Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion.

Background: The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion. Methods: The analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses. Results: Our data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2. Conclusions: These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.

Comparison of Genomic Profiling Data with Clinical Parameters: Implications for Breast Cancer Prognosis.

Precise prognosis is crucial for selection of adjuvant therapy in breast cancer. Molecular subtyping is increasingly used to complement immunohistochemical and pathological classification and to predict recurrence. This study compares both outcomes in a clinical setting. Molecular subtyping (MammaPrint®, TargetPrint®, and BluePrint®) and pathological classification data were compared in a cohort of 143 breast cancer patients. High risk clinical factors were defined by a value of the proliferation factor Ki67 equal or higher than 14% and/or high histological grade. The results from molecular classification were considered as reference. Core needle biopsies were found to be comparable to surgery samples for molecular classification. Discrepancies were found between molecular and pathological subtyping of the samples, including misclassification of HER2-positive tumors and the identification of a significant percentage of genomic high risk T1N0 tumors. In addition, 20% of clinical low-risk tumors showed genomic high risk, while clinical high-risk samples included 42% of cases with genomic low risk. According to pathological subtyping, a considerable number of breast cancer patients would not receive the appropriate systemic therapy. Our findings support the need to determine the molecular subtype of invasive breast tumors to improve breast cancer management.

A Comparative Study between Spanish and British SARS-CoV-2 Variants.

The study of the interaction between the SARS-CoV-2 spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor is key to understanding binding affinity and stability. In the present report, we sought to investigate the differences between two already sequenced genome variants (Spanish and British) of SARS-CoV-2. Methods: In silico model evaluating the homology, identity and similarity in the genome sequence and the structure and alignment of the predictive spike by computational docking methods. Results: The identity results between the Spanish and British variants of the Spike protein were 28.67%. This close correspondence in the results between the Spanish and British SARS-CoV-2 variants shows that they are very similar (99.99%). The alignment obtained results in four deletions. There were 23 nucleotide substitutions also predicted which could affect the functionality of the proteins produced from this sequence. The interaction between the binding receptor domain from the spike protein and the ACE2 receptor produces some of the mutations found and, therefore, the energy of this ligand varies. However, the estimated antigenicity of the British variant is higher than its Spanish counterpart. Conclusions: Our results indicate that minimal mutations could interfere in the infectivity of the virus due to changes in the fitness between host cell recognition and interaction proteins. In particular, the N501Y substitution, situated in the RBD of the spike of the British variant, might be the reason for its extraordinary infective potential.

Spontaneous regression of a thrombosed cerebral arteriovenous malformation in a patient with a prothrombotic state associated with multiple myeloma: A case report and literature review.

BACKGROUND: Cerebral arteriovenous malformations (AVMs) are pathologic communications between veins and arteries of the brain vasculature. Its spontaneous regression is rare, and many factors have been described in the effort to explain this phenomenon, including a hypercoagulable state. CASE DESCRIPTION: We present the case of a spontaneous unruptured AVM regression in a patient where thrombosis of the malformation was found, probably due to a prothrombotic state associated with multiple myeloma (MM). CONCLUSION: We aim to contribute to the study of this rare phenomenon, presenting the relationship between a hypercoagulable state caused by MM and the spontaneous AVM regression that has not been previously reported.

Segmented-Block Poly(ether amide)s Containing Flexible Polydisperse Polyethyleneoxide Sequences and Rigid Aromatic Amide Moieties.

We describe the synthesis and characterization of three novel aromatic diamines containing oxyethylene sequences of different lengths. These diamines were polymerized using the low-temperature solution polycondensation method with isophthaloyl chloride (IPC), terepthaloyl chloride (TPC), [1,1'-biphenyl]-4,4'-dicarbonyl dichloride (BDC), and 4,4'-oxybis(benzoyl chloride) (OBE), obtaining twelve poly(ether amide)s with short segments of polydisperse polyethyleneoxide (PEO) sequences in the polymer backbone. These polymers show reasonably high molecular mass materials (Mw > 12,000), and the relationship between their structure and properties has been carefully studied. Compared with conventional polyamides containing monodisperse PEO sequences, the polydispersity of the PEO segments within the structural units exerts a significant influence on the crystallinity, flexibility, solubility, and the thermal properties of the polymers. For instance, the all-para oriented polyamides (TPCP-A), with an average number of 8.2 ethylenoxide units per structural unit can be transformed conventionally (Tm = 259 °C) in comparison with thermally untransformable polymer with 2 ethylenoxide units (Tm = 425 °C).

ANCORP: Procedimiento para la recuperación de información en sistemas de bibliotecas mediante grafos de conocimiento / ANCORP: Procedure for information retrieval in library systems using knowledge graphs

Las bibliotecas y los centros de documentación carecen de una guía metodológica para transformar sus datos RDF en grafos de conocimiento, lo que impide que puedan aprovechar las facilidades de esta herramienta en la búsqueda y recuperación de información. El artículo propone una metodología para la transformación de datos bibliográficos en grafos de conocimiento. Se presenta ANCORP, a partir del análisis de las técnicas de incrustación, limpieza y chequeo de grafos de conocimiento. Esta metodología se divide en dos partes: la parte 1, dedicada a la construcción del grafo de conocimiento, y la parte 2, dedicada a resolver los procesos de recuperación de información. Con la implementación de la metodología se corroboran saltos cualitativos en la recuperación de información y en la calidad de los datos(AU)

Libraries and documentation centers haven't a methodology guide to transform their RDF data into knowledge graphs, which prevents them from taking advantage of the facilities of this tool in the search and retrieval of information. This methodology was proposed for the transformation of bibliographic data in knowledge graphs. ANCORP was presented from the analysis of the techniques of incrustation, cleaning and checking of knowledge graphs. This methodology was divided into two parts: part I dedicated to the construction of the knowledge graph, and part II dedicated to solving the processes of information retrieval. With the implementation of the methodology, qualitative leaps in the information retrieval and in the quality of the data are corroborated(AU)

Uncovering patterns of freshwater positive interactions using meta-analysis: Identifying the roles of common participants, invasive species and environmental context.

Positive interactions are sensitive to human activities, necessitating synthetic approaches to elucidate broad patterns and predict future changes if these interactions are altered or lost. General understanding of freshwater positive interactions has been far outpaced by knowledge of these important relationships in terrestrial and marine ecosystems. We conducted a global meta-analysis to evaluate the magnitude of positive interactions across freshwater habitats. In 340 studies, we found substantial positive effects, with facilitators increasing beneficiaries by, on average, 81% across all taxa and response variables. Mollusks in particular were commonly studied as both facilitators and beneficiaries. Amphibians were one group benefiting the most from positive interactions, yet few studies investigated amphibians. Invasive facilitators had stronger positive effects on beneficiaries than non-invasive facilitators. We compared positive effects between high- and low-stress conditions and found no difference in the magnitude of benefit in the subset of studies that manipulated stressors. Future areas of research include understudied facilitators and beneficiaries, the stress gradient hypothesis, patterns across space or time and the influence of declining taxa whose elimination would jeopardise fragile positive interaction networks. Freshwater positive interactions occur among a wide range of taxa, influence populations, communities and ecosystem processes and deserve further exploration.

The Evolutionary Significance of RNAi in the Fungal Kingdom.

RNA interference (RNAi) was discovered at the end of last millennium, changing the way scientists understood regulation of gene expression. Within the following two decades, a variety of different RNAi mechanisms were found in eukaryotes, reflecting the evolutive diversity that RNAi entails. The essential silencing mechanism consists of an RNase III enzyme called Dicer that cleaves double-stranded RNA (dsRNA) generating small interfering RNAs (siRNAs), a hallmark of RNAi. These siRNAs are loaded into the RNA-induced silencing complex (RISC) triggering the cleavage of complementary messenger RNAs by the Argonaute protein, the main component of the complex. Consequently, the expression of target genes is silenced. This mechanism has been thoroughly studied in fungi due to their proximity to the animal phylum and the conservation of the RNAi mechanism from lower to higher eukaryotes. However, the role and even the presence of RNAi differ across the fungal kingdom, as it has evolved adapting to the particularities and needs of each species. Fungi have exploited RNAi to regulate a variety of cell activities as different as defense against exogenous and potentially harmful DNA, genome integrity, development, drug tolerance, or virulence. This pathway has offered versatility to fungi through evolution, favoring the enormous diversity this kingdom comprises.

MODIS Sensor Capability to Burned Area Mapping-Assessment of Performance and Improvements Provided by the Latest Standard Products in Boreal Regions.

This paper presents an accuracy assessment of the main global scale Burned Area (BA) products, derived from daily images of the Moderate-Resolution Imaging Spectroradiometer (MODIS) Fire_CCI 5.1 and MCD64A1 C6, as well as the previous versions of both products (Fire_CCI 4.1 and MCD45A1 C5). The exercise was conducted on the boreal region of Alaska during the period 2000-2017. All the BA polygons registered by the Alaska Fire Service were used as reference data. Both new versions doubled the annual BA estimate compared to the previous versions (66% for Fire_CCI 5.1 versus 35% for v4.1, and 63% for MCD64A1 C6 versus 28% for C5), reducing the omission error (OE) by almost one half (39% versus 67% for Fire_CCI and 48% versus 74% for MCD) and slightly increasing the commission error (CE) (7.5% versus 7% for Fire_CCI and 18% versus 7% for MCD). The Fire_CCI 5.1 product (CE = 7.5%, OE = 39%) presented the best results in terms of positional accuracy with respect to MCD64A1 C6 (CE = 18%, OE = 48%). These results suggest that Fire_CCI 5.1 could be suitable for those users who employ BA standard products in geoinformatics analysis techniques for wildfire management, especially in Boreal regions. The Pareto boundary analysis, performed on an annual basis, showed that there is still a potential theoretical capacity to improve the MODIS sensor-based BA algorithms.

Improving the staging of neck injuries using a new index, the Neck Functional Holistic Analysis Score: Clustering approach to determine degrees of impairment.

BACKGROUND: Traumatic cervical spine injuries are amongst the traffic injuries that can cause most harm to a person. Classifying subtypes of clinical presentations has been a method used in other pathologies to diagnose more efficiently and to address the appropriate treatment and the prognosis. The management of patients suffering from cervical injuries could be improved by classifying the severity of the impairment. This will allow clinicians to propose better treatment modalities according to the severity of the injury. MATERIALS AND METHODS: The present study is a retrospective cohort study performed with the clinical data from 772 patients stored at Fisi-(ON) Health Group. All the patients treated for cervical spine injuries are evaluated using the EBI-5® system, which is based on inertial measurement unit (IMU) technology. The normalized range of motion of each patient was incorporated into a single index, the Neck Functional Holistic Analysis Score (NFHAS). RESULTS: Clustering analysis of the patients according to their NFHAS resulted in five groups. The Kruskal-Wallis H test showed that there were statistically relevant differences in the ROM values and NFHAS of the patients depending on the cluster they were assigned to: FE X2(4) = 551.59, p = 0.0005; LB ROM X2(4) = 484.58, p = 0.0005; RT ROM X2(4) = 557.14, p = 0.0005; NFHAS X2(4) = 737.41, p = 0.0005. Effect size with ηp2 for the comparison of groups were: FE = 0.76, LB = 0.68, RT = 0.76 and NFHAS = 0.96. CONCLUSION: The NFHAS is directly correlated to the available ROM of the patient. The NFHAS serves as a good tool for the classification of cervical injury patients. The degree of impairment shown by the cervical injury can now be staged correctly using this new classification.

A Sox2-Sox9 signalling axis maintains human breast luminal progenitor and breast cancer stem cells.

Increased cancer stem cell content during development of resistance to tamoxifen in breast cancer is driven by multiple signals, including Sox2-dependent activation of Wnt signalling. Here, we show that Sox2 increases and estrogen reduces the expression of the transcription factor Sox9. Gain and loss of function assays indicate that Sox9 is implicated in the maintenance of human breast luminal progenitor cells. CRISPR/Cas knockout of Sox9 reduces growth of tamoxifen-resistant breast tumours in vivo. Mechanistically, Sox9 acts downstream of Sox2 to control luminal progenitor cell content and is required for expression of the cancer stem cell marker ALDH1A3 and Wnt signalling activity. Sox9 is elevated in breast cancer patients after endocrine therapy failure. This new regulatory axis highlights the relevance of SOX family transcription factors as potential therapeutic targets in breast cancer.

Easy and inexpensive method for the visual and electronic detection of oxidants in air by using vinylic films with embedded aniline.

Conventional nonconductive vinylic films with dispersed aniline change their color and become conductive in the presence of specific oxidant gases, namely, chlorine and hydrogen peroxide. The color change arises from the polymerization of the aniline to yield the conjugated polymer polyaniline, which at the same time renders the flexible vinylic films conductive. We present a simple and straightforward method using both colorimetric and electrical responses to detect and quantify the presence of oxidants (Cl2 and H2O2) in the air. Using RGB analysis (red, green and blue parameters defining the colors in digital pictures on a computer display) based on different pictures taken with a smartphone of discs extracted from the films and by measuring the UV-vis spectral variation in the presence of different concentrations of Cl2 and H2O2, we obtained limits of detection and quantification between 15 and 200 ppbv for H2O2 and between 37 and 583 ppbv for Cl2. Additionally, the electrical response was measured using a fabricated device to visually detect the electrical conductivity activation of the sensor in the presence of oxidant atmospheres, detecting a rapid decrease in resistivity (three orders of magnitude) when the polymerization of aniline began, changing the film from non-conductive to conductive.

Sensory Polymeric Foams as a Tool for Improving Sensing Performance of Sensory Polymers.

Microcellular sensory polymers prepared from solid sensory polymeric films were tested in an aqueous Hg(II) detection process to analyze their sensory behavior. First, solid acrylic-based polymeric films of 100 µm thickness were obtained via radical copolymerization process. Secondly, dithizone sensoring motifs were anchored in a simple five-step route, obtaining handleable colorimetric sensory films. To create the microporous structure, films were foamed in a ScCO2 batch process, carried out at 350 bar and 60 °C, resulting in homogeneous morphologies with cell sizes around 5 µm. The comparative behavior of the solid and foamed sensory films was tested in the detection of mercury in pure water media at 2.2 pH, resulting in a reduction of the response time (RT) around 25% and limits of detection and quantification (LOD and LOQ) four times lower when using foamed films, due to the increase of the specific surface associated to the microcellular structure.

Hydrocephalus in a patient with an unruptured pial arteriovenous fistula: hydrodynamic considerations, endovascular treatment, and clinical course.

Intracranial pial arteriovenous fistulas, also known as nongalenic fistulas, are rare vascular malformations affecting predominantly the pediatric population. Hydrocephalus is an unusual presentation in which the exact pathophysiology is not fully understood. The aim of treatment in these cases is occlusion of the fistula prior to considering ventricular shunting. Here, the authors describe the hydrodynamic considerations of the paravascular pathway and the resolution of hydrocephalus with endovascular treatment of the fistula.

Functional Aromatic Polyamides.

We describe herein the state of the art following the last 8 years of research into aromatic polyamides, wholly aromatic polyamides or aramids. These polymers belong to the family of high performance materials because of their exceptional thermal and mechanical behavior. Commercially, they have been transformed into fibers mainly for production of advanced composites, paper, and cut and fire protective garments. Huge research efforts have been carried out to take advantage of the mentioned characteristics in advanced fields related to transport applications, optically active materials, electroactive materials, smart materials, or materials with even better mechanical and thermal behavior.

Perforaciones duodenales tras colangiopancreatografía retrógrada endoscópica / Duodenal perforations after endoscopic retrograde cholangiopancreatography

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Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves.

Islands have played a key role in understanding species formation ever since Darwin's work on the Galapagos and Wallace's work in the Malay Archipelago. Like oceanic islands, habitat 'islands', such as mountaintops and caves similarly may drive diversification. Here we examine patterns of diversification in the tailless whip spider genus Phrynus Larmarck, 1809 (Amblypygida: Phrynidae) a system that shows evidence of diversification under the influence of 'islands within islands'. We estimate phylogeographic history and measure genetic diversity among representatives of three nominal Phrynus species from epigean and cave systems of Puerto Rico and nearby islands. Data from five loci (mitochondrial 12S, 16S, Cox1; nuclear H3, 28S) were used to generate phylogenetic hypotheses and to assess species monophyly and phylogeographic relationships. Genetic divergences and population limits were estimated and assessed using the Geneious barcoding plugin and the genealogical sorting index. We find that mtDNA sequence divergences within each of the three Phrynus species range between 15% and 20%. Genetic divergence is structured at three spatial scales: among islands in a manner consistent with the GAARlandia hypothesis, among bedrock formations within Puerto Rico, and among caves within these formations. Every isolated cave system contains a unique mtDNA genetic lineage of Phrynus, with divergence among cave systems far exceeding that within. In some localities epigean specimens nest among cave taxa, in others caves are monophyletic. Remarkably, clades that show up to 20% mtDNA sequence divergence show little or no variation in the nuclear markers. We interpret this pattern as resulting from extreme conservation of our nuclear markers rather than male sex-biased dispersal, based on high conservation of 28S and H3 between our individuals and other amblypygid genera that are restricted to Africa. While this study includes but a tiny fraction of Caribbean caves, our findings suggest Phrynus may be much more diverse than hitherto thought, at least in terms of mtDNA diversity, and that the arthropod fauna of caves may represent a dimension of biodiversity that is yet to be discovered in the Caribbean biodiversity hotspot.

Hepatotoxicity induced by acute and chronic paracetamol overdose in adults. Where do we stand?

Paracetamol (Acetaminophen) poisoning data can reveal the potential deficiencies of paracetamol poisoning management guidelines. We conducted a retrospective cohort study of patients >18years who were attended in the emergency department (ED) of a Spanish tertiary hospital, from 2005 to 2010 for suspected paracetamol overdose and who had measurable paracetamol concentrations. 208 patients suspected of paracetamol poisoning were identified. The annual incidence in the ED increased from 2.0 (95%-CI: 0.2-7.2) cases per 10,000 patients in 2005 to 3.4 (95%-CI: 1.1-8.8) in 2010. Only 7 of 98 patients (7.14%) with acute poisoning at toxic doses showed hepatotoxicity signs, 4 (57.1%) of whom presented acute liver failure (ALF) criteria, while 8 of 10 patients (80%) with chronic paracetamol poisoning at toxic doses presented hepatotoxicity and 3 (37.5%) with ALF criteria. The time required to find medical care was 9.0h for acute poisoning and 49.6h for chronic poisoning (p<0.001). We conclude that the incidence of suspected cases of paracetamol poisoning at our hospital is increasing. The majority of toxicity cases, including ALF, associated with the ingestion of paracetamol were due to chronic poisoning. This finding constitutes an important warning regarding paracetamol chronic poisoning, and clinicians should have a higher index of clinical suspicion for this entity.