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We measure the three-dimensional power spectrum (P3D) of the transmitted flux in the Lyman- |$\alpha$| (Ly  |$\alpha$|⁠) forest using the complete extended Baryon Oscillation Spectroscopic Survey data release 16 (eBOSS DR16). This sample consists of |$\sim$| 205 000 quasar spectra in the redshift range |$2\le z \le 4$| at an effective redshift |$z=2.334$|⁠. We propose a pair-count spectral estimator in configuration space, weighting each pair by |$\exp (i\mathbf {k}\cdot \mathbf {r})$|⁠ , for wave vector |$\mathbf {k}$| and pixel pair separation |$\mathbf {r}$|⁠ , effectively measuring the anisotropic power spectrum without the need for fast Fourier transforms. This accounts for the window matrix in a tractable way, avoiding artefacts found in Fourier-transform based power spectrum estimators due to the sparse sampling transverse to the line of sight of Ly  |$\alpha$| skewers. We extensively test our pipeline on two sets of mocks: (i) idealized Gaussian random fields with a sparse sampling of Ly  |$\alpha$| skewers, and (ii) log-normal LyaCoLoRe mocks including realistic noise levels, the eBOSS survey geometry and contaminants. On eBOSS DR16 data, the Kaiser formula with a non-linear correction term obtained from hydrodynamic simulations yields a good fit to the power spectrum data in the range |$(0.02 \le k \le 0.35)\, h\, {\rm Mpc}^{-1}\,$| at the 1–2σ level with a covariance matrix derived from LyaCoLoRe mocks. We demonstrate a promising new approach for full-shape cosmological analyses of Ly  |$\alpha$| forest data from cosmological surveys such as eBOSS, the currently observing Dark Energy Spectroscopic Instrument and future surveys such as the Prime Focus Spectrograph, WEAVE-QSO, and 4MOST. [ABSTRACT FROM AUTHOR]

Mitochondria have emerged as key actors of innate and adaptive immunity. Mitophagy has a pivotal role in cell homeostasis, but its contribution to macrophage functions and host defense remains to be delineated. Here, we showed that lipopolysaccharide (LPS) in combination with IFN-[gamma] inhibited PINK1-dependent mitophagy in macrophages through a STAT1dependent activation of the inflammatory caspases 1 and 11. In addition, we demonstrated that the inhibition of mitophagy triggered classical macrophage activation in a mitochondrial ROS-dependent manner. In a murine model of polymicrobial infection (cecal ligature and puncture), adoptive transfer of Pink1-deficient bone marrow or pharmacological inhibition of mitophagy promoted macrophage activation, which favored bactericidal clearance and led to a better survival rate. Reciprocally, mitochondrial uncouplers that promote mitophagy reversed LPS/IFN-[gamma]-mediated activation of macrophages and led to immunoparalysis with impaired bacterial clearance and lowered survival. In critically ill patients, we showed that mitophagy was inhibited in blood monocytes of patients with sepsis as compared with nonseptic patients. Overall, this work demonstrates that the inhibition of mitophagy is a physiological mechanism that contributes to the activation of myeloid cells and improves the outcome of sepsis., Introduction Sepsis is one of the leading causes of morbidity and mortality in intensive care units (ICUs) (1). Strategies that blunt inflammatory responses have failed to improve survival, whereas those [...]

We estimate the redshift-dependent, anisotropic clustering signal in the Dark Energy Spectroscopic Instrument (DESI) Year 1 Survey created by tidal alignments of Luminous Red Galaxies (LRGs) and a selection-induced galaxy orientation bias. To this end, we measured the correlation between LRG shapes and the tidal field with DESI's Year 1 redshifts, as traced by LRGs and Emission-Line Galaxies. We also estimate the galaxy orientation bias of LRGs caused by DESI's aperture-based selection, and find it to increase by a factor of seven between redshifts 0.4−1.1 due to redder, fainter galaxies falling closer to DESI's imaging selection cuts. These effects combine to dampen measurements of the quadrupole of the correlation function (ξ2) caused by structure growth on scales of 10–80 h −1 Mpc by about 0.15 per cent for low redshifts (0.4 < z < 0.6) and 0.8 per cent for high (0.8 < z < 1.1), a significant fraction of DESI's error budget. We provide estimates of the ξ2 signal created by intrinsic alignments that can be used to correct this effect, which is necessary to meet DESI's forecasted precision on measuring the growth rate of structure. While imaging quality varies across DESI's footprint, we find no significant difference in this effect between imaging regions in the Legacy Imaging Survey. [ABSTRACT FROM AUTHOR]

The 1D power spectrum P 1D of the Ly α forest provides important information about cosmological and astrophysical parameters, including constraints on warm dark matter models, the sum of the masses of the three neutrino species, and the thermal state of the intergalactic medium. We present the first measurement of P 1D with the quadratic maximum likelihood estimator (QMLE) from the Dark Energy Spectroscopic Instrument (DESI) survey early data sample. This early sample of 54 600 quasars is already comparable in size to the largest previous studies, and we conduct a thorough investigation of numerous instrumental and analysis systematic errors to evaluate their impact on DESI data with QMLE. We demonstrate the excellent performance of the spectroscopic pipeline noise estimation and the impressive accuracy of the spectrograph resolution matrix with 2D image simulations of raw DESI images that we processed with the DESI spectroscopic pipeline. We also study metal line contamination and noise calibration systematics with quasar spectra on the red side of the Ly α emission line. In a companion paper, we present a similar analysis based on the Fast Fourier Transform estimate of the power spectrum. We conclude with a comparison of these two approaches and discuss the key sources of systematic error that we need to address with the upcoming DESI Year 1 analysis. [ABSTRACT FROM AUTHOR]

We present the one-dimensional Ly α forest power spectrum measurement using the first data provided by the Dark Energy Spectroscopic Instrument (DESI). The data sample comprises 26 330 quasar spectra, at redshift z > 2.1, contained in the DESI Early Data Release and the first 2 months of the main survey. We employ a Fast Fourier Transform (FFT) estimator and compare the resulting power spectrum to an alternative likelihood-based method in a companion paper. We investigate methodological and instrumental contaminants associated with the new DESI instrument, applying techniques similar to previous Sloan Digital Sky Survey (SDSS) measurements. We use synthetic data based on lognormal approximation to validate and correct our measurement. We compare our resulting power spectrum with previous SDSS and high-resolution measurements. With relatively small number statistics, we successfully perform the FFT measurement, which is already competitive in terms of the scale range. At the end of the DESI survey, we expect a five times larger Ly α forest sample than SDSS, providing an unprecedented precise one-dimensional power spectrum measurement. [ABSTRACT FROM AUTHOR]

Accurate quasar classifications and redshift measurements are increasingly important to precision cosmology experiments. Broad absorption line (BAL) features are present in 15–20 per cent of all quasars, and these features can introduce systematic redshift errors, and in extreme cases produce misclassifications. We quantitatively investigate the impact of BAL features on quasar classifications and redshift measurements with synthetic spectra that were designed to match observations by the Dark Energy Spectroscopic Instrument (DESI) survey. Over the course of 5 yr, DESI aims to measure spectra for 40 million galaxies and quasars, including nearly three million quasars. Our synthetic quasar spectra match the signal-to-noise ratio and redshift distributions of the first year of DESI observations, and include the same synthetic quasar spectra both with and without BAL features. We demonstrate that masking the locations of the BAL features decreases the redshift errors by about 1 per cent and reduces the number of catastrophic redshift errors by about 80 per cent. We conclude that identifying and masking BAL troughs should be a standard part of the redshift determination step for DESI and other large-scale spectroscopic surveys of quasars. [ABSTRACT FROM AUTHOR]

Purpose: Cardiac surgery with cardiopulmonary bypass triggers sterile inflammation that is responsible for post-operative morbidity. Automated flow cytometry devices used for leucocyte count provide cell population data (CPD) regarding fluorescence intensity, size and granularity of leukocytes that have never been studied in the context of sterile inflammation. Our objective was to explore leukocyte cell population data in patients undergoing cardiac surgery with cardiopulmonary bypass in order to determine whether CPD could be used to monitor immune cell activation. Methods: This is an ancillary study of a cohort of patients undergoing cardiac surgery with cardiopulmonary bypass. Cell population data (CPD) extracted from a routine automated flow cytometer were analyzed (Fluorescence targeted to nucleic acids). The time points of interest were: pre-operative, postoperative and 5 days after surgery. The variations in those parameters were studied. Data were then compared between patients according to the occurrence of a composite criteria (supra-ventricular arrythmia, stroke, acute renal failure, and/or death). Results: Data from 1453 patients were analyzed. The neutrophil count, fluorescence granularity (NE-SCC), intensity (NE-SFL) and size (NE-FSC) increased with surgery. Heterogeneity of neutrophils decreased in terms of fluorescence granularity (NE-WX) and size (NE-WZ) but increased in terms of intensity (NE-WY). The lymphocyte count decreased with surgery. While fluorescence granularity (LY-X) and size increased (LY-Z), Lymphocyte intensity decreased (LY-Y). Lymphocytes were less heterogeneous in terms of their granularity, size and intensity after surgery (LY-WX, LY-WY, LY-WZ). Patients who developed the composite complication criteria had a higher pre-operative neutrophil count (5.08 [3.89;6.95] vs 4.76 [3.60;6.13], p = 0.02; AUC = 0.56 [0.51;0.60]), and more heterogeneous neutrophils in terms of fluorescence granularity (NE-WX, AUC = 0.57 [0.52;0.62]) and intensity (NE-WY, AUC 0.61 [0.56;0.65]). Those patients also had lower pre-operative lymphocyte count (1.49 [1.10;1.14] vs 1.81 [1.39;2.39], p<0.01, AUC = 0.61 [0.57;0.66]) and fluorescence granularity (LY-X, AUC = 0.57 [0.53;0.62]). NE-WX, NE-WY and LYX were associated with post-operative complications after adjustment on the EuroSCORE 2 (adjusted odd ratio of 1.01 [1.00;1.02]; 1.01 [1.00;1.01] and 1.08 [1.02;1.15] respectively). Conclusion: Cardiac surgery with cardiopulmonary bypass was associated with substantial alterations of CPD probably reflecting leukocytes activation in sterile inflammation. Pre-operative NE-WX, NE-WY and LY-X biomarkers levels were associated with post-operative complications, independently of the EuroSCORE 2. Such routine, unexploited and low cost parameters might represent useful tools likely to monitor immune function and predict outcomes for patients undergoing cardiac surgery. Our findings requires validation on a larger external cohort. [ABSTRACT FROM AUTHOR]

Keywords: early assessment; flow cytometry; measurable residual disease; multiple myeloma; outcome EN early assessment flow cytometry measurable residual disease multiple myeloma outcome e82 e85 4 06/14/22 20220615 NES 220615 Multiple myeloma (MM) treatment has evolved remarkably with the introduction of new agents such as proteasome inhibitors, immunomodulatory drugs (IMIDS) and therapeutic antibodies. The level of minimal residual disease in the bone marrow of patients with multiple myeloma before high-dose therapy and autologous blood stem cell transplantation is an independent predictive parameter. The 26 patients with persistent positive MRD had worse PFS compared to the negative MRD post- and pre-ASCT cases (24 months vs 45 months vs 68 months, I p i < 0.0001). [Extracted from the article]

Author(s): D. Andrew Howell (corresponding author) [1]; Mark Sullivan [1]; Peter E. Nugent [2]; Richard S. Ellis [3]; Alexander J. Conley [1]; Damien Le Borgne [4]; Raymond G. Carlberg [1]; [...]

Lymphoid neoplasms are a heterogeneous group of lymphoid neoplastic diseases with multiple presentations, and varying prognoses. They are especially frequent in older patients (OPs) and the atypism of this frail elderly population can make the diagnostic process even more difficult. Blood lymphocyte immunophenotyping (BLI) is essential in rapid noninvasive diagnosis orientation and guides complementary investigations. To our knowledge, BLI prescription has never been evaluated in OPs. We hypothesized that, when there is a suspicion of lymphoid neoplasm in the geriatric population, a BLI is performed in view of various clinical or biological abnormalities. This study aimed to: (1) describe the characteristics of hospitalized OPs having undergone BLI for suspected lymphoid neoplasm, (2) identify the causes leading to BLI prescription, and (3) identify the most profitable criteria for BLI prescription. This was a descriptive retrospective study on 151 OPs aged ≥75 years who underwent BLI over a 2-year period. Regarding BLI prescriptions, eight had lymphocytosis, constituting the "lymphocytosis group" (LG+), while the 143 others had BLI prescribed for reasons other than lymphocytosis (LG−), mainly general weakness and anemia. In the LG−, we compared OPs with positive and negative BLI results. The criteria found to be profitable for BLI prescription were lymphadenopathy, splenomegaly, lymphocytosis, and thrombocytopenia. BLI identified circulating lymphoid neoplasms (positive BLI) in 21/151 OPs, mainly marginal zone lymphoma and chronic lymphocytic leukemia. In polymorbid OPs, as per our study population, the diagnostic and therapeutic complexity explained in part the sole use of indirect and minimally invasive diagnostic techniques such as BLI. [ABSTRACT FROM AUTHOR]

Diagnosis of B-cell chronic lymphocytic leukemia (B-CLL) is usually straightforward, involving clinical, immunophenotypic (Matutes score), and (immuno)genetic analyses (to refine patient prognosis for treatment). CLL cases with atypical presentation (e.g., Matutes ≤ 3) are also encountered, and for these diseases, biology and prognostic impact are less clear. Here we report the genomic characterization of a case of atypical B-CLL in a 70-yr-old male patient; B-CLL cells showed a Matutes score of 3, chromosomal translocation t(14;18)(q32;q21) (BCL2/IGH), mutated IGHV, deletion 17p, and mutations in BCL2, NOTCH1 (subclonal), and TP53 (subclonal). Quite strikingly, a novel PAX5 mutation that was predicted to be loss of function was also seen. Exome sequencing identified, in addition, a potentially actionable BRAF mutation, together with novel somatic mutations affecting the homeobox transcription factor NKX2-3, known to control B-lymphocyte development and homing, and the epigenetic regulator LRIF1, which is implicated in chromatin compaction and gene silencing. Neither NKX2-3 nor LRIF1 mutations, predicted to be loss of function, have previously been reported in B-CLL. Sequencing confirmed the presence of these mutations together with BCL2, NOTCH1, and BRAF mutations, with the t(14;18)(q32;q21) translocation, in the initial diagnostic sample obtained 12 yr prior. This is suggestive of a role for these novel mutations in B-CLL initiation and stable clonal evolution, including upon treatment withdrawal. This case extends the spectrum of atypical B-CLL with t(14;18)(q32;q21) and highlights the value of more global precision genomics for patient follow-up and treatment in these patients. [ABSTRACT FROM AUTHOR]

We evaluate the impact of imaging systematics on the clustering of luminous red galaxies (LRG), emission-line galaxies (ELG), and quasars (QSO) targeted for the upcoming Dark Energy Spectroscopic Instrument (DESI) survey. Using Data Release 7 of the DECam Legacy Survey, we study the effects of astrophysical foregrounds, stellar contamination, differences between north galactic cap and south galactic cap measurements, and variations in imaging depth, stellar density, galactic extinction, seeing, airmass, sky brightness, and exposure time before presenting survey masks and weights to mitigate these effects. With our sanitized samples in hand, we conduct a preliminary analysis of the clustering amplitude and evolution of the DESI main targets. From measurements of the angular correlation functions, we determine power law fits |$r_0 = 7.78 \pm 0.26\, h^{-1}$| Mpc, γ  = 1.98 ± 0.02 for LRGs and |$r_0 = 5.45 \pm 0.1\, h^{-1}$| Mpc, γ  = 1.54 ± 0.01 for ELGs. Additionally, from the angular power spectra, we measure the linear biases and model the scale-dependent biases in the weakly non-linear regime. Both sets of clustering measurements show good agreement with survey requirements for LRGs and ELGs, attesting that these samples will enable DESI to achieve precise cosmological constraints. We also present clustering as a function of magnitude, use cross-correlations with external spectroscopy to infer dN/dz and measure clustering as a function of luminosity, and probe higher order clustering statistics through counts-in-cells moments. [ABSTRACT FROM AUTHOR]

We measure the imprint of primordial baryon acoustic oscillations (BAOs) in the correlation function of Lyα absorption in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) and the extended BOSS (eBOSS) in Data Release 14 (DR14) of the Sloan Digital Sky Survey (SDSS)-IV. In addition to 179 965 spectra with absorption in the Lyman-α (Lyα) region, we use Lyα absorption in the Lyman-β region of 56 154 spectra for the first time. We measure the Hubble distance, DH, and the comoving angular diameter distance, DM, relative to the sound horizon at the drag epoch rd at an effective redshift z = 2.34. Using a physical model of the correlation function outside the BAO peak, we find DH(2.34)/rd = 8.86 ± 0.29 and DM(2.34)/rd = 37.41 ± 1.86, within 1σ from the flat-ΛCDM model consistent with CMB anisotropy measurements. With the addition of polynomial "broadband" terms, the results remain within one standard deviation of the CMB-inspired model. Combined with the quasar-Lyα cross-correlation measurement presented in a companion paper, the BAO measurements at z = 2.35 are within 1.7σ of the predictions of this model. [ABSTRACT FROM AUTHOR]

We present a measurement of the baryon acoustic oscillation (BAO) scale at redshift z = 2.35 from the three-dimensional correlation of Lyman-α (Lyα) forest absorption and quasars. The study uses 266 590 quasars in the redshift range 1.77 <  z <  3.5 from the Sloan Digital Sky Survey (SDSS) Data Release 14 (DR14). The sample includes the first two years of observations by the SDSS-IV extended Baryon Oscillation Spectroscopic Survey (eBOSS), providing new quasars and re-observations of BOSS quasars for improved statistical precision. Statistics are further improved by including Lyα absorption occurring in the Lyβ wavelength band of the spectra. From the measured BAO peak position along and across the line of sight, we determined the Hubble distance DH and the comoving angular diameter distance DM relative to the sound horizon at the drag epoch rd: DH(z = 2.35)/rd = 9.20 ± 0.36 and DM(z = 2.35)/rd = 36.3 ± 1.8. These results are consistent at 1.5σ with the prediction of the best-fit spatially-flat cosmological model with the cosmological constant reported for the Planck (2016) analysis of cosmic microwave background anisotropies. Combined with the Lyα auto-correlation measurement presented in a companion paper, the BAO measurements at z = 2.34 are within 1.7σ of the predictions of this model. [ABSTRACT FROM AUTHOR]

Thrombotic manifestations are a hallmark of many auto-immune diseases (AID), specially of warm autoimmune hemolytic anemia (wAIHA), as 15 to 33% of adults with wAIHA experience venous thromboembolic events (VTE). However, beyond the presence of positive antiphospholipid antibodies and splenectomy, risk factors for developing a VTE during wAIHA have not been clearly identified. The aim of this retrospective study was to characterize VTEs during wAIHA and to identify risk factors for VTE. Forty-eight patients with wAIHA were included, among whom 26 (54%) had secondary wAIHA. Eleven (23%) patients presented at least one VTE, that occurred during an active phase of the disease for 10/11 patients (90%). The frequency of VTE was not different between primary and secondary AIHA (23.7 vs. 19.2%; p = 0.5). The Padua prediction score based on traditional risk factors was not different between patients with and without VTE. On multivariate analysis, total bilirubin ≥ 40 μmol/L [odds ratio (OR) = 7.4; p = 0.02] and leucocyte count above 7x109/L (OR = 15.7; p = 0.02) were significantly associated with a higher risk of thrombosis. Antiphospholipid antibodies were screened in 9 out the 11 patients who presented a VTE and were negative. Thus, the frequency of VTE is high (23%) during wAIHA and VTE preferentially occur within the first weeks of diagnosis. As no clinically relevant predictive factors of VTE could be identified, the systematic use of a prophylactic anticoagulation should be recommended in case of active hemolysis and its maintenance after hospital discharge should be considered. The benefit of a systematic screening for VTE and its procedure remain to be determined. [ABSTRACT FROM AUTHOR]

Background: In this study, we primarily sought to assess the ability of flow cytometry to predict early clinical deterioration and overall survival in patients with sepsis admitted in the ED and ICU.Methods: Patients admitted for community-acquired acute sepsis from 11 hospital centers were eligible. Early (day 7) and late (day 28) deaths were notified. Levels of CD64pos granulocytes, CD16pos monocytes, CD16dim immature granulocytes (IGs), and T and B lymphocytes were assessed by flow cytometry using an identical, cross-validated, robust, and simple consensus standardized protocol in each center.Results: Among 1,062 patients screened, 781 patients with confirmed sepsis were studied (age, 67 ± 48 years; Simplified Acute Physiology Score II, 36 ± 17; Sequential Organ Failure Assessment, 5 ± 4). Patients were divided into three groups (sepsis, severe sepsis, and septic shock) on day 0 and on day 2. On day 0, patients with sepsis exhibited increased levels of CD64pos granulocytes, CD16pos monocytes, and IGs with T-cell lymphopenia. Clinical severity was associated with higher percentages of IGs and deeper T-cell lymphopenia. IG percentages tended to be higher in patients whose clinical status worsened on day 2 (35.1 ± 35.6 vs 43.5 ± 35.2, P = .07). Increased IG percentages were also related to occurrence of new organ failures on day 2. Increased IG percentages, especially when associated with T-cell lymphopenia, were independently associated with early (P < .01) and late (P < .01) death.Conclusions: Increased circulating IGs at the acute phase of sepsis are linked to clinical worsening, especially when associated with T-cell lymphopenia. Early flow cytometry could help clinicians to target patients at high risk of clinical deterioration.Trial Registry: ClinicalTrials.gov; No.: NCT01995448; URL: www.clinicaltrials.gov. [ABSTRACT FROM AUTHOR]

Abstract: Objectives: To investigate the efficacy, safety, and cost of a pomalidomide‐dexamethasone regimen in patients with relapsed and refractory multiple myeloma (RRMM). Methods: All patients (n = 63) treated with pomalidomide‐dexamethasone for RRMM in our university hospital between August 2013 and October 2015 were included. Results: Pomalidomide was discontinued early due to progression (before the 4th cycle) in 17 (27%) patients. No case was discontinued for intolerance. The only independent factor that predicted early pomalidomide discontinuation was time from diagnosis to pomalidomide initiation <3 years. Overall response rate was 51% including complete response in 8%, very good partial response in 25%, and partial response in 19% patients. Thirteen (33%) patients showed stable disease. Median overall survival was 6.4 months in the 17 patients who discontinued pomalidomide early vs 26.8 months in the 14 patients with stable disease vs not achieved in the 32 responders (log‐rank; P < 10−3). The most common grade ≥3 adverse events were neutropenia (14%) and infections (25%). The incremental cost‐effectiveness ratio of pomalidomide‐dexamethasone compared with dexamethasone alone was estimated at €39 911 per life‐year gained. Conclusions: The study demonstrated that pomalidomide‐dexamethasone regimen has a long‐term favorable safety‐efficacy profile in RRMM patients. The survival benefit is substantial even in patients with stable disease. [ABSTRACT FROM AUTHOR]

The assessment of minimal residual disease (MRD) in acute myeloblastic leukemia is of growing interest as a prognostic marker of patients' outcome. Multiparameter flow cytometry (MFC), tracking leukemia-associated immunophenotypic patterns, has been shown in several studies to be a useful tool to investigate MRD. Here, we report a multicenter prospective study which allowed to define a harmonized analysis strategy, as well as the efficacy of MFC MRD to predict outcome. This study included 276 patients, in 10 different MFC centers, of whom 268 had at least 1 MRD check point. The combination of a CD45, CD34, and CD33 backbone, with the addition of CD117, CD13, CD7, and CD15 in 2 five-color tubes allowed to define each patient's multiparameter immunophenotypic characteristics at diagnosis, according to a Boolean combination of gates. The same individual diagnosis gating strategy was then applied at each MRD time point for each patient. MRD levels were stratified according to log by log thresholds, from 5 × 10-2 (the classical morphological threshold to define remission) down to <5 × 10-5 . MRD was found to be constantly negative (<5 × 10-5 ) for 148 patients. Survival analyses significantly associated MRD negativity with a good prognosis and any positive value with poorer outcome. All P values were <0.0001 both for disease-free and overall survival at the earliest time point (post-induction, MRD1) as well as when considering all time points together. Finally, MRD levels were independent of cytogenetics and allowed in fact to further stratify all cytogenetics risk groups. In summary, this multicenter study demonstrates that a simple combination of immunophenotypic markers successfully allows for the detection of MRD in acute myeloblastic leukemia patients, with a strong correlation to outcome. [ABSTRACT FROM AUTHOR]

Background: Expression of SRY [sex-determining region Y]-box11 (SOX11) is specific to mantle cell lymphoma (MCL) and contributes, in conjunction with immunoglobulin variable heavy chain gene mutation status, to the identification of two forms of this disease. Methods: The aim of this report was firstly, to design an easy and suitable RT-qPCR method to quantify SOX11 mRNA expression in mantle cell lymphoma and other B cell malignancies with the proper reference gene; secondly, to define the best threshold of relative quantity of SOX11 mRNA in order to reach the best compromise between sensitivity and specificity. Results: For best discrimination of MCL and non-MCL groups we determined an area under the curve (AUC) of 0.9750 and a threshold of 1.76 with 100% sensitivity and 88% specificity. AUC and threshold values of respectively 0.91/1.346 [87% sensitivity, 80% specificity] and 0.9525/1.7120 [100% sensitivity, 88% specificity] for GAPDH and RPLP0 respectively denote that the RPLP0 reference gene alone is sufficient for PCR housekeeping gene. Conclusion: This work describes an RT-qPCR assay for SOX11 expression in order to better characterize MCL at diagnosis. Further studies on larger cohorts are needed to evaluate this molecular tool, especially for the follow-up of minimal residual disease. [ABSTRACT FROM AUTHOR]

A major hallmark of cortical organization is the existence of a variable number of layers, i.e., sheets of neurons stacked on top of each other, in which neurons have certain commonalities. However, even for the neocortex, variable numbers of layers have been described and it is just a convention to distinguish six layers from each other. Whether cortical layers are a structural epiphenomenon caused by developmental dynamics or represent a functionally important modularization of cortical computation is still unknown. Here we present our insights from the reeler mutant mouse, a model for a developmental, "molecular lesion"-induced loss of cortical layering that could serve as ground truth of what an intact layering adds to the cortex in terms of functionality. We could demonstrate that the reeler neocortex shows no inversion of cortical layers but rather a severe disorganization that in the primary somatosensory cortex leads to the complete loss of layers. Nevertheless, the somatosensory system is well organized. When exploring an enriched environment with specific sets of whiskers, activity-dependent gene expression takes place in the corresponding modules. Precise whisker stimuli lead to the functional activation of somatotopically organized barrel columns as visualized by intrinsic signal optical imaging. Similar results were obtained in the reeler visual system. When analyzing pathways that could be responsible for preservation of tactile perception, lemniscal thalamic projections were found to be largely intact, despite the smearing of target neurons across the cortical mantle. However, with optogenetic experiments we found evidence for a mild dispersion of thalamic synapse targeting on layer IV-spiny stellate cells, together with a general weakening in thalamocortical input strength. This weakening of thalamic inputs was compensated by intracortical mechanisms involving increased recurrent excitation and/or reduced feedforward inhibition. In conclusion, a layer loss so far only led to the detection of subtle defects in sensory processing by reeler mice. This argues in favor of a view in which cortical layers are not an essential component for basic perception and cognition. A view also supported by recent studies in birds, which can have remarkable cognitive capacities despite the lack of a neocortex with multiple cortical layers. In conclusion, we suggest that future studies directed toward understanding cortical functions should rather focus on circuits specified by functional cell type composition than mere laminar location. [ABSTRACT FROM AUTHOR]

GABAergic interneurons represent ∼15% to 20% of all cortical neurons, but their diversity grants them unique roles in cortical circuits. In the barrel cortex, responses of excitatory neurons to stimulation of facial whiskers are direction selective, whereby excitation is maximized over a narrow range of angular deflections. Whether GABAergic interneurons are also direction selective is unclear. Here, we use two-photon-guided whole-cell recordings in the barrel cortex of anesthetized mice and control whisker stimulation to measure direction selectivity in defined interneuron subtypes. Selectivity is ubiquitous in interneurons, but tuning sharpness varies across populations. Vasoactive intestinal polypeptide (VIP) interneurons are as selective as pyramidal neurons, but parvalbumin (PV) interneurons are more broadly tuned. Furthermore, a majority (2/3) of somatostatin (SST) interneurons receive direction-selective inhibition, with the rest receiving direction-selective excitation. Sensory evoked activity in the barrel cortex is thus cell-type specific, suggesting that interneuron subtypes make distinct contributions to cortical representations of stimuli. [Display omitted] • In vivo two-photon-guided patch clamp in identified neuronal types of mouse barrel cortex • Controlled whisker stimulation in eight angular directions • Direction preference exists in all major GABAergic neurons of the cortex • Stimulation hyperpolarizes somatostatin-positive neurons in a direction-dependent manner Assemblies of cortical excitatory neurons encode the properties of sensory stimulus by responding selectively to discrete features such as direction of whisker deflection. Using in vivo patch-clamp recordings in the barrel cortex, Guy et al. show that this property extends to all major subtypes of GABAergic neurons. [ABSTRACT FROM AUTHOR]

Calreticulin (CALR) mutations have recently been reported in 70–84% of JAK2V617F-negative myeloproliferative neoplasms (MPN), and this detection has become necessary to improve the diagnosis of MPN. In a large single-centre cohort of 298 patients suffering from Essential Thrombocythemia (ET), the JAK2V617F, CALR and MPL mutations were noted in 179 (60%), 56 (18.5%) and 13 (4.5%) respectively. For the detection of the CALR mutations, three methods were compared in parallel: high-resolution melting-curve analysis (HRM), product-sizing analysis and Sanger sequencing. The sensitivity for the HRM, product-sizing analysis and Sanger sequencing was 96.4%, 98.2% and 89.3% respectively, whereas the specificity was 96.3%, 100% and 100%. In our cohort, the product-sizing analysis was the most sensitive method and was the easiest to interpret, while the HRM was sometimes difficult to interpret. In contrast, when large series of samples were tested, HRM provided results more quickly than did the other methods, which required more time. Finally, the sequencing method, which is the reference method, had the lowest sensitivity but can be used to describe the type of mutation precisely. Altogether, our results suggest that in routine laboratory practice, product-sizing analysis is globally similar to HRM for the detection of CALR mutations, and that both may be used as first-line screening tests. If the results are positive, Sanger sequencing can be used to confirm the mutation and to determine its type. Product-sizing analysis provides sensitive and specific results, moreover, with the quantitative measurement of CALR, which might be useful to monitor specific treatments. [ABSTRACT FROM AUTHOR]

Our specialized population-based registry has allowed us to explore changes in incidence and survival by subtype over the last 30 years. Between 1980 and 2009, 4790 cases of lymphoid malignancies were registered using the International Classification of Diseases for Oncology. The incidence rate of lymphoid malignancies was 20.5 per 100 000 inhabitants per year, and ranged from 0.1 to 4 according to subtype. Five-year net survival was 65%, and ranged from 41 % to 93% according to subtype. We observed an increase in 5-year net survival between the periods 1980-1989 and 2000-2009 (58% vs. 70%). This was observed in most but not all subtypes. Our long-standing population-based registry allowed us to measure differences in trends according to the subtype of lymphoid malignancy. Incidence rates steadily increased in quite frequent entities, and poor survival probability for most entities indicates that they should be the next objective in therapeutic research programs. [ABSTRACT FROM AUTHOR]

Flow cytometry (FC) instruments settings classically rely on local establishment of photomultipliers (PMT) voltages adapted to the measurements expected to be performed. In the era of multiparameter FC (MFC), it appears more and more desirable that comparable patterns of fluorescence are obtained in different settings. This relies on a harmonization of settings between instruments. Although this has been shown to be feasible within a given brand of flow cytometers, little information is available about broader comparisons in a given center or in a multicenter fashion. Here, we report a two-phase series of experiments first performed between a Canto II (BD Biosciences) and a Navios (Beckman Coulter) instruments in the same center. PMT values adjusted on the reference instrument (RI) Canto II were used to establish target values for PMT settings on the paired Navios practice instrument (PI). This allowed to show the good correlation of all but peaks 1 and 2 of Rainbow® beads between RI and PI. Using 4- or 8-color stained leukocytes, the similitude of the settings was further confirmed. A complex set of matrices was then established between five centers all equipped with both instruments. Using Bland & Altman difference comparisons for median fluorescence values, it was shown that using either Rainbow beads or CD16 stained polymorphonuclears to set-up target values on the RI CantoII, highly superimposable results could be obtained on all 9 PI. The latter were obtained using Rainbow beads or Compbeads® for comparisons. In summary, this two-phase study demonstrates the feasibility of different methods allowing for a robust harmonization of settings for MFC. © 2013 International Society for Advancement of Cytometry [ABSTRACT FROM AUTHOR]

Background: Although immune modulation is a promising therapeutic avenue in coronavirus disease 2019 (COVID-19), the most relevant targets remain to be found. COVID-19 has peculiar characteristics and outcomes, suggesting a unique immunopathogenesis.Methods: Thirty-six immunocompetent non-COVID-19 and 27 COVID-19 patients with severe pneumonia were prospectively enrolled in a single center, most requiring intensive care. Clinical and biological characteristics (including T cell phenotype and function and plasma concentrations of 30 cytokines) and outcomes were compared.Results: At similar baseline respiratory severity, COVID-19 patients required mechanical ventilation for significantly longer than non-COVID-19 patients (15 [7-22] vs. 4 (0-15) days; p = 0.0049). COVID-19 patients had lower levels of most classical inflammatory cytokines (G-CSF, CCL20, IL-1β, IL-2, IL-6, IL-8, IL-15, TNF-α, TGF-β), but higher plasma concentrations of CXCL10, GM-CSF and CCL5, compared to non-COVID-19 patients. COVID-19 patients displayed similar T-cell exhaustion to non-COVID-19 patients, but with a more unbalanced inflammatory/anti-inflammatory cytokine response (IL-6/IL-10 and TNF-α/IL-10 ratios). Principal component analysis identified two main patterns, with a clear distinction between non-COVID-19 and COVID-19 patients. Multivariate regression analysis confirmed that GM-CSF, CXCL10 and IL-10 levels were independently associated with the duration of mechanical ventilation.Conclusion: We identified a unique cytokine response, with higher plasma GM-CSF and CXCL10 in COVID-19 patients that were independently associated with the longer duration of mechanical ventilation. These cytokines could represent the dysregulated immune response in severe COVID-19, as well as promising therapeutic targets. ClinicalTrials.gov: NCT03505281. [ABSTRACT FROM AUTHOR]