Setup and validation of shake-flask procedures for the determinationof partition coefficients (log D) from low drug amounts

Several procedures based on the shake-flask method and designed to require a minimum amount of drug for octanol-water partition coefficient determination have been established and developed. The procedures have been validated by a 28 substance set with a lipophilicity range from -2.0 to 4.5 (logD7.4). The experimental partition is carried out using aqueous phases buffered with phosphate (pH 7.4) and n-octanol saturated with buffered water and the analysis is performed by liquid chromatography. In order to have accurate results, four procedures and eight different ratios between phase volumes are proposed. Each procedure has been designed and optimized (for partition ratios) for a specific range of drug lipophilicity (low, regular and high lipophilicity) and solubility (high and low aqueous solubility). The procedures have been developed to minimize the measurement in the octanolic phase. Experimental logD7.4 values obtained from different procedures and partition ratios show a standard deviation lower than 0.3 and there is a nice agreement when these values are compared with the reference literature one

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks : The GR@ACE project

Introduction: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. Methods: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. Results: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. Discussion: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41–6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain.Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000–2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively.Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p < 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2–79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999–2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin.Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Neovascularización mediada por factor tisular en la placa aterosclerótica

[spa] Las enfermedades cardiovasculares son la primera causa de muerte en todo el mundo y representan uno de los desafíos primordiales en la investigación biomédica. La aterosclerosis es causante de la mayoría de las enfermedades cardiovasculares. Un factor clave en la evolución de la aterosclerosis subclínica hacia un evento isquémico es la vulnerabilidad de la placa aterosclerótica. No se conocen las causas que producen la rotura de alguna de las placas existentes en el árbol arterial mientras que otras se mantienen estables. Se han observado placas coronarias humanas, asociadas a síndromes coronarios agudos, que presentan una mayor acumulación de neovasos. De hecho, se ha descrito que la angiogénesis dentro de las placas ateroscleróticas puede contribuir a la expansión de la íntima, a la transformación pro-trombótica de las células residentes y a crear un fenotipo de placa hemorrágica inestable. Se han localizado células inflamatorias, especialmente monocitos y macrófagos, en áreas de la placa activamente angiogénicas, así como CEs microvasculares (CEm) dentro del núcleo de una placa aterosclerótica coronaria que expresan altos niveles de FT. El FT es una glicoproteína de membrana, considerado el principal responsable de la cascada de coagulación, que contribuye activamente en la formación de neovasos. Nuestra hipótesis de trabajo es que el FT juega un papel clave en la angiogénesis intraplaca. Creemos que la modulación del FT en las CEs podría regular la capacidad angiogénica de éstas, estimular el reclutamiento de pericitos e inducir la formación de vasos maduros, evitando así las continuas hemorragias, favoreciendo la estabilidad de la placa y disminuyendo los episodios trombóticos. El FT conduce a la formación de vasos sanguíneos por medio de una cascada de señalización. Los resultados obtenidos en esta tesis proponen dos vías de señalización desencadenadas a partir de la expresión de FT en las CEm. Por un lado, FT-Akt-ETS1, que estimulan la formación de neovasos; y por otro, el FT-PAR2-SMAD3 que permite que los vasos sean estables. Además, ambas vías estimulan la expresión de CCL2, una proteína que se secreta al medio e induce el reclutamiento de pericitos y células musculares lisas. La inflamación es uno de los factores más influyentes en la placa aterosclerótica, monocitos y macrófagos ejercen un papel protagonista. Los resultados obtenidos en esta tesis determinan que los monocitos ejercen una función esencial en la angiogénesis, ya que estimulan a las CEm a que expresen FT y formen nuevos vasos por medio de la secreción de la proteína Wnt5a y la activación de una vía de señalización de Wnt no canónica. Además, estos monocitos en estrecho contacto con las CEs van diferenciándose en respuesta a los estímulos angiogénicos. El FT endotelial constituye un estímulo para los monocitos, que responden alterando su fenotipo y expresando marcadores típicamente endoteliales. Este cambio fenotípico de los monocitos sugiere una participación activa en la formación y estabilización de neovasos. De esta manera, los monocitos estimulan a las CEs a expresar FT y formar neovasos. Esta expresión de FT endotelial estimula a los monocitos a expandir la población CD16+ y a expresar características endoteliales. De esta manera se genera un ciclo de retroalimentación positiva donde ambos tipos celulares trabajan para la formación y estabilización de los nuevos vasos formados, con el factor tisular como jugador principal.[eng] Cardiovascular disease is the main cause of death worldwide and it is usually the clinical manifestation of underlying atherosclerosis. Our understanding of atherosclerosis has advanced considerably; however, the factors that contribute to its progression and complication are largely unknown. A key factor in the evolution of subclinical atherosclerosis to an ischemic event is the increased vulnerability of atheromatous plaques. Atherosclerosis is characterized by inflammation and neovascular growth that precipitate plaque rupture and subsequent thrombosis. In fact, inflammation in the vessel wall is now considered to play an essential role in the initiation, progression and final steps of atherosclerosis, namely plaque destabilization and eventually plaque rupture. Increasing evidence shows that high neovessel density in atherosclerotic-plaques is associated with hemorrhagic leaky vessels, unstable plaques and high rate of thrombotic episodes. However the mechanisms responsible for neovessel formation are not understood. It has been described that microvascular endothelial cells (mECs), located in the nuclei of coronary atherosclerosis plaque, express high levels of tissue factor (TF). TF is a transmembrane glycoprotein, considered the main trigger of the coagulation cascade. TF expression has been closely linked to angiogenesis and malignancy. Indeed TF is able to initiate cellular signaling mechanisms leading to alteration in patterns of gene expression. In this study, we hypothesized that TF plays a key role in the angiogenic processes intraplaque. TF upregulates the angiogenic activity of mECs and improves microvessel stabilization. TF signaling may induce the formation of mature new vessels that may prevent continuous hemorrhages and improve plaque stability. TF drives the formation of new capillaries through a signaling cascade. We elucidated two signaling pathways triggered by TF expression in mECs. First, TF through the activation of AKT1 and ERK1/2 induce the activation of ETS1, a transcription factor that promote CCL2 expression. Second, TF forms a complex with factor VII, activates PAR2 and, consequently, the transcription factor SMAD3. SMAD3 presents synergisms with ETS1, and also activates expression of CCL2. CCL2 recruits SMC and pericytes to promote vascular stability. Inflammation is a crucial factor in atherosclerosis plaque formation. We demonstrated that monocytes develop an essential role during angiogenesis, since they stimulate mECs to express TF and to form new vessels through Wnt5a secretion. Wnt5a binds to FZD5 receptors in endothelial membrane and triggers intracellular calcium release and NF-.B activation, through a non-canonical pathway. In addition, monocytes have a tight collaboration with ECs and they response to angiogenic stimuli. Moreover, we have observed that monocytes respond to endothelial TF, developing endothelial properties. Thus, there is a positive feedback cycle generation between monocytes and ECs that promotes the formation and stabilization of new vessels

Setup and validation of shake-flask procedures for the determinationof partition coefficients (log D) from low drug amounts

Several procedures based on the shake-flask method and designed to require a minimum amount of drug for octanol-water partition coefficient determination have been established and developed. The procedures have been validated by a 28 substance set with a lipophilicity range from -2.0 to 4.5 (logD7.4). The experimental partition is carried out using aqueous phases buffered with phosphate (pH 7.4) and n-octanol saturated with buffered water and the analysis is performed by liquid chromatography. In order to have accurate results, four procedures and eight different ratios between phase volumes are proposed. Each procedure has been designed and optimized (for partition ratios) for a specific range of drug lipophilicity (low, regular and high lipophilicity) and solubility (high and low aqueous solubility). The procedures have been developed to minimize the measurement in the octanolic phase. Experimental logD7.4 values obtained from different procedures and partition ratios show a standard deviation lower than 0.3 and there is a nice agreement when these values are compared with the reference literature one

Discovering HIV related information by means of association rules and machine learning

Acquired immunodeficiency syndrome (AIDS) is still one of the main health problems worldwide. It is therefore essential to keep making progress in improving the prognosis and quality of life of affected patients. One way to advance along this pathway is to uncover connections between other disorders associated with HIV/AIDS-so that they can be anticipated and possibly mitigated. We propose to achieve this by using Association Rules (ARs). They allow us to represent the dependencies between a number of diseases and other specific diseases. However, classical techniques systematically generate every AR meeting some minimal conditions on data frequency, hence generating a vast amount of uninteresting ARs, which need to be filtered out. The lack of manually annotated ARs has favored unsupervised filtering, even though they produce limited results. In this paper, we propose a semi-supervised system, able to identify relevant ARs among HIV-related diseases with a minimal amount of annotated training data. Our system has been able to extract a good number of relationships between HIV-related diseases that have been previously detected in the literature but are scattered and are often little known. Furthermore, a number of plausible new relationships have shown up which deserve further investigation by qualified medical experts