Robust FCS Parsing: Exploring 211,359 Public Files

When it comes to data storage, the field of flow cytometry is fairly standardized, thanks to the flow cytometry standard (FCS) file format. The structure of FCS files is described in the FCS specification. Software that strictly complies with the FCS specification is guaranteed to be interoperable (in terms of exchange via FCS files). Nowadays, software interoperability is crucial for eco system, as FCS files are frequently shared, and workflows rely on more than one piece of software (e.g., acquisition and analysis software). Ideally, software developers strictly follow the FCS specification. Unfortunately, this is not always the case, which resulted in various nonconformant FCS files being generated over time. Therefore, robust FCS parsers must be developed, which can handle a wide variety of nonconformant FCS files, from different resources. Development of robust FCS parsers would greatly benefit from a fully fledged set of testing files. In this study, readability of 211,359 public FCS files was evaluated. Each FCS file was checked for conformance with the FCS specification. For each data set, within each FCS file, validated parse results were obtained for the TEXT segment. Highly space efficient testing files were generated. FlowCore was benchmarked in depth, by using the validated parse results, the generated testing files, and the original FCS files. Robustness of FlowCore (as measured by testing against 211,359 files) was improved by re-implementing the TEXT segment parser. Altogether, this study provides a comprehensive resource for FCS parser development, an in-depth benchmark of FlowCore, and a concrete proposal for improving FlowCore

High CD33-antigen loads in peripheral blood limit the efficacy of gemtuzumab ozogamicin |(Mylotarg®) treatment in acute myeloid leukemia patients

Gemtuzumab ozogamicin (Mylotarg®) induces remission in approximately 30% of relapsed AML patients. We previously demonstrated that gemtuzumab infusion results in near-complete CD33 saturation in peripheral blood, and that saturating gemtuzumab levels result in continuous binding and internalization of gemtuzumab due to renewed CD33 expression. We now demonstrate that a high CD33-antigen load in peripheral blood is an independent adverse prognostic factor, likely due to peripheral consumption of gemtuzumab. Indeed, CD33 saturation in bone marrow is significantly reduced (40-90% saturation) as compared with CD33 saturation in corresponding peripheral blood samples (>90%). In vitro, such reduced CD33 saturation levels were strongly related with reduced cell kill. Apparently, high CD33-antigen loads in blood consume gemtuzumab and thereby limit its penetration into bone marrow. Consequently, CD33 saturation in bone marrow is reduced, which hampers efficient cell kill. Therefore, gemtuzumab should be administered at higher or repeated doses, or, preferably, after reduction of the leukemic cell burden by classical chemotherapy

Modifications to the Cauchy–Born rule: Applications in the deformation of single-walled carbon nanotubes

AbstractThis paper presents a study of the Cauchy–Born (CB) rule as applied to the deformation analysis of single-walled carbon nanotubes (SWNTs) that are modeled as 2-dimensional manifolds. The C–C bond vectors in the SWNT are assumed to deform according to the local deformation gradient as per the CB rule or a modified version thereof. Aspects of the CB rule related to spatial inhomogeneity of the deformation gradient at the atomic scale are investigated in the context of a specific class of extension–twist deformation problems. Analytic expressions are derived for the deformed bond lengths using the standard CB rule as well as modified versions of the standard CB rule. Since the deformation map is conveniently prescribed in this work, it is possible to compare the performance of these deformation rules with the exact solution (i.e. the exact analytic expression for the deformed bond vectors) given directly by the deformation map. This approach provides insights into the CB rule and its possible modifications for use in more complicated deformations where an explicit deformation map is not available. Specifically, it is concluded that in the case of inhomogeneous deformations at the atomic scale for which the CB rule is only approximate (as demonstrated in Section 1 of this paper), the mean value theorem in calculus can be used as a guide to modify the CB rule and construct a more rigorous and accurate atomistic–continuum connection. The deformed bond lengths are used to formulate an enriched continuum hyperelastic strain energy density function based on interatomic potentials (the multi-body Tersoff–Brenner [Tersoff, J., 1988. New empirical approach for the structure and energy of covalent systems. Phys. Rev. B 37, 6991–7000; Brenner, D.W., 1990. Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Phys. Rev. B 42, 9458–9471] empirical interatomic potential for carbon-carbon bonds is used in this work). The deformation map (and hence the deformation gradient, the bond vectors and the continuum strain energy density) contains certain parameters, some of which are imposed and others determined as a result of energy minimization in the standard variational formulation. Numerical results for kinematic coupling and binding energy per atom are presented in the case of imposed extension and twist deformations on representative chiral, zig-zag and armchair nanotubes using the CB rule and its modifications. These results are compared with the exact solution based on the deformation map which serves as a basis for evaluating the efficacy of these deformation rules. The ideas presented in this paper can also be directly extended to other lattices

Increased group 2 innate lymphoid cells in peripheral blood of adults with mastocytosis

Background: Systemic mastocytosis is a hematological disease in which aberrant mast cells accumulate because of gain-of-function mutations in the KIT receptor. Group 2 innate lymphoid cells (ILC2s) are effector cells of type 2 immune responses that also express KIT and colocalize with mast cells at barrier tissue sites. In mouse models, mast cell-ILC2 crosstalk can drive local inflammation. However, a possible role for ILC2s in the pathophysiology of mastocytosis remains unexplored. Objective: We sought to characterize circulating ILC2s in a clinically diverse cohort of patients with mastocytosis. Methods: We included 21 adults with systemic mastocytosis and 18 healthy controls. Peripheral blood ILC2 abundance and phenotype were analyzed by flow cytometry and correlated to clinical characteristics, including the presence of the D816V KIT mutation. Results: ILC2 levels were significantly higher in D816V+ patients with mastocytosis compared with D816V− patients or healthy controls. We observed increased proportions of KIT+ ILC2s among patients with mastocytosis, regardless of D816V status. Patients with skin involvement and itch showed the highest levels of ILC2s, which was independent from atopy or serum tryptase levels. Allele-specific quantitative PCR showed that the vast majority of ILC2s did not carry the D816V mutation. Conclusions: Our findings suggest a role for ILC2s and pathogenic ILC2-mast cell crosstalk in mastocytosis. We hypothesize that a high cutaneous D816V+

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin

Newborns are unable to mount antibody responses towards certain antigens. This has been related to the restricted repertoire of immunoglobulin (Ig) genes of their B cells. The mechanisms underlying the restricted fetal Ig gene repertoire are currently unresolved. We here addressed this with detailed molecular and cellular analysis of human precursor-B cells from fetal liver, fetal bone marrow (BM), and pediatric BM. In the absence of selection processes, fetal B-cell progenitors more frequently used proximal V, D and J genes in complete IGH gene rearrangements, despite normal Ig locus contraction. Fewer N-nucleotides were added in IGH gene rearrangements in the context of low TdT and XRCC4 expression. Moreover, fetal progenitor-B cells expressed lower levels of IL7Rα than their pediatric counterparts. Analysis of progenitor-B cells from IL7Rα-deficient patients revealed that TdT expression and N-nucleotides additions in Dh-Jh junctions were dependent on functional IL7Rα. Thus, IL7Rα affects TdT expression, and decreased expression of this receptor underlies at least in part the skewed Ig repertoire formation in fetal B-cell precursors. These new insights provide a better understanding of the formation of adaptive immunity in the developing fetus