Deciphering the RRM-RNA recognition code: A computational analysis.

RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.

Design of Two New Sulfur Derivatives of Perezone: In Silico Study Simulation Targeting PARP-1 and In Vitro Study Validation Using Cancer Cell Lines.

Poly-ADP-Ribose Polymerase (PARP-1) is an overexpressed enzyme in several carcinomas; consequently, the design of PARP-1 inhibitors has acquired special attention. Hence, in the present study, three compounds (8-10) were produced through a Michael addition protocol, using phenylmethanethiol, 5-fluoro-2-mercaptobenzyl alcohol, and 4-mercaptophenylacetic acid, respectively, as nucleophiles and perezone as the substrate, expecting them to be convenient candidates that inhibit PARP-1. It is convenient to note that in the first stage of the whole study, the molecular dynamics (MD) simulations and the quantum chemistry studies of four secondary metabolites, i.e., perezone (1), perezone angelate (2), hydroxyperezone (3), and hydroxyperezone monoangelate (4), were performed, to investigate their interactions in the active site of PARP-1. Complementarily, a docking study of a set of eleven sulfur derivatives of perezone (5-15) was projected to explore novel compounds, with remarkable affinity to PARP-1. The molecules 8-10 provided the most adequate results; therefore, they were evaluated in vitro to determine their activity towards PARP-1, with 9 having the best IC50 (0.317 µM) value. Additionally, theoretical calculations were carried out using the density functional theory (DFT) with the hybrid method B3LYP with a set of base functions 6-311++G(d,p), and the reactivity properties were compared between the natural derivatives of perezone and the three synthesized compounds, and the obtained results exhibited that 9 has the best properties to bind with PARP-1. Finally, it is important to mention that 9 displays significant inhibitory activity against MDA-MB-231 and MCF-7 cells, i.e., 145.01 and 83.17 µM, respectively.

b2bTools: online predictions for protein biophysical features and their conservation.

We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata ß-sheet aggregation. These predictions, several of which were previously not available online, capture 'emergent' properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.

Synthesis, Cytotoxic Activity and In Silico Study of Novel Dihydropyridine Carboxylic Acids Derivatives.

To aid the possible prevention of multidrug resistance in tumors and cause lower toxicity, a set of sixteen novel dihydropyridine carboxylic acids derivatives 3a-p were produced; thus, the activation of various ynones with triflic anhydride was performed, involving a nucleophilic addition of several bis(trimethylsilyl) ketene acetals, achieving good yields requiring easy workup. The target molecules were unequivocally characterized by common spectroscopic methods. In addition, two of the tested compounds (3a, and 3b) were selected to perform in silico studies due to the highest cytotoxic activity towards the HCT-15 cell line (7.94 ± 1.6 µM and 9.24 ± 0.9 µM, respectively). Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) showed that the molecular parameters correlate adequately with the experimental results. In contrast, predictions employing Osiris Property Explorer showed that compounds 3a and 3b present physicochemical characteristics that would likely make it an orally active drug. Moreover, the performance of Docking studies with proteins related to the apoptosis pathway allowed a proposal of which compounds could interact with PARP-1 protein. Pondering the obtained results (synthesis, in silico, and cytotoxic activity) of the target compounds, they can be judged as suitable antineoplastic agent candidates.

Thromboembolic and hemorrhagic complications in patients with prosthetic heart valves cared for in a tertiary care center. What have we learned?

BACKGROUND: Heart valve replacement surgery with mechanical or biological prostheses entails a risk of thromboembolism and bleeding complications. OBJECTIVE: To determine the complications related to complementary anticoagulation therapy and the probability of risk. METHODS: One-hundred and sixty-three patients who underwent heart valve replacement between 2002 and 2016 with either mechanical or biological prostheses, and who received vitamin K antagonists after hospital discharge, were studied. Anticoagulation therapy was categorized into optimal and non-optimal according to INR values prior to the development of complications. Patients with comorbidities and other risk factors for thrombosis and/or bleeding were excluded. RESULTS: In total, 68.7 % of patients received mechanical prostheses, and 31.3 %, biological prostheses (p ≤ 0.001); 25.2 % experienced the complications that motivated the study (p ≤ 0.001), which were hemorrhagic in 48.8 %, thromboembolic in 26.8 %, and of both types in 24.4 % (relative risk = 4.229). Among the patients with complications, 95.1 % received mechanical prostheses, and 4.9 %, biological (p = 0.005); non-optimal INR was identified in 49.7 % (p ≤ 0.001). CONCLUSIONS: Given the high risk of thromboembolic and hemorrhagic complications, valve prostheses must be carefully chosen, and care priorities should include prevention and follow-up, especially in those patients who require anticoagulation therapy.

ANTECEDENTES: El reemplazo valvular por prótesis mecánicas o biológicas implica riesgo de tromboembolismo y complicaciones hemorrágicas. OBJETIVO: Determinar las complicaciones relacionadas con la terapia de anticoagulación complementaria y la probabilidad de riesgo en pacientes portadores de prótesis valvulares del corazón. MÉTODOS: Se estudiaron 163 pacientes entre 2002 y 2016, portadores de prótesis mecánicas y biológicas, quienes recibieron antagonistas de la vitamina K posterior al egreso hospitalario. La terapia de anticoagulación se categorizó en óptima y no óptima conforme a los valores de INR previos a las complicaciones. Fueron excluidos los pacientes con comorbilidades y otros factores de riesgo de trombosis y/o sangrado. RESULTADOS: a 68.7 % de los pacientes se les colocó prótesis mecánica y a 31.3 %, biológica (p ≤ 0.001); 25.2 % presentó las complicaciones motivo de estudio (p ≤ 0.001), hemorrágicas en 48.8 %, tromboembólicas en 26.8 % y de ambos tipos en 24.4 % (riesgo relativo = 4.229); a 95.1 % de los pacientes con complicaciones se les colocó prótesis mecánica y a 4.9 %, biológica (p = 0.005); 49.7 % presentó INR no óptimo (p ≤ 0.001). CONCLUSIONES: Ante riesgo alto de complicaciones tromboembólicas y hemorrágicas, la elección de las prótesis valvulares, la prevención y el seguimiento son prioridades, principalmente en quienes requieren terapia de anticoagulación.

Bridging the serodivide: attitudes of PrEP users towards sex partners living with HIV.

The introduction of biomedical HIV prevention methods, such as pre-exposure prophylaxis (PrEP), holds the potential to overcome the serodivide. We investigated the attitudes of PrEP users towards having sex with partners living with HIV. PrEP users in the Netherlands were recruited online and completed three questionnaires over a period of six months. We investigated changes over time in feelings of fear of HIV, comfort, and attitudes towards condom use when having sex with men living with HIV (MLHIV). A majority of PrEP users in our sample (up to 71.6%) had sex with MLHIV. Feeling comfortable to have sex with MLHIV did not change over time, but was already at a high level at T1. Most importantly, feeling safe not to use condoms with HIV-positive partners significantly increased, and did so in a rather short period of time after the onset of PrEP use (3-6 months). Taken together, the findings suggest that that PrEP may contribute to decreasing the serodivide between MSM rather quickly after the onset of PrEP use.

The Ability of Chlorophyll to Trap Carcinogen Aflatoxin B1: A Theoretical Approach.

The coordination of one and two aflatoxin B1 (AFB1, a potent carcinogen) molecules with chlorophyll a (chl a) was studied at a theoretical level. Calculations were performed using the M06-2X method in conjunction with the 6-311G(d,p) basis set, in both gas and water phases. The molecular electrostatic potential map shows the chemical activity of various sites of the AFB1 and chl a molecules. The energy difference between molecular orbitals of AFB1 and chl a allowed for the establishment of an intermolecular interaction. A charge transfer from AFB1 to the central cation of chl a was shown. The energies of the optimized structures for chl a show two configurations, unfolded and folded, with a difference of 15.41 kcal/mol. Chl a appeared axially coordinated to the plane (α-down or ß-up) of the porphyrin moiety, either with the oxygen atom of the ketonic group, or with the oxygen atom of the lactone moiety of AFB1. The complexes of maximum stability were chl a 1-α-E-AFB1 and chl a 2-ß-E-AFB1, at -36.4 and -39.2 kcal/mol, respectively. Additionally, with two AFB1 molecules were chl a 1-D-2AFB1 and chl a 2-E-2AFB1, at -60.0 and -64.8 kcal/mol, respectively. Finally, biosorbents containing chlorophyll could improve AFB1 adsorption.

In Vitro and Computational Studies of Perezone and Perezone Angelate as Potential Anti-Glioblastoma Multiforme Agents.

Glioblastoma multiforme (GBM) represents the most malignant type of astrocytoma, with a life expectancy of two years. It has been shown that Poly (ADP-ribose) polymerase 1 (PARP-1) protein is over-expressed in GBM cells, while its expression in healthy tissue is low. In addition, perezone, a phyto-compound, is a PARP-1 inhibitor with anti-neoplastic activity. As a consequence, in the present study, both in vitro and computational evaluations of perezone and its chemically related compound, perezone angelate, as anti-GBM agents were performed. Hence, the anti-proliferative assay showed that perezone angelate induces higher cytotoxicity in the GBM cell line (U373 IC50 = 6.44 µM) than perezone (U373 IC50 = 51.20 µM) by induction of apoptosis. In addition, perezone angelate showed low cytotoxic activity in rat glial cells (IC50 = 173.66 µM). PARP-1 inhibitory activity (IC50 = 5.25 µM) and oxidative stress induction by perezone angelate were corroborated employing in vitro studies. In the other hand, the performed docking studies allowed explaining the PARP-1 inhibitory activity of perezone angelate, and ADMET studies showed its probability to permeate cell membranes and the blood-brain barrier, which is an essential characteristic of drugs to treat neurological diseases. Finally, it is essential to highlight that the results confirm perezone angelate as a potential anti-GBM agent.

Narratives Shape Cognitive Representations of Immigrants and Immigration-Policy Preferences.

Scholars from across the social and media sciences have issued a clarion call to address a recent resurgence in criminalized characterizations of immigrants. Do these characterizations meaningfully impact individuals' beliefs about immigrants and immigration? Across two online convenience samples (total N = 1,054 adult U.S. residents), we applied a novel analytic technique to test how different narratives-achievement, criminal, and struggle-oriented-impacted cognitive representations of German, Russian, Syrian, and Mexican immigrants and the concept of immigrants in general. All stories featured male targets. Achievement stories homogenized individual immigrant representations, whereas both criminal and struggle-oriented stories racialized them along a White/non-White axis: Germany clustered with Russia, and Syria clustered with Mexico. However, criminal stories were unique in making our most egalitarian participants' representations as differentiated as our least egalitarian participants'. Narratives about individual immigrants also generalized to update representations of nationality groups. Most important, narrative-induced representations correlated with immigration-policy preferences: Achievement narratives and corresponding homogenized representations promoted preferences for less restriction, and criminal narratives promoted preferences for more.

Slow Uptake of PrEP: Behavioral Predictors and the Influence of Price on PrEP Uptake Among MSM with a High Interest in PrEP.

Despite the improved availability and affordability of PrEP in the Netherlands, PrEP uptake is low among men who have sex with men (MSM). To optimize uptake, it is important to identify facilitators and barriers of PrEP use. During our study period, the price of PrEP dropped significantly after generic PrEP was introduced. We investigated whether the price drop predicts PrEP uptake, alongside behavioral and demographic characteristics. Participants (N = 349) were recruited online and completed three questionnaires over a period of 6 months, between February 2017 and March 2019. After 6 months, 159 (45.6%) participants were using PrEP. PrEP uptake was greater among MSM who ever had postexposure prophylaxis (PEP) treatment, among MSM with a better perceived financial situation, and when the price of PrEP dropped. MSM in a tighter perceived financial situation may use PrEP more when it would be free or fully reimbursed.

RESUMEN: A pesar de la disponibilidad y asequibilidad a PrEP en Los Paises Bajos, el consumo de PrEP es bajo entre hombres que tienen sexo con hombres (HSH). Para optimizar su consumo, es importante identificar los factores facilitadores y las barreras del uso de PrEP. Durante nuestro estudio, el precio de PrEP se redujo significativamente, después de que se introdujo la PrEP genérica al mercado. Investigamos las características demograficas y de conducta y si la caída en el precio predice el consumo de PrEP. Participantes (N = 349) fueron reclutados en linea y completaron tres cuestionarios en un periodo de seis meses, entre Febrero de 2017 y Marzo de 2019. Despues de seis meses, 159 participantes (45.6%) estaban usando PrEP. El consumo de PrEP fue mayor cuando el precio de PrEP bajó y entre HSH que se sometieron a un tratamiento de profilaxis posexposición (PEP) y que tenían una buena situación financiera. HSH con una percibida situacion finaciera más precaria podrían usar PrEP más cuando sea gratis o reembolsada totalmente.

Socio-Sexual Experiences and Access to Healthcare Among Informal PrEP Users in the Netherlands.

The aim of this qualitative study was to explore the experiences of informal PrEP users regarding access to PrEP and PrEP-related healthcare, community responses, sexual behavior and well-being. We interviewed 30 men who have sex with men (MSM) in semi-structured online interviews between March and August 2018. Interviews were analyzed using interpretive description. Informal PrEP users were well informed about the use of PrEP, but sometimes did not make use of renal testing. Participants reported a lack of PrEP knowledge among healthcare providers, which limited their access to PrEP and put them at risk, as they received incorrect information. Although some participants reported negative reactions from potential sex partners, most received positive reactions and were sometimes seen as more desirable sex partners. PrEP healthcare services should not only be accessible to formal PrEP users, but also to PrEP users who procure PrEP informally.

Quantifying idiosyncratic and shared contributions to judgment.

Identifying relative idiosyncratic and shared contributions to judgments is a fundamental challenge to the study of human behavior, yet there is no established method for estimating these contributions. Using edge cases of stimuli varying in intrarater reliability and interrater agreement-faces (high on both), objects (high on the former, low on the latter), and complex patterns (low on both)-we showed that variance component analyses (VCAs) accurately captured the psychometric properties of the data (Study 1). Simulations showed that the VCA generalizes to any arbitrary continuous rating and that both sample and stimulus set size affect estimate precision (Study 2). Generally, a minimum of 60 raters and 30 stimuli provided reasonable estimates within our simulations. Furthermore, VCA estimates stabilized given more than two repeated measures, consistent with the finding that both intrarater reliability and interrater agreement increased nonlinearly with repeated measures (Study 3). The VCA provides a rigorous examination of where variance lies in data, can be implemented using mixed models with crossed random effects, and is general enough to be useful in any judgment domain in which agreement and disagreement are important to quantify and in which multiple raters independently rate multiple stimuli.

Alternative mass spectrometry techniques for the validation of the fragmentation pattern of capsaicin and dihydrocapsaicin.

RATIONALE: Capsaicinoids are prevalent secondary metabolites in many natural and synthetic pharmacological compounds. To date, several soft ionization studies related to capsaicinoids have been reported; they all proposed a common fragmentation pattern based on a rearrangement of the aromatic double bonds and the fragmentation of the various positional acyl chains. However, the mechanism has never been validated by high-resolution analyses. Consequently, in this work, a validated fragmentation mechanism of the main capsaicinoids, capsaicin (1) and dihydrocapsaicin (2), is offered. METHODS: In order to propose and validate a common electron ionization (EI) fragmentation mechanism for the target analytes, the following mass spectrometric methods were employed: collision-induced dissociation (CID) by means of linked scans (LS), reinforcing the methodology by high-resolution mass spectrometry (HRMS), in addition to appropriate deuterium-labeled experiments performed using gas chromatography/mass spectrometry (GC/MS) and direct analysis in real time (DART). RESULTS: In a first stage, a common EI fragmentation pattern comprising two pathways was proposed for compounds 1 and 2; then, the suggested mechanism was validated by CID-LS together with HRMS complemented by DART-deuterium-labeling studies. The obtained results are indicative that the corresponding molecular ions were conveniently observed, m/z 305 and m/z 307; it is worth noting that the common base peak is in correspondence with a tropylium ion derivative (m/z 137), as a consequence of a McLafferty rearrangement. In addition to these highlighted fragments, other common ions, m/z 122 and m/z 94, and their corresponding trajectory, were confirmed using the same approach. Finally, the proposed mechanism was complementarily validated by deuterium-labeling studies, taking into account the two exchangeable hydrogens present in the phenolic and the amidic moieties. CONCLUSIONS: A common validated EI fragmentation pattern for both capsaicin and dihydrocapsaicin was established using appropriated mass spectrometric methods together with convenient hydrogen/deuterium labeling. This study provides a new alternative to validate mechanisms of fragmentation of important natural products.

Pre-exposure prophylaxis sorting among men who have sex with men.

Factors such as race, masculinity, and sexually transmitted infections have been documented to influence partner selection in men who have sex with men (MSM). Pre-exposure prophylaxis (PrEP) has received mixed evaluations as a responsible step in HIV prevention and as an enabler of risker sexual practices. PrEP may consequently serve as an additional factor in partner choice. We examine the role that PrEP use and "promiscuity" play in affiliation and dating decisions by men who have sex with men with different HIV and PrEP stati. We invited 450 MSM across the United States from a smartphone geo-locating sex application to complete a survey of which 339 successfully finished the task. The survey contained vignettes of fictional men who were promiscuous or monogamous and either taking PrEP or not. Participants provided responses on whether to affiliate with these characters in three social domains: as friends, dates, or sex partners. Neither PrEP nor promiscuity influenced friendship choices. There was a preference for dating monogamous characters. Critically, PrEP influenced sexual affiliations for HIV negative individuals who showed a preference for PrEP-using characters. The pattern of results provides quantitative evidence for PrEP-based sexual sorting aimed at reducing risk of HIV transmission.

Control Engagement During Sentence and Inhibition fMRI Tasks in Children With Reading Difficulties.

Recent reading research implicates executive control regions as sites of difference in struggling readers. However, as studies often employ only reading or language tasks, the extent of deviation in control engagement in children with reading difficulties is not known. The current study investigated activation in reading and executive control brain regions during both a sentence comprehension task and a nonlexical inhibitory control task in third-fifth grade children with and without reading difficulties. We employed both categorical (group-based) and individual difference approaches to relate reading ability to brain activity. During sentence comprehension, struggling readers had less activation in the left posterior temporal cortex, previously implicated in language, semantic, and reading research. Greater negative activity (relative to fixation) during sentence comprehension in a left inferior parietal region from the executive control literature correlated with poorer reading ability. Greater comprehension scores were associated with less dorsal anterior cingulate activity during the sentence comprehension task. Unlike the sentence task, there were no significant differences between struggling and nonstruggling readers for the nonlexical inhibitory control task. Thus, differences in executive control engagement were largely specific to reading, rather than a general control deficit across tasks in children with reading difficulties, informing future intervention research.

Green Approach Extraction of Perezone from the Roots of Acourtia platyphilla (A. Grey): A Comparison of Four Activating Modes and Supercritical Carbon Dioxide.

Perezone, a sesquiterpene quinone, is a very important molecule due to its pharmacological activities in addition to the fact that it is considered to be the first secondary metabolite isolated in the new world (America-Mexico, 1852). This study aims to offer a green comparative study about the extraction of the target molecule from the roots of the vegetable specimen Acourtia platyphilla (A. Grey). The study was performed comparing five different modes of extraction: supercritical CO2, electromagnetic infrared and microwave irradiations, mechanical-wave ultrasound versus typical mantle heating procedure. An exhaustive comparative-discussion of the obtained results is provided. It is worth noting that the corresponding quantifications were established using 1H NMR, correlating appropriately the integrals of the vinylic proton H-6 of perezone with the aromatic singlet of p-dinitrobenzene employed as an internal reference. It is also important to highlight that the four presented procedures are novel modes to extract perezone. Finally, a complementary study about the solubility of the target sesquiterpene quinone related to the use of supercritical CO2 is also reported.

A pragmatist philosophy of psychological science and its implications for replication.

A pragmatist philosophy of psychological science offers to the direct replication debate concrete recommendations and novel benefits that are not discussed in Zwaan et al. This philosophy guides our work as field experimentalists interested in behavioral measurement. Furthermore, all psychologists can relate to its ultimate aim set out by William James: to study mental processes that provide explanations for why people behave as they do in the world.

Estimation of umbilical cord blood leptin and insulin based on anthropometric data by means of artificial neural network approach: identifying key maternal and neonatal factors.

BACKGROUND: Leptin and insulin levels are key factors regulating fetal and neonatal energy homeostasis, development and growth. Both biomarkers are used as predictors of weight gain and obesity during infancy. There are currently no prediction algorithms for cord blood (UCB) hormone levels using Artificial Neural Networks (ANN) that have been directly trained with anthropometric maternal and neonatal data, from neonates exposed to distinct metabolic environments during pregnancy (obese with or without gestational diabetes mellitus or lean women). The aims were: 1) to develop ANN models that simulate leptin and insulin concentrations in UCB based on maternal and neonatal data (ANN perinatal model) or from only maternal data during early gestation (ANN prenatal model); 2) To evaluate the biological relevance of each parameter (maternal and neonatal anthropometric variables). METHODS: We collected maternal and neonatal anthropometric data (n = 49) in normoglycemic healthy lean, obese or obese with gestational diabetes mellitus women, as well as determined UCB leptin and insulin concentrations by ELISA. The ANN perinatal model consisted of an input layer of 12 variables (maternal and neonatal anthropometric and biochemical data from early gestation and at term) while the ANN prenatal model used only 6 variables (maternal anthropometric from early gestation) in the input layer. For both networks, the output layer contained 1 variable to UCB leptin or to UCB insulin concentration. RESULTS: The best architectures for the ANN perinatal models estimating leptin and insulin were 12-5-1 while for the ANN prenatal models, 6-5-1 and 6-4-1 were found for leptin and insulin, respectively. ANN models presented an excellent agreement between experimental and simulated values. Interestingly, the use of only prenatal maternal anthropometric data was sufficient to estimate UCB leptin and insulin values. Maternal BMI, weight and age as well as neonatal birth were the most influential parameters for leptin while maternal morbidity was the most significant factor for insulin prediction. CONCLUSIONS: Low error percentage and short computing time makes these ANN models interesting in a translational research setting, to be applied for the prediction of neonatal leptin and insulin values from maternal anthropometric data, and possibly the on-line estimation during pregnancy.

Infrared Irradiation: Toward Green Chemistry, a Review.

This review provides a comprehensive overview of where infrared irradiation has been employed, mainly as regards activating green mode for natural products extractions, as well as to favor a reaction, highlighting its actual importance. It is also underlined that infrared irradiation heating has been around for a long time; however, only in the last eighteen years have many of its advantages been applied to satisfy a wide range of chemical processes, natural products extractions, and for the promotion of many kinds of reactions. In addition, it is brought to light that near infrared irradiation is more efficient than middle and far infrared irradiations, being easily controllable and with the quality of a fast responding heat source. Thus, the main objective of this review is to offer infrared irradiation as an alternative clean energy source to activate reactions, in addition to favor the selective extraction of natural products, all of which is within the Green Chemistry protocol. Some recent results from our laboratory are also included.