Hydration free energies in the FreeSolv database calculated with polarized iterative Hirshfeld charges

Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute’s electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol–1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups

Laser-induced tuning of carbon nanosensitizers to maximize nitrogen doping and reactive oxygen species production in the visible range

Carbon nanodots (CNDs) have emerged as novel fluorescent nanosensitizers able to expand the photocatalytic response of conventional semiconductors beyond the ultraviolet spectral window. Key aspects of CNDs related with their high photostability, resistance to photobleaching and optical properties (including downconversion and upconversion luminescence) are often associated with the capacity to dope the carbogenic network with light heteroatoms, especially nitrogen. In this work, we present the use of laser pyrolysis as a versatile and convenient synthesis technique to generate different N-doped CNDs. The level of N doping can be tuned through the selection of a single liquid solvent containing N as carbon precursor. This liquid precursor can be alternatively enriched with additional N sources co-fed in the form of gas (i.e. NH3) or disolved solid precursors (i.e. phtalocyanine-Ph). We demonstrate that the N-CNDs retrieved after the additional N cofeeding treatments improve their photoactivity when assembled to P25 nanoparticles towards the conversion of methyl orange (MO) under white LED illumination. All the N-CNDs act as photosensitizers expanding the response of P25 beyond the UV region and exhibit an active role generating different types of Reactive Oxygen Species (ROS) via singlet oxygen, superoxide and hydroxyl radicals that can pave the way for multiple potential applications in environmental and green processes

RAF1 kinase activity is dispensable for KRAS/p53 mutant lung tumor progression.

We thank Dr. Shiva Malek and her colleagues (Genentech Inc.) for sharing their results with us before publication. We also thank M. San Roman, R. Villar, M.C. Gonzalez, A. Lopez, N. Cabrera, P. Villanueva, J. Condo, O. Dominguez, and S. Ortega for excellent technical support. This work was supported by grants from the European Research Council (ERC-2015-AdG/695566, THERACAN); the Spanish Ministry of Science, Innovation, and Universities (RTC-2017-6576-1 and RTI2018094664-B-I00) and the Autonomous Community of Madrid (B2017/BMD-3884 iLUNG-CM) to M.B., as well as by a grant from the Spanish Ministry of Science, Innovation and Universities (RTI2018-094664-B-I00) to M.B. and M.M. M.B. is a recipient of an Endowed Chair from the AXA Research Fund. M.S., P.N., and F.F.-G. were supported by FPU fellowships from the Spanish Ministry of Education. L.E.-B. was a recipient of an FPI fellowship from the Spanish Ministry of Economy and Competitiveness. S.G.-A. is a recipient of a postdoctoral fellowship from the Asociacion Espanola Contra el Cancer (AECC).S

Clinical and Ambulatory Gait Speed in Older Adults: Associations With Several Physical, Mental, and Cognitive Health Outcomes

Background: Although clinical gait speed may indicate health and well-being in older adults, there is a lack of studies comparing clinical tests with ambulatory gait speed with regard to several health outcomes. Objective: The objective of this study was to examine the associations of clinical gait speed, measured by the 2.44-m walk test and the ambulatory gait speed with several physical, mental, and cognitive health outcomes in older adults. Design: A cross-sectional design was used. Methods: The study population comprised 432 high-functioning, community-dwelling older adults (287 women) aged between 65 and 92 years. Clinical and ambulatory gait speeds were measured using the 2.44-m walk test and a portable gait analysis device, respectively. Multiple linear regressions were used to examine the association of clinical and ambulatory gait speeds with several health outcomes (body mass index, waist circumference, systolic and diastolic blood pressure, chronic conditions, self-rated health, exhaustion, upper- and lower-body strength, physical and mental health status, cognitive status, and self-rated cognitive status). Results: The results showed that the average gait speed for clinical and ambulatory measures cannot be directly compared. Clinical gait speed was associated with 7 health outcomes, and the ambulatory gait speed was associated with 6 health outcomes. The significant associations between measures of gait speed and the health outcomes converged in 5 of the 13 health outcomes studied; however, the strength of associations was singly different between measures. Limitations: The short monitoring time, the inability to distinguish between the ambulatory gait speed inside the home and outdoor gait speed, and the under-representative sample are limitations of the study. Conclusion: The results indicated differences in the number and strength of associations between clinical and ambulatory gait speed. Both measures have construct validity because they have been associated with physical and health outcomes; however, they may have different predictive validity. Further research should be conducted to compare their predictive validity in longitudinal design

Spatial repellents transfluthrin and metofluthrin affect the behavior of \u3cem\u3eDermacentor variabilis\u3c/em\u3e, \u3cem\u3eAmblyomma americanum\u3c/em\u3e, and \u3cem\u3eIxodes scapularis\u3c/em\u3e in an \u3cem\u3ein vitro\u3c/em\u3e vertical climb assay

Repellents serve an important role in bite protection. Tick repellents largely rely on biomechanisms that induce responses with direct contact, but synthetic pyrethroids used as spatial repellents against insects have received recent attention for potential use in tick protection systems. An in vitro vertical climb assay was designed to assess spatial repellency against Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis adult, female ticks. Climbing behavior was assessed with and without the presence of two spatial repellents, transfluthrin and metofluthrin. Repellency parameters were defined to simulate the natural questing behavior of ambushing ticks, including measures of detachment, pseudo-questing duration, climbing deterrence, and activity. Significant effects were observed within each parameter. D. variabilis showed the greatest general susceptibility to each repellent, followed by A. americanum, and I. scapularis. The most important and integrative measure of repellency was climbing deterrence–a measure of the spatial repellent’s ability to disrupt a tick’s natural propensity to climb. Transfluthrin deterred 75% of D. variabilis, 67% of A. americanum, and 50% of I. scapularis. Metofluthrin was slightly more effective, deterring 81% of D. variabilis, 73% of A. americanum, and 72% of I. scapularis. The present study poses a novel paradigm for repellency and reports a preliminary assessment of spatial repellent effect on tick behavior. Further research will assess spatial repellency in a more natural setting, scale exposure conditions, and incorporate host cues

Tumor regression and resistance mechanisms upon CDK4 and RAF1 inactivation in KRAS/P53 mutant lung adenocarcinomas.

KRAS mutant lung adenocarcinomas remain intractable for targeted therapies. Genetic interrogation of KRAS downstream effectors, including the MAPK pathway and the interphase CDKs, identified CDK4 and RAF1 as the only targets whose genetic inactivation induces therapeutic responses without causing unacceptable toxicities. Concomitant CDK4 inactivation and RAF1 ablation prevented tumor progression and induced complete regression in 25% of KRAS/p53-driven advanced lung tumors, yet a significant percentage of those tumors that underwent partial regression retained a population of CDK4/RAF1-resistant cells. Characterization of these cells revealed two independent resistance mechanisms implicating hypermethylation of several tumor suppressors and increased PI3K activity. Importantly, these CDK4/RAF1-resistant cells can be pharmacologically controlled. These studies open the door to new therapeutic strategies to treat KRAS mutant lung cancer, including resistant tumors.We thank S. Ortega for the generation of the Cdk4FxKD mouse model; and M. San Roman, R. Villar, M. C. Gonzalez, A. Lopez, N. Cabrera, P. Villanueva, J. Condo, J. Klett, A. Cebria, A. Otero, O. Dominguez, G. Luengo, G. Garaulet, F. Mulero, and D. Megias for excellent technical support. This work was supported by European Research Council Grant ERC-2015-AdG/695566, THERACAN, Spanish Ministry of Science, Innovation, and Universities Grant RTC-2017-6576-1, and the Autonomous Community of Madrid Grant B2017/BMD-3884 iLUNG-CM (to M.B.); Spanish Ministry of Science, Innovation, and Universities Grant RTI2018-094664B-I00 (to M.B. and M.M.); and National Natural Science Foundation of China Grant 31771469 (to H.W.). M.B. is a recipient of an Endowed Chair from the AXA Research Fund. L.E.-B. is the recipient of an FPI fellowship from the Spanish Ministry of Economy and Competitiveness. F.F.-G., M.S., and P.N. were supported by an FPU fellowships from the Spanish Ministry of Education.S

Dolutegravir Monotherapy as Maintenance Strategy: A Meta-Analysis of Individual Participant Data From Randomized Controlled Trials

Background Dolutegravir monotherapy (DTG-m) results in virological failure (VF) in some people with human immunodeficiency virus (PWH). We sought to identify the independent factors associated with the risk of VF and to explore the effect size heterogeneity between subgroups of PWH enrolled in DTG-m trials. Methods We searched for randomized clinical trials (RCTs) evaluating DTG-m versus combined antiretroviral therapy (cART) among PWH virologically controlled for at least 6 months on cART. We performed an individual participant data meta-analysis of VF risk factors and quantified their explained heterogeneity in random-effect models. Definition of VF was a confirmed plasma human immunodeficiency virus (HIV)-1 ribonucleic acid (RNA) >50 copies/mL by week 48. Results Among 416 PWH from 4 RCTs, DTG-m significantly increased the risk of VF (16 of 227 [7%] versus 0 of 189 for cART; risk difference 7%; 95% confidence interval [CI], 1%-2%; P = .02; I$^{2}$ = 51%). Among 272 participants exposed to DTG-m, VF were more likely in participants with the following: first cART initiated ≥90 days from HIV acute infection (adjusted hazard ratio [aHR], 5.16; 95% 95% CI, 1.60-16.65), CD4 T cells nadir <350/mm$^{3}$ (aHR, 12.10; 95% CI, 3.92-37.40), HIV RNA signal at baseline (aHR, 4.84; 95% CI, 3.68-6.38), and HIV-deoxyribonucleic acid (DNA) copy number at baseline ≥2.7 log/10$^{6}$ peripheral blood mononuclear cells (aHR, 3.81; 95% CI, 1.99-7.30). Among these independent risk factors, the largest effect size heterogeneity was found between HIV DNA subgroups (I$^{2}$ = 80.2%; P for interaction = .02). Conclusions Our study supports the importance of a large viral reservoir size for explaining DTG-m simplification strategy failure. Further studies are needed to link size and genetic diversity of the HIV-1 reservoir

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.Comment: 26 pages, 6 figures, and supporting informatio

No association between polymorphisms/haplotypes of the vascular endothelial growth factor gene and preeclampsia

<p>Abstract</p> <p>Background</p> <p>Preeclampsia (PE) is the first worldwide cause of death in pregnant women, intra-uterine growth retardation, and fetal prematurity. Some vascular endothelial grown factor gene (<it>VEGF</it>) polymorphisms have been associated to PE and other pregnancy disturbances. We evaluated the associations between <it>VEGF </it>genotypes/haplotypes and PE in Mexican women.</p> <p>Methods</p> <p>164 pregnant women were enrolled in a case-control study (78 cases and 86 normotensive pregnant controls). The rs699947 (-2578C/A), rs1570360 (-1154G/A), rs2010963 (+405G/C), and rs25648 (-7C/T), <it>VEGF </it>variants were discriminated using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) methods or Taqman single nucleotide polymorphism (SNP) assays.</p> <p>Results</p> <p>The proportions of the minor allele for rs699947, rs1570360, rs2010963, and rs25648 <it>VEGF </it>SNPs were 0.33, 0.2, 0.39, and 0.17 in controls, and 0.39, 0.23, 0.41, and 0.15 in cases, respectively (<it>P </it>values > 0.05). The most frequent haplotypes of rs699947, rs1570360, rs2010963, and rs25648 <it>VEGF </it>SNPs, were C-G-C-C and C-G-G-C with frequencies of 0.39, 0.21 in cases and 0.37, 0.25 in controls, respectively (<it>P </it>values > 0.05)</p> <p>Conclusion</p> <p>There was no evidence of an association between <it>VEGF </it>alleles, genotypes, or haplotypes frequencies and PE in our study.</p