Practical causal mediation analysis: extending nonparametric estimators to accommodate multiple mediators and multiple intermediate confounders.

Mediation analysis is appealing for its ability to improve understanding of the mechanistic drivers of causal effects, but real-world data complexities challenge its successful implementation, including (i) the existence of post-exposure variables that also affect mediators and outcomes (thus, confounding the mediator-outcome relationship), that may also be (ii) multivariate, and (iii) the existence of multivariate mediators. All three challenges are present in the mediation analysis we consider here, where our goal is to estimate the indirect effects of receiving a Section 8 housing voucher as a young child on the risk of developing a psychiatric mood disorder in adolescence that operate through mediators related to neighborhood poverty, the school environment, and instability of the neighborhood and school environments, considered together and separately. Interventional direct and indirect effects (IDE/IIE) accommodate post-exposure variables that confound the mediator-outcome relationship, but currently, no readily implementable nonparametric estimator for IDE/IIE exists that allows for both multivariate mediators and multivariate post-exposure intermediate confounders. The absence of such an IDE/IIE estimator that can easily accommodate both multivariate mediators and post-exposure confounders represents a significant limitation for real-world analyses, because when considering each mediator subgroup separately, the remaining mediator subgroups (or a subset of them) become post-exposure intermediate confounders. We address this gap by extending a recently developed nonparametric estimator for the IDE/IIE to allow for easy incorporation of multivariate mediators and multivariate post-exposure confounders simultaneously. We apply the proposed estimation approach to our analysis, including walking through a strategy to account for other, possibly co-occurring intermediate variables when considering each mediator subgroup separately.

EFFECT OF PAXLOVID TREATMENT DURING ACUTE COVID-19 ON LONG COVID ONSET: AN EHR-BASED TARGET TRIAL EMULATION FROM THE N3C AND RECOVER CONSORTIA.

Preventing and treating post-acute sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, has become a public health priority. In this study, we examined whether treatment with Paxlovid in the acute phase of COVID-19 helps prevent the onset of PASC. We used electronic health records from the National Covid Cohort Collaborative (N3C) to define a cohort of 426,352 patients who had COVID-19 since April 1, 2022, and were eligible for Paxlovid treatment due to risk for progression to severe COVID-19. We used the target trial emulation (TTE) framework to estimate the effect of Paxlovid treatment on PASC incidence. We estimated overall PASC incidence using a computable phenotype. We also measured the onset of novel cognitive, fatigue, and respiratory symptoms in the post-acute period. Paxlovid treatment did not have a significant effect on overall PASC incidence (relative risk [RR] = 0.98, 95% confidence interval [CI] 0.95-1.01). However, it had a protective effect on cognitive (RR = 0.90, 95% CI 0.84-0.96) and fatigue (RR = 0.95, 95% CI 0.91-0.98) symptom clusters, which suggests that the etiology of these symptoms may be more closely related to viral load than that of respiratory symptoms.

Using instrumental variables to address unmeasured confounding in causal mediation analysis.

Mediation analysis is a strategy for understanding the mechanisms by which interventions affect later outcomes. However, unobserved confounding concerns may be compounded in mediation analyses, as there may be unobserved exposure-outcome, exposure-mediator, and mediator-outcome confounders. Instrumental variables (IVs) are a popular identification strategy in the presence of unobserved confounding. However, in contrast to the rich literature on the use of IV methods to identify and estimate a total effect of a non-randomized exposure, there has been almost no research into using IV as an identification strategy to identify mediational indirect effects. In response, we define and nonparametrically identify novel estimands-double complier interventional direct and indirect effects-when 2, possibly related, IVs are available, one for the exposure and another for the mediator. We propose nonparametric, robust, efficient estimators for these effects and apply them to a housing voucher experiment.

URI-CADS: A Fully Automated Computer-Aided Diagnosis System for Ultrasound Renal Imaging.

Ultrasound is a widespread imaging modality, with special application in medical fields such as nephrology. However, automated approaches for ultrasound renal interpretation still pose some challenges: (1) the need for manual supervision by experts at various stages of the system, which prevents its adoption in primary healthcare, and (2) their limited considered taxonomy (e.g., reduced number of pathologies), which makes them unsuitable for training practitioners and providing support to experts. This paper proposes a fully automated computer-aided diagnosis system for ultrasound renal imaging addressing both of these challenges. Our system is based in a multi-task architecture, which is implemented by a three-branched convolutional neural network and is capable of segmenting the kidney and detecting global and local pathologies with no need of human interaction during diagnosis. The integration of different image perspectives at distinct granularities enhanced the proposed diagnosis. We employ a large (1985 images) and demanding ultrasound renal imaging database, publicly released with the system and annotated on the basis of an exhaustive taxonomy of two global and nine local pathologies (including cysts, lithiasis, hydronephrosis, angiomyolipoma), establishing a benchmark for ultrasound renal interpretation. Experiments show that our proposed method outperforms several state-of-the-art methods in both segmentation and diagnosis tasks and leverages the combination of global and local image information to improve the diagnosis. Our results, with a 87.41% of AUC in healthy-pathological diagnosis and 81.90% in multi-pathological diagnosis, support the use of our system as a helpful tool in the healthcare system.

A Robust Method for the Unsupervised Scoring of Immunohistochemical Staining.

Immunohistochemistry is a powerful technique that is widely used in biomedical research and clinics; it allows one to determine the expression levels of some proteins of interest in tissue samples using color intensity due to the expression of biomarkers with specific antibodies. As such, immunohistochemical images are complex and their features are difficult to quantify. Recently, we proposed a novel method, including a first separation stage based on non-negative matrix factorization (NMF), that achieved good results. However, this method was highly dependent on the parameters that control sparseness and non-negativity, as well as on algorithm initialization. Furthermore, the previously proposed method required a reference image as a starting point for the NMF algorithm. In the present work, we propose a new, simpler and more robust method for the automated, unsupervised scoring of immunohistochemical images based on bright field. Our work is focused on images from tumor tissues marked with blue (nuclei) and brown (protein of interest) stains. The new proposed method represents a simpler approach that, on the one hand, avoids the use of NMF in the separation stage and, on the other hand, circumvents the need for a control image. This new approach determines the subspace spanned by the two colors of interest using principal component analysis (PCA) with dimension reduction. This subspace is a two-dimensional space, allowing for color vector determination by considering the point density peaks. A new scoring stage is also developed in our method that, again, avoids reference images, making the procedure more robust and less dependent on parameters. Semi-quantitative image scoring experiments using five categories exhibit promising and consistent results when compared to manual scoring carried out by experts.

Second generation of pyrimidin-quinolone hybrids obtained from virtual screening acting as sphingosine kinase 1 inhibitors and potential anticancer agents.

We report here the virtual screening design, synthesis and activity of eight new inhibitors of SphK1. For this study we used a pre-trained Graph Convolutional Network (GCN) combined with docking calculations. This exploratory analysis proposed nine compounds from which eight displayed significant inhibitory effect against sphingosine kinase 1 (SphK1) demonstrating a high level of efficacy for this approach. Four of these compounds also displayed anticancer activity against different tumor cell lines, and three of them (5), (6) and (7) have shown a wide inhibitory action against many of the cancer cell line tested, with GI50 below 5 µM, being (5) the most promising with TGI below 10 µM for the half of cell lines. Our results suggest that the three most promising compounds reported here are the pyrimidine-quinolone hybrids (1) and (6) linked by p-aminophenylsulfanyl and o-aminophenol fragments respectively, and (8) without such aryl linker. We also performed an exhaustive study about the molecular interactions that stabilize the different ligands at the binding site of SphK1. This molecular modeling analysis was carried out by using combined techniques: docking calculations, MD simulations and QTAIM analysis. In this study we also included PF543, as reference compound, in order to better understand the molecular behavior of these ligands at the binding site of SphK1.These results provide useful information for the design of new inhibitors of SphK1 possessing these structural scaffolds.

Causal survival analysis under competing risks using longitudinal modified treatment policies.

Longitudinal modified treatment policies (LMTP) have been recently developed as a novel method to define and estimate causal parameters that depend on the natural value of treatment. LMTPs represent an important advancement in causal inference for longitudinal studies as they allow the non-parametric definition and estimation of the joint effect of multiple categorical, ordinal, or continuous treatments measured at several time points. We extend the LMTP methodology to problems in which the outcome is a time-to-event variable subject to a competing event that precludes observation of the event of interest. We present identification results and non-parametric locally efficient estimators that use flexible data-adaptive regression techniques to alleviate model misspecification bias, while retaining important asymptotic properties such as [Formula: see text]-consistency. We present an application to the estimation of the effect of the time-to-intubation on acute kidney injury amongst COVID-19 hospitalized patients, where death by other causes is taken to be the competing event.

The application of target trials with longitudinal targeted maximum likelihood estimation to assess the effect of alcohol consumption in adolescence on depressive symptoms in adulthood.

Time-varying confounding is a common challenge for causal inference in observational studies with time-varying treatments, long follow-up periods, and participant dropout. Confounder adjustment using traditional approaches can be limited by data sparsity, weight instability and computational issues. The Nicotine Dependence in Teens (NDIT) study is a prospective cohort study involving 24 data collection cycles from 1999 to date, among 1,294 students recruited from 10 high schools in Montreal, Canada, including follow-up into adulthood. Our aim is to estimate associations between the timing of alcohol initiation and the cumulative duration of alcohol use on depression symptoms in adulthood. Based on the target trials framework, we define intention-to-treat and as-treated parameters in a marginal structural model with sex as a potential effect-modifier. We then use the observational data to emulate the trials. For estimation, we use pooled longitudinal target maximum likelihood estimation (LTMLE), a plug-in estimator with double robust and local efficiency properties. We describe strategies for dealing with high-dimensional potential drinking patterns and practical positivity violations due to a long follow-up time, including modifying the effect of interest by removing sparsely observed drinking patterns from the loss function and applying longitudinal modified treatment policies to represent the effect of discouraging drinking.

Independent and joint contributions of physical disability and chronic pain to incident opioid use disorder and opioid overdose among Medicaid patients.

BACKGROUND: Chronic pain has been extensively explored as a risk factor for opioid misuse, resulting in increased focus on opioid prescribing practices for individuals with such conditions. Physical disability sometimes co-occurs with chronic pain but may also represent an independent risk factor for opioid misuse. However, previous research has not disentangled whether disability contributes to risk independent of chronic pain. METHODS: Here, we estimate the independent and joint adjusted associations between having a physical disability and co-occurring chronic pain condition at time of Medicaid enrollment on subsequent 18-month risk of incident opioid use disorder (OUD) and non-fatal, unintentional opioid overdose among non-elderly, adult Medicaid beneficiaries (2016-2019). RESULTS: We find robust evidence that having a physical disability approximately doubles the risk of incident OUD or opioid overdose, and physical disability co-occurring with chronic pain increases the risks approximately sixfold as compared to having neither chronic pain nor disability. In absolute numbers, those with neither a physical disability nor chronic pain condition have a 1.8% adjusted risk of incident OUD over 18 months of follow-up, those with physical disability alone have an 2.9% incident risk, those with chronic pain alone have a 3.6% incident risk, and those with co-occurring physical disability and chronic pain have a 11.1% incident risk. CONCLUSIONS: These findings suggest that those with a physical disability should receive increased attention from the medical and healthcare communities to reduce their risk of opioid misuse and attendant negative outcomes.

Governing the emissive properties of 4-aminobiphenyl-2-pyrimidine push-pull systems via the restricted torsion of N,N-disubstituted amino groups.

Donor-acceptor-substituted biphenyl derivatives are particularly interesting model compounds, which exhibit intramolecular charge transfer because of the extent of charge transfer between both substituents. The connection of a 4-[1,1'-biphenyl]-4-yl-2-pyrimidinyl) moiety to differently disubstituted amino groups at the biphenyl terminal can offer push-pull compounds with distinctive photophysical properties. Herein, we report a comprehensive study of the influence of the torsion angle of the disubstituted amino group on the emissive properties of two pull-push systems: 4-[4-(4-N,N-dimethylaminophenyl)phenyl]-2,6-diphenylpyrimidine (D1) and 4-[4-(4-N,N-diphenylaminophenyl)phenyl]-2,6-diphenylpyrimidine (D2). The torsion angle of the disubstituted amino group, either N,N-dimethyl-amine or N,N-diphenyl-amine, at the biphenyl end governs their emissive properties. A drastic fluorescence quenching occurs in D1 as the solvent polarity increases, whereas D2 maintains its emission independently of the solvent polarity. Theoretical calculations on D1 support the presence of a twisted geometry for the lowest energy, charge-transfer excited state (S1,90), which corresponds to the minimum energy structure in polar solvents and presents a small energy barrier to move from the excited to the ground state, thereby favoring the non-radiative pathway and reducing the fluorescence efficiency. In contrast, this twisted structure is absent in D2 due to the steric hindrance of the phenyl groups attached to the amine group, making the non-radiative decay less favorable. Our findings provide insights into the crucial role of the substituent in the donor moiety of donor-acceptor systems on both the singlet excited state and the intramolecular charge-transfer process.

A causal roadmap for generating high-quality real-world evidence.

Increasing emphasis on the use of real-world evidence (RWE) to support clinical policy and regulatory decision-making has led to a proliferation of guidance, advice, and frameworks from regulatory agencies, academia, professional societies, and industry. A broad spectrum of studies use real-world data (RWD) to produce RWE, ranging from randomized trials with outcomes assessed using RWD to fully observational studies. Yet, many proposals for generating RWE lack sufficient detail, and many analyses of RWD suffer from implausible assumptions, other methodological flaws, or inappropriate interpretations. The Causal Roadmap is an explicit, itemized, iterative process that guides investigators to prespecify study design and analysis plans; it addresses a wide range of guidance within a single framework. By supporting the transparent evaluation of causal assumptions and facilitating objective comparisons of design and analysis choices based on prespecified criteria, the Roadmap can help investigators to evaluate the quality of evidence that a given study is likely to produce, specify a study to generate high-quality RWE, and communicate effectively with regulatory agencies and other stakeholders. This paper aims to disseminate and extend the Causal Roadmap framework for use by clinical and translational researchers; three companion papers demonstrate applications of the Causal Roadmap for specific use cases.

Caracterización de las cirugías laparoscópicas en el Servicio de Ginecología del Hospital Materno-Infantil Ángel Arturo Aballí

Introducción: La cirugía laparoscópica ginecológica permite intervenir a la paciente sin tener que abrir el abdomen, pues consiste en realizar pequeñas incisiones. Actualmente se emplea en enfermedades como el cáncer o en la extracción de quistes y miomas, por lo que se puede aplicar en casi cualquier intervención de cirugía ginecológica. Objetivo: Caracterizar los procedimientos laparoscópicos del Servicio de Ginecología en el Hospital Materno-Infantil Ángel Arturo Aballí en el período comprendido entre enero del 2018 y diciembre del 2021. Métodos: Se realizó un estudio observacional, descriptivo, retrospectivo de corte longitudinal con el fin de describir la actividad asistencial laparoscópica. La muestra fue de 180 pacientes, según el criterio de selección no probabilístico de los investigadores. Resultados: La edad promedio fue 41,6 años. Según los antecedentes, predominó el tamaño del útero con 91,1 % (n = 164). Dentro de las indicaciones quirúrgicas, se encontró la paridad satisfecha en un 34,4 %, seguido del tumor de ovario (18,9 %), las neoplasias intraepiteliales cervicales (13,4 %) y el fibroma uterino sintomático. En cuanto a la cirugía mayor, se encontró la histerectomía abdominal laparoscópica en un 49,0 % (n = 78), seguido de la salpingectomía con un 38,9 %, resultados con significación desde el punto de vista estadístico (p = 0,004). En cuanto a la cirugía menor, el 11,6 % de la muestra recibió la ablación de los focos endometriales. Las complicaciones fueron escasas. Conclusiones: Los procederes laparoscópicos del Servicio de Ginecología del Hospital Materno-Infantil Ángel Arturo Aballí se consideraron adecuados de acuerdo a los indicadores quirúrgicos.

Introduction: Laparoscopic gynecological surgery allows for the patient to undergo surgery without having to open their abdomen, since it consists in making small incisions. It is currently used in diseases such as cancer or in the removal of cysts and myomas; therefore, it can be applied in almost any gynecological surgery. Objective: To characterize the laparoscopic procedures of the gynecology service at Hospital Materno-Infantil Ángel Arturo Aballí, in the period from January 2018 to December 2021. Methods: An observational, descriptive, retrospective and longitudinal study was carried out in order to describe the laparoscopic assistance activity. The sample consisted of 180 patients, according to the researchers' nonprobabilistic selection criteria. Results: The mean age was 41.6 years. Concerning antecedents, uterine size predominated, with 91.1% (n = 164). Among surgical indications, satisfied parity was found in 34.4%, followed by ovarian tumor (18.9%), cervical intraepithelial neoplasms (13.4 %) and symptomatic uterine fibroid. With respect to major surgery, laparoscopic abdominal hysterectomy was found in 49.0 % (n = 78), followed by salpingectomy, with 38.9%; such results are statistically significant (p = 0.004). Regarding minor surgery, 11.6% of the sample received ablation of endometrial focuses. Complications were rare. Conclusions: The laparoscopic procedures of the gynecology service at Hospital Materno-Infantil Ángel Arturo Aballí are considered adequate according to the surgical indicators.

Mature iPSC-derived astrocytes of an ALS/FTD patient carrying the TDP43A90V mutation display a mild reactive state and release polyP toxic to motoneurons.

Astrocytes play a critical role in the maintenance of a healthy central nervous system and astrocyte dysfunction has been implicated in various neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). There is compelling evidence that mouse and human ALS and ALS/FTD astrocytes can reduce the number of healthy wild-type motoneurons (MNs) in co-cultures or after treatment with astrocyte conditioned media (ACM), independently of their genotype. A growing number of studies have shown that soluble toxic factor(s) in the ACM cause non-cell autonomous MN death, including our recent identification of inorganic polyphosphate (polyP) that is excessively released from mouse primary astrocytes (SOD1, TARDBP, and C9ORF72) and human induced pluripotent stem cells (iPSC)-derived astrocytes (TARDBP) to kill MNs. However, others have reported that astrocytes carrying mutant TDP43 do not produce detectable MN toxicity. This controversy is likely to arise from the findings that human iPSC-derived astrocytes exhibit a rather immature and/or reactive phenotype in a number of studies. Here, we have succeeded in generating a highly homogenous population of functional quiescent mature astrocytes from control subject iPSCs. Using identical conditions, we also generated mature astrocytes from an ALS/FTD patient carrying the TDP43A90V mutation. These mutant TDP43 patient-derived astrocytes exhibit key pathological hallmarks, including enhanced cytoplasmic TDP-43 and polyP levels. Additionally, mutant TDP43 astrocytes displayed a mild reactive signature and an aberrant function as they were unable to promote synaptogenesis of hippocampal neurons. The polyP-dependent neurotoxic nature of the TDP43A90V mutation was further confirmed as neutralization of polyP in ACM derived from mutant TDP43 astrocytes prevented MN death. Our results establish that human astrocytes carrying the TDP43A90V mutation exhibit a cell-autonomous pathological signature, hence providing an experimental model to decipher the molecular mechanisms underlying the generation of the neurotoxic phenotype.

Antispasmodic Effect of Valeriana pilosa Root Essential Oil and Potential Mechanisms of Action: Ex Vivo and In Silico Studies.

Infusions of Valeriana pilosa are commonly used in Peruvian folk medicine for treating gastrointestinal disorders. This study aimed to investigate the spasmolytic and antispasmodic effects of Valeriana pilosa essential oil (VPEO) on rat ileum. The basal tone of ileal sections decreased in response to accumulative concentrations of VPEO. Moreover, ileal sections precontracted with acetylcholine (ACh), potassium chloride (KCl), or barium chloride (BaCl2) were relaxed in response to VPEO by a mechanism that depended on atropine, hyoscine butylbromide, solifenacin, and verapamil, but not glibenclamide. The results showed that VPEO produced a relaxant effect by inhibiting muscarinic receptors and blocking calcium channels, with no apparent effect on the opening of potassium channels. In addition, molecular docking was employed to evaluate VPEO constituents that could inhibit intestinal contractile activity. The study showed that α-cubebene, ß-patchoulene, ß-bourbonene, ß-caryophyllene, α-guaiene, γ-muurolene, valencene, eremophyllene, and δ-cadinene displayed the highest docking scores on muscarinic acetylcholine receptors and voltage-gated calcium channels, which may antagonize M2 and/or M3 muscarinic acetylcholine receptors and block voltage-gated calcium channels. In summary, VPEO has both spasmolytic and antispasmodic effects. It may block muscarinic receptors and calcium channels, thus providing a scientific basis for its traditional use for gastrointestinal disorders.

Protection provided by a commercial modified-live porcine reproductive and respiratory syndrome virus (PRRSV) 1 vaccine (PRRSV1-MLV) against a Japanese PRRSV2 field strain.

BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) vaccines do not provide full cross-protection, mainly due to the virus genetic variability. Despite this, vaccines based on modified-live PRRSV (PRRSV-MLV) reduce the disease impact. OBJECTIVES: To assess the efficacy of two commercial vaccines-one based on PRRSV1 (PRRSV1-MLV) and another on PRRSV2 (PRRSV2-MLV)-against a Japanese PRRSV2 field strain. METHODS: Two groups of three-week-old piglets were vaccinated (G1: PRRSV1-MLV; G2: PRRSV2-MLV) and two were kept as non-vaccinated (INF and CTRL). One month later, G1, G2, and INF were challenged with a PRRSV2 field strain. RESULTS: After the challenge, clinical signs were only observed in INF. Moreover, the highest rectal temperatures and values for the area under the curve (AUC) were observed in INF. Regarding viral detection, both AUC and the proportion of positive samples in blood were higher in INF. In G1, viremic animals never reached 100%. At necropsy (21 d after the challenge), differences for titers among groups were only found in tonsils (G1 < G2 and INF). One animal (belonging to G1) was negative in all tissues. Regarding humoral responses, G1 and G2 seroconverted after vaccination, as detected in the corresponding enzyme-linked immunosorbent assay. Specific neutralizing antibodies (NA) against PRRSV1-MLV were already detected at 14 d after vaccination in G1, showing a significant booster after the challenge, while PRRSV2-MLV NA were detected in G2 at the end of the experiment. CONCLUSIONS: Despite genetic differences, PRRSV1-MLV has been demonstrated to confer partial protection against a Japanese PRRSV2 strain, at least as good as PRRSV2-MLV.

On the importance of equatorial metal-centered excited states in the photophysics of cyclometallated Ir(III) complexes.

In the present contribution, the following three cyclometallated Ir(III) complexes were theoretically investigated using density functional theory calculations to explain their different photophysical properties: [Ir(ppy)2(bpy)]+, where Hppy is 2-phenylpyridine and bpy is 2,2'-bipyridine, [Ir(ppy)2(pbpy)]+, where pbpy is 6-phenyl-2,2'-bipyridine, and [Ir(ppy)2(dpbpy)]+, where dpbpy is 6,6'-diphenyl-2,2'-bipyridine. Despite sharing the same molecular skeleton, with the only difference being the addition of one or two phenyl groups attached to the ancillary bpy ligand, the complexes show different emission quantum yields in CH2Cl2 solution (0.196, 0.049 and 0.036, respectively). Such a behavior was previously justified as a consequence of a different ability to non-radiatively decay through an axial metal-centered (MC) triplet state. In the present contribution, a new non-radiative decay path has been characterized to be mediated by the so-called equatorial MC states, in which an Ir-Nbpy bond is elongated instead of an Ir-Nppy bond as observed in the axial MC states. The decay path involving the equatorial MC states is more favorable than that associated with the axial MC states, and the different ability to decay through the former better explains the photoemission properties exhibited by the three complexes.

Molecular network of the oil palm root response to aluminum stress.

BACKGROUND: The solubilization of aluminum ions (Al3+) that results from soil acidity (pH < 5.5) is a limiting factor in oil palm yield. Al can be uptaken by the plant roots affecting DNA replication and cell division and triggering root morphological alterations, nutrient and water deprivation. In different oil palm-producing countries, oil palm is planted in acidic soils, representing a challenge for achieving high productivity. Several studies have reported the morphological, physiological, and biochemical oil palm mechanisms in response to Al-stress. However, the molecular mechanisms are just partially understood. RESULTS: Differential gene expression and network analysis of four contrasting oil palm genotypes (IRHO 7001, CTR 3-0-12, CR 10-0-2, and CD 19 - 12) exposed to Al-stress helped to identify a set of genes and modules involved in oil palm early response to the metal. Networks including the ABA-independent transcription factors DREB1F and NAC and the calcium sensor Calmodulin-like (CML) that could induce the expression of internal detoxifying enzymes GRXC1, PER15, ROMT, ZSS1, BBI, and HS1 against Al-stress were identified. Also, some gene networks pinpoint the role of secondary metabolites like polyphenols, sesquiterpenoids, and antimicrobial components in reducing oxidative stress in oil palm seedlings. STOP1 expression could be the first step of the induction of common Al-response genes as an external detoxification mechanism mediated by ABA-dependent pathways. CONCLUSIONS: Twelve hub genes were validated in this study, supporting the reliability of the experimental design and network analysis. Differential expression analysis and systems biology approaches provide a better understanding of the molecular network mechanisms of the response to aluminum stress in oil palm roots. These findings settled a basis for further functional characterization of candidate genes associated with Al-stress in oil palm.

Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain.

BACKGROUND: The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized. RESULTS: PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (> 90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries. CONCLUSIONS: Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered.

Modeling the Interaction of Coronavirus Membrane Phospholipids with Photocatalitically Active Titanium Dioxide.

The outbreak of viral infectious diseases urges airborne droplet and surface disinfection strategies, which may rely on photocatalytic semiconductors. A lipid bilayer membrane generally encloses coronaviruses and promotes the anchoring on the semiconductor surface, where, upon photon absorption, electron-hole pairs are produced, which can react with adsorbed oxygen-containing species and lead to the formation of reactive oxygen species (ROSs). The photogenerated ROSs may support the disruptive oxidation of the lipidic membrane and pathogen death. Density functional theory calculations are employed to investigate adsorption modes, energetics, and electronic structure of a reference phospholipid on anatase TiO2 nanoparticles. The phospholipid covalently bound on TiO2, engaging a stronger adsorption on the (101) than on the (001) surface. The energetically most stable structure involves the formation of four covalent bonds through phosphate and carbonyl oxygen atoms. The adsorbates show a reduction of the band gap compared with standalone TiO2, suggesting a significant interfacial coupling.