Py3BR: A software for computing atomic three-body recombination rates.

The three-body recombination reaction, or ternary association, is a termolecular reaction leading to a molecule after a three-body encounter that plays a vital role in many relevant scenarios in chemical physics. Here, we introduce the Python 3-Body Recombination program, which is dedicated to the computation of atomic three-body recombination rate coefficients. The software is based on a classical trajectory approach in hyperspherical coordinates after mapping the three-body problem as a single particle in a higher-dimensional space. This theoretical approach is fully general and applicable to any ion-atom-atom or atom-atom-atom three-body process. The predictive power of the methodology has been tested in several different experimental scenarios, reaching a good description of every system. The code structure is presented alongside examples and tests to ensure the software's capacity. In addition, the performance of the software after parallelization is shown.

On the role of non-additive interactions in three-body recombination.

Non-additive forces are a cornerstone of molecular spectroscopy and reaction dynamics. However, the relevance of non-additive forces in three-body recombination remains largely unexplored. In this work, we present a global study on the impact of non-additive interactions in three-body recombination: atom-atom-atom and ion-atom-atom. Our study explores these reactions in a wide range of energies, from the cold to the hyperthermal regime, finding no effect of non-additive interactions. Therefore, pair-wise interactions are enough to describe the three-body recombination dynamics adequately.

Molecular dynamics-driven global potential energy surfaces: Application to the AlF dimer.

In this work, we present a full-dimensional potential energy surface for AlF-AlF. We apply a general machine learning approach for full-dimensional potential energy surfaces, employing an active learning scheme trained on ab initio points, whose size grows based on the accuracy required. The training points are selected based on molecular dynamics simulations, choosing the most suitable configurations for different collision energy and mapping the most relevant part of the potential energy landscape of the system. The present approach does not require long-range information and is entirely general. As a result, it is possible to provide the full-dimensional AlF-AlF potential energy surface, requiring ≲0.01% of the configurations to be calculated ab initio. Furthermore, we analyze the general properties of the AlF-AlF system, finding critical differences with other reported results on CaF or bi-alkali dimers.

Anthropogenic Contamination in the Free Aquifer of the San Luis Potosí Valley.

The San Luis Potosí valley is an endorheic basin that contains three aquifers: a shallow unconfined aquifer of alluvial material and two deep aquifers, free and confined. The groundwater contamination documented for the shallow aquifer generates contamination of the deep unconfined type aquifer, from which part of the population's drinking water needs are met. This study records incipient anthropogenic contamination of two types: biogenic and potentially toxic trace elements. The studied contaminants include fecal coliform bacteria, total coliform, nitrate, and potentially toxic elements such as: manganese (Mn), mercury (Hg), arsenic (As), and cadmium (Cd). This contamination in some locations exceeds the permissible limit for human consumption. Some major consequences to health, including severe illness, may be caused by the trace elements. The present results give a first signal about the contamination of the deep unconfined type aquifer due to anthropogenic activity in the valley. This is a priority issue because this aquifer supplies drinking water, and in the short or medium term it will have an effect on public health.

Barrier Height Prediction by Machine Learning Correction of Semiempirical Calculations.

Different machine learning (ML) models are proposed in the present work to predict density functional theory-quality barrier heights (BHs) from semiempirical quantum mechanical (SQM) calculations. The ML models include a multitask deep neural network, gradient-boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute errors are similar to those of previous models considering the same number of data points. The ML corrections proposed in this paper could be useful for rapid screening of the large reaction networks that appear in combustion chemistry or in astrochemistry. Finally, our results show that 70% of the features with the highest impact on model output are bespoke predictors. This custom-made set of predictors could be employed by future Δ-ML models to improve the quantitative prediction of other reaction properties.

Ion-atom-atom three-body recombination: From the cold to the thermal regime.

We present a study on ion-atom-atom reaction A + A + B+ in a wide range of systems and collision energies ranging from 100 µK to 105 K, analyzing two possible products: molecules and molecular ions. The dynamics is performed via a direct three-body formalism based on a classical trajectory method in hyperspherical coordinates developed in Pérez-Ríos et al. [J. Chem. Phys. 140, 044307 (2014)]. Our chief finding is that the dissociation energy of the molecular ion product acts as a threshold energy, separating the low- and high-energy regimes. In the low-energy regime, the long-range tail of the three-body potential dictates the fate of the reaction and the main reaction product. On the contrary, in the high-energy regime, the short-range of atom-atom and atom-ion interaction potential dominate the dynamics, enhancing molecular formation.

The performance of CCSD(T) for the calculation of dipole moments in diatomics.

This work analyzes the accuracy of the coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] method for predicting dipole moments. In particular, we benchmark CCSD(T) predictions for the equilibrium bond length, vibrational frequency, and dipole moment versus accurate experimental data. As a result, we find that CCSD(T) leads to accurate dipole moments. However, in some cases, it disagrees with the experimental values, and the disagreement can not be satisfactorily explained via relativistic or multi-reference effects. Therefore, our results indicate that benchmark studies for energy and geometry properties do not accurately describe other electron density magnitudes.

AlF-AlF Reaction Dynamics between 200 K and 1000 K: Reaction Mechanisms and Intermediate Complex Characterization.

AlF is a relevant molecule in astrochemistry as a tracer of F-bearing molecules. Additionally, AlF presents diagonal Franck-Condon factors and can be created very efficiently in the lab, which makes it a prototypical molecular for laser cooling. However, very little is known about the reaction dynamics of AlF. In this work, we report on the reaction dynamics of AlF-AlF between 200 and 1000 K using ab initio molecular dynamics and a highly efficient active learning approach for the potential energy surface, including all degrees of freedom. As a result, we identify the main reaction mechanisms and the lifetime of the intermediate complex AlF-AlF relevant to astrochemistry environments and regions in buffer gas cells.

Leishmaniasis visceral con hemorragia masiva

RESUMEN Las complicaciones potencialmente mortales por el uso de la anfotericina B desoxicolato se presentan en menos del 1% de los casos. Entre ellas se describe el sangrado masivo principalmente por trombocitopenia. Se presenta caso de un paciente de sexo masculino de 38 años de edad, oriundo de una zona endémica, portador de leishmaniasis visceral grave que posterior al inicio de tratamiento con anfotericina B desoxicolato presenta hemorragia alveolar masiva por trombocitopenia.

ABSTRACT Life-threatening complications from the use of amphotericin B deoxycholate occur in less than 1% of cases. Among them, massive bleeding is described mainly due to thrombocytopenia. We present the case of a 38-year-old male patient, from an endemic area, with severe visceral leishmaniasis who, after starting treatment with amphotericin B deoxycholate, presented massive alveolar hemorrhage due to thrombocytopenia.

Subclavian-Brachial Bypass for Chronic Limb Threatening Ischemia Associated with an Old Motorcycle Accident.

Chronic limb-threatening ischemia is rarely associated with previous traumatic injury. We present a case of a 28-year-old male with progressive digit ulcers, a weak pulse, cyanosis, and a cold limb. Eight months prior, he had a motorcycle accident resulting in a right clavicle fracture and brachial plexus injury. Computed tomography angiography revealed occlusion of the right subclavian artery near a surgically implanted reduction plate. The patient underwent an open subclavian-brachial bypass with a reversed saphenous vein graft. His postoperative recovery was uneventful. After 3 months, he had a euthermic right hand with a palpable pulse and his ulcers had completely healed. This case reinforces the need for patients with a neurological deficit in the upper extremity caused by blunt trauma to undergo thorough vascular examination to identify potential arterial injury and compromised perfusion.

Ozone Formation in Ternary Collisions: Theory and Experiment Reconciled.

The present Letter shows that the formation of ozone in ternary collisions O+O_{2}+M-the primary mechanism of ozone formation in the stratosphere-at temperatures below 200 K (for M=Ar) proceeds through a formation of a temporary complex MO_{2}, while at temperatures above ∼700 K, the reaction proceeds mainly through a formation of long-lived vibrational resonances of O_{3}^{*}. At intermediate temperatures 200-700 K, the process cannot be viewed as a two-step mechanism, often used to simplify and approximate collisions of three atoms or molecules. The developed theoretical approach is applied to the reaction O+O_{2}+Ar because of extensive experimental data available. The rate coefficients for the formation of O_{3} in ternary collisions O+O_{2}+Ar without using two-step approximations were computed for the first time as a function of collision energy. Thermally averaged coefficients were derived for temperatures 5-900 K. It is found that the majority of O_{3} molecules formed initially are weakly bound. Accounting for the process of vibrational quenching of the nascent population, a good agreement with available experimental data for temperatures 100-900 K is obtained.

Classical threshold law for the formation of van der Waals molecules.

We study the role of pairwise long-range interactions in the formation of van der Waals molecules through direct three-body recombination processes A + B + B → AB + B, based on a classical trajectory method in hyperspherical coordinates developed in our earlier works [J. Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014); M. Mirahmadi and J. Pérez-Ríos, J. Chem. Phys. 154, 034305 (2021)]. In particular, we find the effective long-range potential in hyperspherical coordinates with an exact expression in terms of dispersion coefficients of pairwise potentials. Exploiting this relation, we derive a classical threshold law for the total cross section and the three-body recombination rate yielding an analytical expression for the three-body recombination rate as a function of the pairwise long-range coefficients of the involved partners.

Complex Reaction Network Thermodynamic and Kinetic Autoconstruction Based on Ab Initio Statistical Mechanics: A Case Study of O2 Activation on Ag4 Clusters.

An approach based on ab initio statistical mechanics is demonstrated for autoconstructing complex reaction networks. Ab initio molecular dynamics combined with Markov state models are employed to study relevant transitions and corresponding thermodynamic and kinetic properties of a reaction. To explore the capability and flexibility of this approach, we present a study of oxygen activation on Ag4 as a model reaction. Specifically, with the same sampled trajectories, it is possible to study the structural effects and the reaction rate of the cited reaction. The results show that this approach is suitable for automatized construction of reaction networks, especially for non-well-studied reactions, which can benefit from this ab initio molecular dynamics based approach to construct comprehensive reaction networks with Markov state models without prior knowledge about the potential energy landscape.

Predicting second virial coefficients of organic and inorganic compounds using Gaussian process regression.

We show that by using intuitive and accessible molecular features it is possible to predict the temperature-dependent second virial coefficient of organic and inorganic compounds with Gaussian process regression. In particular, we built a low dimensional representation of features based on intrinsic molecular properties, topology and physical properties relevant for the characterization of molecule-molecule interactions. The featurization was used to predict second virial coefficients in the interpolative regime with a relative error ⪅1% and to extrapolate the prediction to temperatures outside of the training range for each compound in the dataset with a relative error of 2.1%. Additionally, the model's predictive abilities were extended to organic molecules unseen in the training process, yielding a prediction with a relative error of 2.7%. Test molecules must be well-represented in the training set by instances of their families, which are high in variety. The method shows a generally better performance when compared to several semi-empirical procedures employed in the prediction of the quantity. Therefore, apart from being robust, the present Gaussian process regression model is extensible to a variety of organic and inorganic compounds.

On the formation of van der Waals complexes through three-body recombination.

In this work, we show that van der Waals molecules X-RG (where RG is the rare gas atom) may be created through direct three-body recombination collisions, i.e., X + RG + RG → X-RG + RG. In particular, the three-body recombination rate at temperatures relevant for buffer gas cell experiments is calculated via a classical trajectory method in hyperspherical coordinates [Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014)]. As a result, it is found that the formation of van der Waals molecules in buffer gas cells (1 K ≲ T ≲ 10 K) is dominated by the long-range tail (distances larger than the LeRoy radius) of the X-RG interaction. For higher temperatures, the short-range region of the potential becomes more significant. Moreover, we notice that the rate of formation of van der Walls molecules is of the same order of the magnitude independent of the chemical properties of X. As a consequence, almost any X-RG molecule may be created and observed in a buffer gas cell under proper conditions.

On the relationship between spectroscopic constants of diatomic molecules: a machine learning approach.

Through a machine learning approach, we show that the equilibrium distance, harmonic vibrational frequency and binding energy of diatomic molecules are related, independently of the nature of the bond of a molecule; they depend solely on the group and period of the constituent atoms. As a result, we show that by employing the group and period of the atoms that form a molecule, the spectroscopic constants are predicted with an accuracy of <5%, whereas for the A-excited electronic state it is needed to include other atomic properties leading to an accuracy of <11%.

Heat shock proteins and antioxidants as mechanisms of response to ivermectin in the dung beetle Euoniticellus intermedius.

Ivermectin is the most common antiparasitic drug used in livestock in many regions of the world. Its residues are excreted in dung, threatening non-target fauna such as dung beetles, fundamental for cleaning dung in pastures. However, it is unclear which are the physiological mechanisms used by dung beetles to cope with ivermectin. Here we evaluated experimentally the physiological responses of the dung beetle Euoniticellus intermedius to ivermectin-induced stress. We measured metabolic rates, heat shock protein 70 (Hsp70) expression, antioxidant capacity, and oxidative damage in lipids in both males and females exposed to a sublethal dose. Compared to control beetles, ivermectin-treated males and females had increased metabolic rates. Moreover, ivermectin-treated females increased their expression of Hsp70 whereas males increased their antioxidant capacity. No changes in the levels of oxidative damage to lipids were detected for either sex, suggesting a process of hormesis, such that exposure to a moderate concentration of ivermectin could stimulate the action of a protective mechanism against oxidative stress, that differs between sexes. However, it does not exclude the possibility that damage to other biomolecules might have occurred. Sexual differences in physiological responses can be interpreted as the result of hormonal differences or life-history trade-offs that favor different mechanisms in females and males. Hsps and antioxidants are involved in the physiological response of beetles to ivermectin and may be key in providing resistance to this contaminant in target and non-target species, including dung beetles.

A data-driven approach to determine dipole moments of diatomic molecules.

We present a data-driven approach for the prediction of the electric dipole moment of diatomic molecules, which is one of the most relevant molecular properties. In particular, we apply Gaussian process regression to a novel dataset to show that dipole moments of diatomic molecules can be learned, and hence predicted, with a relative error ⪅5%. The dataset contains the dipole moment of 162 diatomic molecules, the most exhaustive and unbiased dataset of dipole moments up to date. Our findings show that the dipole moment of diatomic molecules depends on atomic properties of the constituents atoms: electron affinity and ionization potential, as well as on (a feature related to) the first derivative of the electronic kinetic energy at the equilibrium distance.

Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial.

ObjectivesAn IFN-2b and IFN-{gamma} combination has demonstrated favorable pharmacodynamics for genes underlying antiviral activity which might be involved in the defense of a host from a SARS-CoV-2 infection. Considering this synergy, we conducted a randomized controlled clinical trial for efficacy and safety evaluation of subcutaneous IFN - 2b and IFN-{gamma} administration in patients positive for SARS-CoV-2. MethodsWe enrolled 19-82 years-old inpatients at the Military Central Hospital Luis Diaz Soto, Havana, Cuba. They were hospitalized after confirmed diagnosis for SARS-CoV-2 RNA by real-time reverse transcription polymerase chain reaction. Patients were randomly assigned in a 1:1 ratio to receive either, subcutaneous treatment with a co-lyophilized combination of 3.0 MIU IFN-2b and 0.5 MIU IFN-{gamma} (HeberFERON, CIGB, Havana, Cuba), twice a week for two weeks, or thrice a week intramuscular injection of 3.0 MIU IFN-2b (Heberon(R) Alpha R, CIGB, Havana, Cuba). Additionally, all patients received lopinavir-ritonavir (200/50 mg every 12 h) and chloroquine (250 mg every 12 h, i.e.standard of care). The primary endpoints were, from the start of treatment, the time to elimination of viral RNA and the time to progression to severe COVID-19. The protocol was approved by the Ethics Committee on Clinical Investigation from the Hospital and the Center for the State Control of Medicines, Equipment and Medical Devices in Cuba. Informed consent was obtained from each participant (INSTITUTION PROTOCOL IG/IAG/CV/2001). ResultsA total of 79 patients with laboratory-confirmed SARS-CoV-2 infection, including symptomatic or asymptomatic conditions, fulfilled the inclusion criteria and underwent randomization. Thirty-three subjects were assigned to the HeberFERON group, and 33 to the Heberon Alpha R group. Sixty-three patients were analyzed for viral elimination, of these 78.6% in the HeberFERON group eliminated the virus after 4 days of treatment versus 40.6% of patients in the Heberon Alpha R groups (p=0.004). Time to reach the elimination of SARS-CoV-2, as measured by RT-PCR was 3.0 and 5.0 days for the HeberFERON and Heberon Alpha R groups, respectively. A significant improvement in the reduction of time for virus elimination was attributable to HeberFERON (p=0.0027, Log-rank test) with a Hazard Ratio of 3.2 and 95% CI of 1.529 to 6.948, as compared to the Heberon Alpha R treated group. Worsening of respiratory symptoms was detected in two (6.6%) and one (3.3%) patients in HeberFERON and IFN-2b groups, respectively. However, none of the subjects transited to severe COVID-19 during the study or during the following clinical evaluation (21 more days). RT-PCR on day 14 after the start of the treatment was negative to SARS-CoV-2 in 100% and 91% of patients of the combination of IFNs and IFN-2b, respectively. Elimination in HeberFERON treated patients was related to a significant increase in lymphocytes counts and also a significant reduction in CRP as early as 7 days after commencing the therapeutic schedule. All the patients in both cohorts recovered and had their laboratory parameters return to normal values by day 14 after treatment initiation. Adverse events were identified in 31.5% of patients, 28.5% in the control group, and 34.4% in the HeberFERON group, with the most frequent adverse event being headaches (17.4%). ConclusionsIn a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly eliminated the virus on day 4 of treatment when compared to treatment with IFN-2b alone. However, Heberon Alpha R alone also showed efficacy for the treatment of the viral infection. Both treatments were safe and positively impacted on the resolution of the symptoms. None of the patients developed severe COVID-19.

Panorama histórico de la enfermedad diarreica aguda en México y el futuro de su prevención / Historical overview of acute infectious diarrhea in Mexico and future preventive strategies

Resumen: Objetivo: Revisar los aspectos epidemiológicos de la enfermedad diarreica aguda (EDA) a través de la historia de México y analizar las estrategias que potencialmente podrán prevenir su aparición en la población mexicana. Material y métodos: Se realizó una búsqueda sistematizada utilizando los siguientes descriptores de las ciencias de la salud: diarrea, morbilidad, mortalidad, México y promoción de la salud de los últimos 20 años (1878-2018). Resultados: Se obtuvieron más de 8 600 artículos que fueron evaluados en función de los objetivos de la presente publicación. Conclusión: Como resultado de una revisión sistemática se observó que, gracias a las estrategias implementadas a lo largo del tiempo, se ha logrado graduar los matices de riesgo de la EDA; ello permite ahora plantear estrategias que guiarán a la prevención de ese padecimiento, de la mano de políticas que incluyan aspectos higiénico-dietéticos, innovaciones farmacéuticas y aplicaciones tecnológicas en medidas sanitarias.

Abstract: Objective: To analyze the epidemiological aspects of AID through Mexican history and the potential strategies to prevent AID in Mexican population. Materials and methods: A systematic review was performed exploring the key words, diarrhea, morbidity, mortality, Mexico, health promotion for the last 20 years (1978-2018). Results: Over 8 600 articles were obtained; all of them were evaluated to consider those follow the aim of the present work. Conclusion: The result of the performed systematic review denoted the influence of AID in Mexican public health policy the adopted actions diminished the AID's associated risks and allowed future strategies to prevent it; those actions must include hygienic and dietetic measures, pharmaceutical innovations and technological tools applied to health policies.