The study on Silurian-Devonian conodonts from the Precordillera has shown a significant increase in the last 5 years. In the new conodont collections, particular specimens of Ozarkodina were obtained ...from the middle and upper parts of the Los Espejos Formation in the Talacasto region. The taxonomic study allows us to propose a new species of the genus Ozarkodina, named Ozarkodina huenickeni sp. nov., which shows three different morphotypes, α, β and γ, respectively, based on the presence of ornamentation above the platform lobes. The species ranges from the Pedavis latialata-Ozarkodina snajdri interval Zone to the Icriodus hesperius Zone, Ludfordian to early Lochkovian in age. The phylogenetic analysis of Oz. huenickeni sp. nov. allows us to propose that this species could belong to the bohemica lineage, probably representing a South American endemic taxon.
•The taxonomic study allows us to propose a new species of the genus Ozarkodina.•The carminate P1 element is characterized by a discrete leaf-shaped platform expanded.•The lobes of the platform may or may not be ornamented by nodes and/or ridge.•In the middle part of the blade, the denticles have the same height or they are fused.
Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic ...control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/.
Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation ...identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript to be more abundant in Alzheimer's disease with more severe tau and amyloid pathological burden. Thus, we demonstrate potential association of human-lineage-specific sequences in brain development and neurological disease.
Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of ...the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity. Saliva samples were processed for viral metagenomics (
= 15) and SVGs (
= 3). A total of 1328 uncultured single viruses were sorted by fluorescence-activated virus sorting followed by whole genome amplification. Sequencing of 24 viral single amplified genomes (vSAGs) showed that half of the vSAGs contained viral hallmark genes. Among those bona fide viruses, the uncultured single virus 92-C13 putatively infecting oral Streptococcus-like species was within the top ≈10 most abundant viruses in the oral virome. Viral gene network and viral metagenomics analyses of 439 oral viruses from cultures, metagenomics, and SVGs revealed that salivary viruses were tentatively structured into ≈200 major viral clusters, corresponding to approximately genus-level groupings. Data showed that none of the publicly available viral isolates, excepting an Actinomyces phage, were significantly abundant in the oral viromes. In addition, none of the obtained viral contigs and vSAGs from this study were present in all viromes. Overall, the data demonstrates that most viral isolates are not naturally abundant in saliva, and furthermore, the predominant viruses in the oral cavity are yet uncharacterized. Results suggest a variable, complex, and interpersonal viral profile. Finally, we demonstrated the power of SVGs in combination with viral metagenomics to unveil the genetic information of the uncultured viruses of the human virome.
We performed exploratory and descriptive analyses of data from our 8 years of experience in hospital-at-home (HaH) treatment to characterize the clinical profile of patients with exacerbated ...underlying chronic obstructive pulmonary disease (COPD). Our study had a retrospective research design, using historical electronic health records from patients admitted to the HaH setting between 2012 and 2019. We collected demographic, administrative, and clinical data from patients diagnosed with exacerbated COPD. Between 2012 and 2019, 420 patients diagnosed with acute respiratory infectious disease related to COPD were treated in our HaH setting (18% of all admissions to HaH). Most patients were referred from the Internal Medicine Department. The median length of the hospital stay was 10 days. Most patients (78.8%) presented acute exacerbation with no pneumonia. One-third of the patients required domiciliary oxygen therapy, and half required ventilatory devices for nebulized bronchodilator therapy. All patients were successfully discharged as clinically stable. Our HaH experience in managing patients with exacerbated COPD indicates a means of obtaining cost savings and increased quality of life for patients in which antibiotic and ventilatory therapy is not compromised.
ECLIM-SEHOP platform was created in 2017. Its main objective is to establish the infrastructure to allow Spanish participation into international academic collaborative clinical trials, observational ...studies, and registries in pediatric oncology. The aim of this manuscript is to describe the activity conducted by ECLIM-SEHOP since its creation.
The platform's database was queried to provide an overview of the studies integrally and partially supported by the organization. Data on trial recruitment and set-up/conduct metrics since its creation until November 2023 were extracted.
ECLIM-SEHOP has supported 47 studies: 29 clinical trials and 18 observational studies/registries that have recruited a total of 5250 patients. Integral support has been given to 25 studies: 16 trials recruiting 584 patients and nine observational studies/registries recruiting 278 patients. The trials include front-line studies for leukemia, lymphoma, brain and solid extracranial tumors, and other key transversal topics such as off-label use of targeted therapies and survivorship. The mean time from regulatory authority submission to first patient recruited was 12.2 months and from first international site open to first Spanish site open was 31.3 months.
ECLIM-SEHOP platform has remarkably improved the availability and accessibility of international academic clinical trials and has facilitated the centralization of resources in childhood cancer treatment. Despite the progressive improvement on clinical trial set-up metrics, timings should still be improved. The program has contributed to leveling survival rates in Spain with those of other European countries that presented major differences in the past.
Antigen tests or polymerase chain reaction (PCR) amplification are currently COVID-19 diagnostic tools. However, developing complementary diagnosis tools is mandatory. Thus, we performed a plasma ...cytokine array in COVID-19 patients to identify novel diagnostic biomarkers. A discovery–validation study in two independent prospective cohorts was performed. The discovery cohort included 136 COVID-19 and non-COVID-19 patients recruited consecutively from 24 March to 11 April 2020. Forty-five cytokines’ quantification by the MAGPIX system (Luminex Corp., Austin, TX, USA) was performed in plasma samples. The validation cohort included 117 patients recruited consecutively from 15 to 25 April 2020 for validating results by ELISA. COVID-19 patients showed different levels of multiple cytokines compared to non-COVID-19 patients. A single chemokine, IP-10, accurately identified COVID-19 patients who required hospital admission (AUC: 0.962; 95%CI (0.933–0.992); p < 0.001)). The results were validated in an independent cohort by multivariable analysis (OR: 25.573; 95%CI (8.127–80.469); p < 0.001) and AUROC (AUC: 0.900; 95%CI (0.846–0.954); p < 0.001). Moreover, showing IP-10 plasma levels over 173.35 pg/mL identified COVID-19 with higher sensitivity (86.20%) than the first SARS-CoV-2 PCR. Our discover–validation study identified IP-10 as a robust biomarker in clinical practice for COVID-19 diagnosis at hospital. Therefore, IP-10 could be used as a complementary tool in clinical practice, especially in emergency departments.
Early recognition of sepsis is a key factor to improve survival to this disease in surgical patients, since it allows prompt control of the infectious source. Combining pro-inflammatory and ...immunosupression biomarkers could represent a good strategy to improve sepsis detection. Here we evaluated the combination of procalcitonin (PCT) with gene expression levels of HLA-DRA to detect sepsis in a cohort of 154 surgical patients (101 with sepsis and 53 with no infection). HLA-DRA expression was quantified using droplet digital PCR, a next-generation PCR technology. Area under the receiver operating curve analysis (AUROC) showed that the PCT/HLA-DRA ratio outperformed PCT to detect sepsis (AUROC CI95%, p): PCT: 0.80 0.73-0.88, <0.001; PCT/HLA-DRA: 0.85 0.78-0.91, <0.001. In the multivariate analysis, the ratio showed a superior ability to predict sepsis compared to that of PCT (OR CI 95%, p): PCT/HLA-DRA: 7.66 1.82-32.29, 0.006; PCT: 4.21 1.15-15.43 0.030. Multivariate analysis was confirmed using a new surgical cohort with 74 sepsis patients and 21 controls: PCT/HLA-DRA: 34.86 1.22-995.08, 0.038; PCT: 5.52 0.40-75.78, 0.201. In conclusion, the combination of PCT with HLA-DRA is a promising strategy for improving sepsis detection in surgical patients.
► We propose a new scale for colour specification of virgin olive oils named MUOCS. ► MUOCS was proposed on the basis of a wide dataset of 1700 virgin olive oils. ► MUOCS improved previous Bromthymol ...Blue (BTB) scale in more than a factor 2. ► A low-cost electronic device measuring MUOCS and BTB colours was designed. ► This device is portable and may avoid the use of expensive colour instrumentation.
The Modified Uniform Oil Colour Scale (MUOCS) is proposed for the colour specification of virgin olive oils. MUOCS has 60 standard colours, the same number as the two previous scales available for the same purpose: Uniform Oil Colour Scale (UOCS) and Bromthymol Blue (BTB). A remarkable improvement in accuracy can be achieved from MUOCS standards: For a broad dataset of 1700 virgin olive oils produced in Spain during four different harvests, the average colour differences to the closest standards were 2.86, 3.99, and 8.17 CIELAB units using MUOCS, UOCS and BTB, respectively. A low-cost (<60 Euros) portable electronic device is proposed for the colour specification of virgin olive oils based on MUOCS and BTB standards. This device can operate with USB connection to a computer or AAA batteries, and is based on fast (<0.25s) transmittance measurements of the virgin-olive-oil sample placed in a 5-mm pathlength quartz cell. The device may avoid the use of expensive laboratory instrumentation for colour measurement and can be easily employed by non-technician users. For a reduced set of commercial virgin olive oils with random colours, the MUOCS classifications provided by our device agreed with those given by conventional spectrophotometric measurements in 92% of the cases.
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