Many studies of the human brain have explored the relationship between cortical thickness and cognition, phenotype, or disease. Due to the subjectivity and time requirements in manual measurement of ...cortical thickness, scientists have relied on robust software tools for automation which facilitate the testing and refinement of neuroscientific hypotheses. The most widely used tool for cortical thickness studies is the publicly available, surface-based FreeSurfer package. Critical to the adoption of such tools is a demonstration of their reproducibility, validity, and the documentation of specific implementations that are robust across large, diverse imaging datasets. To this end, we have developed the automated, volume-based Advanced Normalization Tools (ANTs) cortical thickness pipeline comprising well-vetted components such as SyGN (multivariate template construction), SyN (image registration), N4 (bias correction), Atropos (n-tissue segmentation), and DiReCT (cortical thickness estimation). In this work, we have conducted the largest evaluation of automated cortical thickness measures in publicly available data, comparing FreeSurfer and ANTs measures computed on 1205 images from four open data sets (IXI, MMRR, NKI, and OASIS), with parcellation based on the recently proposed Desikan–Killiany–Tourville (DKT) cortical labeling protocol. We found good scan–rescan repeatability with both FreeSurfer and ANTs measures. Given that such assessments of precision do not necessarily reflect accuracy or an ability to make statistical inferences, we further tested the neurobiological validity of these approaches by evaluating thickness-based prediction of age and gender. ANTs is shown to have a higher predictive performance than FreeSurfer for both of these measures. In promotion of open science, we make all of our scripts, data, and results publicly available which complements the use of open image data sets and the open source availability of the proposed ANTs cortical thickness pipeline.
•A complete, volumetric-based cortical thickness pipeline is proposed.•The pipeline consists of well-vetted components fine-tuned by the original developers.•Approximately 1200 data were analyzed with no major failures.•All software is open source as part of the ANTs repository.•Analysis and visualization scripts using the R statistical package are also publicly available.
The Advanced Normalizations Tools ecosystem, known as ANTsX, consists of multiple open-source software libraries which house top-performing algorithms used worldwide by scientific and research ...communities for processing and analyzing biological and medical imaging data. The base software library, ANTs, is built upon, and contributes to, the NIH-sponsored Insight Toolkit. Founded in 2008 with the highly regarded Symmetric Normalization image registration framework, the ANTs library has since grown to include additional functionality. Recent enhancements include statistical, visualization, and deep learning capabilities through interfacing with both the R statistical project (ANTsR) and Python (ANTsPy). Additionally, the corresponding deep learning extensions ANTsRNet and ANTsPyNet (built on the popular TensorFlow/Keras libraries) contain several popular network architectures and trained models for specific applications. One such comprehensive application is a deep learning analog for generating cortical thickness data from structural T1-weighted brain MRI, both cross-sectionally and longitudinally. These pipelines significantly improve computational efficiency and provide comparable-to-superior accuracy over multiple criteria relative to the existing ANTs workflows and simultaneously illustrate the importance of the comprehensive ANTsX approach as a framework for medical image analysis.
Plasma cell neoplasms including multiple myeloma (MM) and related terminally differentiated B-cell neoplasms are characterized by secretion of monoclonal immunoglobulin and stepwise development from ...a preneoplastic clonal B and/or plasma cell proliferation called monoclonal gammopathy of undetermined significance (MGUS). Diagnosis of these disorders requires integration of clinical, laboratory, and morphological features. While their classification mostly remains unchanged compared to the revised 2016 WHO classification and the 2014 International Myeloma Working Group consensus, some changes in criteria and terminology were proposed in the 2022 International Consensus Classification (ICC) of mature lymphoid neoplasms. MGUS of IgM type is now divided into IgM MGUS of plasma cell type, precursor to the rare IgM MM and characterized by MM-type cytogenetics, lack of clonal B-cells and absence of
MYD88
mutation, and IgM MGUS, NOS including the remaining cases. Primary cold agglutinin disease is recognized as a new entity. MM is now formally subdivided into cytogenetic groups, recognizing the importance of genetics for clinical features and prognosis. MM with recurrent genetic abnormalities includes MM with
CCND
family translocations, MM with
MAF
family translocations, MM with
NSD2
translocation, and MM with hyperdiploidy, with the remaining cases classified as MM, NOS. For diagnosis of localized plasma cell tumors, solitary plasmacytoma of bone, and primary extraosseous plasmacytoma, the importance of excluding minimal bone marrow infiltration by flow cytometry is emphasized. Primary systemic amyloidosis is renamed immunoglobulin light chain amyloidosis (AL), and a localized AL amyloidosis is recognized as a distinct entity. This review summarizes the updates on plasma cell neoplasms and related entities proposed in the 2022 ICC.
Key points
• Lymphoplasmacytic lymphoma can be diagnosed with lymphoplasmacytic aggregates in trephine biopsies < 10% of cellularity and evidence of clonal B-cells and plasma cells
.
• IgM MGUS is subdivided into a plasma cell type and a not otherwise specified (NOS) type.
• Primary cold agglutinin disease is recognized as a new entity
.
• The term “multiple myeloma” replaces the term “plasma cell myeloma” used in the 2016 WHO classification
.
• Multiple myeloma is subdivided into 4 mutually exclusive cytogenetic groups and MM NOS
.
• Minimal bone marrow infiltration detected by flow cytometry is of major prognostic importance for solitary plasmacytoma of bone and to a lesser extent for primary extraosseous plasmacytoma
.
• Localized IG light chain amyloidosis is recognized as a separate entity, distinct from systemic immunoglobulin light chain (AL) amyloidosis
.
To evaluate the clinical utility of immune receptor translocation-associated protein 1 (IRTA1) and myeloid nuclear differentiation antigen (MNDA) expression in the diagnosis and classification of ...marginal zone lymphomas (MZLs).
IRTA1 was examined using a novel RNA in situ hybridization assay and MNDA expression determined by immunohistochemistry in 127 small B-cell neoplasms, including 80 cases of MZL.
IRTA1 expression was detected in 31 (42%) of 74 MZLs vs one (2%) of 43 other small B-cell neoplasms (P < .001). MNDA staining was positive in 51 (64%) of 79 MZLs vs 21 (45%) of 46 non-MZLs (P = .06). MNDA expression was particularly uncommon in follicular lymphoma (3/14, 21%; P = .003 vs MZL). There was no association between MNDA and IRTA1 expression and the presence of monocytoid cytology. IRTA1 expression was less frequent in cases with a diffuse growth pattern.
IRTA1 and MNDA are useful markers in the differential diagnosis of MZLs.
We report herein a comparison of the photophysics of a series of polythiophenes with ionization potentials ranging from 4.8 to 5.6 eV as pristine films and when blended with 5 wt % ...1-(3-methoxycarbonyl)propyl-1-phenyl-6,6C61 (PCBM). Three polymers are observed to give amorphous films, attributed to a nonplanar geometry of their backbone while the other five polymers, including poly(3-hexylthiophene), give more crystalline films. Optical excitation of the pristine films of the amorphous polymers is observed by transient absorption spectroscopy to give rise to polymer triplet formation. For the more crystalline pristine polymers, no triplet formation is observed, but rather a short-lived (∼100 ns), broad photoinduced absorption feature assigned to polymer polarons. For all polymers, the addition of 5 wt % PCBM resulted in 70−90% quenching of polymer photoluminescence (PL), indicative of efficient quenching of polythiophene excitons. Remarkably, despite this efficient exciton quenching, the yield of dissociated polymer+ and PCBM- polarons, assayed by the appearance of a long-lived, power-law decay phase assigned to bimolecular recombination of these polarons, was observed to vary by over 2 orders of magnitude depending upon the polymer employed. In addition to this power-law decay phase, the blend films exhibited short-lived decays assigned, for the amorphous polymers, to neutral triplet states generated by geminate recombination of bound radical pairs and, for the more crystalline polymers, to the direct observation of the geminate recombination of these bound radical pairs to ground. These observations are discussed in terms of a two-step kinetic model for charge generation in polythiophene/PCBM blend films analogous to that reported to explain the observation of exciplex-like emission in poly(p-phenylenevinylene)-based blend films. Remarkably, we find an excellent correlation between the free energy difference for charge separation (ΔG CS rel) and yield of the long-lived charge generation, with efficient charge generation requiring a much larger ΔG CS rel than that required to achieve efficient PL quenching. We suggest that this observation is consistent with a model where the excess thermal energy of the initially formed polaron pairs is necessary to overcome their Coulombic binding energy. This observation has important implications for synthetic strategies to optimize organic solar cell performance, as it implies that, at least devices based on polythiophene/PCBM blend films, a large ΔG CS rel (or LUMO level offset) is required to achieve efficient charge dissociation.
Microfluidics with fluid walls Walsh, Edmond J; Feuerborn, Alexander; Wheeler, James H R ...
Nature communications,
10/2017, Letnik:
8, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method - Freestyle Fluidics - that overcomes many key limitations. ...In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications - triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.
Follicular lymphoma (FL) and marginal zone lymphoma (MZL) are indolent mature B-cell neoplasms with variable clinical presentation and distinct histopathologic features. Recent advances in the ...biology and molecular characteristics of these lymphomas have further expanded our understanding of the heterogeneous nature of these lymphomas, with increasing recognition of specific disease entities within the broader categories of FL and MZL. Here, we discuss the conclusions of the 2022 International Consensus Classification of Mature Lymphoid Neoplasms (2022 ICC) dealing with FL, and review differences with the proposed WHO 5th Edition classification. We review issues related to grading and alternative forms of FL especially those lacking the genetic hallmark of FL, the t(14;18) chromosomal alteration. Among them, t(14;18)-negative CD23
+
follicle center lymphoma has been proposed by the 2022 ICC as a provisional entity. Other follicle center–derived lymphomas such as pediatric-type follicular lymphoma, testicular follicular lymphoma, primary cutaneous follicle center lymphoma, and large B-cell lymphoma with
IRF4
rearrangement are considered distinct entities separate from conventional FL. Importantly, large B-cell lymphoma with
IRF4
rearrangement introduced as a provisional entity in the WHO 2017 is upgraded to a definite entity in the 2022 ICC. We also discuss diagnostic strategies for recognition of MZLs including splenic MZL, extranodal MZL (MALT lymphoma), and primary nodal MZL. The importance of molecular studies in the distinction among marginal zone lymphoma subtypes is emphasized, as well as their value in the differential diagnosis with other B-cell lymphomas.
Prussian blue (PB) and its analogues are promising materials for electrochemical energy storage, yet their use in flow-type devices is limited by their lack of redox responsiveness as colloidal ...suspensions. We have investigated the redox chemistry amine functionalization of PB along with its Cu analogue (CuPBA). No redox response of colloidal PB was observed and suspensions of CuPBA formed films on electrode surfaces with and without applied potentials; the films were redox-active but the material that remained suspended in solution did not participate in redox chemistry. Propylamine (pa), ethylenediamine (en), or tetramethylethylenediamine (TMEDA) were added in an attempt to maintain well dispersed suspensions through nanoparticle surface functionalization. Propylamine modifications resulted in a loss of the CuPBA network and subsequent precipitation of insoluble materials. Coordination of ethylenediamine prompted the formation of Cu and Fe monomers (Cu(en)2 m+/Fe(CN)6 n− ) that remained soluble in aqueous electrolytes. In the absence of supporting electrolytes, these monomers formed a one-dimensional (1D) polymeric structure (Cu2Fe-1D). TMEDA modification preserved the CuPBA extended structure with only modest precipitate formation over 30 min. The redox responsiveness of these suspensions depended on conditions; in 1 M KCl, no redox chemistry was observed for the CuPBA. In pH 4 potassium hydrogen phthalate buffer, a signal was observed that was attributed to the Fe centers of CuPBA. Under these conditions, the material precipitated in ∼15 min and the signal was lost. Although the Fe centers in these networks are redox-active, additional work is needed to realize longer-term redox activity and stability. Ligand modifications can alter the properties of these networks but within a given ligand class, e.g., amines, the effects can vary greatly from the deconstruction of the framework to preventing film formation.
Primary cutaneous marginal zone lymphoma (PCMZL) can be subdivided into 2 groups based on immunoglobulin (Ig) heavy chain usage: IgM-positive cases that constitute a less common and more T-helper ...type 1-driven process, and more common heavy chain class-switched cases that are predominantly T-helper type 2-driven. Although some report a significant IgG4-positive subset, others have found a much smaller proportion. To further evaluate the proportion of IgG4-positive PCMZL, to address whether IgG4-positive cases have any distinctive characteristics, and to assess whether additional features separating IgM-positive and class-switched cases could be identified, the clinicopathologic features of 26 PCMZL obtained from 19 patients were investigated. Twenty of 26 (77%) PCMZL were heavy chain class-switched (19 IgG-positive, 1 IgA-positive), including 9 that were IgG4-positive (35%). IgG4-positive and other class-switched PCMZL were morphologically similar. IgM-positive cases occurred in older individuals (median: 69 vs. 46.5 y; P=0.0001), more often involved the subcutis (P=0.002), demonstrated plasma cells diffusely scattered versus at the periphery of the lymphoid infiltrate (P=0.005), uniformly showed follicular colonization (P=0.0001), contained more numerous B cells (P=0.0004), and were more likely to have a T-cell CD4:CD8 ratio of <3:1 (P=0.03). None of the IgM-positive PCMZL harbored a MYD88 L265P mutation. No significant differences in clinical outcome were documented. These results highlight the high frequency of IgG4-positive PCMZL, which are otherwise similar to other class-switched cases, provide additional evidence supporting the distinction between class-switched and IgM-positive cases, and emphasize the indolent nature of at least the class-switched PCMZL, which may warrant their categorization as a clonal chronic lymphoproliferative disorder.
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