University of Havana

Molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has been proven to balance accuracy and computational efficiency, especially when dealing with large systems. As a result of its popularity, several programs have been developed for performing MM/PB(GB)SA calculations within the GROMACS community. These programs, however, present several limitations. Here we present gmx_MMPBSA, a new tool to perform end-state free energy calculations from GROMACS molecular dynamics trajectories. gmx_MMPBSA provides the user with several options, including binding free energy calculations with different solvation models (PB, GB, or 3D-RISM), stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Noteworthy, several promising methodologies to calculate relative binding free energies such as alanine scanning with variable dielectric constant and interaction entropy have also been implemented in gmx_MMPBSA. Two additional tools-gmx_MMPBSA_test and gmx_MMPBSA_ana-have been integrated within gmx_MMPBSA to improve its usability. Multiple illustrating examples can be accessed through gmx_MMPBSA_test, while gmx_MMPBSA_ana provides fast, easy, and efficient access to different graphics plotted from gmx_MMPBSA output files. The latest version (v1.4.3, 26/05/2021) is available free of charge (documentation, test files, and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.

Humans express a wide array of ideal mate preferences. Around the world, people desire romantic partners who are intelligent, healthy, kind, physically attractive, wealthy, and more. In order for these ideal preferences to guide the choice of actual romantic partners, human mating psychology must possess a means to integrate information across these many preference dimensions into summaries of the overall mate value of their potential mates. Here we explore the computational design of this mate preference integration process using a large sample of n = 14,487 people from 45 countries around the world. We combine this large cross-cultural sample with agent-based models to compare eight hypothesized models of human mating markets. Across cultures, people higher in mate value appear to experience greater power of choice on the mating market in that they set higher ideal standards, better fulfill their preferences in choice, and pair with higher mate value partners. Furthermore, we find that this cross-culturally universal pattern of mate choice is most consistent with a Euclidean model of mate preference integration.

BACKGROUND: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.

Non-alcoholic fatty liver disease (NAFLD) is a potentially serious liver disease that affects approximately one-quarter of the global adult population, causing a substantial burden of ill health with wide-ranging social and economic implications. It is a multisystem disease and is considered the hepatic component of metabolic syndrome. Unlike other highly prevalent conditions, NAFLD has received little attention from the global public health community. Health system and public health responses to NAFLD have been weak and fragmented, and, despite its pervasiveness, NAFLD is largely unknown outside hepatology and gastroenterology. There is only a nascent global public health movement addressing NAFLD, and the disease is absent from nearly all national and international strategies and policies for non-communicable diseases, including obesity. In this global Delphi study, a multidisciplinary group of experts developed consensus statements and recommendations, which a larger group of collaborators reviewed over three rounds until consensus was achieved. The resulting consensus statements and recommendations address a broad range of topics — from epidemiology, awareness, care and treatment to public health policies and leadership — that have general relevance for policy-makers, health-care practitioners, civil society groups, research institutions and affected populations. These recommendations should provide a strong foundation for a comprehensive public health response to NAFLD. Non-alcoholic fatty liver disease (NAFLD) is a potentially serious liver disease with a substantial burden worldwide. In this Consensus Statement, a global multidisciplinary group of experts develop consensus statements and recommendations addressing a broad range of topics on NAFLD to raise awareness and spur action.

Quercetin (Que) and its derivatives are naturally occurring phytochemicals with promising bioactive effects. The antidiabetic, anti-inflammatory, antioxidant, antimicrobial, anti-Alzheimer's, antiarthritic, cardiovascular, and wound-healing effects of Que have been extensively investigated, as well as its anticancer activity against different cancer cell lines has been recently reported. Que and its derivatives are found predominantly in the Western diet, and people might benefit from their protective effect just by taking them via diets or as a food supplement. Bioavailability-related drug-delivery systems of Que have also been markedly exploited, and Que nanoparticles appear as a promising platform to enhance their bioavailability. The present review aims to provide a brief overview of the therapeutic effects, new insights, and upcoming perspectives of Que.

The grafting of the triangular 1,3,5-benzene tricarboxylate linkers (denoted trim) on tetrahedral ε-Keggin polyoxometalates (POMs) capped by Zn(II) ions, formed in situ under hydrothermal conditions, has generated three novel POM-based metal organic frameworks (POMOFs). (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(36)(OH)(4)Zn(4)][C(6)H(3)(COO)(3)](4/3)·6H(2)O (ε(trim)(4/3)) is a 3D open-framework built of molecular Keggin units connected by trim linkers, with channels occupied by tetrabutylammonium (TBA) counterions. ε(trim)(4/3) is a novel (3,4)-connected net, named ofp for open-framework polyoxometalate, and computer simulations have been used to evaluate its relative stability in comparison with ctn- and bor-like polymorphs, showing the stability of this novel phase directly related to its greatest density. A computational study was also undertaken with the aim of locating TBA molecules, the positions of which could not be deduced from single crystal X-ray diffraction, and further rationalizes their structure directing role. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)] (ε(2)(trim)(2)), the building unit is not the molecular Keggin but a dimerized form of this POM. Their connection via trim linkers generates a 3D framework with channels filled by TBA cations. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)]·8H(2)O ([ε(trim)](∞)), zigzag chains are connected via the organic linkers, forming 2D grids. Modified electrodes were fabricated by direct adsorption of the POMOFs on glassy carbon or entrapment in carbon paste (CPE). A remarkable electrocatalytic hydrogen evolution reaction (HER) was detected with a yield greater than 95%, and a turnover number as high as 1.2 × 10(5) was obtained after 5 h. The reported POMOF-based electrodes are more active than platinum, with a roughly 260 mV anodic shift. Finally, the electrocatalytic activities of ε(trim)(4/3)/CPE electrodes in various XCl (X = Li, Na, K, Cs) media have been studied. This allowed us to detect a cation effect and propose an electrocatalytic mechanistic pathway for the HER.

Glycoconjugate vaccines provide effective prophylaxis against bacterial infections. To date, however, no commercial vaccine has been available in which the key carbohydrate antigens are produced synthetically. We describe the large-scale synthesis, pharmaceutical development, and clinical evaluation of a conjugate vaccine composed of a synthetic capsular polysaccharide antigen of Haemophilus influenzae type b (Hib). The vaccine was evaluated in clinical trials in Cuba and showed long-term protective antibody titers that compared favorably to licensed products prepared with the Hib polysaccharide extracted from bacteria. This demonstrates that access to synthetic complex carbohydrate-based vaccines is feasible and provides a basis for further development of similar approaches for other human pathogens.

The main source of commercial chitosan is the extensive deacetylation of its parent polymer chitin. It is present in green algae, the cell walls or fungi and in the exoskeleton of crustaceans. A novel procedure for preparing chitosan from shrimp shells was developed. The procedure involves two 10-minutes bleaching steps with ethanol after the usual demineralization and deproteinization processes. Before deacetylation, chitin was immersed in 12.5 M NaOH, cooled down and kept frozen for 24 h. The obtained chitosan was characterized using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), UV, X-ray diffraction (XRD) and viscosimetry. Samples of white chitosan with acetylation degrees below 9 % were obtained, as determined by FTIR and UV-first derivative spectroscopy. The change in the morphology of samples was followed by SEM. The ash content of chitosan samples were all below 0.063 % . Chitosan was soluble in 1 % acetic acid with insoluble contents of 0.62 % or less. XRD patterns exhibited the characteristic peaks of chitosan centered at 10 and 20 degrees in 2 θ . The molecular weight of chitosan was between 2.3 and 2.8 × 10 5 g/mol. It is concluded that the procedure developed in the present work allowed obtaining chitosans with physical and chemical properties suitable for pharmaceutical applications.

Innate immunity is a semi-specific and widely distributed form of immunity, which represents the first line of defence against pathogens. This type of immunity is critical to maintain homeostasis and prevent microbe invasion, eliminating a great variety of pathogens and contributing with the activation of the adaptive immune response. The components of innate immunity include physical and chemical barriers, humoral and cell-mediated components, which are present in all jawed vertebrates. The understanding of innate defence mechanisms in non-mammalian vertebrates is the key to comprehend the general picture of vertebrate innate immunity and its evolutionary history. This is also essential for the identification of new molecules with applications in immunopharmacology and immunotherapy. In this review, we describe and discuss the main elements of vertebrate innate immunity, presenting core findings in this field and identifying areas that need further investigation.

Molybdenum carbide (Mo 2 C) based catalysts were found to be one of the most promising electrocatalysts for hydrogen evolution reaction (HER) in acid media in comparison with Pt-based catalysts but were seldom investigated in alkaline media, probably due to the limited active sites, poor conductivity, and high energy barrier for water dissociation. In this work, Mo 2 C-embedded nitrogen-doped porous carbon nanosheets (Mo 2 C@2D-NPCs) were successfully achieved with the help of a convenient interfacial strategy. As a HER electrocatalyst in alkaline solution, Mo 2 C@2D-NPC exhibited an extremely low onset potential of ∼0 mV and a current density of 10 mA cm –2 at an overpotential of ∼45 mV, which is much lower than the values of most reported HER electrocatalysts and comparable to the noble metal catalyst Pt. In addition, the Tafel slope and the exchange current density of Mo 2 C@2D-NPC were 46 mV decade –1 and 1.14 × 10 –3 A cm –2, respectively, outperforming the state-of-the-art metal-carbide-based electrocatalysts in alkaline media. Such excellent HER activity was attributed to the rich Mo 2 C/NPC heterostructures and synergistic contribution of nitrogen doping, outstanding conductivity of graphene, and abundant active sites at the heterostructures.

AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock's functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS . REVIEWERS: This article was reviewed by Alexander Krah and Thomas Gaillard.

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela-Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSupramolecular Chemistry of Cyclodextrins in Enzyme TechnologyReynaldo Villalonga, Roberto Cao, and Alex FragosoView Author Information Laboratory of Bioinorganic Chemistry, Faculty of Chemistry, University of Havana, Vedado, Havana 10400, Cuba, Center for Enzyme Technology, University of Matanzas, Matanzas 44740, Cuba, and Nanobiotechnology & Bioanalysis Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, Tarragona 43007, Spain Cite this: Chem. Rev. 2007, 107, 7, 3088–3116Publication Date (Web):June 23, 2007Publication History Received29 June 2006Published online23 June 2007Published inissue 1 July 2007https://pubs.acs.org/doi/10.1021/cr050253ghttps://doi.org/10.1021/cr050253gresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views6214Altmetric-Citations334LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Biotechnology,Cadmium sulfide,Oligosaccharides,Peptides and proteins,Reaction products Get e-Alerts

BACKGROUND: Latin America, China and India are experiencing unprecedentedly rapid demographic ageing with an increasing number of people with dementia. The 10/66 Dementia Research Group's title refers to the 66% of people with dementia that live in developing countries and the less than one tenth of population-based research carried out in those settings. This paper describes the protocols for the 10/66 population-based and intervention studies that aim to redress this imbalance. METHODS/DESIGN: Cross-sectional comprehensive one phase surveys have been conducted of all residents aged 65 and over of geographically defined catchment areas in ten low and middle income countries (India, China, Nigeria, Cuba, Dominican Republic, Brazil, Venezuela, Mexico, Peru and Argentina), with a sample size of between 1000 and 3000 (generally 2000). Each of the studies uses the same core minimum data set with cross-culturally validated assessments (dementia diagnosis and subtypes, mental disorders, physical health, anthropometry, demographics, extensive non communicable disease risk factor questionnaires, disability/functioning, health service utilisation, care arrangements and caregiver strain). Nested within the population based studies is a randomised controlled trial of a caregiver intervention for people with dementia and their families (ISRCTN41039907; ISRCTN41062011; ISRCTN95135433; ISRCTN66355402; ISRCTN93378627; ISRCTN94921815). A follow up of 2.5 to 3.5 years will be conducted in 7 countries (China, Cuba, Dominican Republic, Venezuela, Mexico, Peru and Argentina) to assess risk factors for incident dementia, stroke and all cause and cause-specific mortality; verbal autopsy will be used to identify causes of death. DISCUSSION: The 10/66 DRG baseline population-based studies are nearly complete. The incidence phase will be completed in 2009. All investigators are committed to establish an anonymised file sharing archive with monitored public access. Our aim is to create an evidence base to empower advocacy, raise awareness about dementia, and ensure that the health and social care needs of older people are anticipated and met.

In the past decade, multicomponent reactions have experienced a renaissance as powerful peptide macrocyclization tools enabling the rapid creation of skeletal complexity and diversity with low synthetic cost. This review provides both a historical and modern overview of the development of the peptide multicomponent macrocyclization as a strategy capable to compete with the classic peptide cyclization methods in terms of chemical efficiency and synthetic scope. We prove that the utilization of multicomponent reactions for cyclizing peptides by either their termini or side chains provides a key advantage over those more established methods; that is, the possibility to explore the cyclic peptide chemotype space not only at the amino acid sequence but also at the ring-forming moiety. Owing to its multicomponent nature, this type of peptide cyclization process is well-suited to generate diversity at both the endo - and exo -cyclic fragments formed during the ring-closing step, which stands as a distinctive and useful characteristic for the creation and screening of cyclic peptide libraries. Examples of the novel multicomponent peptide stapling approach and heterocycle ring-forming macrocyclizations are included, along with multicomponent methods incorporating macrocyclization handles and the one-pot syntheses of macromulticyclic peptide cages. Interesting applications of this strategy in the field of drug discovery and chemical biology are provided.

Considerable research has examined human mate preferences across cultures, finding universal sex differences in preferences for attractiveness and resources as well as sources of systematic cultural variation. Two competing perspectives—an evolutionary psychological perspective and a biosocial role perspective—offer alternative explanations for these findings. However, the original data on which each perspective relies are decades old, and the literature is fraught with conflicting methods, analyses, results, and conclusions. Using a new 45-country sample ( N = 14,399), we attempted to replicate classic studies and test both the evolutionary and biosocial role perspectives. Support for universal sex differences in preferences remains robust: Men, more than women, prefer attractive, young mates, and women, more than men, prefer older mates with financial prospects. Cross-culturally, both sexes have mates closer to their own ages as gender equality increases. Beyond age of partner, neither pathogen prevalence nor gender equality robustly predicted sex differences or preferences across countries.

-acetylglucosamine). It is biocompatible, biodegradable, mucoadhesive, and non-toxic. These excellent biological properties make chitosan a good candidate for a platform in developing drug delivery systems having improved biodistribution, increased specificity and sensitivity, and reduced pharmacological toxicity. In particular, chitosan nanoparticles are found to be appropriate for non-invasive routes of drug administration: oral, nasal, pulmonary and ocular routes. These applications are facilitated by the absorption-enhancing effect of chitosan. Many procedures for obtaining chitosan nanoparticles have been proposed. Particularly, the introduction of hydrophobic moieties into chitosan molecules by grafting to generate a hydrophobic-hydrophilic balance promoting self-assembly is a current and appealing approach. The grafting agent can be a hydrophobic moiety forming micelles that can entrap lipophilic drugs or it can be the drug itself. Another suitable way to generate self-assembled chitosan nanoparticles is through the formation of polyelectrolyte complexes with polyanions. This paper reviews the main approaches for preparing chitosan nanoparticles by self-assembly through both procedures, and illustrates the state of the art of their application in drug delivery.

Bullying is a phenomenon of unjustified aggression which actually takes place in two formats: face to face and as a behavior that is carried out through digital devices (cyberbullying). Both have been widely studied, though currently there is little knowledge about the homogeneity of both phenomena and we do not have measuring instruments for evaluating their two dimensions: aggression and cyber-aggression, victimization and cyber-victimization. This paper presents the validation of the European Bullying Intervention Project Questionnaire and the European Cyberbullying Intervention Project Questionnaire, that assess respectively the involvement in bullying and cyberbullying. Both have been administered to 792 high school students and have achieved good fit and good psychometric properties. The use of a structural equations modelling has allowed us to evaluate the concurrence and the relations between the two phenomena, finding the influence of bullying on cyberbullying, but not vice versa. These results show the suitability of the two instruments to assess together bullying and cyberbullying, given their important relationship and similarity, which makes them good tools for educational intervention to prevent and reduce both phenomena.

PURPOSE: To evaluate safety and preliminary efficacy of the humanized anti-epidermal growth factor receptor monoclonal antibody h-R3 in combination with radiotherapy (RT) in unresectable head and neck cancer patients. Secondary end points were the measurement of h-R3 serum levels and the assessment of the potential mechanisms of antitumor effect on patient biopsies. Anti-idiotypic response to h-R3 was assessed. To predict pharmacologic effect, a mathematical model for antibodies recognizing antigens expressed in tumors and normal tissues was built. PATIENTS AND METHODS: Twenty-four patients with advanced carcinomas of the head and neck received six once-weekly infusions of h-R3 at four dose levels in combination with RT. Pretreatment tumor biopsies were obtained to evaluate epidermal growth factor receptor expression as an enrollment criterion. Second biopsies were taken to evaluate the proliferative activity and angiogenesis in comparison with the pretreatment samples. Patient serum samples were collected to measure h-R3 levels and anti-idiotypic response. RESULTS: The combination of h-R3 and RT was well tolerated. Antibody-related adverse events consisted in infusion reactions. No skin or allergic toxicity appeared. Overall survival significantly increased after the use of the higher antibody doses. Immunohistochemistry studies of tumor specimens before and after treatment revealed that antitumor response correlated with antiproliferative and antiangiogenic effect. One patient developed antibodies to h-R3. The mathematical model predicted that the maximum difference between the area under the curve in tumors and normal tissues is reached when the antibody has intermediate affinity. CONCLUSION: h-R3 is a well-tolerated drug that may enhance radiocurability of unresectable head and neck neoplasms.

Abstract Chitosan is a weak cationic polysaccharide composed essentially of β (1 → 4) linked glucosamine units together with some N ‐acetylglucosamine units. It is obtained by extensive deacetylation of chitin, a polysaccharide common in nature. Chitosan is a biocompatible, biodegradable, and nontoxic natural polymer that exhibits excellent film‐forming ability. As a result of its cationic character, chitosan is able to react with polyanions giving rise to polyelectrolyte complexes. Therefore, because of these interesting properties, it has become the subject of numerous scientific reports and patents on the preparation of microspheres and microcapsules. The techniques employed to microencapsulate with chitosan include, among others, ionotropic gelation, spray drying, emulsion phase separation, simple and complex coacervation, and polymerization of a vinyl monomer in the presence of chitosan. The aim of this work is to review some of the more common techniques used and to put forward the results obtained by our research group in preparing chitosan‐based microcapsules: for taste masking and improving the stability of a nutritional oil, the sustained release of drugs, as well as the preparation of chitosan superparamagnetic microcapsules for the immobilization of enzymes. Scanning electron micrograph of some superparamagnetic chitosan particles and magnetic hysteresis loop of the microparticles. magnified image Scanning electron micrograph of some superparamagnetic chitosan particles and magnetic hysteresis loop of the microparticles.