Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms.

Hybrid density functional approximations (DFAs) offer compelling accuracy for ab initio electronic-structure simulations of molecules, nanosystems, and bulk materials, addressing some deficiencies of computationally cheaper, frequently used semilocal DFAs. However, the computational bottleneck of hybrid DFAs is the evaluation of the non-local exact exchange contribution, which is the limiting factor for the application of the method for large-scale simulations. In this work, we present a drastically optimized resolution-of-identity-based real-space implementation of the exact exchange evaluation for both non-periodic and periodic boundary conditions in the all-electron code FHI-aims, targeting high-performance central processing unit (CPU) compute clusters. The introduction of several new refined message passing interface (MPI) parallelization layers and shared memory arrays according to the MPI-3 standard were the key components of the optimization. We demonstrate significant improvements of memory and performance efficiency, scalability, and workload distribution, extending the reach of hybrid DFAs to simulation sizes beyond ten thousand atoms. In addition, we also compare the runtime performance of the PBE, HSE06, and PBE0 functionals. As a necessary byproduct of this work, other code parts in FHI-aims have been optimized as well, e.g., the computation of the Hartree potential and the evaluation of the force and stress components. We benchmark the performance and scaling of the hybrid DFA-based simulations for a broad range of chemical systems, including hybrid organic-inorganic perovskites, organic crystals, and ice crystals with up to 30 576 atoms (101 920 electrons described by 244 608 basis functions).

Quantum rates in dissipative systems with spatially varying friction.

We investigate whether making the friction spatially dependent on the reaction coordinate introduces quantum effects into the thermal reaction rates for dissipative reactions. Quantum rates are calculated using the numerically exact multi-configuration time-dependent Hartree method, as well as the approximate ring-polymer molecular dynamics (RPMD), ring-polymer instanton methods, and classical molecular dynamics. By conducting simulations across a wide range of temperatures and friction strengths, we can identify the various regimes that govern the reactive dynamics. At high temperatures, in addition to the spatial-diffusion and energy-diffusion regimes predicted by Kramer's rate theory, a (coherent) tunneling-dominated regime is identified at low friction. At low temperatures, incoherent tunneling dominates most of Kramer's curve, except at very low friction, when coherent tunneling becomes dominant. Unlike in classical mechanics, the bath's influence changes the equilibrium time-independent properties of the system, leading to a complex interplay between spatially dependent friction and nuclear quantum effects even at high temperatures. More specifically, a realistic friction profile can lead to an increase (or decrease) of the quantum (classical) rates with friction within the spatial-diffusion regime, showing that classical and quantum rates display qualitatively different behaviors. Except at very low frictions, we find that RPMD captures most of the quantum effects in the thermal reaction rates.

Molecular diversity and polyparasitism of avian trypanosomes in the Brazilian Atlantic Rainforest.

The current study proposes to investigate the diversity and phylogeny of trypanosomes parasitizing wild birds from the Brazilian Atlantic Forest. Cytological examination was carried out by light microscopy of blood smears and positive birds were selected for amplification of the 18S rDNA sequence through PCR. The resulting amplicons were subjected to purification, cloning, and sequencing analysis. Phylogenetic reconstruction was conducted, including all avian trypanosomes representative's lineages. A total of ten bird samples from species of Turdus flavipes (N=1/12), T. albicollis (N=1/8), Tachyphonus coronatus (N=6/121), Thamnophilus caerulescens (N=1/22) and Synallaxis spixi (N=1/8) were positive for Trypanosoma spp. In the six specimens of T. coronatus, five distinct lineages of Trypanosoma spp. 18S-rRNA were observed in ninety sequences obtained, and using the strategy of cloning independent PCR, it was possible to observe that two of them were related to T. avium (JB01/JB02), and three were closed related to T. bennetti (JB03/ JB04/JB05). Addionaly, all fifteen sequences obtained from T. caerulescens/ S. spixi/T. flavipes/T. albicollis were identical. The present research is the first study to access molecular diversity and polyparasitism by avian trypanosomes in Brazil. The current research exhibits the wide genetic variability in avian trypanosomes and its non-specific relationship with its avian hosts.

Assessing the role of taxonomic impediment in the knowledge on geographic distribution of Physidae (Gastropoda: Hygrophila) in South America, using an intensive-data approach.

There is a marked disparity in the state of knowledge of Holartic x Neotropical species of the freshwater snail family Physidae; the incipiency of data on Neotropical physids reflecting the lower number of dedicated specialists. The gaps in the knowledge on Neotropical physids have led to historical uncertainty about species validity. Revisiting the species is essential to reduce taxonomic impediment and delineating their probable distribution is the first step to attain this purpose. We aimed at critically analyze occurrence records of South American physids, compiled through an intensive search in the literature, biodiversity and molecular databases. We present a provisional characterization of the distribution of this family in South America, considering the probable versus the poorly documented distribution of the species. The critical underrepresentation of South American physids in collections, molecular databases and literature reinforces the role of taxonomic impediment in delaying the advance of the knowledge on species diversity. Malacological collections represented the main source of records, evidencing the relevance of unpublished data associated to specimens to assess distributional information on neglected groups. As most of the species are represented by shells, the reassessment of species identity and distribution must be done, using molecular and anatomical criteria for species delimitation.

First record of Trypanosoma (Ornithotrypanum) infecting Neotropical birds.

Parasites play a pivotal role in ecosystem health, influencing human and zoonotic diseases, as well as biodiversity preservation. The genus Trypanosoma comprises approximately 500 species mostly found in wildlife animals. This study focuses on identifying trypanosomes found in the white-necked thrush (Turdus albicollis) and the yellow-legged thrush (Turdus flavipes) in the Neotropics. First, we demonstrate the utility of an 18S rDNA sequence-structure phylogeny as an alternative method for trypanosome classification, especially when gGAPDH sequences are unavailable. Subsequently, the sequence-structure phylogeny is employed to classify new trypanosome sequences discovered in wild birds, placing them within the Ornithotrypanum subgenus. This marks the first identification of Ornithotrypanum in Neotropical birds, contributing to the understanding of the distribution and ecological adaptation of avian trypanosomes. Beyond taxonomy, this study broadens our comprehension of the ecological implications of avian trypanosomes in the Neotropics, emphasizing the need for continued research in this field. These findings underscore the importance of alternative classification methods, which are essential to unravel the complex interactions between parasites, wildlife hosts, and their ecosystems.

High infestation and phylogenetic position of Epistylis sp. (Ciliophora, Peritrichia) on Aegla serrana Buckup & Rossi (Crustacea, Anomura) from southern Brazil.

High infestations of epibiont ciliates on vertebrates or invertebrates are normally related to aquaculture tanks or similar environments, and the importance of this relationship in natural habitats is often disregarded. Here, we describe the first record of high infestation of ciliates on Aegla serrana in South America and conduct a brief morphological and phylogenetic characterization of these ciliates. Our findings confirm that cases of high infestation of ciliates on metazoans can indeed occur in natural environments.

Systematic review of the genera Rhabdostyla Kent 1880 and Orborhabdostyla Foissner et al. 2010 (Ciliophora, Peritrichia, Epistylididae).

The genus Rhabdostyla is one of the oldest of the family Epistylididae, it was described over 120 years ago and has more than 40 species considered valid. This group went through several systematic changes throughout its existence and due to the lack of taxonomic information, said to be essential, for most species that compose it, some of these changes are still questioned. In order to better understand and validate the species and relationships identified for this genus, the present work makes a brief review for the genus Rhabdostyla and its related genera, Opisthostyla and Orborhabdostyla. A 18S-rDNA phylogenetic analysis was also performed to understand the relationship between these groups. As a result of this review, 45 diagnoses were compiled and reorganized for the current model, accompanied by new graphical representations for the species considered valid for the genus Rhabdostyla and its associates. The major changes that the genus underwent, such as synonymy and separation to a new genus, were discussed in light of new phylogenetic information, but despite this, other information is still needed for a better validation of these changes.

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy.

Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.

First-Principles Simulations of Tip Enhanced Raman Scattering Reveal Active Role of Substrate on High-Resolution Images.

Tip-enhanced Raman scattering (TERS) has emerged as a powerful tool to obtain subnanometer spatial resolution fingerprints of atomic motion. Theoretical calculations that can simulate the Raman scattering process and provide an unambiguous interpretation of TERS images often rely on crude approximations of the local electric field. In this work, we present a novel and first-principles-based method to compute TERS images by combining Time Dependent Density Functional Theory (TD-DFT) and Density Functional Perturbation Theory (DFPT) to calculate Raman cross sections with realistic local fields. We present TERS results on free-standing benzene and C60 molecules, and on the TCNE molecule adsorbed on Ag(100). We demonstrate that chemical effects on chemisorbed molecules, often ignored in TERS simulations of larger systems, dramatically change the TERS images. This observation calls for the inclusion of chemical effects for predictive theory-experiment comparisons and an understanding of molecular motion at the nanoscale.

Predicting the electronic density response of condensed-phase systems to electric field perturbations.

We present a local and transferable machine-learning approach capable of predicting the real-space density response of both molecules and periodic systems to homogeneous electric fields. The new method, Symmetry-Adapted Learning of Three-dimensional Electron Responses (SALTER), builds on the symmetry-adapted Gaussian process regression symmetry-adapted learning of three-dimensional electron densities framework. SALTER requires only a small, but necessary, modification to the descriptors used to represent the atomic environments. We present the performance of the method on isolated water molecules, bulk water, and a naphthalene crystal. Root mean square errors of the predicted density response lie at or below 10% with barely more than 100 training structures. Derived polarizability tensors and even Raman spectra further derived from these tensors show good agreement with those calculated directly from quantum mechanical methods. Therefore, SALTER shows excellent performance when predicting derived quantities, while retaining all of the information contained in the full electronic response. Thus, this method is capable of predicting vector fields in a chemical context and serves as a landmark for further developments.

Urinary Aspergillosis in a Patient with Systemic Lupus Erythematosus (SLE).

Aspergillosis is an opportunistic mycosis that generally affects the lungs. The fungus was cleared by the immune system of a healthy host. Extrapulmonary forms are very rare, and there are few reports of urinary aspergillosis. In this case report, we describe a 62-year-old woman with systemic lupus erythematosus (SLE) with complaints of fever and dysuria. The patient had recurrent episodes of urinary tract infection and several hospitalizations. A computed tomography revealed an amorphous mass in the left kidney and bladder. After partial resection of the material was referred for analysis, Aspergillus infection was suspected and confirmed by culture. Successful treatment with voriconazole was provided. Diagnosis of localized primary renal Aspergillus infection in a patient with SLE requires careful investigation due to its benign presentation and lack of associated systemic clinical features.

Ab initio study of water dissociation on a charged Pd(111) surface.

The interactions between molecules and electrode surfaces play a key role in electrochemical processes and are a subject of extensive research, both experimental and theoretical. In this paper, we address the water dissociation reaction on a Pd(111) electrode surface, modeled as a slab embedded in an external electric field. We aim at unraveling the relationship between surface charge and zero-point energy in aiding or hindering this reaction. We calculate the energy barriers with dispersion-corrected density-functional theory and an efficient parallel implementation of the nudged-elastic-band method. We show that the lowest dissociation barrier and consequently the highest reaction rate take place when the field reaches a strength where two different geometries of the water molecule in the reactant state are equally stable. The zero-point energy contributions to this reaction, on the other hand, remain nearly constant across a wide range of electric field strengths, despite significant changes in the reactant state. Interestingly, we show that the application of electric fields that induce a negative charge on the surface can make nuclear tunneling more significant for these reactions.

Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble.

Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.

Electronic-Structure Properties from Atom-Centered Predictions of the Electron Density.

The electron density of a molecule or material has recently received major attention as a target quantity of machine-learning models. A natural choice to construct a model that yields transferable and linear-scaling predictions is to represent the scalar field using a multicentered atomic basis analogous to that routinely used in density fitting approximations. However, the nonorthogonality of the basis poses challenges for the learning exercise, as it requires accounting for all the atomic density components at once. We devise a gradient-based approach to directly minimize the loss function of the regression problem in an optimized and highly sparse feature space. In so doing, we overcome the limitations associated with adopting an atom-centered model to learn the electron density over arbitrarily complex data sets, obtaining very accurate predictions using a comparatively small training set. The enhanced framework is tested on 32-molecule periodic cells of liquid water, presenting enough complexity to require an optimal balance between accuracy and computational efficiency. We show that starting from the predicted density a single Kohn-Sham diagonalization step can be performed to access total energy components that carry an error of just 0.1 meV/atom with respect to the reference density functional calculations. Finally, we test our method on the highly heterogeneous QM9 benchmark data set, showing that a small fraction of the training data is enough to derive ground-state total energies within chemical accuracy.

Experiencias subjetivas del personal de salud durante la emergencia sanitaria en Uruguay / Experiences of health personnel during the health emergency in Uruguay / Vivências subjetivas dos trabalhadores de saúde na emergência sanitária en Uruguay

La emergencia sanitaria COVID-19 impactó en los/as trabajadores de salud, dejando en evidencia: el malestar subjetivo y altos índices de ansiedad y depresión. El objetivo del presente trabajo es analizar las experiencias y vivencias de trabajadores/as de la salud durante la pandemia. La misma se realizó a partir del análisis de las respuestas obtenidas en la pregunta abierta del formulario autoadministrado del proyecto Héroes Uruguay. La población objetivo fue el personal de los servicios de salud integrados al Sistema Nacional Integrado de Salud en los tres niveles de atención. Las respuestas fueron agrupadas y categorizadas en base a su frecuencia. La categoría condiciones de trabajo fue la temática más mencionada, seguida de organización del trabajo y vivencias. Realizamos otra categorización sobre los sentidos subjetivos durante la pandemia, nueve categorías son las frecuentes, siendo el 86% de los sentidos subjetivos: ansiedad y estrés, miedo, cansancio, no apoyo social y sobrecarga son los más mencionados. Los resultados muestran que la mayoría de las respuestas remite a las condiciones y a la organización del trabajo, se trata de dimensiones claves en la salud del trabajador, en su entorno, y en los procesos de asistencia al paciente y su familia. Este estudio nos permite afirmar la importancia a nivel organizacional y de políticas de salud, de generar entornos laborales seguros y saludables. La emergencia sanitaria generada por el COVID 19, expuso y agudizó la tensión de los sistemas sanitarios y su impacto en la salud y bienestar del personal.

The COVID-19 health emergency impacted health workers, revealing: subjective discomfort and high rates of anxiety and depression. The objective of this work is to analyze the experiences of health workers during the pandemic. It was carried out from the analysis of the answers obtained in the open question of the self-administered form of the Héroes Uruguay project. The target population was the staff of the health services integrated into the National Integrated Health System at the three levels of care. The responses were grouped and categorized based on recurring themes. The working conditions category was the most mentioned theme, followed by work organization and experiences. We carry out another categorization of the subjective senses during the pandemic, nine categories are the most frequent, with 86% of the subjective senses: anxiety and stress, fear, tiredness, lack of social support and overload are the most mentioned. The results show that most of the answers refer to the conditions and organization of work, these are key dimensions in the worker's health, in his environment, and in the patient assisted and his family. This study allows us to affirm the importance at the organizational and health policy level of generating safe and healthy work environments. The health emergency generated by COVID 19 exposed and exacerbated the tension in health systems and its impact on the health and well-being of personnel.

A emergência sanitária da COVID-19 impactou os trabalhadores da saúde, revelando: desconforto subjetivo e altos índices de ansiedade e depressão. O objetivo deste trabalho é analisar as vivências dos trabalhadores da saúde durante a pandemia. Foi realizada a partir da análise das respostas obtidas na questão aberta do formulário autoaplicável do projeto Héroes Uruguai. A população alvo foram os trabalhadores dos serviços de saúde integrados no Sistema Único de Saúde Integrado nos três níveis de cuidados. As respostas foram agrupadas e categorizadas com base em temas recorrentes. A categoria condições de trabalho foi o tema mais citado, seguido de organização do trabalho e experiências. Realizamos outra categorização dos sentidos subjetivos durante a pandemia, nove categorias são as mais frequentes, com 86% dos sentidos subjetivos: ansiedade e estresse, medo, cansaço, falta de apoio social e sobrecarga são os mais citados. Os resultados mostram que a maioria das respostas se refere às condições e organização do trabalho, dimensões fundamentais na saúde do trabalhador, em seu ambiente, e no paciente assistido e sua família. Este estudo permite afirmar a importância a nível organizacional e da política de saúde de gerar ambientes de trabalho seguros e saudáveis. A emergência de saúde gerada pelo COVID 19 expôs e exacerbou a tensão nos sistemas de saúde e seu impacto na saúde e bem-estar do pessoal.

Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating.

Although the diversity (~35 species) and worldwide distribution of goats (Ruminantia, Bovidae, Caprinae) are significant, studies on the diversity of symbiont ciliates in these mammals are scarce in comparison to other ruminants. The present work is a review and checklist of species based on taxonomic, morphologic, and ecologic studies of rumen ciliate protozoa in goats, presenting geographic distribution and hosts, as well as estimating the macroevolutionary relationships of the species observed in the studies. To that end, all of the available literature on databases was reviewed, the schematic drawings were made based on information present in the original description of the taxa, and the phylogenetic relationships were inferred based on Maximum Likelihood and Bayesian Inference analyses. According to our review, 72 species and 14 genera of ciliates have been associated with goats. Through the analysis of the association between ciliate genera and caprine hosts, it was shown that ciliates are more associated with domestic animals (Capra hircus14 genera) than wild ones (Rupicapra rupicaprasix genera, Capra ibexone genus, Capra pyrenaicaone genus). Thirteen countries were identified in the distribution map as having had reports of ciliate species associated with goats. The interaction networks of ciliates and their hosts showed that the species of ciliates associated with goats also occur in other herbivore mammal species. The recovered phylogenetic hypotheses show that the ciliate species in goats form a non-monophyletic group with maximum and minimum ages of ~8.2My and ~2.4My. We have also found that a large portion of the studies on the diversity of ciliates in goats does not employ all necessary techniques in an integrative way, despite it being essential for detailed descriptions and better knowledge of this fraction of biodiversity.

Production of Cytotoxic Antibodies After Intra-Articular Injection of Allogeneic Synovial Membrane Mesenchymal Stem Cells With and Without LPS Administration.

Allogeneic mesenchymal stem cells (MSC) are widely used in clinical routine due to the shorter expansion time and reliability of its quality. However, some recipients can produce alloantibodies that recognize MSCs and activate the immune system, resulting in cell death. Although antibody production was already described after MSC injection, no previous studies described the immune response after intra-articular MSC injection in acute synovitis. This study aimed to evaluate the influence of inflammation on immune response after single and repeated intra-articular injections of synovial membrane MSC (SMMSC). Horses were divided in three groups: control group (AUTO) received autologous synovial membrane MSCs; whereas group two (ALLO) received allogeneic SMMSCs and group three (ALLO LPS) was submitted to acute experimental synovitis 8 h before SMMSCs injection. The procedure was repeated for all groups for 28 days. Physical and lameness evaluations and synovial fluid analysis were performed. Sera from all animals were obtained before and every 7 days after each injection up to 4 weeks, to perform microcytotoxicity assays incubating donor SMMSCs with recipients' sera. The first injection caused a mild and transient synovitis in all groups, becoming more evident and longer in ALLO and ALLO LPS groups after the second injection. Microcytotoxicity assays revealed significant antibody production as soon as 7 days after SMMSC injection in ALLO and ALLO LPS groups, and cytotoxicity scores of both groups showed no differences at any time point, being equally different from AUTO group. Although inflammation is capable of inducing MHC expression in MSCs, which enhances immune recognition, cytotoxicity scores were equally high in ALLO and ALLO LPS groups, making it difficult to determine the potentiation effect of inflammation on antibody production. Our findings suggest that inflammation does not display a pivotal role in immune recognition on first allogeneic MSC injection. In a translational way, since specific antibodies were produced against MSCs, patients that need more than one MSC injection may benefit from a first allogeneic injection followed by subsequent autologous injections.

Charge Transfer-Mediated Dramatic Enhancement of Raman Scattering upon Molecular Point Contact Formation.

Charge-transfer enhancement of Raman scattering plays a crucial role in current-carrying molecular junctions. However, the microscopic mechanism of light scattering in such nonequilibrium systems is still imperfectly understood. Here, using low-temperature tip-enhanced Raman spectroscopy (TERS), we investigate how Raman scattering evolves as a function of the gap distance in the single C60-molecule junction consisting of an Ag tip and various metal surfaces. Precise gap-distance control allows the examination of two distinct transport regimes, namely tunneling regime and molecular point contact (MPC). Simultaneous measurement of TERS and the electric current in scanning tunneling microscopy shows that the MPC formation results in dramatic Raman enhancement that enables one to observe the vibrations undetectable in the tunneling regime. This enhancement is found to commonly occur not only for coinage but also transition metal substrates. We suggest that the characteristic enhancement upon the MPC formation is rationalized by charge-transfer excitation.

Low Mg content on Ti-Nb-Sn alloy when in contact with eBMMSCs promotes improvement of its biological functions.

Magnesium is a metal used in the composition of titanium alloys and imparts porosity. Due to its osteoconductive, biocompatible and biodegradable characteristics, its application in the development of biomedical materials has become attractive. This study aimed to evaluate the influence of magnesium present in porous Ti-Nb-Sn alloys, which have a low elastic modulus in adhesive, osteogenic properties and the amount of reactive intracellular oxygen species released in mesenchymal stem cells derived from bone marrow equine bone (eBMMSCs). Mechanical properties of the alloy, such as hardness, compressive strength and elastic modulus, were analyzed, as well as surface morphological characteristics through scanning electron microscopy. The evaluation of magnesium ion release was performed by atomic force spectroscopy. The biological characteristics of the alloy, when in contact with the alloy surface and with the culture medium conditioned with the alloy, were studied by SEM and optical microscopy. Confirmation of osteogenic differentiation by alizarin red and detection of ROS using a Muse® Oxidative Stress Kit based on dihydroetide (DHE). The alloy showed an elastic modulus close to cortical bone values. The hardness was close to commercial Ti grade 2, and the compressive strength was greater than the value of cortical bone. The eBMMSCs adhered to the surface of the alloy during the experimental time. Osteogenic differentiation was observed with the treatment of eBMMMSCs with conditioned medium. The eBMMSCs treated with conditioned medium decreased ROS production, indicating a possible antioxidant defense potential of magnesium release.