A stellar stream remnant of a globular cluster below the metallicity floor.

Stellar ejecta gradually enrich the gas out of which subsequent stars form, making the least chemically enriched stellar systems direct fossils of structures formed in the early Universe1. Although a few hundred stars with metal content below 1,000th of the solar iron content are known in the Galaxy2-4, none of them inhabit globular clusters, some of the oldest known stellar structures. These show metal content of at least approximately 0.2% of the solar metallicity [Formula: see text]. This metallicity floor appears universal5,6, and it has been proposed that protogalaxies that merged into the galaxies we observe today were simply not massive enough to form clusters that survived to the present day7. Here we report observations of a stellar stream, C-19, whose metallicity is less than 0.05% of the solar metallicity [Formula: see text]. The low metallicity dispersion and the chemical abundances of the C-19 stars show that this stream is the tidal remnant of the most metal-poor globular cluster ever discovered, and is significantly below the purported metallicity floor: clusters with significantly lower metallicities than observed today existed in the past and contributed their stars to the Milky Way halo.

Nightside condensation of iron in an ultrahot giant exoplanet.

Ultrahot giant exoplanets receive thousands of times Earth's insolation1,2. Their high-temperature atmospheres (greater than 2,000 kelvin) are ideal laboratories for studying extreme planetary climates and chemistry3-5. Daysides are predicted to be cloud-free, dominated by atomic species6 and much hotter than nightsides5,7,8. Atoms are expected to recombine into molecules over the nightside9, resulting in different day and night chemistries. Although metallic elements and a large temperature contrast have been observed10-14, no chemical gradient has been measured across the surface of such an exoplanet. Different atmospheric chemistry between the day-to-night ('evening') and night-to-day ('morning') terminators could, however, be revealed as an asymmetric absorption signature during transit4,7,15. Here we report the detection of an asymmetric atmospheric signature in the ultrahot exoplanet WASP-76b. We spectrally and temporally resolve this signature using a combination of high-dispersion spectroscopy with a large photon-collecting area. The absorption signal, attributed to neutral iron, is blueshifted by -11 ± 0.7 kilometres per second on the trailing limb, which can be explained by a combination of planetary rotation and wind blowing from the hot dayside16. In contrast, no signal arises from the nightside close to the morning terminator, showing that atomic iron is not absorbing starlight there. We conclude that iron must therefore condense during its journey across the nightside.

Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories.

The medial temporal lobe (MTL) cortex, located adjacent to the hippocampus, is crucial for memory and prone to the accumulation of certain neuropathologies such as Alzheimer's disease neurofibrillary tau tangles. The MTL cortex is composed of several subregions which differ in their functional and cytoarchitectonic features. As neuroanatomical schools rely on different cytoarchitectonic definitions of these subregions, it is unclear to what extent their delineations of MTL cortex subregions overlap. Here, we provide an overview of cytoarchitectonic definitions of the entorhinal and parahippocampal cortices as well as Brodmann areas (BA) 35 and 36, as provided by four neuroanatomists from different laboratories, aiming to identify the rationale for overlapping and diverging delineations. Nissl-stained series were acquired from the temporal lobes of three human specimens (two right and one left hemisphere). Slices (50 µm thick) were prepared perpendicular to the long axis of the hippocampus spanning the entire longitudinal extent of the MTL cortex. Four neuroanatomists annotated MTL cortex subregions on digitized slices spaced 5 mm apart (pixel size 0.4 µm at 20× magnification). Parcellations, terminology, and border placement were compared among neuroanatomists. Cytoarchitectonic features of each subregion are described in detail. Qualitative analysis of the annotations showed higher agreement in the definitions of the entorhinal cortex and BA35, while the definitions of BA36 and the parahippocampal cortex exhibited less overlap among neuroanatomists. The degree of overlap of cytoarchitectonic definitions was partially reflected in the neuroanatomists' agreement on the respective delineations. Lower agreement in annotations was observed in transitional zones between structures where seminal cytoarchitectonic features are expressed less saliently. The results highlight that definitions and parcellations of the MTL cortex differ among neuroanatomical schools and thereby increase understanding of why these differences may arise. This work sets a crucial foundation to further advance anatomically-informed neuroimaging research on the human MTL cortex.

DNA methylation profiling of myelodysplastic syndromes and clinical response to azacitidine: A multicentre retrospective study.

Real-world data have revealed that a substantial portion of patients with myelodysplastic syndromes (MDS) does not respond to epigenetic therapy with hypomethylating agents (HMAs). The cellular and molecular reasons for this resistance to the demethylating agent and biomarkers that would be able to predict the treatment refractoriness are largely unknown. In this study, we shed light on this enigma by characterizing the epigenomic profiles of patients with MDS treated with azacitidine. Our approach provides a comprehensive view of the evolving DNA methylation architecture of the disease and holds great potential for advancing our understanding of MDS treatment responses to HMAs.

Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer.

BACKGROUND: RNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors. METHODS: Combining data mining and conventional experimental procedures, NSUN7 methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity. RESULTS: In this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner. NSUN7 epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibiting NSUN7 epigenetic silencing. The DNA methylation-associated loss of NSUN7 was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly, NSUN7 unmethylated status was enriched in the immune active subclass of liver tumors. CONCLUSION: The 5-methylcytosine RNA methyltransferase NSUN7 undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore, NSUN7 DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability.

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools.

MOTIVATION: The analysis of cancer genomes provides fundamental information about its etiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i.e. those that have been acquired during their evolution). For that purpose, a wide range of computational tools have been developed in recent years to detect somatic mutations in sequencing data from tumor samples. While there have been some efforts to benchmark somatic variant calling tools and strategies, the extent to which variant calling decisions impact the results of downstream analyses of tumor genomes remains unknown. RESULTS: Here, we quantify the impact of variant calling decisions by comparing the results obtained in three important analyses of cancer genomics data (identification of cancer driver genes, quantification of mutational signatures and detection of clinically actionable variants) when changing the somatic variant caller (MuSE, MuTect2, SomaticSniper and VarScan2) or the strategy to combine them (Consensus of two, Consensus of three and Union) across all 33 cancer types from The Cancer Genome Atlas. Our results show that variant calling decisions have a significant impact on these analyses, creating important differences that could even impact treatment decisions for some patients. Moreover, the Consensus of three calling strategy to combine the output of multiple variant calling tools, a very widely used strategy by the research community, can lead to the loss of some cancer driver genes and actionable mutations. Overall, our results highlight the limitations of widespread practices within the cancer genomics community and point to important differences in critical analyses of tumor sequencing data depending on variant calling, affecting even the identification of clinically actionable variants. AVAILABILITY AND IMPLEMENTATION: Code is available at https://github.com/carlosgarciaprieto/VariantCallingClinicalBenchmark. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cutaneous lesions and mitochondrial hearing loss: A case report.

Pathogenic sequence changes in mitochondrial DNA (mtDNA) are one of the most common causes of genetic hearing loss. We report an infant with palmoplantar hyperkeratosis, extrapalmoplantar cutaneous features and mitochondrial sensorineural hearing loss caused by the previously reported pathogenic NC_012920:m.7445A > G sequence change in the mitochondrial gene COX1 (COX1, MT-CO1). Next generation sequencing- based technology was key for the diagnosis and management of this patient.

Associations of phosphorylated tau pathology with whole-hemisphere ex vivo morphometry in 7 tesla MRI.

INTRODUCTION: Neurodegenerative disorders are associated with different pathologies that often co-occur but cannot be measured specifically with in vivo methods. METHODS: Thirty-three brain hemispheres from donors with an Alzheimer's disease (AD) spectrum diagnosis underwent T2-weighted magnetic resonance imaging (MRI). Gray matter thickness was paired with histopathology from the closest anatomic region in the contralateral hemisphere. RESULTS: Partial Spearman correlation of phosphorylated tau and cortical thickness with TAR DNA-binding protein 43 (TDP-43) and α-synuclein scores, age, sex, and postmortem interval as covariates showed significant relationships in entorhinal and primary visual cortices, temporal pole, and insular and posterior cingulate gyri. Linear models including Braak stages, TDP-43 and α-synuclein scores, age, sex, and postmortem interval showed significant correlation between Braak stage and thickness in the parahippocampal gyrus, entorhinal cortex, and Broadman area 35. CONCLUSION: We demonstrated an association of measures of AD pathology with tissue loss in several AD regions despite a limited range of pathology in these cases. HIGHLIGHTS: Neurodegenerative disorders are associated with co-occurring pathologies that cannot be measured specifically with in vivo methods. Identification of the topographic patterns of these pathologies in structural magnetic resonance imaging (MRI) may provide probabilistic biomarkers. We demonstrated the correlation of the specific patterns of tissue loss from ex vivo brain MRI with underlying pathologies detected in postmortem brain hemispheres in patients with Alzheimer's disease (AD) spectrum disorders. The results provide insight into the interpretation of in vivo structural MRI studies in patients with AD spectrum disorders.

The volume of ERCP per endoscopist is associated with a higher technical success and a lower post-ERCP pancreatitis rate. A prospective analysis.

INTRODUCTION: conflicting results have been reported regarding the influence of the annual volume of endoscopic retrograde cholangiopancreatography (ERCP) on outcome. OBJECTIVE: to evaluate the influence of case volume on ERCP outcomes. PATIENTS AND METHODS: an analysis of a prospective database was performed, comparing the outcomes of ERCP in three consecutive periods defined by the number of endoscopists performing ERCP: five endoscopists in period I (P1), four in period II (P2) and three in period III (P3). Only patients with biliary ERCP in accessible and naïve papilla were included. Primary variables were cannulation rates and adverse effects (AE). The American Society of Gastrointestinal Endoscopy (ASGE) complexity grades III and IV were considered as highly complex procedures. RESULTS: a total of 2,561 patients were included: 727 (P1), 972 (P2) and 862 (P3). There were no differences in age and sex between groups (p > 0.05). The cannulation rate was significantly higher in P2 and P3: 92.4 % vs 93.3 % vs 93 % (p = 0.037). The AE rate was 13.8 %, 12.6 % and 10.3 % (p > 0.05), respectively. The rate of post-ERCP pancreatitis was significantly lower in P3: 8.5 %, 7.3 % and 5 % (p = 0.01). The rate of complex procedures was 12 %, 14.8 % and 27 % (p < 0.0001), respectively. Two endoscopists participated in all periods and only one had significantly improved outcomes. Cannulation and post-ERCP pancreatitis rates remained significantly better in P3 after adjusting for sex, complexity and endoscopist. CONCLUSION: a higher annual volume of ERCP per endoscopist was associated with a higher rate of cannulation and a lower rate of post-ERCP pancreatitis, despite the greater complexity of the procedures. These beneficial effects seem to differ between endoscopists.

Three-dimensional mapping of neurofibrillary tangle burden in the human medial temporal lobe.

Tau protein neurofibrillary tangles are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimer's disease and related dementias. Our knowledge of the pattern of neurofibrillary tangle progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in Alzheimer's disease, is based on conventional two-dimensional histology studies that only sample the brain sparsely. To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe specimens (age 75.3 ± 11.4 years, range 45 to 93) were used to construct three-dimensional quantitative maps of neurofibrillary tangle burden in the medial temporal lobe at individual and group levels. Group-level maps were obtained in the space of an in vivo brain template, and neurofibrillary tangles were measured in specific anatomical regions defined in this template. Three-dimensional maps of neurofibrillary tangle burden revealed significant variation along the anterior-posterior axis. While early neurofibrillary tangle pathology is thought to be confined to the transentorhinal region, we found similar levels of burden in this region and other medial temporal lobe subregions, including amygdala, temporopolar cortex, and subiculum/cornu ammonis 1 hippocampal subfields. Overall, the three-dimensional maps of neurofibrillary tangle burden presented here provide more complete information about the distribution of this neurodegenerative pathology in the region of the cortex where it first emerges in Alzheimer's disease, and may help inform the field about the patterns of pathology spread, as well as support development and validation of neuroimaging biomarkers.

Genomics-based higher classification of the species-rich Hairstreaks (Lepidoptera: Lycaenidae: Eumaeini).

We propose a higher classification of the lycaenid hairstreak tribe Eumaeini - one of the youngest and most species-rich butterfly tribes - based on autosome, Lepidopteran Z sex chromosome, and mitochondrial protein-coding genes. The subtribe Neolycaenina Korb is a synonym of Callophryidina Tutt, and subtribe Tmolusina Bálint is a synonym of Strephonotina K. Johnson, Austin, Le Crom, & Salazar. Proposed names are Rhammina Prieto & Busby, new subtribe; Timaetina Busby & Prieto, new subtribe; Atlidina Martins & Duarte, new subtribe; Evenina Faynel & Grishin, new subtribe; Jantheclina Robbins & Faynel, new subtribe; Paiwarriina Lamas & Robbins, new subtribe; Cupatheclina Lamas & Grishin, new subtribe; Parrhasiina Busby & Robbins, new subtribe; Ipideclina Martins & Grishin, new subtribe; and Trichonidina Duarte & Faynel, new subtribe. Phylogenetic results from the autosome and Z sex chromosome analyses are similar. Future analyses of datasets with hundreds of terminal taxa may be more practical time-wise by focussing on the smaller number of sex chromosome sequences (2.6% of nuclear protein-coding sequences). The phylogenetic classification and biological summaries for each subtribe suggest that a variety of factors affected Eumaeini diversification. About a dozen kinds of male secondary sexual organs with frequent evolutionary gains and losses occur in Atlidina, Evenina, and Jantheclina (141 species combined). Females have been shown to use these organs to discriminate between conspecific and non-conspecific males, facilitating sympatry among close relatives. Eumaeina, Rhammina, and Timaetina (140 species combined) are overwhelmingly montane with some evidence for a higher incidence of sympatric diversification. Seven Neotropical lineages in five subtribes invaded the temperate parts of the Nearctic Region with a diversification increase in the Callophryidina (262 species). North American Satyrium and Callophrys then invaded the Palearctic at least once each, with a major species-richness increase in Satyrium. The evolution of litter feeding detritivores within Calycopidina (172 species) resulted in an increase in diversification rate compared with its flower-feeding sister lineage. Atlidina, Strephonotina, Parrhasiina, and Strymonina (562 species combined) each contain a mixture of genera that specialize on one or two caterpillar food plant families and genera that are polyphagous. These would be appropriate subtribes to assess how the breadth of caterpillar food plants and the frequency of host shifts affected diversification.

Induction of antiviral and cell mediated immune responses significantly reduce viral load in an acute foot-and-mouth disease virus infection in cattle.

Foot-and-mouth disease virus (FMDV) causes a severe infection in ruminant animals. Here we present an in-depth transcriptional analysis of soft-palate tissue from cattle experimentally infected with FMDV. The differentially expressed genes from two Indian cattle (Bos indicus) breeds (Malnad Gidda and Hallikar) and Holstein Friesian (HF) crossbred calves, highlighted the activation of metabolic processes, mitochondrial functions and significant enrichment of innate antiviral immune response pathways in the indigenous calves. The results of RT-qPCR based validation of 12 genes was in alignment with the transcriptome data. The indigenous calves showing lesser virus load, elicited early neutralizing antibodies and IFN-γ immune responses. This study revealed that induction of potent innate antiviral response and cell mediated immunity in indigenous cattle, especially Malnad Gidda, significantly restricted FMDV replication during acute infection. These data highlighting the molecular processes associated with host-pathogen interactions, could aid in the conception of novel strategies to prevent and control FMDV infection in cattle.

Colectomy rate in ulcerative colitis 15 years after diagnosis: Results from the 2001-2003 Navarra cohort. / Tasas de colectomía en colitis ulcerosa 15 años después del diagnóstico. Datos de la cohorte Navarra 2001-2003.

INTRODUCTION: Knowing the natural history of ulcerative colitis (UC) is essential to understand the course of the disease, assess the impact of different treatment strategies and identify poor prognostic factors. One of the most significant matters in this regard is the need for surgery. OBJECTIVES: To analyse the Colectomy Incidence Rate (CIR) from diagnosis to end of follow-up (31/12/2017) and identify predictive factors for colectomy. MATERIAL AND METHODS: A retrospective study enrolling patients with a definitive diagnosis (DD) of UC or Unclassified Colitis (UnC) in the 2001-03 Navarra cohort. RESULTS: We enrolled 174 patients with a DD of UC (E2 42.8%; E3 26.6%) and 5 patients with a DD of UnC: 44.1% women, median age 39.2 years (range 7-88) and median follow-up 15.7 years. A total of 8 patients underwent surgery (CIR 3 colectomies/103 patient-years: 3 at initial diagnosis (<1 month), 2 in the first 2 years, 2 at 5 years from diagnosis and 1 at 12 years from diagnosis. All had previously received steroids; 5 had received immunomodulators and 2 had received biologics. In 7 patients (87%), surgery was performed on an emergency basis. The indication was megacolon in 3 (37.5%), severe flare-up in 3 (37.5%) and medical treatment failure in 2 (25%). In 5 cases (62.5%), an ileoanal pouch was made, and in 3 cases, a definitive ileostomy was performed. In the univariate analysis, patients with loss of more than 5 kg at diagnosis and admission at diagnosis had a lower rate of colectomy-free survival. CONCLUSIONS: In our series, colectomy rates are lower than usually reported. Most colectomies were performed in the first 5 years following diagnosis and had an emergency indication.

Frequency and prognostic impact of KIT and other genetic variants in indolent systemic mastocytosis.

Indolent systemic mastocytosis (ISM) patients have a normal life expectancy, except in the 5% to 10% of cases that progress to more advanced SM (advSM), which has a significantly poorer outcome. Mutations in genes other than KIT frequently found in myeloid neoplasms have been associated with a poorer outcome among advSM, whereas limited information exists about their frequency and prognostic impact in ISM. We investigated the frequency and prognostic impact of variants in 18 genes, found to be altered in advSM, in 322 ISM patients (median follow-up, 5.7 years) divided into discovery (n = 200) and validation (n = 122) cohorts. Overall, 71 genetic variants were detected in 55 of 322 (17%) patients. Mutated ISM cases, particularly those carrying ASXL1, RUNX1, and/or DNMT3A (A/R/D) pathogenic variant allele frequencies (VAFs) ≥ 30%, exhibited significantly shortened (P < .001) progression-free survival (PFS) and overall survival (OS). Multivariate analysis showed that serum ß2-microglobulin (sß2M) levels > 2.5 µg/mL (hazard ratio [HR], 9.8; P = .001), together with a KIT D816V VAF ≥ 1% in bone marrow (BM) (HR, 10.1; P = .02) and pathogenic variants of A/R/D VAFs ≥ 30% (HR, 4.2; P = .02), were the best combination of independent predictors for PFS. In turn, A/R/D gene pathogenic VAF ≥ 30% was the only independent predictor for OS (HR, 51.8; P < .001). Based on these variables, 2 scoring systems were constructed for risk stratification of ISM at diagnosis with significantly different 10-year PFS (100%, 91%, 0% for scores of 0, 1, ≥2, respectively) and OS (100% and 50% for scores of 0 and 1) rates.

RaNA-Seq: Interactive RNA-Seq analysis from FASTQ files to functional analysis.

SUMMARY: RaNA-Seq is a cloud platform for the rapid analysis and visualization of RNA-Seq data. It performs a full analysis in minutes by quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the explanation of results with functional analyses. Our analysis pipeline applies generally accepted and reproducible protocols that can be applied with two simple steps in its web interface. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication. AVAILABILITY: RaNA-Seq web service is freely available online at https://ranaseq.eu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Neuronal volume of the hippocampal regions in ageing.

The hippocampal formation (HF) has an important role in different human capacities, such as memory processing and emotional expression. Both extensive changes and limited variations of its components can cause clinically expressed dysfunctions. Although there remains no effective treatment for diseases caused by pathological changes in this brain region, detection of these changes, even minimally, could allow us to develop early interventions and establish corrective measures. This study analysed the neuronal islands of layer II of the entorhinal cortex (EC), the neuronal clumps of the external principal layer of the presubiculum (PrS) and the dentate granule cells of the dentate gyrus (DG), which represent the prominent structural regions within the HF circuit. Subjects from two age groups (younger or older than 65 years) were studied and their neuronal size assessed by the point-sampled intercepts stereological method. The quantitative v¯v(soma) estimate was a volume of roughly 8,500 µm3 for EC layer II neurons, and DG granule neurons and presubicular neurons were five and 10 times smaller, respectively. The older age group showed a v¯v(soma) increase of 2%, 18% and 28% with respect to the younger group in the PrS, DG and EC regions, respectively. None of these regions showed interhemispheric differences. This quantitative estimation is relevant because the observed variance in the v¯v(soma) estimates suggests that biological variation is the main contributory factor, with intercepts and measurements having a smaller impact. Therefore, we suggest that age has a limited influence on neuronal volume variation in these HF regions, which needs to be compared with similar measurements in neurodegenerative disorders such as Alzheimer's.

Comparative study of two different perimodiolar and a straight cochlear implant electrode array: surgical and audiological outcomes.

PURPOSE: To compare the surgical and audiological outcomes with two perimodiolar electrode arrays (Nucleus 512-Contour Advance® y Nucleus 532-Slim Perimodiolar®) and a straight electrode array (Nucleus 422/522). METHODS: Patients were retrospectively selected from our cochlear implant program database. Only patients with a history of bilateral, sensorineural postlingually profound hearing loss who underwent cochlear implant surgery with either a N512, a N532 or a N422 were included. Throughout a year of follow-up, pure tone audiometry (PTA), speech perception, Impedances and T-C Thresholds levels were analyzed. Surgical data were also analyzed. RESULTS: 66 patients were included (19-CI532, 20-CI512 and 27-CI422). The most common type of cochlea access with the N532, N512 and N422 was through an extended round window, a promontorial cochleostomy and a pure round window, respectively. No significant differences were observed after 12 months in Mean PTA and Speech recognition. No significant differences were seen in the levels of hearing preservation at frequencies of 250 and 500. The average values of the impedances were significantly higher in the CI group N532 and N422 than in the N512. The mean values of the T and C levels were significantly lower in the CI groups N532 and N422 compared with the N512. CONCLUSIONS: No significant differences were observed after 12 months in Mean PTA and Speech recognition; however, a faster acquisition of auditory results were observed in the group of patients treated with the CI N532. The type of electrode array influences in the type of cochleostomy.

Defects in memory B-cell and plasma cell subsets expressing different immunoglobulin-subclasses in patients with CVID and immunoglobulin subclass deficiencies.

BACKGROUND: Predominantly antibody deficiencies (PADs) are the most prevalent primary immunodeficiencies, but their B-cell defects and underlying genetic alterations remain largely unknown. OBJECTIVE: We investigated patients with PADs for the distribution of 41 blood B-cell and plasma cell (PC) subsets, including subsets defined by expression of distinct immunoglobulin heavy chain subclasses. METHODS: Blood samples from 139 patients with PADs, 61 patients with common variable immunodeficiency (CVID), 68 patients with selective IgA deficiency (IgAdef), 10 patients with IgG subclass deficiency with IgA deficiency, and 223 age-matched control subjects were studied by using flow cytometry with EuroFlow immunoglobulin isotype staining. Patients were classified according to their B-cell and PC immune profile, and the obtained patient clusters were correlated with clinical manifestations of PADs. RESULTS: Decreased counts of blood PCs, memory B cells (MBCs), or both expressing distinct IgA and IgG subclasses were identified in all patients with PADs. In patients with IgAdef, B-cell defects were mainly restricted to surface membrane (sm)IgA+ PCs and MBCs, with 2 clear subgroups showing strongly decreased numbers of smIgA+ PCs with mild versus severe smIgA+ MBC defects and higher frequencies of nonrespiratory tract infections, autoimmunity, and affected family members. Patients with IgG subclass deficiency with IgA deficiency and those with CVID showed defects in both smIgA+ and smIgG+ MBCs and PCs. Reduced numbers of switched PCs were systematically found in patients with CVID (absent in 98%), with 6 different defective MBC (and clinical) profiles: (1) profound decrease in MBC numbers; (2) defective CD27+ MBCs with almost normal IgG3+ MBCs; (3) absence of switched MBCs; and (4) presence of both unswitched and switched MBCs without and; (5) with IgG2+ MBCs; and (6) with IgA1+ MBCs. CONCLUSION: Distinct PAD defective B-cell patterns were identified that are associated with unique clinical profiles.

Raman amplification in the ultra-small limit of Ag nanoparticles on SiO2 and graphene: Size and inter-particle distance effects.

Size, shape and hot spots are crucial to optimize Raman amplification from metallic nanoparticle (NPs). The amplification from radius = 1.8 ± 0.4 nm ultra-small silver NPs was explored. Increasing NP density redshifts and widens their plasmon that, according to simulations for NPs arrays, is originated by the reduction of the interparticle distance, d, becoming remarkable for d ≤ R. Inter-particle interaction red-shifts (N130 nm) and widens (N90 nm) the standard plasmon of non-interacting spherical particles. Graphene partly delocalizes the carriers enhancing the NIR spectral weight. Raman amplification of graphene phonons is moderate and depends smoothly on d while that of Rhodamine 6G (R6G) varies almost exponentially due to their location at hotspots that depend strongly on d. The experimental correlation between amplification and plasmon position is well reproduced by simulations. The amplification originated by the ultra-small NPs is compared to that of larger particles, granular silver films with 7 < R < 15 nm grains, with similar extinction values. The amplification is found to be larger for the 1.8nm NPs due to the higher surface/volume ration that allows higher density of hot spots. It is demonstrated that Raman amplification can be efficiently increased by depositing low density layers of ultra-small NPs on top of granular films.

Measuring the Tangle of Three-Qubit States.

We present a quantum circuit that transforms an unknown three-qubit state into its canonical form, up to relative phases, given many copies of the original state. The circuit is made of three single-qubit parametrized quantum gates, and the optimal values for the parameters are learned in a variational fashion. Once this transformation is achieved, direct measurement of outcome probabilities in the computational basis provides an estimate of the tangle, which quantifies genuine tripartite entanglement. We perform simulations on a set of random states under different noise conditions to asses the validity of the method.