Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules.

CONTEXT: Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well. METHODS: Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).

A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium.

Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH2 , CHCH3 , NH2 , COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizable-continuum model calculations.

Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules.

The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.

Domestic violence against children detected and managed in the routine of dentistry - A systematic review.

The domestic violence against children (DVAC) interferes in the psychological development leading to sequels that manifest and persist up to the adulthood. The physical evidences of domestic violence are more easily observed in the orofacial complex, becoming eventually detected by dentists. The present systematic literature review aimed to investigate the perception, knowledge and attitude of dentists towards the detection and management of DVAC cases. A systematic search was performed in 6 databases: PubMed, ScienceDirect, LILACS, SciELO, GoogleScholar, and OpenGrey. Cross-sectional articles assessing the perception, knowledge, and attitude of dentists facing potential cases of DVAC were selected. No restriction of language, time, and publication status was considered. The search resulted in 1.024 articles, of which 18 fit the eligibility criteria. The knowledge for detecting cases of DVAC obtained during the undergraduation course was classified by the dentists (in 39% of the articles) as "insufficient". When suspecting of cases involving domestic violence, most of the dentists (in 77.75% of the articles) considered reporting to the competent authorities. However, the dentists are not sure about who these authorities are (in 31.25% of the articles). More attention must be given to the Forensic education in Dentistry. Specifically, proper training is necessary to support the dentists on the detection and management of pediatric patients under domestic violence. Systematic Review Registration Number: PROSPERO CRD42015026747 (http://www.crd.york.ac.uk/PROSPERO).

Evaluation of the effectiveness of semen processing techniques to remove bovine viral diarrhea virus from experimentally contaminated semen samples.

The aim of this study was to evaluate the capacity of three semen processing techniques, Percoll gradient centrifugation, Swim-up and a combination of Swim-up and Percoll gradient centrifugation, to reduce the viral load of bovine viral diarrhea virus (BVDV) in experimentally infected semen samples. The evaluation was performed using two approaches: first, searching for the presence of virus in the processed samples (via virus titration and RT-PCR) and second, ascertaining the possible interference on in vitro embryo production. The sperm count and DNA integrity (Comet assay) of the processed samples were analyzed (Experiment 1). The amount of virus in the processed samples was determined by titration in cell culture (Experiment 2). The samples processed by Swim up/Percoll gradient centrifugation were utilized for in vitro embryo production, and the embryos produced were tested for BVDV by RT-PCR (Experiment 3). Sperm concentration, Comet assay and embryo production were analyzed by chi-squared tests (P<0.05). There was a significant difference between sperm separation techniques when the sperm count and Comet assay were analyzed. The sperm count obtained from the Swim up/Percoll gradient centrifugation group was lower than that obtained in either of the two other groups (Swim up and Percoll gradient centrifugation), and the Comet assay showed that the combination of the two semen processing techniques (Swim up/Percoll gradient) produced a 1.1% prevalence of Comet level 2, which was not observed in the other groups. The BVDV titer (10(6.68)TCID(50)/mL) added to experimentally infected semen samples decreased after Percoll gradient centrifugation to 10(2.3)-10(1)TCID(50)/mL; for the Swim up group, the titer range was 10(3.3)-10(1.87)TCID(50)/mL, and in the Swim up/Percoll gradient centrifugation group, BVDV was undetectable. The decreases in titer varied from 99.9% in the Swim up-processed group to 100% in the Swim up/Percoll gradient centrifugation group. In vitro embryo production displayed similar blastocyst development rates among all groups, and RT-PCR was negative for the produced embryos. The data showed that the combination of Swim up/Percoll gradient centrifugation promoted the elimination of BVDV from the semen samples without damaging spermatozoa cells and also allowed successful in vitro embryo production free of BVDV. Hence, the risk of BVDV contamination is negligible for the embryo recipient.

Preliminary study on determining stereotypical motor movements.

Stereotypical motor movements are one of the most common and least understood behaviors occurring in individuals with Autism Spectrum Disorder (ASD). To overcome problems with traditional methods for measuring stereotypical motor movements in persons with ASD, the Kinect sensor from Microsoft and gesture recognition algorithms were used to automatically detect hand flapping. This study provides a valuable tool to monitor stereotypes in order to understand and to cope with this problem. At the end it facilitates to identify behavioral patterns especially relevant when studying interaction skills in children with ASD.

Survival of vitrifi ed mouse blastocysts loaded intoglass micro-capillaries / Sobrevivencia embrionaria de blastocistos murinos vitrificados en microcapilares de vidrio / Sobrevivência embrionária de blastocistos murinos vitrificados em micro capilares de vidro

The purpose of this study was to determine the in vitro expansion and hatching rates of vitrified mouseblastocysts loaded into glass micro-capillaries (Brand® - 5 μL). Early morning on day 4 of pregnancy,blastocysts were collected from donors, morphologically evaluated, and then allocated in three groups:Group 1 (Control): embryos were transferred into 100 μL of KSOM medium drops and in vitro culturedduring 72 h; Groups 2 and 3: embryos initially exposed to the equilibration solution (PBSm + 10% EG+ 10% PROH and 0.5% PVA) for 1 min, and then to vitrification solution (PBSm + 20% EG + 20%PROH + 0.5% PVA) for 30 sec. After that, blastocysts were loaded into glass micropipettes (GMP) or glassmicrocapillaries (GMC) and plunged into super-cooled liquid nitrogen (-200 °C). Embryo warming andcryoprotectant dilution were carried out into 500 μL droplets of PBSm supplemented with 0.25 M sucrosemaintained at 37 °C. After 5 min embryos were transferred to 100 mL droplets of KSOM medium andcultured in vitro for 72 h. Blastocyst expansion rates after in vitro culture were 77% (138/177) and 74%(131/175), for blastocysts vitrified in GMP and GMC, respectively. Blastocyst hatching rate (control group)was 91% (134/146), which was higher than for embryos loaded in GMP 61% (108/177) and GMC 53%(93/175). ICM number in control group embryos contained 25.7 ± 2.5 cells and did not differ from themean cell number observed in vitrified embryos loaded in GMP (24.2±2.3) or GMC (22.5±2.59). Regardingthe trophoectoderm cell number, Group 1 embryos displayed 63.1±3.0 cells, and also not differ from the cellnumbers of the embryos loaded into GMP (58.0±1.8) or GMC (58.0±.3.7). In conclusion, manufacturedGMC (Brand®) tested in this study showed same efficiency as GMP for vitrification of mouse blastocysts.

El objetivo de este estudio fue determinar las tazas de expansión y eclosión in vitro de los blastocistosmurinos vitrificados en micro-capilares de vidrio (Brand® - 5 μL). En el día 4 de preñez, los blastocistoseran colectados de las donantes, evaluados morfológicamente y localizados en tres diferentes grupos:Grupo 1 (Control): compuesto por los embriones que eran transferidos a gotas de 100 μL de medio KSOMy cultivados in vitro por un periodo de 72 h; Grupos 2 y 3: compuesto por los embriones que eran expuestosinicialmente a la solución de equilibrio (PBSm + 10% EG + 10% PROH and 0.5% PVA) por 1 min,y posteriormente a la solución de vitrificación (PBSm + 20% EG + 20% PROH + 0.5% PVA) por unperiodo de 30 seg. Posteriormente, los blastocistos, eran almacenados dentro de micro-pipetas de vidrio(GMP) o micro-capilares de vidrio (GMC) y sumergidos en nitrógeno líquido (-200 °C). La dilución delos crioprotectores y desvitrificación de los embriones fue realizada al colocarlos en gotas de 500 μLde PBSm suplementado con 0.25 M de sacarosa a una temperatura de 37 °C. Después de 5 minutos losembriones fueron transferidos a gotas de 100 μL de medio KSOM y cultivados in vitro por 72 h. Las tazasde expansión de los blastocistos, posteriores al cultivo fueron de 77% (138/177) y 74% (131/175), para losblastocistos vitrificados en GMP y GMC, respectivamente. Las tazas de eclosión fueron de 91% (134/146)para el grupo control, siendo mayores que para los embriones vitrificados en GMP 61% (108/177) y GMC53% (93/175). El número del índice de masa celular interna (ICM) para los embriones del grupo controlfue de 25.7 ± 2.5 células, no teniendo diferencia significativa con el número de células observado en losembriones vitrificados en GMP (24.2±2.3) ó GMC (22.5±2.59).

O objectivo de este estudo foi determinar as taxas de expansão e eclosão in vitro dos blastocitos murinosvitrificados em micro capilares de vidro (Brand® - 5 μL). No quarto dia de prenhes, os blastocitos foramcolectados das doadoras, avaliados morfologicamente e localizados em três diferentes grupos: Grupo 1(Controle): composto por os embriões que foram transferidos a gotas de 100 μL de KSOM e cultivados invitro por um período de 72 h; Grupos 2 e 3: composto por os embriões que foram expostos inicialmente ásolução de equilíbrio (PBSm + 10% EG + 10% PROH e 0.5% PVA) por 1 min, e posteriormente á soluçãode vitrificação (PBSm + 20% EG + 20% PROH + 0.5% PVA) por um período de 30 seg. Posteriormente,os blastocistos, foram armazenados dentro de micro pipetas de vidro (GMP) ou micro capilares de vidro(GMC) e submergidos em nitrogénio líquido super-resfriado (-200°C). A diluição dos crioprotetores edesvitrificação dos embriões foi realizada ao colocar-lhos em gotas de 500 μL de PBSm suplementadocom 0.25 M de sacarose a uma temperatura de 37 °C. Depois de 5 minutos, os embriões foram transferidosa gotas de 100 μL de KSOM e cultivados in vitro por 72 h. As taxas de expansão dos blastocistos, posterioresao cultivo foram de 77% (138/177) e 74% (131/175), para os blastocistos vitrificados em GMP e GMC,respectivamente. As taxas de eclosão foram de 91% (134/146) para o grupo controle, e foram maioresos embriões vitrificados em GMP 61% (108/177) e GMC 53% (93/175). O número do índice de massacelular interna (ICM) para os embriões do grupo controle foi de 25.7 ± 2.5 células, não havendo diferenciasignificativa com o número de células observado em embriões vitrificados em GMP (24.2±2.3) ou GMC(22.5±2.59). Alem do mais, as células do trofoectodermo, no grupo controle apresentaram 63.1±3.0células, no sendo diferente às células dos embriões vitrificados em GMP (58.0±1.8) ou GMC (58.0±.3.7).