of the jaws of extant and extinct species, and we compare these results to those obtained using a phylogenetic comparative approach based on extant species. The results show a marked phylogenetic structure in the mandibular morphology of platyrrhines. Principal component analyses highlight the morphological diversity among modern forms, and reveal a similar range of variation for the clade when fossil specimens are included. Disparity-Through-Time analysis shows that most of the shape variation between platyrrhines originated early in their evolution (between 20 and 15 Ma). Our results converge with previous studies of body mass, cranial shape, the brain and the basicranium to show that platyrrhine evolution might have been shaped by an early increase in morphological variation followed by a decelerated rate of diversification and evolutionary stasis., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Primates constitute one of the most diverse mammalian clades, and a notable feature of their diversification is the evolution of brain morphology. However, the evolutionary processes and ecological factors behind these changes are largely unknown. In this work, we investigate brain shape diversification of New World monkeys during their adaptive radiation in relation to different ecological dimensions. Our results reveal that brain diversification in this clade can be explained by invoking a model of adaptive peak shifts to unique and shared optima, defined by a multidimensional ecological niche hypothesis. Particularly, we show that the evolution of convergent brain phenotypes may be related to ecological factors associated with group size (e.g., social complexity). Together, our results highlight the complexity of brain evolution and the ecological significance of brain shape changes during the evolutionary diversification of a primate clade.

The cranial base, composed of the midline and lateral basicranium, is a structurally important region of the skull associated with several key traits, which has been extensively studied in anthropology and primatology. In particular, most studies have focused on the association between midline cranial base flexion and relative brain size, or encephalization. However, variation in lateral basicranial morphology has been studied less thoroughly. Platyrrhines are a group of primates that experienced a major evolutionary radiation accompanied by extensive morphological diversification in Central and South America over a large temporal scale. Previous studies have also suggested that they underwent several evolutionarily independent processes of encephalization. Given these characteristics, platyrrhines present an excellent opportunity to study, on a large phylogenetic scale, the morphological correlates of primate diversification in brain size. In this study we explore the pattern of variation in basicranial morphology and its relationship with phylogenetic branching and with encephalization in platyrrhines. We quantify variation in the 3D shape of the midline and lateral basicranium and endocranial volumes in a large sample of platyrrhine species, employing high-resolution CT-scans and geometric morphometric techniques. We investigate the relationship between basicranial shape and encephalization using phylogenetic regression methods and calculate a measure of phylogenetic signal in the datasets. The results showed that phylogenetic structure is the most important dimension for understanding platyrrhine cranial base diversification; only Aotus species do not show concordance with our molecular phylogeny. Encephalization was only correlated with midline basicranial flexion, and species that exhibit convergence in their relative brain size do not display convergence in lateral basicranial shape. The evolution of basicranial variation in primates is probably more complex than previously believed, and understanding it will require further studies exploring the complex interactions between encephalization, brain shape, cranial base morphology, and ecological dimensions acting along the species divergence process., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

A phytochemical investigation of the whole plant of Crassocephalum bauchiense Huch. resulted in the isolation of a new clerodane diterpenoid, ent-2β,18,19-trihydroxycleroda-3,13-dien-16,15-olide (1), together with two known flavonoids 3',5-dihydroxy-4',5',6,7,8-pentamethoxyflavone (2) and 4',5-dihydroxy-3',5',6,7,8-pentamethoxyflavone (3). The compounds were tested against the chloroquine-sensitive 3D7 strain of Plasmodium falciparum. Compound 2 showed weak activity (IC50 = 10.1 g/mL) whilst compounds 1 and 3 were inactive. The structures of the compounds were elucidated by using detailed spectral analyses, especially (1)H and (13)C NMR, (1)H-(1)H COSY, NOESY, HMBC and HR-ESI-MS.

Adaptive radiations that have taken place in the distant past can now be more thoroughly studied with the availability of large molecular phylogenies and comparative data drawn from extant and fossil species. Platyrrhines are a good example of a major mammalian evolutionary radiation confined to a single continent, involving a relatively large temporal scale and documented by a relatively small but informative fossil record. Here, we present comparative evidence using data on extant and fossil species to explore alternative evolutionary models in an effort to better understand the process of platyrrhine lineage and phenotypic diversification. Specifically, we compare the likelihood of null models of lineage and phenotypic diversification versus various models of adaptive evolution. Moreover, we statistically explore the main ecological dimension behind the platyrrhine diversification. Contrary to the previous proposals, our study did not find evidence of a rapid lineage accumulation in the phylogenetic tree of extant platyrrhine species. However, the fossil-based diversity curve seems to show a slowdown in diversification rates toward present times. This also suggests an early high rate of extinction among lineages within crown Platyrrhini. Finally, our analyses support the hypothesis that the platyrrhine phenotypic diversification appears to be characterized by an early and profound differentiation in body size related to a multidimensional niche model, followed by little subsequent change (i.e., stasis)., (Copyright © 2013 Elsevier Inc. All rights reserved.)

The estimation of phylogenetic relationships and divergence times among a group of organisms is a fundamental first step toward understanding its biological diversification. The time of the most recent or last common ancestor (LCA) of extant platyrrhines is one of the most controversial among scholars of primate evolution. Here we use two molecular based approaches to date the initial divergence of the platyrrhine clade, Bayesian estimations under a relaxed-clock model and substitution rate plus generation time and body size, employing the fossil record and genome datasets. We also explore the robustness of our estimations with respect to changes in topology, fossil constraints and substitution rate, and discuss the implications of our findings for understanding the platyrrhine radiation. Our results suggest that fossil constraints, topology and substitution rate have an important influence on our divergence time estimates. Bayesian estimates using conservative but realistic fossil constraints suggest that the LCA of extant platyrrhines existed at ca. 29 Ma, with the 95% confidence limit for the node ranging from 27-31 Ma. The LCA of extant platyrrhine monkeys based on substitution rate corrected by generation time and body size was established between 21-29 Ma. The estimates based on the two approaches used in this study recalibrate the ages of the major platyrrhine clades and corroborate the hypothesis that they constitute very old lineages. These results can help reconcile several controversial points concerning the affinities of key early Miocene fossils that have arisen among paleontologists and molecular systematists. However, they cannot resolve the controversy of whether these fossil species truly belong to the extant lineages or to a stem platyrrhine clade. That question can only be resolved by morphology. Finally, we show that the use of different approaches and well supported fossil information gives a more robust divergence time estimate of a clade.