ATENA: A Web-Based Tool for Modelling Metal Oxide Nanoparticles Based on NanoFingerprint Quantitative Structure-Activity Relationships

Modelling size-realistic nanomaterials to analyse some of their properties, such as toxicity, solubility, or electronic structure, is a current challenge in computational and theoretical chemistry. The representation of the all-atom three-dimensional structure of a nanocompound would be ideal, as it could account explicitly for structural effects. However, the use of the whole structure is tedious due to the high data management and the structural complexity that accompanies the surface of the nanoparticle. Developing appropriate tools that enable a quantitative analysis of the structure, as well as the selection of regions of interest such as the core-shell, is a crucial step toward enabling the efficient analysis and processing of model nanostructures. The aim of this study was twofold. First, we defined the NanoFingerprint, which is a representation of a nanocompound in the form of a vector based on its 3D structure. The local relationship between atoms, i.e., their coordination within successive layers of neighbours, allows the characterisation of the local structure through the atom connectivity, maintaining the information of the three-dimensional structure but increasing the management ability. Second, we present a web server, called ATENA, to generate NanoFingerprints and other tools based on the 3D structure of the nanocompounds. A case study is reported to show the validity of our new fingerprint tool and the usefulness of our server. The scientific community and also private companies have a new tool based on a public web server for exploring the toxicity of nanocompounds.

Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus

KEY MESSAGE

Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.

Comprehensive Oral Diagnosis and Management for Women with Turner Syndrome

Turner Syndrome (TS) is a rare genetic disorder that affects females when one of the X chromosomes is partially or completely missing. Due to high genetic and phenotypic variability, TS diagnosis is challenging and is often delayed until adolescence, resulting in poor clinical management. Numerous oral, dental and craniofacial anomalies have been associated with TS, yet a comprehensive description is still lacking. This study addresses this gap through a detailed analysis of oral health and craniofacial characteristics in a cohort of 15 females with TS and their first-degree relatives. Subjects with TS ranged from 3 to 48 years old, none showed evidence of periodontal disease and only the youngest was in mixed dentition. Using the Multifunction System, we identified an aggregation of multiple signs and symptoms in each TS subject, including tooth anomalies (supernumerary molars, agenesis, microdontia, enamel defects, alterations in eruption patterns -advanced and delayed for chronological age-, crowding, rotations and transpositions), malocclusion (class II/1 and II/2) and Class II facial profile, while relatives exhibited fewer manifestations. The early detection of these signs and symptoms is crucial for appropriate referral and the optimal clinical management of TS, especially during the critical period of 9 to 10 years when congenital dental anomalies appear. The use of an established taxonomy to describe these phenotypic features is essential for early detection. Multidisciplinary teams are required to ensure holistic care management in rare diseases like TS.

Structural Stabilization of Clinically Oriented Oligomeric Proteins During their Transit through Synthetic Secretory Amyloids

Developing time-sustained drug delivery systems is a main goal in innovative medicines. Inspired by the architecture of secretory granules from the mammalian endocrine system it has generated non-toxic microscale amyloid materials through the coordination between divalent metals and poly-histidine stretches. Like their natural counterparts that keep the functionalities of the assembled protein, those synthetic structures release biologically active proteins during a slow self-disintegration process occurring in vitro and upon in vivo administration. Being these granules formed by a single pure protein species and therefore, chemically homogenous, they act as highly promising time-sustained drug delivery systems. Despite their enormous clinical potential, the nature of the clustering process and the quality of the released protein have been so far neglected issues. By using diverse polypeptide species and their protein-only oligomeric nanoscale versions as convenient models, a conformational rearrangement and a stabilization of the building blocks during their transit through the secretory granules, being the released material structurally distinguishable from the original source is proved here. This fact indicates a dynamic nature of secretory amyloids that act as conformational arrangers rather than as plain, inert protein-recruiting/protein-releasing granular depots.

Correlates of protection and determinants of SARS-CoV-2 breakthrough infections 1 year after third dose vaccination

BACKGROUND

The emergence of new SARS-CoV-2 variants and the waning of immunity raise concerns about vaccine effectiveness and protection against COVID-19. While antibody response has been shown to correlate with the risk of infection with the original variant and earlier variants of concern, the effectiveness of antibody-mediated protection against Omicron and the factors associated with protection remain uncertain.

METHODS

We evaluated antibody responses to SARS-CoV-2 spike (S) and nucleocapsid (N) antigens from Wuhan and variants of concern by Luminex and their role in preventing breakthrough infections 1 year after a third dose of mRNA vaccination, in a cohort of health care workers followed since the pandemic onset in Spain (N = 393). Data were analyzed in relation to COVID-19 history, demographic factors, comorbidities, vaccine doses, brand, and adverse events.

RESULTS

Higher levels of anti-S IgG and IgA to Wuhan, Delta, and Omicron were associated with protection against vaccine breakthroughs (IgG against Omicron S antigen HR, 0.06, 95%CI, 0.26-0.01). Previous SARS-CoV-2 infection was positively associated with antibody levels and protection against breakthroughs, and a longer time since last infection was associated with lower protection. In addition, priming with BNT162b2 followed by mRNA-1273 booster was associated with higher antibody responses than homologous mRNA-1273 vaccination.

CONCLUSIONS

Data show that IgG and IgA induced by vaccines against the original strain or by hybrid immunization are valid correlates of protection against Omicron BA.1 despite immune escape and support the benefits of heterologous vaccination regimens to enhance antibodies and the prioritization of booster vaccination in individuals without recent infections.

Nanoparticle-Based Secretory Granules Induce a Specific and Long-Lasting Immune Response through Prolonged Antigen Release

Developing prolonged antigen delivery systems that mimic long-term exposure to pathogens appears as a promising but still poorly explored approach to reach durable immunities. In this study, we have used a simple technology by which His-tagged proteins can be assembled, assisted by divalent cations, as supramolecular complexes with progressive complexity, namely protein-only nanoparticles and microparticles. Microparticles produced out of nanoparticles are biomimetics of secretory granules from the mammalian hormonal system. Upon subcutaneous administration, they slowly disintegrate, acting as an endocrine-like secretory system and rendering the building block nanoparticles progressively bioavailable. The performance of such materials, previously validated for drug delivery in oncology, has been tested here regarding the potential for time-prolonged antigen release. This has been completed by taking, as a building block, a nanostructured version of p30, a main structural immunogen from the African swine fever virus (ASFV). By challenging the system in both mice and pigs, we have observed unusually potent pro-inflammatory activity in porcine macrophages, and long-lasting humoral and cellular responses in vivo, which might overcome the need for an adjuvant. The robustness of both innate and adaptive responses tag, for the first time, these dynamic depot materials as a novel and valuable instrument with transversal applicability in immune stimulation and vaccinology.

Cognitive Vergence Recorded with a Webcam-Based Eye-Tracker during an Oddball Task in an Elderly Population

(1) Background: Our previous research provides evidence that vergence eye movements may significantly influence cognitive processing and could serve as a reliable measure of cognitive issues. The rise of consumer-grade eye tracking technology, which uses sophisticated imaging techniques in the visible light spectrum to determine gaze position, is noteworthy. In our study, we explored the feasibility of using webcam-based eye tracking to monitor the vergence eye movements of patients with Mild Cognitive Impairment (MCI) during a visual oddball paradigm. (2) Methods: We simultaneously recorded eye positions using a remote infrared-based pupil eye tracker. (3) Results: Both tracking methods effectively captured vergence eye movements and demonstrated robust cognitive vergence responses, where participants exhibited larger vergence eye movement amplitudes in response to targets versus distractors. (4) Conclusions: In summary, the use of a consumer-grade webcam to record cognitive vergence shows potential. This method could lay the groundwork for future research aimed at creating an affordable screening tool for mental health care.

Implementing Horizon Scanning as a tool for the strategic development of regulatory guidelines for nanotechnology-enabled health products

Strategic regulatory development is essential to ensure that new innovations in nanotechnology-enabled health products (NHPs) successfully reach the market and benefit patients. Currently, the lack of specific regulatory guidelines for NHPs is considered one of the primary causes of the so-called "valley of death" in these products, impacting both current and future advancements. In this study, we have implemented a methodology to anticipate key trends in NHP development and compare them with the current regulatory landscape applicable to NHPs. This methodology relies on Horizon Scanning, a tool commonly used by policymakers to foresee future needs and proactively shape a regulatory framework tailored to those needs. Through the application of this methodology, different trends in NHP have been identified, notably NHPs for drug delivery and dental applications. Furthermore, the most disruptive elements involve NHPs that are multicomposite and multifunctional, harnessing nano-scale properties to combine therapeutic and diagnostic purposes within a single product. When compared with the regulatory landscape, current regulations are gradually adapting to accommodate emerging trends, with specific guidelines being developed. However, for the most disruptive elements, multicomposite and multifunctional NHPs, their novelty still poses significant regulatory challenges, requiring a strategic development of guidelines by regulatory agencies to ensure their safe and effective integration into healthcare practices. This study underscores the importance of proactive regulatory planning to bridge the gap between NHP innovation and market implementation.

Exploring Metabolic and Gut Microbiome Responses to Paraquat Administration in Male Wistar Rats: Implications for Oxidative Stress

In this study, we examined the metabolic and gut microbiome responses to paraquat (PQ) in male Wistar rats, focusing on oxidative stress effects. Rats received a single intraperitoneal injection of PQ at 15 and 30 mg/kg, and various oxidative stress parameters (i.e., MDA, SOD, ROS, 8-isoprostanes) were assessed after three days. To explore the omic profile, GC-qTOF and UHPLC-qTOF were performed to assess the plasma metabolome; 1H-NMR was used to assess the urine metabolome; and shotgun metagenomics sequencing was performed to study the gut microbiome. Our results revealed reductions in body weight and tissue changes, particularly in the liver, were observed, suggesting a systemic effect of PQ. Elevated lipid peroxidation and reactive oxygen species levels in the liver and plasma indicated the induction of oxidative stress. Metabolic profiling revealed changes in the tricarboxylic acid cycle, accumulation of ketone body, and altered levels of key metabolites, such as 3-hydroxybutyric acid and serine, suggesting intricate links between energy metabolism and redox reactions. Plasma metabolomic analysis revealed alterations in mitochondrial metabolism, nicotinamide metabolism, and tryptophan degradation. The gut microbiome showed shifts, with higher PQ doses influencing microbial populations (e.g., Escherichia coli and Akkermansia muciniphila) and metagenomic functions (pyruvate metabolism, fermentation, nucleotide and amino acid biosynthesis). Overall, this study provides comprehensive insights into the complex interplay between PQ exposure, metabolic responses, and gut microbiome dynamics. These findings enhance our understanding of the mechanisms behind oxidative stress-induced metabolic alterations and underscore the connections between xenobiotic exposure, gut microbiota, and host metabolism.

Outcome improvement over time in reduced intensity conditioning hematopoietic transplantation: a 20-year experience

The current study includes all consecutive patients (N = 484) who received a reduced-intensity conditioning regimen (RIC) allogeneic hematopoietic stem cell transplantation in our center from 1999 to 2020. Conditioning regimens were based on fludarabine with melphalan or busulfan, with low-dose thiotepa and pharmacological GVHD prophylaxis consisted of cyclosporine A (CsA)-methotrexate (MTX)/mofetil (MMF) (n = 271), tacrolimus-sirolimus (n = 145), and post-transplantation cyclophosphamide (PTCy)-tacrolimus (n = 68). The median time of overall follow-up in survivors was 8 years (1-22 years) and was at least 3 years in all three GVHD prophylaxis groups. Thirty-three percent had a high or very high disease risk index, 56% ≥ 4 European bone marrow transplantation risk, and 65% ≥ 3 hematopoietic stem cell transplantation comorbidity index score-age score. Neutrophil and platelet engraftment was longer for PTCy-tacro (p 0.0001). Cumulative incidence of grade III-IV aGVHD was 17% at 200 days, and that of moderate-severe cGvHD was 36% at 8 years. GVHD prophylaxis was the only prognostic factor in the multivariable analyses for the development of aGVHD and moderate-severe cGVHD (p 0.0001). NRM and relapse incidences were 29% and 30% at 8 years, while OS and PFS rates were 43% and 39% at 8 years. At 3 years, OS was highest in the PTCy-tacro group (68%) than in the tacro-siro (61%) and CsA-MTX/MMF (49%) cohorts (p < 0.01). In the three groups, respectively, the 200-day incidence of grade III-IV aGvHD (6% vs. 12% vs. 23%) and 3-year moderate-severe cGVHD (8% vs. 40% vs. 38%) were lower in the PTCy cohort. These better outcomes were confirmed in multivariable analyses. Based on our recent results, the PTCy could be considered as a real GvHD prophylaxis in the RIC setting due to improve best 3-year GvHD and survival outcomes.

Concordance of in vivo reflectance confocal microscopy and horizontal-sectioning histology in skin tumours

BACKGROUND

In vivo reflectance confocal microscopy (RCM) enables the study of architectural and cytological aspects in horizontal sections, which closely correlate with histologic features. However, traditional histopathological vertical sections cannot totally reproduce the image of the in vivo RCM horizontal section.

OBJECTIVE

To evaluate the concordance between in vivo RCM and histopathologic transverse sections for melanocytic lesions, basal cell carcinoma and seborrheic keratoses.

METHODS

Prospectively collected benign melanocytic and non-melanocytic tumours diagnosed by dermoscopy were evaluated for common RCM features and compared to histopathology in horizontal sections with haematoxylin and eosin staining.

RESULTS

A total of 44 skin tumours including 19 melanocytic lesions (nine compound, five junctional and five intradermal nevi), 12 basal cell carcinomas and 13 seborrheic keratoses were collected in the Department of Dermatology of Hospital Clinic of Barcelona. The RCM features that had statistically significant agreement with the histopathological horizontal sections were the preserved and visible honeycomb pattern, well defined DEJ, small bright particles, dermal nests, tumour islands and dark silhouettes, clefting, collagen bundles, thickened collagen bundles and cytologic atypia.

CONCLUSIONS

Histopathology evaluation of horizontal sections of skin tumours can be correlated with main RCM findings. The results of this study have improved the understanding and interpretation of RCM features in relation to skin tumours, thus reinforcing the utility of RCM as a diagnostic tool.

Prediction models using artificial intelligence and longitudinal data from electronic health records: a systematic methodological review

OBJECTIVE

To describe and appraise the use of artificial intelligence (AI) techniques that can cope with longitudinal data from electronic health records (EHRs) to predict health-related outcomes.

METHODS

This review included studies in any language that: EHR was at least one of the data sources, collected longitudinal data, used an AI technique capable of handling longitudinal data, and predicted any health-related outcomes. We searched MEDLINE, Scopus, Web of Science, and IEEE Xplorer from inception to January 3, 2022. Information on the dataset, prediction task, data preprocessing, feature selection, method, validation, performance, and implementation was extracted and summarized using descriptive statistics. Risk of bias and completeness of reporting were assessed using a short form of PROBAST and TRIPOD, respectively.

RESULTS

Eighty-one studies were included. Follow-up time and number of registers per patient varied greatly, and most predicted disease development or next event based on diagnoses and drug treatments. Architectures generally were based on Recurrent Neural Networks-like layers, though in recent years combining different layers or transformers has become more popular. About half of the included studies performed hyperparameter tuning and used attention mechanisms. Most performed a single train-test partition and could not correctly assess the variability of the model's performance. Reporting quality was poor, and a third of the studies were at high risk of bias.

CONCLUSIONS

AI models are increasingly using longitudinal data. However, the heterogeneity in reporting methodology and results, and the lack of public EHR datasets and code sharing, complicate the possibility of replication.

REGISTRATION

PROSPERO database (CRD42022331388).

Anandamide and 2-arachidonoylglycerol baseline plasma concentrations and their clinical correlate in gambling disorder

INTRODUCTION

Different components of the endocannabinoid (eCB) system such as their most well-known endogenous ligands, anandamide (AEA) and 2-arachidonoylglycerol (2-AG), have been implicated in brain reward pathways. While shared neurobiological substrates have been described among addiction-related disorders, information regarding the role of this system in behavioral addictions such as gambling disorder (GD) is scarce.

AIMS

Fasting plasma concentrations of AEA and 2-AG were analyzed in individuals with GD at baseline, compared with healthy control subjects (HC). Through structural equation modeling, we evaluated associations between endocannabinoids and GD severity, exploring the potentially mediating role of clinical and neuropsychological variables.

METHODS

The sample included 166 adult outpatients with GD (95.8% male, mean age 39 years old) and 41 HC. Peripheral blood samples were collected after overnight fasting to assess AEA and 2-AG concentrations (ng/ml). Clinical (i.e., general psychopathology, emotion regulation, impulsivity, personality) and neuropsychological variables were evaluated through a semi-structured clinical interview and psychometric assessments.

RESULTS

Plasma AEA concentrations were higher in patients with GD compared with HC (p = .002), without differences in 2-AG. AEA and 2-AG concentrations were related to GD severity, with novelty-seeking mediating relationships.

CONCLUSIONS

This study points to differences in fasting plasma concentrations of endocannabinoids between individuals with GD and HC. In the clinical group, the pathway defined by the association between the concentrations of endocannabinoids and novelty-seeking predicted GD severity. Although exploratory, these results could contribute to the identification of potential endophenotypic features that help optimize personalized approaches to prevent and treat GD.

The earliest basketry in southern Europe: Hunter-gatherer and farmer plant-based technology in Cueva de los Murciélagos (Albuñol)

Plant material culture can offer unique insights into the ways of life of prehistoric societies; however, its perishable nature has prevented a thorough understanding of its diverse and complex uses. Sites with exceptional preservation of organic materials provide a unique opportunity for further research. The burial site of Cueva de los Murciélagos in southern Iberia, uncovered during 19th-century mining activities, contained the best-preserved hunter-gatherer basketry in southern Europe, together with other unique organic artifacts associated with the first farming communities, such as sandals and a wooden hammer. We present 14 14C dates for the perishable artifacts (N = 76), situating the assemblage between the Early and Middle Holocene (c. 7500 to 4200 cal BCE). Our integrated analysis includes raw material determination and technological and chrono-cultural contextualization of this unique and important set of materials.

Coupling Capillary-Driven Microfluidics with Lateral Flow Immunoassay for Signal Enhancement

Microfluidics has emerged as a versatile technology that is applied to enhance the performance of analytical techniques, among others. Pursuing this, we present a capillary-driven microfluidic device that improves the sensitivity of lateral flow immunoassay rapid tests thanks to offering an automated washing step. A novel multilevel microfluidic chip was 3D-printed with a photocurable black resin, sealed by an optically clear pressure-sensitive adhesive, and linked to the lateral flow strip. To depict the efficacy of microfluidics and the washing step, cortisol was measured quantitatively within the proposed device. Measuring cortisol levels is a way to capture physiological stress responses. Among biofluids, saliva is less infectious and easier to sample than others. However, higher sensitivity is demanded because the salivary cortisol concentrations are much lower than in blood. We carried out a competitive lateral flow immunoassay protocol with the difference that the microfluidic device applies an automated washing step after the sample is drained downstream. It washes the trapped quantum-dot-labeled antibodies out from nitrocellulose, diminishing background noise as these are bonded to cortisols and not to the immobilized receptors. Fluorescence spectroscopy, as a high-precision analysis, was successfully applied to determine clinically relevant salivary cortisol concentrations within a buffer quantitatively. The microfluidic design relied on a 3D valve that avoids reagent cross-contamination. This cross-contamination could make the washing buffer impure and undesirably dilute the sample. The proposed device is cost-effective, self-powered, robust, and ideal for non-expert users.

Enhanced recombinant protein capture, purity and yield from crude bacterial cell extracts by N-Lauroylsarcosine-assisted affinity chromatography

BACKGROUND

Recombinant proteins cover a wide range of biomedical, biotechnological, and industrial needs. Although there are diverse available protocols for their purification from cell extracts or from culture media, many proteins of interest such as those containing cationic domains are difficult to purify, a fact that results in low yields of the final functional product. Unfortunately, this issue prevents the further development and industrial or clinical application of these otherwise interesting products.

RESULTS

Aiming at improving the purification of such difficult proteins, a novel procedure has been developed based on supplementing crude cell extracts with non-denaturing concentrations of the anionic detergent N-Lauroylsarcosine. The incorporation of this simple step in the downstream pipeline results in a substantial improvement of the protein capture by affinity chromatography, an increase of protein purity and an enhancement of the overall process yield, being the detergent not detectable in the final product.

CONCLUSION

By taking this approach, which represents a smart repurposing of N-Lauroylsarcosine applied to protein downstream, the biological activity of the protein is not affected. Being technologically simple, the N-Lauroylsarcosine-assisted protein purification might represent a critical improvement in recombinant protein production with wide applicability, thus smothering the incorporation of promising proteins into the protein market.

Recombinant Proteins for Assembling as Nano- and Micro-Scale Materials for Drug Delivery: A Host Comparative Overview

By following simple protein engineering steps, recombinant proteins with promising applications in the field of drug delivery can be assembled in the form of functional materials of increasing complexity, either as nanoparticles or nanoparticle-leaking secretory microparticles. Among the suitable strategies for protein assembly, the use of histidine-rich tags in combination with coordinating divalent cations allows the construction of both categories of material out of pure polypeptide samples. Such molecular crosslinking results in chemically homogeneous protein particles with a defined composition, a fact that offers soft regulatory routes towards clinical applications for nanostructured protein-only drugs or for protein-based drug vehicles. Successes in the fabrication and final performance of these materials are expected, irrespective of the protein source. However, this fact has not yet been fully explored and confirmed. By taking the antigenic RBD domain of the SARS-CoV-2 spike glycoprotein as a model building block, we investigated the production of nanoparticles and secretory microparticles out of the versions of recombinant RBD produced by bacteria (Escherichia coli), insect cells (Sf9), and two different mammalian cell lines (namely HEK 293F and Expi293F). Although both functional nanoparticles and secretory microparticles were effectively generated in all cases, the technological and biological idiosyncrasy of each type of cell factory impacted the biophysical properties of the products. Therefore, the selection of a protein biofabrication platform is not irrelevant but instead is a significant factor in the upstream pipeline of protein assembly into supramolecular, complex, and functional materials.

EndoTrainer: a novel hybrid training platform for endoscopic surgery

PURPOSE

Endoscopy implies high demanding procedures, and their practice requires structured formation curricula supported by adequate training platforms. Physical platforms are the most standardised solution for surgical training, but over the last few years, virtual platforms have been progressively introduced. This research work presents a new hybrid, physic-virtual, endoscopic training platform that exploits the benefits of the two kind of platforms combining realistic tools and phantoms together with the capacity of measuring all relevant parameters along the execution of the exercises and of providing an objective assessment performance.

METHODS

The developed platform, EndoTrainer, has been designed to train and assess surgical skills in hysteroscopy and cystoscopy following a structured curricula. The initial development and validation is focused on hysteroscopic exercises proposed in the Gynaecological Endoscopic Surgical Education and Assessment (GESEA) Certification Programme from The Academy and European Society for Gynaecological Endoscopy (ESGE) and analyses the obtained results of an extensive study with 80 gynaecologists executing 30 trials of the standard 30 degree endoscope navigation exercise.

RESULTS

The experiments demonstrate the benefits of the presented hybrid platform. Multi-variable statistical analysis points out that all subjects have obtained statistically significant improvement in all relevant parameters: shorter and safer trajectories, improved 30-degree endoscope navigation, accurate positioning over the targets and reduction of the execution time.

CONCLUSION

This paper presents a new hybrid approach for training, and evaluating whether it provides an objectivable improvement of camera navigation endoscopic basic skills. The obtained results demonstrate the initial hypothesis: all subjects have improved their camera handling and navigation skills.

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues

BACKGROUND

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.

RESULTS

More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.

CONCLUSIONS

The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.

Essential and Non-essential Trace Elements in Milks and Plant-Based Drinks

Although milk and plant-based drinks are widely consumed foodstuffs with high nutritional value, their consumption may also mean intake of non-essential/toxic elements becoming a risk for human health. This study was aimed at determining the concentrations of essential (Ca, Co, K, Mg, Mn, Na, Ni and P) and non-essential/toxic (Hg, Pb, U and V) elements in milks (cow and goat), plant-based drinks (soy, almond, rice and oat) and infant formulas from organic and conventional production systems. Lactose-free, fresh and ultra-high-temperature (UHT) milks were also included. Chemical analyses were performed by means of inductively coupled plasma-mass spectrometry (ICP-MS). The content of the elements hereby assessed did not depend on the production system and the presence of lactose. However, significant differences were found in the concentrations of multiple elements when comparing sterilization methods, source (animal vs. plant-based) and animal species. Non-essential elements were not detected in milks and plant-based drinks, excepting Pb, which was detected in three samples. While the consumption of goat milk is recommended, considering the global intake of essential elements and the absence of non-essential elements, further studies should be conducted to confirm the absence of non-target toxic elements at very low trace levels. On the other hand, the best plant-based drinks are those made up with almonds (intake of Ca) and soy (K and Mg). The current results should be useful to help the population to balance the benefits and risks from milks and plant-based drinks consumption, as well as to adapt their dietary habits.

Sexual dimorphism in the first rib of Homo sapiens

This work aimed to study sexual dimorphism in the first rib of modern humans, with a special focus on whether differences in shape are due to divergent allometric growth in males and females. Also, we compare the accuracy of sex classification using different approaches based on two methodologies, traditional morphometry based on linear measurements and geometric morphometric analysis based on 2D landmark coordinates. The sample studied here comprised 121 right and left first ribs from 65 female and male adult recent Euro-American Homo sapiens individuals. For traditional morphometrics, 12 metric variables were collected from each rib using a digital caliper, and for geometric morphometrics, six landmarks and 31 semilandmarks were captured from photographs using digital software. Both geometric morphometric and metric data were analyzed to calculate the index of sexual dimorphism, variation related to lateral asymmetry, variation in size and shape, and allometric trends between males and females. Finally, a linear discriminant analysis (LDA) was performed comparing both methodologies to test the best approach for sex classification. Results indicated that there are significant sex differences in the size and shape of the first ribs of recent Euro-American Homo sapiens. Regression analysis revealed different allometric patterns for males and females, and this could partially explain shape differences between sexes. Additionally, traditional morphometrics showed that all characteristics analyzed are significantly dimorphic, with the midshaft minimum craniocaudal diameter, the sternal end minimum diameter, and the neck minimum craniocaudal diameter displaying the most dimorphic scores. Similarly, geometric morphometrics results indicated that males have more curved and interno-exteriorly wider first ribs. Finally, analysis of sex classification using LDA yielded slightly better accuracy for traditional morphometry (83.8%) than the geometric morphometrics approach (81.3%) based on form Procrustes coordinates. This study demonstrates the usefulness of applying two different morphometric approaches to obtain more comprehensive results.

Unveiling the Multitarget Anti-Alzheimer Drug Discovery Landscape: A Bibliometric Analysis

Multitarget anti-Alzheimer agents are the focus of very intensive research. Through a comprehensive bibliometric analysis of the publications in the period 1990-2020, we have identified trends and potential gaps that might guide future directions. We found that: (i) the number of publications boomed by 2011 and continued ascending in 2020; (ii) the linked-pharmacophore strategy was preferred over design approaches based on fusing or merging pharmacophores or privileged structures; (iii) a significant number of in vivo studies, mainly using the scopolamine-induced amnesia mouse model, have been performed, especially since 2017; (iv) China, Italy and Spain are the countries with the largest total number of publications on this topic, whereas Portugal, Spain and Italy are the countries in whose scientific communities this topic has generated greatest interest; (v) acetylcholinesterase, β-amyloid aggregation, oxidative stress, butyrylcholinesterase, and biometal chelation and the binary combinations thereof have been the most commonly pursued, while combinations based on other key targets, such as tau aggregation, glycogen synthase kinase-3β, NMDA receptors, and more than 70 other targets have been only marginally considered. These results might allow us to spot new design opportunities based on innovative target combinations to expand and diversify the repertoire of multitarget drug candidates and increase the likelihood of finding effective therapies for this devastating disease.

Effects of exercise on fitness in adults with intellectual disability: a protocol of an overview of systematic reviews

INTRODUCTION

Adults with intellectual disability (ID) have lower physical fitness levels than their peers without disabilities, representing a risk to their health since physical activity and cardiorespiratory fitness are directly related to better health and quality of life. Therefore, it is essential to determine the effects that exercise can have on them, as adults with ID present high comorbidities and lower life expectancy, altogether with lower rates of physical activity. The current overview of systematic reviews aims to provide an outline of the exercise benefits in health-related and skill-related fitness in adults with ID.

METHODS AND ANALYSIS

Research will be conducted in PubMed, CENTRAL, EMBASE, PEDro, SPORTDiscus and CINAHL. The search terms will be categorised through population (eg, adult, ID); intervention (eg, exercise, physical activity) and outcomes (eg, cardiorespiratory fitness, body composition, muscular strength, muscular endurance, flexibility, balance, power, speed, agility, coordination, mobility and reaction time). Each database will be searched from their earliest available record up to 30 September 2021.Inclusion criteria will be: systematic reviews including at least one RCT that compare exercise interventions with a control group or another type of intervention; measure of fitness using objectives methods; inclusion of adults with ID (≥18 years old), and published in any language, with at least their abstract in English, Spanish, French and/or Portuguese.

ETHICS AND DISSEMINATION

To our knowledge, our overview will be the first of its kind to address the topic in people with ID. The results could be used to determine which fitness components can be improved by exercise and to provide a valuable tool to develop comprehensive exercise programmes specific to people with ID. Ethical approval is not required. The knowledge generated will be disseminated electronically and in print and presented at conferences.

PROSPERO REGISTRATION NUMBER

CRD42021237580.

PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans

Adaptive challenges that humans faced as they expanded across the globe left specific molecular footprints that can be decoded in our today's genomes. Different sets of metrics are used to identify genomic regions that have undergone selection. However, there are fewer methods capable of pinpointing the allele ultimately responsible for this selection. Here, we present PopHumanVar, an interactive online application that is designed to facilitate the exploration and thorough analysis of candidate genomic regions by integrating both functional and population genomics data currently available. PopHumanVar generates useful summary reports of prioritized variants that are putatively causal of recent selective sweeps. It compiles data and graphically represents different layers of information, including natural selection statistics, as well as functional annotations and genealogical estimations of variant age, for biallelic single nucleotide variants (SNVs) of the 1000 Genomes Project phase 3. Specifically, PopHumanVar amasses SNV-based information from GEVA, SnpEFF, GWAS Catalog, ClinVar, RegulomeDB and DisGeNET databases, as well as accurate estimations of iHS, nSL and iSAFE statistics. Notably, PopHumanVar can successfully identify known causal variants of frequently reported candidate selection regions, including EDAR in East-Asians, ACKR1 (DARC) in Africans and LCT/MCM6 in Europeans. PopHumanVar is open and freely available at https://pophumanvar.uab.cat.

Heat-Up Colloidal Synthesis of Shape-Controlled Cu-Se-S Nanostructures-Role of Precursor and Surfactant Reactivity and Performance in N2 Electroreduction

Copper selenide-sulfide nanostructures were synthesized using metal-organic chemical routes in the presence of Cu- and Se-precursors as well as S-containing compounds. Our goal was first to examine if the initial Cu/Se 1:1 molar proportion in the starting reagents would always lead to equiatomic composition in the final product, depending on other synthesis parameters which affect the reagents reactivity. Such reaction conditions were the types of precursors, surfactants and other reagents, as well as the synthesis temperature. The use of 'hot-injection' processes was avoided, focusing on 'non-injection' ones; that is, only heat-up protocols were employed, which have the advantage of simple operation and scalability. All reagents were mixed at room temperature followed by further heating to a selected high temperature. It was found that for samples with particles of bigger size and anisotropic shape the CuSe composition was favored, whereas particles with smaller size and spherical shape possessed a Cu2-xSe phase, especially when no sulfur was present. Apart from elemental Se, Al2Se3 was used as an efficient selenium source for the first time for the acquisition of copper selenide nanostructures. The use of dodecanethiol in the presence of trioctylphosphine and elemental Se promoted the incorporation of sulfur in the materials crystal lattice, leading to Cu-Se-S compositions. A variety of techniques were used to characterize the formed nanomaterials such as XRD, TEM, HRTEM, STEM-EDX, AFM and UV-Vis-NIR. Promising results, especially for thin anisotropic nanoplates for use as electrocatalysts in nitrogen reduction reaction (NRR), were obtained.

New-Generation Ligand Design for the Gold-Catalyzed Asymmetric Activation of Alkynes

Gold(I) catalysts are ideal for the activation of alkynes under very mild conditions. However, unlike allenes or alkenes, the triple bond of alkynes cannot be prochiral. In addition, the linear coordination displayed by gold(I) complexes places the chiral ligand far away from the substrate resulting in an inefficient transfer of chiral information. This poses a significant challenge for the achievement of high enantiocontrol in gold(I)-catalyzed reactions of alkynes. Although considerable progress on enantioselective gold(I)-catalyzed transformations has recently been achieved, the asymmetric activation of non-prochiral alkyne-containing small molecules still represents a great challenge. Herein we summarize recent advances in intra- and intermolecular enantioselective gold(I)-catalyzed reactions involving alkynes, discussing new chiral ligand designs that lie at the basis of these developments. We also focus on the mode of action of these catalysts, their possible limitations towards a next-generation of more efficient ligand designs. Finally, square planar chiral gold(III) complexes, which offer an alternative to chiral gold(I) complexes, are also discussed.

Light signals generated by vegetation shade facilitate acclimation to low light in shade-avoider plants

When growing in search for light, plants can experience continuous or occasional shading by other plants. Plant proximity causes a decrease in the ratio of R to far-red light (low R:FR) due to the preferential absorbance of R light and reflection of FR light by photosynthetic tissues of neighboring plants. This signal is often perceived before actual shading causes a reduction in photosynthetically active radiation (low PAR). Here, we investigated how several Brassicaceae species from different habitats respond to low R:FR and low PAR in terms of elongation, photosynthesis, and photoacclimation. Shade-tolerant plants such as hairy bittercress (Cardamine hirsuta) displayed a good adaptation to low PAR but a poor or null response to low R:FR exposure. In contrast, shade-avoider species, such as Arabidopsis (Arabidopsis thaliana), showed a weak photosynthetic performance under low PAR but they strongly elongated when exposed to low R:FR. These responses could be genetically uncoupled. Most interestingly, exposure to low R:FR of shade-avoider (but not shade-tolerant) plants improved their photoacclimation to low PAR by triggering changes in photosynthesis-related gene expression, pigment accumulation, and chloroplast ultrastructure. These results indicate that low R:FR signaling unleashes molecular, metabolic, and developmental responses that allow shade-avoider plants (including most crops) to adjust their photosynthetic capacity in anticipation of eventual shading by nearby plants.

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

Metabolomics and proteomics, like other omics domains, usually face a data mining challenge in providing an understandable output to advance in biomarker discovery and precision medicine. Often, statistical analysis is one of the most difficult challenges and it is critical in the subsequent biological interpretation of the results. Because of this, combined with the computational programming skills needed for this type of analysis, several bioinformatic tools aimed at simplifying metabolomics and proteomics data analysis have emerged. However, sometimes the analysis is still limited to a few hidebound statistical methods and to data sets with limited flexibility. POMAShiny is a web-based tool that provides a structured, flexible and user-friendly workflow for the visualization, exploration and statistical analysis of metabolomics and proteomics data. This tool integrates several statistical methods, some of them widely used in other types of omics, and it is based on the POMA R/Bioconductor package, which increases the reproducibility and flexibility of analyses outside the web environment. POMAShiny and POMA are both freely available at https://github.com/nutrimetabolomics/POMAShiny and https://github.com/nutrimetabolomics/POMA, respectively.

Metabolomics and proteomics are two growing areas in human health and personalized medicine fields. Often, one of the main applications of metabolomics and proteomics is the discovery of novel biomarkers and new therapeutic targets in these areas. However, these data are extremely complex and hard to analyse, since they have a large number of features, several missing values, and often important clinical variables to consider in the analyses. Therefore, powerful and versatile tools are needed to provide efficient methods for data visualization and exploration, as well as a wide range of robust statistical methods to meet all data and users requirements. Although powerful tools do exist for the analysis of these data, many of them are still limiting the analyses in terms of visualization and statistical analysis. To address this limitation and complement the existing tools, we have developed a web-based application, named POMAShiny, for the data analysis of metabolomics and proteomics. This novel and versatile tool offers a wholly interactive and easy-to-use environment for the analysis of these data, including numerous methods for preprocessing, data visualization and statistical analysis. The POMAShiny open-source tool is extremely flexible and portable, as it can be installed locally and freely accessed online at https://webapps.nutrimetabolomics.com/POMAShiny.

An ensemble learning approach for modeling the systems biology of drug-induced injury

BACKGROUND

Drug-induced liver injury (DILI) is an adverse reaction caused by the intake of drugs of common use that produces liver damage. The impact of DILI is estimated to affect around 20 in 100,000 inhabitants worldwide each year. Despite being one of the main causes of liver failure, the pathophysiology and mechanisms of DILI are poorly understood. In the present study, we developed an ensemble learning approach based on different features (CMap gene expression, chemical structures, drug targets) to predict drugs that might cause DILI and gain a better understanding of the mechanisms linked to the adverse reaction.

RESULTS

We searched for gene signatures in CMap gene expression data by using two approaches: phenotype-gene associations data from DisGeNET, and a non-parametric test comparing gene expression of DILI-Concern and No-DILI-Concern drugs (as per DILIrank definitions). The average accuracy of the classifiers in both approaches was 69%. We used chemical structures as features, obtaining an accuracy of 65%. The combination of both types of features produced an accuracy around 63%, but improved the independent hold-out test up to 67%. The use of drug-target associations as feature obtained the best accuracy (70%) in the independent hold-out test.

CONCLUSIONS

When using CMap gene expression data, searching for a specific gene signature among the landmark genes improves the quality of the classifiers, but it is still limited by the intrinsic noise of the dataset. When using chemical structures as a feature, the structural diversity of the known DILI-causing drugs hampers the prediction, which is a similar problem as for the use of gene expression information. The combination of both features did not improve the quality of the classifiers but increased the robustness as shown on independent hold-out tests. The use of drug-target associations as feature improved the prediction, specially the specificity, and the results were comparable to previous research studies.

A multiscale model of complex endothelial cell dynamics in early angiogenesis

We introduce a hybrid two-dimensional multiscale model of angiogenesis, the process by which endothelial cells (ECs) migrate from a pre-existing vascular bed in response to local environmental cues and cell-cell interactions, to create a new vascular network. Recent experimental studies have highlighted a central role of cell rearrangements in the formation of angiogenic networks. Our model accounts for this phenomenon via the heterogeneous response of ECs to their microenvironment. These cell rearrangements, in turn, dynamically remodel the local environment. The model reproduces characteristic features of angiogenic sprouting that include branching, chemotactic sensitivity, the brush border effect, and cell mixing. These properties, rather than being hardwired into the model, emerge naturally from the gene expression patterns of individual cells. After calibrating and validating our model against experimental data, we use it to predict how the structure of the vascular network changes as the baseline gene expression levels of the VEGF-Delta-Notch pathway, and the composition of the extracellular environment, vary. In order to investigate the impact of cell rearrangements on the vascular network structure, we introduce the mixing measure, a scalar metric that quantifies cell mixing as the vascular network grows. We calculate the mixing measure for the simulated vascular networks generated by ECs of different lineages (wild type cells and mutant cells with impaired expression of a specific receptor). Our results show that the time evolution of the mixing measure is directly correlated to the generic features of the vascular branching pattern, thus, supporting the hypothesis that cell rearrangements play an essential role in sprouting angiogenesis. Furthermore, we predict that lower cell rearrangement leads to an imbalance between branching and sprout elongation. Since the computation of this statistic requires only individual cell trajectories, it can be computed for networks generated in biological experiments, making it a potential biomarker for pathological angiogenesis.

Angiogenesis, the process by which new blood vessels are formed by sprouting from the pre-existing vascular bed, plays a key role in both physiological and pathological processes, including tumour growth. The structure of a growing vascular network is determined by the coordinated behaviour of endothelial cells in response to various signalling cues. Recent experimental studies have highlighted the importance of cell rearrangements as a driver for sprout elongation. However, the functional role of this phenomenon remains unclear. We formulate a new multiscale model of angiogenesis which, by accounting explicitly for the complex dynamics of endothelial cells within growing angiogenic sprouts, is able to reproduce generic features of angiogenic structures (branching, chemotactic sensitivity, cell mixing, etc.) as emergent properties of its dynamics. We validate our model against experimental data and then use it to quantify the phenomenon of cell mixing in vascular networks generated by endothelial cells of different lineages. Our results show that there is a direct correlation between the time evolution of cell mixing in a growing vascular network and its branching structure, thus paving the way for understanding the functional role of cell rearrangements in angiogenesis.

Polish is quantitatively different on quartzite flakes used on different worked materials

Metrology has been successfully used in the last decade to quantify use-wear on stone tools. Such techniques have been mostly applied to fine-grained rocks (chert), while studies on coarse-grained raw materials have been relatively infrequent. In this study, confocal microscopy was employed to investigate polished surfaces on a coarse-grained lithology, quartzite. Wear originating from contact with five different worked materials were classified in a data-driven approach using machine learning. Two different classifiers, a decision tree and a support-vector machine, were used to assign the different textures to a worked material based on a selected number of parameters (Mean density of furrows, Mean depth of furrows, Core material volume-Vmc). The method proved successful, presenting high scores for bone and hide (100%). The obtained classification rates are satisfactory for the other worked materials, with the only exception of cane, which shows overlaps with other materials. Although the results presented here are preliminary, they can be used to develop future studies on quartzite including enlarged sample sizes.

3D tracking of extracellular vesicles by holographic fluorescence imaging

Fluorescence microscopy is the method of choice in biology for its molecular specificity and super-resolution capabilities. However, it is limited to a narrow z range around one observation plane. Here, we report an imaging approach that recovers the full electric field of fluorescent light with single-molecule sensitivity. We expand the principle of digital holography to fast fluorescent detection by eliminating the need for phase cycling and enable three-dimensional (3D) tracking of individual nanoparticles with an in-plane resolution of 15 nm and a z-range of 8 mm. As a proof-of-concept biological application, we image the 3D motion of extracellular vesicles (EVs) inside live cells. At short time scales (<4 s), we resolve near-isotropic 3D diffusion and directional transport. For longer lag times, we observe a transition toward anisotropic motion with the EVs being transported over long distances in the axial plane while being confined in the horizontal dimension.

Cerebellar Astrocyte Transduction as Gene Therapy for Megalencephalic Leukoencephalopathy

Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare genetic disorder belonging to the group of vacuolating leukodystrophies. It is characterized by megalencephaly, loss of motor functions, epilepsy, and mild mental decline. In brain biopsies of MLC patients, vacuoles were observed in myelin and in astrocytes surrounding blood vessels. There is no therapy for MLC patients, only supportive treatment. We show here a preclinical gene therapy approach for MLC using the Mlc1 knock-out mouse. An adeno-associated virus coding for human MLC1 under the control of the glial fibrillary acidic protein promoter was injected in the cerebellar subarachnoid space of Mlc1 knock-out and wild-type animals at 2 months of age, before the onset of the disease, as a preventive approach. We also tested a therapeutic strategy by injecting the animals at 5 months, once the histopathological abnormalities are starting, or at 15 months, when they have progressed to a more severe pathology. MLC1 expression in the cerebellum restored the adhesion molecule GlialCAM and the chloride channel ClC-2 localization in Bergmann glia, which both are mislocalized in Mlc1 knock-out model. More importantly, myelin vacuolation was extremely reduced in treated mice at all ages and correlated with the amount of expressed MLC1 in Bergmann glia, indicating not only the preventive potential of this strategy but also its therapeutic capacity. In summary, here we provide the first therapeutic approach for patients affected with MLC. This work may have also implications to treat other diseases affecting motor function such as ataxias.

Recommendations for standardizing nomenclature for dietary (poly)phenol catabolites

There is a lack of focus on the protective health effects of phytochemicals in dietary guidelines. Although a number of chemical libraries and databases contain dietary phytochemicals belonging to the plant metabolome, they are not entirely relevant to human health because many constituents are extensively metabolized within the body following ingestion. This is especially apparent for the highly abundant dietary (poly)phenols, for which the situation is compounded by confusion regarding their bioavailability and metabolism, partially because of the variety of nomenclatures and trivial names used to describe compounds arising from microbial catabolism in the gastrointestinal tract. This confusion, which is perpetuated in online chemical/metabolite databases, will hinder future discovery of bioactivities and affect the establishment of future dietary guidelines if steps are not taken to overcome these issues. In order to resolve this situation, a nomenclature system for phenolic catabolites and their human phase II metabolites is proposed in this article and the basis of its format outlined. Previous names used in the literature are cited along with the recommended nomenclature, International Union of Pure and Applied Chemistry terminology, and, where appropriate, Chemical Abstracts Service numbers, InChIKey, and accurate mass.

Hemopexin and α1-microglobulin heme scavengers with differential involvement in preeclampsia and fetal growth restriction

Hemopexin and α1-microglobulin act as scavengers to eliminate free heme-groups responsible for hemoglobin-induced oxidative stress. The present study evaluated maternal and fetal plasma concentrations of these scavengers in the different phenotypes of placenta-mediated disorders. Singleton pregnancies with normotensive fetal growth restriction [FGR] (n = 47), preeclampsia without FGR (n = 45) and preeclampsia with FGR (n = 51) were included prospectively as well as uncomplicated pregnancies (n = 49). Samples were collected at delivery and ELISA analysis was applied to measure the hemopexin and α1-microglobulin concentrations. In maternal blood in preeclampsia with and without FGR, hemopexin was significantly lower (p = 0.003 and p<0.001, respectively) and α1-microglobulin was significantly higher (p<0.001 in both) whereas no difference existed in normotensive FGR mothers compared to controls. In contrast, in fetal blood in growth restricted fetuses with and without preeclampsia, both hemopexin and α1-microglobulin were significantly lower (p<0.001 and p = 0.001 for hemopexin, p = 0.016 and p = 0.013 for α1-microglobulin, respectively) with no difference in fetuses from preeclampsia without FGR in comparison to controls. Thus, hemopexin and α1-microglobulin present significantly altered concentrations in maternal blood in the maternal disease -preeclampsia- and in cord blood in the fetal disease -FGR-, which supports their differential role in placenta-mediated disorders in accordance with the clinical presentation of these disorders.

Exploring the use of leucine zippers for the generation of a new class of inclusion bodies for pharma and biotechnological applications

BACKGROUND

Inclusion bodies (IBs) are biologically active protein aggregates forming natural nanoparticles with a high stability and a slow-release behavior. Because of their nature, IBs have been explored to be used as biocatalysts, in tissue engineering, and also for human and animal therapies. To improve the production and biological efficiency of this nanomaterial, a wide range of aggregation tags have been evaluated. However, so far, the presence in the IBs of bacterial impurities such as lipids and other proteins coexisting with the recombinant product has been poorly studied. These impurities could strongly limit the potential of IB applications, being necessary to control the composition of these bacterial nanoparticles. Thus, we have explored the use of leucine zippers as alternative tags to promote not only aggregation but also the generation of a new type of IB-like protein nanoparticles with improved physicochemical properties.

RESULTS

Three different protein constructs, named GFP, J-GFP-F and J/F-GFP were engineered. J-GFP-F corresponded to a GFP flanked by two leucine zippers (Jun and Fos); J/F-GFP was formed coexpressing a GFP fused to Jun leucine zipper (J-GFP) and a GFP fused to a Fos leucine zipper (F-GFP); and, finally, GFP was used as a control without any tag. All of them were expressed in Escherichia coli and formed IBs, where the aggregation tendency was especially high for J/F-GFP. Moreover, those IBs formed by J-GFP-F and J/F-GFP constructs were smaller, rougher, and more amorphous than GFP ones, increasing surface/mass ratio and, therefore, surface for protein release. Although the lipid and carbohydrate content were not reduced with the addition of leucine zippers, interesting differences were observed in the protein specific activity and conformation with the addition of Jun and Fos. Moreover, J-GFP-F and J/F-GFP nanoparticles were purer than GFP IBs in terms of protein content.

CONCLUSIONS

This study proved that the use of leucine zippers strategy allows the formation of IBs with an increased aggregation ratio and protein purity, as we observed with the J/F-GFP approach, and the formation of IBs with a higher specific activity, in the case of J-GFP-F IBs. Thus, overall, the use of leucine zippers seems to be a good system for the production of IBs with more promising characteristics useful for pharma or biotech applications.

Prevalence and pattern of cardiovascular magnetic resonance late gadolinium enhancement in highly trained endurance athletes

BACKGROUND

Intensive endurance exercise may induce a broad spectrum of right ventricular (RV) adaptation/remodelling patterns. Late gadolinium enhancement (LGE) has also been described in cardiovascular magnetic resonance (CMR) of some endurance athletes and its clinical meaning remains controversial. Our aim was to characterize the features of contrast CMR and the observed patterns of the LGE distribution in a cohort of highly trained endurance athletes.

METHODS

Ninety-three highly trained endurance athletes (> 12 h training/week at least during the last 5 years; 36 ± 6 years old; 53% male) and 72 age and gender-matched controls underwent a resting contrast CMR. In a subgroup of 28 athletes, T1 mapping was also performed.

RESULTS

High endurance training load was associated with larger bi-ventricular and bi-atrial sizes and a slight reduction of biventricular ejection fraction, as compared to controls in both genders (p < 0.05). Focal LGE was significantly more prevalent in athletes than in healthy subjects (37.6% vs 2.8%; p < 0.001), with a typical pattern in the RV insertion points. In T1 mapping, those athletes who had focal LGE had higher extracellular volume (ECV) at the remote myocardium than those without (27 ± 2.2% vs 25.2 ± 2.1%; p < 0.05).

CONCLUSIONS

Highly trained endurance athletes showed a ten-fold increase in the prevalence of focal LGE as compared to control subjects, always confined to the hinge points. Additionally, those athletes with focal LGE demonstrated globally higher myocardial ECV values. This matrix remodelling and potential presence of myocardial fibrosis may be another feature of the athlete's heart, of which the clinical and prognostic significance remains to be determined.

The DNA methylation landscape of hematological malignancies: an update

The rapid advances in high-throughput sequencing technologies have made it more evident that epigenetic modifications orchestrate a plethora of complex biological processes. During the last decade, we have gained significant knowledge about a wide range of epigenetic changes that crucially contribute to some of the most aggressive forms of leukemia, lymphoma, and myelodysplastic syndromes. DNA methylation is a key epigenetic player in the abnormal initiation, development, and progression of these malignancies, often acting in synergy with other epigenetic alterations. It also contributes to the acquisition of drug resistance. In this review, we summarize the role of DNA methylation in hematological malignancies described in the current literature. We discuss in detail the dual role of DNA methylation in normal and aberrant hematopoiesis, as well as the involvement of this type of epigenetic change in other aspects of the disease. Finally, we present a comprehensive overview of the main clinical implications, including a discussion of the therapeutic strategies that regulate or reverse aberrant DNA methylation patterns in hematological malignancies, including their combination with (chemo)immunotherapy.

A multilevel analytical framework for studying cultural evolution in prehistoric hunter-gatherer societies

Over the past decade, a major debate has taken place on the underpinnings of cultural changes in human societies. A growing array of evidence in behavioural and evolutionary biology has revealed that social connectivity among populations and within them affects, and is affected by, culture. Yet the interplay between prehistoric hunter-gatherer social structure and cultural transmission has typically been overlooked. Interestingly, the archaeological record contains large data sets, allowing us to track cultural changes over thousands of years: they thus offer a unique opportunity to shed light on long-term cultural transmission processes. In this review, we demonstrate how well-developed methods for social structure analysis can increase our understanding of the selective pressures underlying cumulative culture. We propose a multilevel analytical framework that considers finer aspects of the complex social structure in which regional groups of prehistoric hunter-gatherers were embedded. We put forward predictions of cultural transmission based on local- and global-level network metrics of small-scale societies and their potential effects on cumulative culture. By bridging the gaps between network science, palaeodemography and cultural evolution, we draw attention to the use of the archaeological record to depict patterns of social interactions and transmission variability. We argue that this new framework will contribute to improving our understanding of social interaction patterns, as well as the contexts in which cultural changes occur. Ultimately, this may provide insights into the evolution of human behaviour.

Involvement of the 14-3-3 Gene Family in Autism Spectrum Disorder and Schizophrenia: Genetics, Transcriptomics and Functional Analyses

The 14-3-3 protein family are molecular chaperones involved in several biological functions and neurological diseases. We previously pinpointed YWHAZ (encoding 14-3-3ζ) as a candidate gene for autism spectrum disorder (ASD) through a whole-exome sequencing study, which identified a frameshift variant within the gene (c.659-660insT, p.L220Ffs*18). Here, we explored the contribution of the seven human 14-3-3 family members in ASD and other psychiatric disorders by investigating the: (i) functional impact of the 14-3-3ζ mutation p.L220Ffs*18 by assessing solubility, target binding and dimerization; (ii) contribution of common risk variants in 14-3-3 genes to ASD and additional psychiatric disorders; (iii) burden of rare variants in ASD and schizophrenia; and iv) 14-3-3 gene expression using ASD and schizophrenia transcriptomic data. We found that the mutant 14-3-3ζ protein had decreased solubility and lost its ability to form heterodimers and bind to its target tyrosine hydroxylase. Gene-based analyses using publicly available datasets revealed that common variants in YWHAE contribute to schizophrenia (p = 6.6 × 10-7), whereas ultra-rare variants were found enriched in ASD across the 14-3-3 genes (p = 0.017) and in schizophrenia for YWHAZ (meta-p = 0.017). Furthermore, expression of 14-3-3 genes was altered in post-mortem brains of ASD and schizophrenia patients. Our study supports a role for the 14-3-3 family in ASD and schizophrenia.

A new generation of recombinant polypeptides combines multiple protein domains for effective antimicrobial activity

BACKGROUND

Although most of antimicrobial peptides (AMPs), being relatively short, are produced by chemical synthesis, several AMPs have been produced using recombinant technology. However, AMPs could be cytotoxic to the producer cell, and if small they can be easily degraded. The objective of this study was to produce a multidomain antimicrobial protein based on recombinant protein nanoclusters to increase the yield, stability and effectivity.

RESULTS

A single antimicrobial polypeptide JAMF1 that combines three functional domains based on human α-defensin-5, human XII-A secreted phospholipase A2 (sPLA2), and a gelsolin-based bacterial-binding domain along with two aggregation-seeding domains based on leucine zippers was successfully produced with no toxic effects for the producer cell and mainly in a nanocluster structure. Both, the nanocluster and solubilized format of the protein showed a clear antimicrobial effect against a broad spectrum of Gram-negative and Gram-positive bacteria, including multi-resistant strains, with an optimal concentration between 1 and 10 µM.

CONCLUSIONS

Our findings demonstrated that multidomain antimicrobial proteins forming nanoclusters can be efficiently produced in recombinant bacteria, being a novel and valuable strategy to create a versatile, highly stable and easily editable multidomain constructs with a broad-spectrum antimicrobial activity in both soluble and nanostructured format.

Infrared electric field sampled frequency comb spectroscopy

Probing matter with light in the mid-infrared provides unique insight into molecular composition, structure, and function with high sensitivity. However, laser spectroscopy in this spectral region lacks the broadband or tunable light sources and efficient detectors available in the visible or near-infrared. We overcome these challenges with an approach that unites a compact source of phase-stable, single-cycle, mid-infrared pulses with room temperature electric field-resolved detection at video rates. The ultrashort pulses correspond to laser frequency combs that span 3 to 27 μm (370 to 3333 cm-1), and are measured with dynamic range of >106 and spectral resolution as high as 0.003 cm-1. We highlight the brightness and coherence of our apparatus with gas-, liquid-, and solid-phase spectroscopy that extends over spectral bandwidths comparable to thermal or infrared synchrotron sources. This unique combination enables powerful avenues for rapid detection of biological, chemical, and physical properties of matter with molecular specificity.

Functional high-throughput screening reveals miR-323a-5p and miR-342-5p as new tumor-suppressive microRNA for neuroblastoma

Current therapies for most non-infectious diseases are directed at or affect functionality of the human translated genome, barely 2% of all genetic information. By contrast, the therapeutic potential of targeting the transcriptome, ~ 70% of the genome, remains largely unexplored. RNA therapeutics is an emerging field that widens the range of druggable targets and includes elements such as microRNA. Here, we sought to screen for microRNA with tumor-suppressive functions in neuroblastoma, an aggressive pediatric tumor of the sympathetic nervous system that requires the development of new therapies. We found miR-323a-5p and miR-342-5p to be capable of reducing cell proliferation in multiple neuroblastoma cell lines in vitro and in vivo, thereby providing a proof of concept for miRNA-based therapies for neuroblastoma. Furthermore, the combined inhibition of the direct identified targets such as CCND1, CHAF1A, INCENP and BCL-XL could reveal new vulnerabilities of high-risk neuroblastoma.

Identification and validation of circulating miRNAs as endogenous controls in obstructive sleep apnea

microRNAs (miRNAs) are non-coding RNAs highly relevant as biomarkers for disease. A seminal study that explored the role of miRNAs in obstructive sleep apnea syndrome (OSA) demonstrated their usefulness in clinical management. Nevertheless, the miRNAs that may act as endogenous controls (ECs) have not yet been established. The identification of ECs would contribute to the standardization of these biomarkers in OSA. The objective of the study is to identify miRNAs that can be used as ECs in OSA. We evaluated 100 patients divided into two different cohorts: a learning cohort of 10 non-OSA and 30 OSA patients, and a validation cohort (20 non-OSA and 40 OSA patients). In the learning cohort, a profile of 188 miRNAs was determined in plasma by TaqMan Low Density Array. The best EC candidates were identified by mean center+SD normalization and concordance correlation restricted normalization. The results were validated using NormFinder and geNorm to assess the stability of those ECs. Eight miRNAs were identified as EC candidates. The combination miRNA-106a/miRNA-186 was identified as the most stable among all candidates. We identified a set of ECs to be used in the determination of circulating miRNA in OSA that may contribute to the homogeneity of results.

Transcriptomic Analysis of Planarians under Simulated Microgravity or 8 g Demonstrates That Alteration of Gravity Induces Genomic and Cellular Alterations That Could Facilitate Tumoral Transformation

The possibility of humans to live outside of Earth on another planet has attracted the attention of numerous scientists around the world. One of the greatest difficulties is that humans cannot live in an extra-Earth environment without proper equipment. In addition, the consequences of chronic gravity alterations in human body are not known. Here, we used planarians as a model system to test how gravity fluctuations could affect complex organisms. Planarians are an ideal system, since they can regenerate any missing part and they are continuously renewing their tissues. We performed a transcriptomic analysis of animals submitted to simulated microgravity (Random Positioning Machine, RPM) (s-µg) and hypergravity (8 g), and we observed that the transcriptional levels of several genes are affected. Surprisingly, we found the major differences in the s-µg group. The results obtained in the transcriptomic analysis were validated, demonstrating that our transcriptomic data is reliable. We also found that, in a sensitive environment, as under Hippo signaling silencing, gravity fluctuations potentiate the increase in cell proliferation. Our data revealed that changes in gravity severely affect genetic transcription and that these alterations potentiate molecular disorders that could promote the development of multiple diseases such as cancer.

Collagen and fibronectin surface modification of nanoporous anodic alumina and macroporous silicon for endothelial cell cultures

BACKGROUND

The ability to direct the cellular response by means of biomaterial surface topography is important for biomedical applications. Substrate surface topography has been shown to be an effective cue for the regulation of cellular response. Here, the response of human aortic endothelial cells to nanoporous anodic alumina and macroporous silicon with collagen and fibronectin functionalization has been studied.

METHODS

Confocal microscopy and scanning electron microscopy were employed to analyse the effects of the material and the porosity on the adhesion, morphology, and proliferation of the cells. Cell spreading and filopodia formation on macro- and nanoporous material was characterized by atomic force microscopy. We have also studied the influence of the protein on the adhesion.

RESULTS

It was obtained the best results when the material is functionalized with fibronectin, regarding cells adhesion, morphology, and proliferation.

CONCLUSION

These results permit to obtain chemical modified 3D structures for several biotechnology applications such as tissue engineering, organ-on-chip or regenerative medicine.

Open problems, questions and challenges in finite- dimensional integrable systems

The paper surveys open problems and questions related to different aspects of integrable systems with finitely many degrees of freedom. Many of the open problems were suggested by the participants of the conference 'Finite-dimensional Integrable Systems, FDIS 2017' held at CRM, Barcelona in July 2017.This article is part of the theme issue 'Finite dimensional integrable systems: new trends and methods'.

Singular fibres of the Gelfand-Cetlin system on 𝔲(n)

In this paper, we show that every singular fibre of the Gelfand-Cetlin system on co-adjoint orbits of unitary groups is a smooth isotropic submanifold which is diffeomorphic to a two-stage quotient of a compact Lie group by free actions of two other compact Lie groups. In many cases, these singular fibres can be shown to be homogeneous spaces or even diffeomorphic to compact Lie groups. We also give a combinatorial formula for computing the dimensions of all singular fibres, and give a detailed description of these singular fibres in many cases, including the so-called (multi-)diamond singularities. These (multi-)diamond singular fibres are degenerate for the Gelfand-Cetlin system, but they are Lagrangian submanifolds diffeomorphic to direct products of special unitary groups and tori. Our methods of study are based on different ideas involving complex ellipsoids, Lie groupoids and also general ideas coming from the theory of singularities of integrable Hamiltonian systems.This article is part of the theme issue 'Finite dimensional integrable systems: new trends and methods'.

CXCR7 expression in diffuse large B-cell lymphoma identifies a subgroup of CXCR4+ patients with good prognosis

The CXCR4/CXCL12 axis has been extensively associated with different types of cancer correlating with higher aggressiveness and metastasis. In diffuse large B-cell lymphoma (DLBCL), the expression of the chemokine receptor CXCR4 is involved in the dissemination of malignant B cells and is a marker of poor prognosis. CXCR7 is a chemokine receptor that binds to the same ligand as CXCR4 and regulates de CXCR4-CXCL12 axis. These findings together with the report of CXCR7 prognostic value in several tumor types, led us to evaluate the expression of CXCR7 in diffuse large B-cell lymphoma biopsies. Here, we describe that CXCR7 receptor is an independent prognostic factor that associates with good clinical outcome. Moreover, the expression of CXCR7 associates with increased survival in CXCR4+ but not in CXCR4- DLBCL patients. Thus, the combined immunohistochemical evaluation of both CXCR7 and CXCR4 expression in DLBCL biopsies may improve their prognostic value as single markers. Finally, we show that CXCR7 overexpression in vitro is able to diminish DLBCL cell survival and increase their sensitivity to antitumor drugs. Hence, further studies on the CXCR7 receptor may establish its role in DLBCL and the molecular mechanisms that modulate CXCR4 activity.

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples

BACKGROUND

Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts.

RESULTS

In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions.

CONCLUSIONS

MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica .