Utility of immunocytochemistry in diagnosing leptomeningeal metastases from an intrahepatic cholangiocarcinoma

Isolated spinal leptomeningeal metastases (LMM) without brain metastases are infrequent, accounting for about 1% of all solid tumors. In LMM, cerebrospinal fluid (CSF) analyses are mostly abnormal. Demonstrations of intrathecal tumor markers are highly suggestive, but only a positive cytology is diagnostic. The initial CSF cytology can give a false negative result in up to 40–50% of patients with pathologically proven LMM on autopsy. We report a case of intrahepatic cholangiocarcinoma with spinal LMM confirmed using cytokeratin7 and pancytokeratin (AE1/AE3) immunocytochemical studies on paucicellular cerebrospinal fluid cytospin preparation. Given the paucicellularity of the smears and difficult morphologic categorization, immunocytochemistry is vital for confirmatory diagnosis and can help reduce false negative results. To the best of our knowledgethis is the first case report of cytologically confirmed LMM from an intrahepatic cholangiocarcinoma while the patient was undergoing treatment. Diagn. Cytopathol. 2014;42:54–57. © 2013 Wiley Periodicals, Inc.     

Structural,magnetic and magneto-optical studies of Mn/Al bilayer thin films on GaAs substrates

Ferromagnetism and magnetic anisotropy in Mn–Al thin films can be of great interest due to their applications in spintronic components and as rare-earth free magnets. Temperature-dependent uniaxial anisotropy has been observed in ferromagnetic MnAl thin films, which is attributed to the modification of the tetragonal lattice distortion with the change in annealing temperature, confirmed by VSM, MOKE and XRD results; the annealing time did not affect the magnetic anisotropy. A simple evaporation technique was used to deposit the Mn/Al bilayer thin films (thickness ∼ 64 nm) on GaAs substrates. A comprehensive study of the effect of annealing temperature as well as annealing time on structural, microstructural, magnetic and magneto-optical properties are reported in this paper. The ferromagnetic phase was enriched in annealed samples, which was confirmed by XRD, MOKE and magnetic hysteresis loops. XRD results revealed that the ferromagnetic τ-phase was enhanced in annealed films with the increase in annealing temperature ≥ 400 °C. Surface roughness was estimated from the AFM micrographs and was found to be increased, whereas the mean grain size was decreased on annealing the as-deposited Mn/Al bilayer thin film. The gradual increase in magnetic coercivity was found on increasing the annealing temperature. It is interesting to note that the magnetic easy axis can be tuned by changing the annealing temperature of MnAl thin films, and the easy axis changes from perpendicular to parallel direction of the film plane when the annealing temperature varies from 400 °C to 500 °C. MOKE results were also found to be consistent with the magnetic results.

Ferromagnetism and magnetic anisotropy in Mn–Al thin films can be of great interest due to their applications in spintronic components and as rare-earth free magnets.     

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.The realization that all organisms on Earth are related by common descent (1) was one of the most profound insights in scientific history. The goal of reconstructing the tree of life is one of the most daunting challenges in biology. The scope of the problem is immense: there are ∼1.8 million named species, and most species have yet to be described (2–4). Despite decades of effort and thousands of phylogenetic studies on diverse clades, we lack a comprehensive tree of life, or even a summary of our current knowledge. One reason for this shortcoming is lack of data. GenBank contains DNA sequences for ∼411,000 species, only 22% of estimated named species. Although some gene regions (e.g., rbcL, 16S, COI) have been widely sequenced across some lineages, they are insufficient for resolving relationships across the entire tree (5). Most recognized species have never been included in a phylogenetic analysis because no appropriate molecular or morphological data have been collected.There is extensive publication of new phylogenies, data, and inference methods, but little attention to synthesis. We therefore focus on constructing, to our knowledge, the first comprehensive tree of life through the integration of published phylogenies with taxonomic information. Phylogenies by systematists with expertise in particular taxa likely represent the best estimates of relationships for individual clades. By focusing on trees instead of raw data, we avoid issues of dataset assembly (6). However, most published phylogenies are available only as journal figures, rather than in electronic formats that can be integrated into databases and synthesis methods (7–9). Although there are efforts to digitize trees from figures (10), we focus instead on synthesis of published, digitally available phylogenies.When source phylogenies are absent or sparsely sampled, taxonomic hierarchies provide structure and completeness (11, 12). Given the limits of data availability, synthesizing phylogeny and taxonomic classification is the only way to construct a tree of life that includes all recognized species. One obstacle has been the absence of a complete, phylogenetically informed taxonomy that spans traditional taxonomic codes (13). We therefore assembled a comprehensive global reference taxonomy via alignment and merging of multiple openly available taxonomic resources. The Open Tree Taxonomy (OTT) is open, extensible, and updatable, and reflects the overall phylogeny of life. With the continued updating of phylogenetic information from published studies, this framework is poised to update taxonomy in a phylogenetically informed manner far more rapidly than has occurred historically (see Fig. S1 for workflow).Open in a separate windowFig. S1.The Open Tree of Life workflow. External taxonomies (and synonym lists) are merged into the Open Tree Taxonomy, OTT. Published phylogenies are curated (rooted, and names mapped to OTT) and stored, with full edit history, in a GitHub repository. The source trees are decomposed into subproblems, and the loaded along with OTT into a common graph database. We traverse the resulting graph and extract a tree of life based on priority of inputs. Components with stars indicate the presence of application programming interfaces (APIs) to access data and services.We used recently developed graph methods (14) to synthesize a tree of life of over 2.3 million operational taxonomic units (OTUs) from the reference taxonomy and curated phylogenies. Taxonomies contribute to the structure only where we do not have phylogenetic trees. Advantages of graph methods include easy storage of topological conflict among underlying source trees in a single database, the construction of alternative synthetic trees, and the ability to continuously update the tree with new phylogenetic and/or taxonomic information. Importantly, our methodology also highlights the current state of knowledge for any given clade and reveals those portions of the tree that most require additional study. Although a massive undertaking in its own right, this draft tree of life represents only a first step. Through feedback, addition of new data, and development of new methods, the broader community can improve this tree.     

Homozygous <Emphasis Type="Italic">GRID2</Emphasis> missense mutation predicts a shift in the D-serine binding domain of GluD2 in a case with generalized brain atrophy and unusual clinical features

Background

Spinocerebellar ataxias comprise a large and heterogeneous group of disorders that may present with isolated ataxia, or ataxia in combination with other neurologic or non-neurologic symptoms. Monoallelic or biallelic GRID2 mutations were recently reported in rare cases with cerebellar syndrome and variable degree of ataxia, ocular symptoms, hypotonia and developmental delay.

Case presentation

We report on a consanguineous family with autosomal recessive childhood onset of slowly progressive cerebellar ataxia and delayed psychomotor development in three siblings. MRI of an adult and affected family member revealed slightly widened cerebral and cerebellar sulci, suggesting generalized brain atrophy, and mild cerebellar atrophy. Using whole exome sequencing we identified a novel homozygous missense variant [c.2128C?>?T, p.(Arg710Trp)] in GRID2 that segregates with the disease. The missense variant is located in a conserved region encoding the extracellular serine-binding domain of the GluD2 protein and predicts a change in conformation of the protein.

Conclusion

The widespread supratentorial brain abnormalities, absence of oculomotor symptoms, increased peripheral muscle tone and the novel missense mutation add to the clinical and genetic variability in GRID2 associated cerebellar syndrome. The neuroradiological findings in our family indicate a generalized neurodegenerative process to be taken into account in other families segregating complex clinical features and GRID2 mutations.