Stmol: A component for building interactive molecular visualizations within streamlit web-applications.

Streamlit is an open-source Python coding framework for building web-applications or "web-apps" and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.

In vitro and in silico studies of terpenes, terpenoids and related compounds with larvicidal and pupaecidal activity against Culex quinquefasciatus Say (Diptera: Culicidae).

BACKGROUND: In order to develop new larvicidal agents derived from phytochemicals, the larvicidal activity of fifty molecules that are constituent of essential oils was evaluated against Culex quinquefasciatus Say. Terpenes, terpenoids and phenylpropanoids molecules were included in the in vitro evaluation, and QSAR models using genetic algorithms were built to identify molecular and structural properties of biological interest. Further, to obtain structural details on the possible mechanism of action, selected compounds were submitted to docking studies on sterol carrier protein-2 (SCP-2) as possible target. RESULTS: Results showed high larvicidal activity of carvacrol and thymol on the third and fourth larval stage with a median lethal concentration (LC50) of 5.5 and 11.1 µg/mL respectively. Myrcene and carvacrol were highly toxic for pupae, with LC50 values of 31.8 and 53.2 µg/mL. Structure-activity models showed that the structural property π-bonds is the largest contributor of larvicidal activity while ketone groups should be avoided. Similarly, property-activity models attributed to the molecular descriptor LogP the most contribution to larvicidal activity, followed by the absolute total charge (Qtot) and molar refractivity (AMR). The models were statistically significant; thus the information contributes to the design of new larvicidal agents. Docking studies show that all molecules tested have the ability to interact with the SCP-2 protein, wherein α-humulene and ß-caryophyllene were the compounds with higher binding energy. CONCLUSIONS: The description of the molecular properties and the structural characteristics responsible for larvicidal activity of the tested compounds were used for the development of mathematical models of structure-activity relationship. The identification of molecular and structural descriptors, as well as studies of molecular docking on the SCP-2 protein, provide insight on the mechanism of action of the active molecules, and the information can be used for the design of new structures for synthesis as potential new larvicidal agents.

QSAR, DFT and molecular modeling studies of peptides from HIV-1 to describe their recognition properties by MHC-I.

Human immunodeficiency virus type-1 (HIV-1) has infected more than 40 million people around the world. HIV-1 treatment still has several side effects, and the development of a vaccine, which is another potential option for decreasing human infections, has faced challenges. This work presents a computational study that includes a quantitative structure activity relationship(QSAR) using density functional theory(DFT) for reported peptides to identify the principal quantum mechanics descriptors related to peptide activity. In addition, the molecular recognition properties of these peptides are explored on major histocompatibility complex I (MHC-I) through docking and molecular dynamics (MD) simulations accompanied by the Molecular Mechanics Generalized Born Surface Area (MMGBSA) approach for correlating peptide activity reported elsewhere vs. theoretical peptide affinity. The results show that the carboxylic acid and hydroxyl groups are chemical moieties that have an inverse relationship with biological activity. The number of sulfides, pyrroles and imidazoles from the peptide structure are directly related to biological activity. In addition, the HOMO orbital energy values of the total absolute charge and the Ghose-Crippen molar refractivity of peptides are descriptors directly related to the activity and affinity on MHC-I. Docking and MD simulation studies accompanied by an MMGBSA analysis show that the binding free energy without considering the entropic contribution is energetically favorable for all the complexes. Furthermore, good peptide interaction with the most affinity is evaluated experimentally for three proteins. Overall, this study shows that the combination of quantum mechanics descriptors and molecular modeling studies could help describe the immunogenic properties of peptides from HIV-1.

Synthesis, electronic, and spectral properties of novel geranylated chalcone derivatives: a theoretical and experimental study.

Novel chalcone derivatives with different substituents attached to A and B-rings: hydroxyl, methoxyl, geranyl, and prenyl groups were synthesized. The obtained compounds were characterized by NMR, HRMS, UV-Vis, IR, and MS. The theoretical analysis was carried out in all the compounds using density functional theory (DFT) with the B3LYP, PBE0, and M06-2X functionals in combination with the 6-311G(d,p) Pople-type basis set. The excited state properties were calculated by time dependent density functional theory (TD-DFT) using the same methodology applied for the ground state properties. The calculated vertical absorption wavelengths (λmax) in gas phase and in ethanol as a solvent are consistent with the experimental ones, being the TD-DFT:B3LYP/6-311G(d,p) and PCM-TD-DFT:PBE0/6-311G(d,p) the best methodologies for these calculations with good approximation to the experimental values. The calculated reorganization energies indicated that, the four chalcone derivatives present an electron transfer character due to the smaller registered values. From these parameters it is proposed that these show an n-type semiconductor character. The localization of the frontier orbitals (HOMO and LUMO) shows that only the compound containing a hydroxyl group on the A-ring displays a marked delocalization favoring the charge-transfer process in this system. The HOMO-LUMO gap energies indicate that the inclusion of different donor groups in the rings does not improve the obtained values for this property. Graphical Abstract Relationship between spectroscopic and geometrical properties of chalcones were carried out using quantum-chemical calculations and compared with experimental values.

[The injured pedestrian in motor vehicle traffic accidents: mortality in Mexico, 1985-1996]. / El peatón lesionado en accidentes de tráfico de vehículo de motor: mortalidad en México, 1985-1996.

OBJECTIVE: To describe the mortality of pedestrians injured at motor vehicle traffic accidents (PIMVTA) in Mexico. METHODS: Analysis of death certificates registered in Mexico (1985-1996), identified by E codes of the International Classification of Diseases, 9th Revision. Mortality rates were stratified by age group. RESULTS: From 1985 to 1996, 60,566 deaths in PIMVTA (rate of 7.42/100,000) were registered: 78.1% in men (11.7/100,000), and 21.9% in women (3.2/100,000). The mortality increased in direct relationship to age, the general mortality trend lightly descending in both sexes, but more marked from the 80 and more years old. The higher rate was is observed for Jalisco (9.7/100,000) and the lower rate was for Coahuila (2.1/100,000). According to the location size, the mortality shows a bimodal distribution: higher for localities of 15.000 to 19.999 and 1,000,000 (8.0/100,000 and 8.2/100,000 person-years, respectively. CONCLUSIONS: The deaths of PLATVM are presented, mainly, in men, their frequency is incremented with the age, they show a tendency lightly descending, and they are observed with greater frequency in urban centers.

Combination drug therapy for cryptosporidiosis in AIDS.

Aside from effective antiretroviral therapy, there is no consistently effective antiparasitic therapy for cryptosporidiosis in AIDS. The purpose of this study was to assess safety, efficacy, and durability of combination therapy with paromomycin and azithromycin for chronic cryptosporidiosis. Patients with AIDS, chronic cryptosporidiosis, and < 100 CD4 cells/microL were treated with open-label paromomycin (1.0 g twice a day) plus azithromycin (600 mg once a day) for 4 weeks, followed by paromomycin alone for 8 weeks. In 11 patients, median stool frequency decreased from 6.5/day (baseline) to 4.9/day (week 4) and 3.0/day (week 12). Median reductions in 24-h oocyst excretion were 84%, 95%, and >99% at 2, 4, and 12 weeks, respectively. None of the responses were attributable to antiretrovirals. Of 5 survivors at 12-30 months of follow-up, 3 remain asymptomatic off medications, and 2 have chronic, mild diarrhea. Treatment of cryptosporidiosis with azithromycin and paromomycin was associated with significant reduction in oocyst excretion and some clinical improvement.

Prophylactic effect of bovine anti-Cryptosporidium hyperimmune colostrum immunoglobulin in healthy volunteers challenged with Cryptosporidium parvum.

Bovine hyperimmune anti-Cryptosporidium colostrum immunoglobulin (BACI) decreases the intensity of Cryptosporidium parvum infection in vitro. We investigated the prophylactic effect of BACI in healthy adults challenged with C. parvum. After we established an oocyst dose that resulted in 100% infection in four volunteers (baseline group), 16 volunteers were randomized to receive (1) BACI prior to C. parvum challenge (BACI group) and a nonfat milk placebo 30 minutes later, (2) BACI prior to and 30 minutes after challenge (reinforced BACI group), or (3) nonfat milk placebo prior to and 30 minutes after challenge. Subjects received BACI (10 g) or nonfat milk placebo three times a day for a total of 5 days and were followed for clinical symptoms and oocyst excretion for 30 days. A trend toward less diarrhea (P = .08) was observed for subjects receiving BACI in comparison with occurrences in placebo recipients. Subjects receiving BACI or nonfat milk placebo had a 100-fold reduction in oocyst excretion as compared with excretion in the baseline group.

Flow cytometric detection of Cryptosporidium oocysts in human stool samples.

Cryptosporidium parvum is an important pathogen that causes diarrhea in virtually all human populations. Improved diagnostic methods are needed to understand the risk factors, modes of transmission, and impact of cryptosporidiosis. In the present study, we fluorescently labeled and counted C. parvum oocysts by flow cytometry (FC) and developed a simple and efficient method of processing human stool samples for FC analysis. Formed stool (suspended in phosphate-buffered saline) from an asymptomatic, healthy individual was seeded with known concentrations of oocysts, and oocysts were labeled with a cell wall-specific monoclonal antibody and detected by FC. The method described herein resulted in a mean oocyst recovery rate of 45% +/- 16% (median, 42%), which consistently yielded a fourfold increase in sensitivity compared to direct fluorescent-antibody assay of seeded stool samples. However, in many instances, FC detected as few as 10(3) oocysts per ml. Thus, FC provides a reproducible and sensitive method for C. parvum oocyst detection.

Practical guidelines for the treatment of cholera.

Cholera is a dramatic clinical illness that requires rapid diagnosis and aggressive therapy. Clinical signs and symptoms of mild, moderate and severe dehydration must be determined, before beginning fluid therapy. Fluid therapy has 2 phases: rehydration (first 3 to 4 hours to correct deficits) and maintenance (to match continuing losses). The route and speed of fluid administration will depend on the degree of dehydration. Patients with severe dehydration should be treated intravenously, as should those patients who do not tolerate oral rehydration solution (ORS). Ringer's lactate is the preferred intravenous solution, although normal saline may be used along with ORS. For most patients with cholera, an ORS using one of the higher sodium-containing solutions and plain water optimally provide the fluid and salt needed. Close monitoring of intake, outputs and hydration status should be performed for all patients. Antimicrobial therapy should be given to moderately and severely ill patients in order to decrease the volume of fluids lost and to shorten the period of excretion of vibrios.