Detection of single DNA mismatches by force spectroscopy in short DNA hairpins.

Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson-Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force-distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects.

Force feedback effects on single molecule hopping and pulling experiments.

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

[EVALUATION OF SEDATION USING THE RICHMOND AGITATION SEDATION SCALE IN PATIENTS WITH PROLONGED MECHANICAL VENTILATION]. / Evaluación de la sedación mediante la escala Richmond Agitation Sedation Scale. EN PACIENTES CON VENTILACIÓN MECÁNICA DE LARGA DURACIÓN.

INTRODUCTION: Sedation is monitored to avoid both under- and oversedation. OBJECTIVES: Determine the most prevalent sedation levels in the ICU according to RASS categories and whether treatment is individualized on the basis of these scores. METHODS: Prospective cohort study of patients connected to mechanical ventilation ≥ 96 hours in the intensive care unit between January 1 and August 31. Daily assessments were recorded in the intensive care unit, together with sedoanalgesic treatment, ventilation modes, or vital signs. RESULTS: We analyzed 1021 RASS scores collected over a total of 220 MV days, categorized in the following ranges: 404 (39.6%) deep sedation, 474 (46.4%) conscious sedation, and 54 (5.3%) agitation; 89 (8.7%) were missing scores. Patients receiving continuous sedoanalgesia were more likely to be in the deep sedation than conscious sedation range (87.1% vs. 32.3%, p < 0.001). Analysis of patients under continuous sedation and in ventilation mode found more changes in the conscious sedation range than in deep sedation (42.5% vs. 22.3% and 12.6% vs. 2.9%, respectively; p < 0.001 in both cases). In conscious sedation range there was increased use of opiates in bolus (6.4%). CONCLUSIONS: Deep sedation was clearly prevalent in patients with mechanical ventilation under continuous sedation, with few changes in ventilation mode, because it is prevalent control ventilation mode and no changes in sedonalagesic perfusion in that range.

Safety and immunogenicity of heterologous COVID-19 vaccine regimens to deal with product shortage: A randomised clinical trial in an elderly population.

Objectives: In a context of COVID-19 vaccine shortages, this study sought to evaluate the safety and efficacy of receiving one dose of Gam-COVID-Vac rAd26 followed by a second COVID-19 vaccine dose of either Gam-COVID-Vac rAd5, ChAdOx1 nCoV-19 or BBIBP-CorV in a cohort of older adults. Study design: Single-centre, randomised, open label, non-inferiority trial. Methods: Adults aged ≥65 years who had received one dose of Gam-COVID-Vac rAd26 were randomised in a 1:1:1 ratio to receive a second-dose COVID-19 vaccination of either Gam-COVID-Vac rAd5, ChAdOx1 nCoV-19 or BBIBP-CorV. The primary outcome was the assessment of the humoral immune response to vaccination (i.e. antibody titres of SARS-CoV-2 spike protein at 28 days after second-dose vaccination). In addition, neutralising antibody titres at day 28 for the three schedules were measured. Results: Of 85 participants who were enrolled in the study between 26 and July 30, 2021, 31 individuals were randomised to receive Gam-COVID-Vac rAd5, 27 to ChAdOx1 nCoV-19 and 27 to BBIBP-CorV. The mean age of participants was 68.2 years (SD 2.9) and 49 (57.6%) were female. Participants who received Gam-COVID-Vac rAd5 and ChAdOx1 nCoV1-19 showed significantly increased anti-S titres at 28 days after second-dose vaccination, but this magnitude of difference was not observed for those who received BBIBP-CorV. The ratio between the geometric mean at day 28 and baseline within each group was 11.8 (6.98-19.89) among patients assigned to Gam-COVID-Vac rAd26/rAd5, 4.81 (2.14-10.81) for the rAd26/ChAdOx1 nCoV-19 group and 1.53 (0.74-3.20) for the rAd26/BBIBP-CorV group. All of the schedules were shown to be safe. Conclusions: The findings in this study contribute to the scarce information published on the safety and immunogenicity of Gam-COVID-Vac heterologous regimens and will help the development of guidelines and vaccine programme management.

A model for assessing habitat fragmentation caused by new infrastructures in extensive territories - evaluation of the impact of the Spanish strategic infrastructure and transport plan.

The aim of the present work is to design a model for evaluating the impact of planned infrastructures on species survival at the territorial scale by calculating a connectivity index. The method developed involves determining the effective distance of displacement between patches of the same habitat, simplifying earlier models so that there is no dependence on specific variables for each species. A case study is presented in which the model was used to assess the impact of the forthcoming roads and railways included in the Spanish Strategic Infrastructure and Transport Plan (PEIT, in its Spanish initials). This study took into account the habitats of peninsular Spain, which occupies an area of some 500,000 km(2). In this territory, the areas deemed to provide natural habitats are defined by Directive 92/43/EEC. The impact of new infrastructures on connectivity was assessed by comparing two scenarios, with and without the plan, for the major new road and railway networks. The calculation of the connectivity index (CI) requires the use of a raster methodology based on the Arc/Info geographical information system (GIS). The actual calculation was performed using a program written in Arc/Info Macro Language (AML); this program is available in FragtULs (Mancebo Quintana, 2007), a set of tools for calculating indicators of fragmentation caused by transport infrastructure (http://topografia.montes.upm.es/fragtuls.html). The indicator of connectivity proposed allows the estimation of the connectivity between all the patches of a territory, with no artificial (non-ecologically based) boundaries imposed. The model proposed appears to be a useful tool for the analysis of fragmentation caused by plans for large territories.

Analysis of the relationship between interleukin polymorphisms within miRNA-binding regions and alcoholic liver disease. / Análisis de la relación entre polimorfismos en regiones diana de micro-ARN y la enfermedad hepática alcohólica.

INTRODUCTION: Alcohol consumption promotes inflammation through the Toll-like receptor 4 (TLR4)/nuclear factor (NF)-?B pathway, leading to organic damage. Some micro-RNA (miRNA) molecules modulate this inflammatory response by downregulating TLR4/NF-?B pathway mediators, like interleukins (ILs). Thus, polymorphisms within IL genes located near miRNA binding sites could modify the risk of ethanol-induced damage. The present study analyzed potential relationships between alcoholism or alcoholic liver disease (ALD) and IL12B 2124 G>T (rs1368439), IL16 5000 C>T (rs1131445), IL1R1 3114 C>T (rs3917328), and NFKB1 3400 A>G (rs4648143) polymorphisms. PATIENTS AND METHODS: The study included 301 male alcoholic patients and 156 male healthy volunteers. Polymorphisms were genotyped using TaqMan® PCR assays for allelic discrimination. Allele and genotype frequencies were compared between groups. Logistic regression analysis was performed to analyze the inheritance model. RESULTS: Analysis of the IL1R1 (rs3917328) polymorphism showed that the proportion of alleleT carriers (CT and TT genotypes) was higher in healthy controls (9.7%) than in alcoholic patients (6.5%; P=.042). However, multivariable logistic regression analyses did not yield a significant result. No differences between groups were found for other analyzed polymorphisms. CONCLUSIONS: Our study describes, for the first time, the expected frequencies of certain polymorphisms within miRNA-binding sites in alcoholic patients with and without ALD. Further studies should be developed to clarify the potential relevance of these polymorphisms in alcoholism and ALD development.

Charge transport in luminescent polymers studied by in situ fluorescence spectroscopy.

Modulation of the photoluminescence of poly-[2,7-(fluorene)-1,4-(phenylene)] can be attained by reversible electrochemical modification of the conjugated chain (p- or n-doping). Controlled injection of charge quenches the fluorescent emission of the conjugated polymer. The injection of holes completely eliminates the emission, while the electrons only quench up to one-third of the initial fluorescence of the polymer. Analogous quenching effects have been previously reported for solid-state organoelectronic devices. Electrochemical Stern-Volmer plots permit the estimation of the relative mobility of charge carriers in the polymer layer. The mobility of holes is 1 order of magnitude higher that the mobility of electrons, as determined by this method.

The human glutathione S-transferases: comparison of isoenzyme expression in normal and astrocytoma brain.

We describe expression of alpha, mu and pi class glutathione S-transferases (GST) in brain tissue from 21 controls and uninfiltrated and tumour tissue from 17 glioma patients. GST were sequentially resolved by chromatofocusing into the GST2, GST1, GST5, GST2 (5.5), GST3, GST6 sets and the contribution of each to total activity determined. The immunological identity of these isoforms was studied using immunoblotting. The pi class GST3 isoform was the major contributor to activity in control tissue (70.9%) and, uninfiltrated (75.1%) and tumour samples (82.4%). Expression was significantly greater in the tumours (P less than 0.05). Expression of alpha isoforms GST2 and GST2 (5.5) was variable with most subjects demonstrating no detectable GST2 (B1 and B2 chromatofocused monomers). An isoform termed GST2 (5.5) chromatofocussed at pH 5.5 and cross-reacted with antisera to B1. It was detected in most control and glioma patients and comprised about 5% of total activity. The contribution of GST2 and GST2 (5.5) to activity was similar in control, uninfiltrated and tumour tissue. Two mu class enzymes, GST1 and GST5, were identified. GST1 isoforms were detected in 9 of 21 control samples, the phenotype of these and matched liver samples were identical. GST1 isoforms were detected in 4 of 16 tumour samples, a significantly lower incidence than in a previously established control group. GST5 was expressed in most samples, the contribution of this locus to activity was significantly reduced in the tumours (5.2%) compared with control samples (14.5%).

Profile structures of TJ-II stellarator plasmas

Fine structures are found in the TJ-II stellarator electron temperature and density profiles, when they are measured using a high spatial resolution Thomson scattering system. These structures consist of peaks and valleys superimposed to a smooth average. Some irregularities remain in an ensemble average of discharges with similar macroscopic parameters such as line density, central temperature, and plasma current. They are found in all the magnetic configurations explored in plasmas heated by electron cyclotron waves. Their characteristics are shown and their possible origin is discussed.

The contribution of modern imaging to planning separation strategies in conjoined twins.

BACKGROUND/AIM: An accurate knowledge of the often complex and unexpected anatomy of conjoined twins is required in order to devise appropriate surgical strategies for separation. The recent progress of imaging techniques prompts an assessment of their contribution to planning separation strategies. MATERIAL AND METHODS: From 1990, we treated 8 consecutive sets of conjoined twins: 1 acardiac-acephalus, 1 epigastric heteropagus, 2 omphalopagus, 2 omphalothoracopagus, 1 ischiopagus tetrapus and 1 parapagus tripus. The first two sets were separated straightforwardly after birth and were excluded. Ultrasonographic and plain and contrast X-ray studies were used in all the remaining sets, angiography in 5, CT in 4, and MRI in 4. Helical CT and magnetic resonance angiography (MRA) were used in 3 sets. RESULTS: Two sets of omphalopagus twins and one of omphalothoracopagus twins were separated after birth due to brain damage of one twin, cloacal exstrophy and large arterial shunting, respectively. They were assessed using barium studies (3 sets), IVP (3), angiography (2), CT (2) and MRI (1). Three of six babies survived after separation. In the second set of omphalothoracopagus ecocardiography and MRA revealed that the extent of cardiovascular sharing precluded separation. In the remaining two sets of twins respectively ischiopagus and parapagus, the extent of organ sharing was depicted using three-dimensional helical CT and MRI; the four babies are alive after separation. CONCLUSIONS: Conventional imaging contributes only modestly to separation planning. In contrast, advanced imaging techniques are amazingly efficient in depicting complex fusions that have to be accurately recognised when planning realistic separation strategies.

[Comparative study of nicardipine versus placebo in the prevention of cognitive deterioration in patients with transient ischemic attack]. / Estudio comparativo de nicardipina frente a placebo en la prevención del deterioro cognitivo en los pacientes con accidentes isquémicos transitorios.

The neuropsychological follow up of transient ischemic attacks can provide a model for evaluating the efficiency of a drug in vascular dementia. A double blind study has been conducted using nicardipine, a calcium-antagonist, as opposed to a placebo in 40 patients with transient ischemic attacks, over a six month period. The patients were evaluated according to a Wechsler's intelligence scale, and their memory was also tested before and after this period. Although no alterations were registered on either scale, some differences did appear in certain sub-tests, especially as regards the verbal coefficient. This pilot study has provided information concerning the possible beneficial effect of the drug, which should be proven by means of a larger-scale study.

[Determination of basal GH in dementias]. / Determinación de la hormona de crecimiento basal en demencias.

We have studied the plasmatic levels of the growth hormone (GH) in a control group consisting of 72 subjects with an average age of 69.7 +/- 8.4 years and in a group of 37 patients with an average age of 69.3 +/- 9.6, of which 28 were demented (15 with degenerative dementia and 13 with non-degenerative dementia); 8 suffered from Parkinson's disease, and the rest showed signs of failing memory due to age. When comparing the plasmatic levels of GH between the patients' group and the control group we did not find significant differences between the demented and the control group, nor between the sub-groups of non-degenerative dementia or of those suffering from Parkinson's disease, when compared to the control group. However, we did find a reduction of GH that was statistically significant in the sub-group of degenerative dementia and the control group. This reduction in GH plasmatic values indicates a specific alteration in this type of process, which may be of certain use when searching for a hormonal marker for degenerative type dementia.

[Gallbladder torsion: report of a case]. / Torsión de la vesícula biliar: a propósito de un caso.

A case of an 81 year old woman who had fever, abdominal pain and a palpable mass in epigastrium and right hypochondriac region is presented. She was diagnosed as having acute cholecystitis and hydrops of the gallbladder. The surgical operation was performed and the findings were: dilated gallbladder with necrotic aspect, free floating with torsion of the cystic duct (greater than 180 degrees) wrapped in the mentum. There was no hepatic bed of the gallbladder. After correcting the torsion, the gallbladder was extirpated, with good clinical evolution. The etiopathogenia is discussed and the literature is reviewed. Despite the rareness of the gallbladder's torsion and the disease being relatively unknown, it has to be considered in the differential diagnosis of acute abdomen in the elderly.

A genetic variant in the microRNA-146a gene is associated with susceptibility to alcohol use disorders.

BACKGROUND: Polymorphisms in the microRNA (miRNA) regulatory pathways are novel functional genetic variants whose association with alcoholism susceptibility has not been previously studied. Given the potential relationship between certain miRNAs and alcohol use disorders (AUDs), this study was designed to explore the association between two polymorphisms within hsa-miR-146a and hsa-miR-196a2 genes and susceptibility to these diseases. METHODS: Three hundred and one male patients with AUDs and 156 sex-matched healthy volunteers were enrolled. Polymorphisms were genotyped using TaqMan(®) PCR assays. Allele and genotype frequencies were compared between groups and logistic regression analysis was also performed to analyze the model of inheritance. RESULTS: There was a significantly higher prevalence of allele C carriers (47.8%) of the miR-146a G>C polymorphism (rs2910164) among patients with AUDs when compared with controls (35.9%), and multivariable logistic regression analysis showed that the C allele was associated with these AUDs (OR=1.615, 95% CI 1.067-2.442; P=0.023). Neither the genotype nor the allele distribution of miR-196a2 polymorphism (rs11614913) was significantly different between groups. CONCLUSIONS: This is the first genetic association study to explore the relationship of miRNA polymorphisms with AUDs and to show an association of the miR-146a C>G rs2910164 allelic variant with this disease.

Implementation of a multichannel soft x-ray diagnostic for electron temperature measurements in TJ-II high-density plasmas.

Based on the multi-foil technique, a multichannel soft x-ray diagnostic for electron temperature measurements has been recently implemented in the TJ-II stellarator. The diagnostic system is composed by four photodiodes arrays with beryllium filters of different thickness. An in-vacuum amplifier board is coupled to each array, aiming at preventing induced noise currents. The Thomson scattering and the vacuum ultraviolet survey diagnostics are used for assessing plasma profiles and composition, being the analysis carried out with the radiation code IONEQ. The electron temperature is determined through the different signal-pair ratios with temporal and spatial resolution. The design and preliminary results from the diagnostic are presented.

Central electron temperature estimations of TJ-II neutral beam injection heated plasmas based on the soft x ray multi-foil technique.

The core electron temperature (T(e0)) of neutral beam heated plasmas is determined in TJ-II stellarator by using soft x ray detectors with beryllium filters of different thickness, based on the method known as the foil absorption technique. T(e0) estimations are done with the impurity code IONEQ, making use of complementary information from the TJ-II soft x ray tomography and the VUV survey diagnostics. When considering the actual electron density and temperature profile shapes, an acceptable agreement is found with Thomson scattering measurements for 8 different magnetic configurations. The impact of the use of both neutral beam injectors on the T(e0) measurements is addressed. Also, the behaviour of T(e0) during spontaneous profile transitions is presented.

Meta-analysis: glutathione-S-transferase allelic variants are associated with alcoholic liver disease.

BACKGROUND: Only a minority of alcoholics develop alcoholic liver disease (ALD) and allelic variants within genes encoding glutathione-S-transferases (GST) have been associated with ALD vulnerability with controversial results. AIM: To assess the effects of GST polymorphisms on ALD by means of a genetic association study and meta-analysis. METHODS: We retrieved published studies on the relationship between allelic variants within GST genes and ALD by means of electronic database search. A meta-analysis was conducted in a fixed or random effects model. Calculations of odds ratios (OR) and their confidence intervals (CI), tests for heterogeneity of the results and sensitivity analysis, have been performed. A genetic association study comparing GSTM1, GSTT1 and GSTP1 genotype distribution among 279 alcoholics with or without ALD and 144 controls was also performed. Results Fifteen previous studies were identified analysing the association of ALD with polymorphisms within GST genes. After meta-analysis, we found a significant association between the possession of the GSTM1 null allele and the presence of ALD (OR=1.43; 95% CI: 1.14, 1.78; P=0.002) among alcoholic patients. A significant association was also found for the possession of the GSTP1 Val/Val genotype and the presence of ALD (OR=2.04; 95% CI: 1.09, 3.80; P=0.03). CONCLUSIONS: Our results suggest that, among alcoholics, carriers of GSTM1 null genetic variant or Val/Val genotype of Ile/Val GSTP1 polymorphism have an increased risk to suffer from alcoholic liver disease. The role of glutathione-S-transferase as a potential therapeutic target in alcoholic liver disease is reinforced.

Multienzymatic system immobilization in sol-gel slides: fluorescent superoxide biosensors development.

One of the potential areas of research in the development of biosensors is the production of analytical devices based on the use of immobilized multienzymatic systems. In this work, we report the development of three analytical systems for superoxide radical detection using sol-gel technology to immobilize enzyme systems. These systems are based on the connected reactions of three enzymes (xanthine oxidase, superoxide dismutase and horseradish peroxidase) coupled to the probe Amplex red. The difference between these three systems lies in the immobilization of two or three enzymes into a single or in different sol-gel slides. We check the potential use of each designed systems to quantify superoxide radical and potential evaluation of radical scavenging properties of several antioxidant compounds.

Accurate and reliable image classification by using conformal predictors in the TJ-II Thomson scattering.

The charge-coupled device camera of the TJ-II Thomson scattering (TS) can capture five different classes of images. Typically, different data processing is performed depending on the kind of image that is acquired. The procedure can be automated to recognize the type of image. To this end, machine learning methods (MLM) are applied. However, usually, MLM classify without confidence estimates. An image classifier based on conformal predictors has been developed for the TJ-II TS. It provides a couple of indicators (confidence and credibility) for each classification that measures the accuracy and reliability of the prediction. Results achieve success rates of about 97%. The implemented classifier is valid for any kind of images.