An atlas of cells in the human tonsil.

Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.

Molecular Epidemiology of Underreported Emerging Zoonotic Pathogen Streptococcus suis in Europe.

Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infections in Europe. To procure data, we surveyed 7 reference laboratories and performed a systematic review of the scientific literature. We identified 236 cases of human S. suis infection from those sources and an additional 87 by scanning gray literature. We performed whole-genome sequencing to type 46 zoonotic S. suis isolates and combined them with 28 publicly available genomes in a core-genome phylogeny. Clonal complex (CC) 1 isolates accounted for 87% of typed human infections; CC20, CC25, CC87, and CC94 also caused infections. Emergence of diverse zoonotic clades and notable severity of illness in humans support classifying S. suis infection as a notifiable condition.

A single-cell tumor immune atlas for precision oncology.

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing published data sets of >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying colocalization patterns of immune, stromal, and cancer cells in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immunotherapy.

First case of Oropouche fever detected in the international border region of the Colombian Amazon: clinical characteristics and molecular diagnosis.

OBJECTIVES: We report the first case of Oropouche fever detected in the border region of Colombia. METHODS: Using a multiplex real-time polymerase chain reaction (PCR), genetic sequencing and clinical characteristics during the dengue epidemic in 2019, a total of 175 samples were analysed, from cases notified to the system epidemiological surveillance such as dengue. FINDINGS: The Oropouche virus (OROV) isolate from Leticia belongs to lineage 2 according to both M and S genome segments maximum likelihood (ML) analysis, shares a common ancestor with samples obtained in Esmeraldas, Ecuador and Turbaco, Colombia. The patient: a woman resident in the border neighbourhood of the municipality of Leticia had the following symptoms: fever, headache, retro-orbital pain and myalgias. MAIN CONCLUSION: This cross-border surveillance can be useful to give an alert about the entry or exit of arboviruses circulation in the region, which are often underreported in public health surveillance systems.

Genomic Epidemiology Linking Nonendemic Coccidioidomycosis to Travel.

Coccidioidomycosis is a fungal infection endemic to hot, arid regions of the western United States, northern Mexico, and parts of Central and South America. Sporadic cases outside these regions are likely travel-associated; alternatively, an infection could be acquired in as-yet unidentified newly endemic locales. A previous study of cases in nonendemic regions with patient self-reported travel history suggested that infections were acquired during travel to endemic regions. We sequenced 19 Coccidioides isolates from patients with known travel histories from that earlier investigation and performed phylogenetic analysis to identify the locations of potential source populations. Our results show that those isolates were phylogenetically linked to Coccidioides subpopulations naturally occurring in 1 of the reported travel locales, confirming that these cases were likely acquired during travel to endemic regions. Our findings demonstrate that genomic analysis is a useful tool for investigating travel-related coccidioidomycosis.

Starkeya nomas sp. nov., a prosthecate and budding bacterium isolated from an immunocompromized patient.

Strain HF14-78462T is an environmental bacterium found in clinical samples from an immunocompromized patient in 2014 at Hospital Universitari i Politècnic La Fe (Valencia, Spain). Phenotypically, strain HF14-78462T cells were Gram-stain-negative, aerobic, non-spore forming and non-motile small rods which formed mucous and whitish-translucent colonies when incubated at 20-36 °C. Phylogenetic analyses based on the 16S rRNA genes and the whole genomes of closest sequenced relatives confirmed that strain HF14-78462T is affiliated with the genus Starkeya. The strain was oxidase, catalase and urease positive; but indole, lysine decarboxylase, ornithine decarboxylase and DNase negative, did not produce H2S and was able to utilize a wide variety of carbon sources including acetamide, adonitol, amygdalin, l-arabinose, citric acid, glucose, mannitol and melibiose. Unlike Starkeya novella and Starkeya koreensis, strain HF14-78462T failed to grow in thiosulphate-oxidizing media and had a narrower temperature growth range. Its genome was characterized by a size of 4.83 Mbp and a C+G content of 67.75 mol%. Major fatty acids were C18:1 ω7c, cyclo C19 : 0 and C16 : 0, its polar acids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an aminophospholipid; while the ubiquinones were Q9 (1.8 %) and Q10 (98.2 %). Digital DNA-DNA hybridization values were 41 and 41.4 against S. novella and S. koreensis, respectively, while average nucleotide identity values were around 84 %. Phenotypic, average nucleotide identity and phylogenomic comparative studies suggest that strain HF14-78462T is a new representative of the genus Starkeya and the name Starkeya nomas sp. nov. is proposed. The type strain is HF14-78462T (=CECT 30124T=LMG 31874T).

Implication of the Polymeric Phenolic Fraction and Matrix Effect on the Antioxidant Activity, Bioaccessibility, and Bioavailability of Grape Stem Extracts.

The bioaccessibility and bioavailability of phenolics compounds of two grape stem extracts with different composition were studied. High polymeric extract (HPE) presented a higher content of total phenolics (TPC), procyanidins, hemicelluloses, proteins, and ashes, whereas low procyanidin extract (LPE) showed a higher fat, soluble sugars, and individual phenolic compounds content. Corresponding to its higher total phenolics content, HPE possesses a higher antioxidant activity (TEAC value). The digestion process reduced the antioxidant activity of the HPE up to 69%, due to the decrease of TPC (75%) with a significant loss of polymeric compounds. LPE antioxidant activity was stable, and TPC decreased by only 13% during the digestion process. Moreover, a higher antioxidant phenolic compounds bioavailability was shown in LPE in contrast to HPE. This behaviour was ascribed mainly to the negative interaction of polymeric fractions and the positive interaction of lipids with phenolic compounds. Therefore, this study highlights the convenience of carrying out previous studies to identify the better extraction conditions of individual bioavailable phenolic compounds with antioxidant activity, along with those constituents that could increase their bioaccessibility and bioavailability, such as lipids, although the role played by other components, such as hemicelluloses, cannot be ruled out.

Dynamics of Fractional Delayed Reaction-Diffusion Equations.

The long-term behavior of the weak solution of a fractional delayed reaction-diffusion equation with a generalized Caputo derivative is investigated. By using the classic Galerkin approximation method and comparison principal, the existence and uniqueness of the solution is proved in the sense of weak solution. In addition, the global attracting set of the considered system is obtained, with the help of the Sobolev embedding theorem and Halanay inequality.

MicroRNAs control the apoptotic threshold in primed pluripotent stem cells through regulation of BIM.

Mammalian primed pluripotent stem cells have been shown to be highly susceptible to cell death stimuli due to their low apoptotic threshold, but how this threshold is regulated remains largely unknown. Here we identify microRNA (miRNA)-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Moreover, we found that three miRNA families, miR-20, miR-92, and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the proapoptotic protein BIM. These families therefore represent an essential buffer needed to maintain cell survival in stem cells that are primed for not only differentiation but also cell death.

Impact of optimal vaccination and social distancing on COVID-19 pandemic.

The first COVID-19 case was reported at Wuhan in China at the end of December 2019 but till today the virus has caused millions of deaths worldwide. Governments of each country, observing the severity, took non-pharmaceutical interventions from the very beginning to break the chain of higher transmission. Fortunately, vaccines are available now in most countries and people are asked to take recommended vaccines as precautionary measures. In this work, an epidemiological model on COVID-19 is proposed where people from the susceptible and asymptomatically infected phase move to the vaccinated class after a full two-dose vaccination. The overall analysis says that the disease transmission rate from symptomatically infected people is most sensitive on the disease prevalence. Moreover, better disease control can be achieved by vaccination of the susceptible class. In the later part of the work, a corresponding optimal control problem is considered where maintaining social distancing and vaccination procedure change with time. The result says that even in absence of social distancing, only the vaccination to people can significantly reduce the overall infected population. From the analysis, it is observed that maintaining physical distancing and taking vaccines at an early stage decreases the infection level significantly in the environment by reducing the probability of becoming infected.

Cell free circulating tumor DNA in cerebrospinal fluid detects and monitors central nervous system involvement of B-cell lymphomas.

The levels of cell free circulating tumor DNA (ctDNA) in plasma correlated with treatment response and outcome in systemic lymphomas. Notably, in brain tumors, the levels of ctDNA in the cerebrospinal fluid (CSF) are higher than in plasma. Nevertheless, their role in central nervous system (CNS) lymphomas remains elusive. We evaluated the CSF and plasma from 19 patients: 6 restricted CNS lymphomas, 1 systemic and CNS lymphoma, and 12 systemic lymphomas. We performed whole exome sequencing or targeted sequencing to identify somatic mutations of the primary tumor, then variant-specific droplet digital PCR was designed for each mutation. At time of enrolment, we found ctDNA in the CSF of all patients with restricted CNS lymphoma but not in patients with systemic lymphoma without CNS involvement. Conversely, plasma ctDNA was detected in only 2/6 patients with restricted CNS lymphoma with lower variant allele frequencies than CSF ctDNA. Moreover, we detected CSF ctDNA in 1 patient with CNS lymphoma in complete remission and in 1 patient with systemic lymphoma, 3 and 8 months before CNS relapse was confirmed; indicating CSF ctDNA might detect CNS relapse earlier than conventional methods. Finally, in 2 cases with CNS lymphoma, CSF ctDNA was still detected after treatment even though a complete decrease in CSF tumor cells was observed by flow cytometry (FC), indicating CSF ctDNA better detected residual disease than FC. In conclusion, CSF ctDNA can better detect CNS lesions than plasma ctDNA and FC. In addition, CSF ctDNA predicted CNS relapse in CNS and systemic lymphomas.

Frailty in outpatients with cirrhosis: A prospective observational study.

BACKGROUND AND AIM: Frailty is increasingly recognized as a major prognostic factor in cirrhosis in addition to conventional liver insufficiency scores. The aim was to compare the prevalence and characteristics of frailty between patients with cirrhosis and controls, and to analyse its prognostic value. METHODS: We included outpatients with cirrhosis and age- and gender-matched non-cirrhotic controls. Frailty was defined according to the Fried frailty criteria. In patients with cirrhosis, we analysed the ability of the degree of frailty to predict a composite endpoint, consisting of hospitalization, admission to a long-term care centre, falls or death. RESULTS: We included 135 patients with cirrhosis and 135 controls. The prevalence of frailty was higher among patients with cirrhosis: 35 (25.9%) frail, 74 (54.8%) pre-frail and 26 (19.2%) robust vs 14 (10.4%) frail, 67 (49.6%) pre-frail and 54 (40%) robust (P < .001) in controls. This difference was mainly as a result of decreased muscle strength in patients with cirrhosis. During follow-up, frail patients with cirrhosis showed a higher probability of composite endpoint, hospitalization and falls than pre-frail and robust cirrhotic patients but mortality was similar. MELD-Na score and frailty were independent predictive factors for hospitalization, frailty for falls, and MELD-Na score and albumin for survival. Vitamin D deficiency and increased cystatin C were associated with frailty. CONCLUSIONS: Frailty was more frequent in outpatients with cirrhosis than in controls, mainly because of a decrease in muscle strength, and it could be a predictive factor for hospitalization and falls in these patients.

Invasive Streptococcus pyogenes disease in Spain: a microbiological and epidemiological study covering the period 2007-2019.

The aim of this study is to present the first nationwide microbiological and epidemiological study of invasive group A Streptococcus (iGAS) disease in Spain. One thousand eight hundred ninety-three iGAS isolates were analyzed over 2007-2019. emm typing was performed by sequencing the gene's variable 5' end, exotoxin genes were identified by PCR, and antimicrobial susceptibility explored via the E test and disk diffusion. Five hundred twenty-three isolates were associated with sepsis, 292 with cellulitis, 232 with scarlet fever, 153 with pneumonia, 141 with streptococcal toxic shock syndrome, and 94 with necrotizing fasciitis. The most prevalent emm types were emm1 (449/1893 isolates), emm89 (210/1893), emm3 (208/1893), emm4 (150/1893), emm12 (112/1893) emm6 (107/1893), emm87 (89/1893), emm28 (88/1893), emm75 (78/1893), emm77 (78/1893), emm11 (58/1893), and emm22 (35/1893). emm1, emm3, emm4, and emm6 were the predominant types affecting children (mostly respiratory infections), while emm11, emm77, and emm89 prevailed in the elderly (mostly skin infections). Each emm type was associated with one or more exotoxin gene (spe, sme, and ssa) profiles. speA was detected in 660 isolates, speB in 1829, speC in 1014, speF in 1826, speG in 1651, speJ in 716, speH in 331, smeZ in 720, and ssa in 512. Isolates with speA were associated with the most severe infections. Penicillin susceptibility was universal. Two hundred twenty-four isolates were resistant to tetracycline, 169 to erythromycin, and 81 to clindamycin. Tetracycline, erythromycin, and clindamycin resistance rates declined over the study period. The above information could serve as the basis for continued surveillance efforts designed to control disease cause by this bacterium.

Clinical impact of confinement due to the COVID-19 pandemic on patients with fibromyalgia: a cohort study.

OBJECTIVES: To our knowledge, the impact of the COVID-19 pandemic on fibromyalgia (FM) patients has not been studied before. FM patients often experience clinical impairment with stress. The aim of this study was to determine whether severity of FM increases because of confinement by the COVID-19 pandemic. METHODS: This prospective study includes patients from the Combined Index of Severity of Fibromyalgia (ICAF) cohort who met the 2010 ACR FM criteria. In this cohort, all patients have a periodical evaluation of their quality of life through two questionnaires, the ICAF, which assesses the ability to perform daily living activities, anxiety and depression, and through the Patient Global Impression of Change (PGIC), which assesses overall change after a therapeutical intervention. Pre- and post-confinement measurements were analysed. Inferential statistical analysis and ANOVA for repeated measurements were used. RESULTS: A total of 93 patients received a phone consultation, (95.5% females), mean (SD) age of 48.23 (8.38) years. Four patients were excluded as presenting COVID-19 and 51 (57%) completed the post-confinement ICAF. Following confinement, 25 (49%) patients got worse (group-worse) and 26 (51%) patients experienced no change or improved (group-stable). Comparisons between pre- and post-confinement ICAF did not show significant differences in both groups. Passive coping was significantly different in group-worse in pre-confinement evaluation. In the 80% of patients with passive coping predominance there were no changes in coping strategy. CONCLUSIONS: No clinical impairment due to COVID-19 confinement occurred. The perceived worsening among FM patients relies primarily on how patients cope with their disease, without a real impact on clinical manifestations.

FACE MASK CONTAMINATION DURING COVID-19 PANDEMIA. A STUDY ON PATIENTS RECEIVING INTRAVITREAL INJECTIONS.

PURPOSE: To investigate the bacterial growth in the surgical face masks used by patients who received intravitreal injections and study the effect of povidone-iodine on the periocular area (PA) of masks. METHODS: Forty patients who attended for intravitreal injections were divided in those with less (<4 hours) and more (>4 hours) than 4 hours of mask use. Each group was divided depending on the application or not of povidone-iodine in the PA of the mask. Bacterial load was studied on PA and mouth area samples. RESULTS: The bacterial load in the PA was higher in the >4 hours group compared with the <4 hours group (13.2 vs. 48.75 colony-forming units/µL; P = 0.03). The contamination in the PA significantly decreased after applying povidone-iodine in the >4 hours group (P = 0.01). The use or not of povidone-iodine was strongly correlated to a positive culture (OR = 9.0, P = 0.00. CI 1.63-49.44). CONCLUSION: Surgical face masks worn for more than 4 hours present higher contamination in the PA than those with less use. Bacterial load in the PA is reduced with povidone-iodine on masks used for more than 4 hours. This contamination should be considered in the asepsis protocol of intravitreal injections.

Interdisciplinary Approaches to COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic has been a significant concern worldwide. The pandemic has demonstrated that public health issues are not merely a health concern but also affect society as a whole. In this chapter, we address the importance of bringing together the world's scientists to find appropriate solutions for controlling and managing the COVID-19 pandemic. Interdisciplinary cooperation, through modern scientific methods, could help to handle the consequences of the pandemic and to avoid the recurrence of future pandemics.

Fractional model of COVID-19 applied to Galicia, Spain and Portugal.

A fractional compartmental mathematical model for the spread of the COVID-19 disease is proposed. Special focus has been done on the transmissibility of super-spreaders individuals. Numerical simulations are shown for data of Galicia, Spain, and Portugal. For each region, the order of the Caputo derivative takes a different value, that is not close to one, showing the relevance of considering fractional models.

Forecasting the Effects of the New SARS-CoV-2 Variant in Europe.

Due to the emergence of a new SARS-CoV-2 variant, we use a previous model to simulate the behaviour of this new SARS-CoV-2 variant. The analysis and simulations are performed for Europe, in order to provide a global analysis of the pandemic. In this context, numerical results are obtained in the first 100 days of the pandemic assuming an infectivity of 70%, 56%, and 35%, respectively, higher for the new SAR-CoV-2 variant, as compared with the real data.

Rhizopus microsporus Infections Associated with Surgical Procedures, Argentina, 2006-2014.

Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients. During 2005-2017, an abnormally high number of Rhizopus infections in surgery patients, with no apparent epidemiologic links, were reported in Argentina. To determine the likelihood of a common source of the cluster, we performed whole-genome sequencing on samples collected during 2006-2014. Most isolates were separated by >60 single-nucleotide polymorphisms, and we found no evidence for recombination or nonneutral mutation accumulation; these findings do not support common source or patient-to-patient transmission. Assembled genomes of most isolates were ≈25 Mbp, and multiple isolates had substantially larger assembled genomes (43-51 Mbp), indicative of infections with strain types that underwent genome expansion. Whole-genome sequencing has become an essential tool for studying epidemiology of fungal infections. Less discriminatory techniques may miss true relationships, possibly resulting in inappropriate attribution of point source.

The urgent need for integrated science to fight COVID-19 pandemic and beyond.

The COVID-19 pandemic has become the leading societal concern. The pandemic has shown that the public health concern is not only a medical problem, but also affects society as a whole; so, it has also become the leading scientific concern. We discuss in this treatise the importance of bringing the world's scientists together to find effective solutions for controlling the pandemic. By applying novel research frameworks, interdisciplinary collaboration promises to manage the pandemic's consequences and prevent recurrences of similar pandemics.