Entropy-based particle correspondence for shape populations

Purpose

Statistical shape analysis of anatomical structures plays an important role in many medical image analysis applications such as understanding the structural changes in anatomy in various stages of growth or disease. Establishing accurate correspondence across object populations is essential for such statistical shape analysis studies.

Methods

In this paper, we present an entropy-based correspondence framework for computing point-based correspondence among populations of surfaces in a groupwise manner. This robust framework is parameterization-free and computationally efficient. We review the core principles of this method as well as various extensions to deal effectively with surfaces of complex geometry and application-driven correspondence metrics.

Results

We apply our method to synthetic and biological datasets to illustrate the concepts proposed and compare the performance of our framework to existing techniques.

Conclusions

Through the numerous extensions and variations presented here, we create a very flexible framework that can effectively handle objects of various topologies, multi-object complexes, open surfaces, and objects of complex geometry such as high-curvature regions or extremely thin features.

     

Plasmacytoid dendritic cells prime IL-10-producing T regulatory cells by inducible costimulator ligand

Although there is evidence for distinct roles of myeloid dendritic cells (DCs [mDCs]) and plasmacytoid pre-DCs (pDCs) in regulating T cell-mediated adaptive immunity, the concept of functional DC subsets has been questioned because of the lack of a molecular mechanism to explain these differences. In this study, we provide direct evidence that maturing mDCs and pDCs express different sets of molecules for T cell priming. Although both maturing mDCs and pDCs upregulate the expression of CD80 and CD86, only pDCs upregulate the expression of inducible costimulator ligand (ICOS-L) and maintain high expression levels upon differentiation into mature DCs. High ICOS-L expression endows maturing pDCs with the ability to induce the differentiation of naive CD4 T cells to produce interleukin-10 (IL-10) but not the T helper (Th)2 cytokines IL-4, -5, and -13. These IL-10-producing T cells are T regulatory cells, and their generation by ICOS-L is independent of pDC-driven Th1 and Th2 differentiation, although, in the later condition, some contribution from endogenous IL-4 cannot be completely ruled out. Thus, in contrast to mDCs, pDCs are poised to express ICOS-L upon maturation, which leads to the generation of IL-10-producing T regulatory cells. Our findings demonstrate that mDC and pDCs are intrinsically different in the expression of costimulatory molecules that drive distinct types of T cell responses.     

Functional mRNA analysis reveals aberrant splicing caused by novel intronic mutation in WDR45 in NBIA patient

WDR45 gene‐associated neurodegeneration with brain iron accumulation (NBIA), referred to as beta‐propeller protein‐associated neurodegeneration (BPAN), is a rare disorder that presents with a very nonspecific clinical phenotype in children constituting global developmental delay. This case report illustrates the power of a combination of trio exome sequencing, in silico splicing analysis, and mRNA analysis to provide sufficient evidence for pathogenicity of a relatively intronic variant in WDR45, and in so doing, find a genetic diagnosis for a 6‐year‐old patient with developmental delay and seizures, a diagnosis which may otherwise have only been found once the characteristic MRI patterns of the disease became more obvious in young adulthood.     

Shank–cortactin interactions control actin dynamics to maintain flexibility of neuronal spines and synapses

The family of Shank scaffolding molecules (comprising Shank1, 2 and 3) are core components of the postsynaptic density (PSD) in neuronal synapses. Shanks link surface receptors to other scaffolding molecules within the PSD, as well as to the actin cytoskeleton. However, determining the function of Shank proteins in neurons has been complicated because the different Shank isoforms share a very high degree of sequence and domain homology. Therefore, to control Shank content while minimizing potential compensatory effects, a miRNA‐based knockdown strategy was developed to reduce the expression of all synaptically targeted Shank isoforms simultaneously in rat hippocampal neurons. Using this approach, a strong (>75%) reduction in total Shank protein levels was achieved at individual dendritic spines, prompting an approximately 40% decrease in mushroom spine density. Furthermore, Shank knockdown reduced spine actin levels and increased sensitivity to the actin depolymerizing agent Latrunculin A. A SHANK2 mutant lacking the proline‐rich cortactin‐binding motif (SHANK2‐ΔPRO) was unable to rescue these defects. Furthermore, Shank knockdown reduced cortactin levels in spines and increased the mobility of spine cortactin as measured by single‐molecule tracking photoactivated localization microscopy, suggesting that Shank proteins recruit and stabilize cortactin at the synapse. Furthermore, it was found that Shank knockdown significantly reduced spontaneous remodelling of synapse morphology that could not be rescued by the SHANK2‐ΔPRO mutant. It was concluded that Shank proteins are key intermediates between the synapse and the spine interior that, via cortactin, permit the actin cytoskeleton to dynamically regulate synapse morphology and function.     

Real-Time Adherence Monitoring for HIV Antiretroviral Therapy

Current adherence assessments typically detect missed doses long after they occur. Real-time, wireless monitoring strategies for antiretroviral therapy may provide novel opportunities to proactively prevent virologic rebound and treatment failure. Wisepill, a wireless pill container that transmits a cellular signal when opened, was pilot tested in ten Ugandan individuals for 6 months. Adherence levels measured by Wisepill, unannounced pill counts, and self-report were compared with each other, prior standard electronic monitoring, and HIV RNA. Wisepill data was initially limited by battery life and signal transmission interruptions. Following device improvements, continuous data was achieved with median (interquartile range) adherence levels of 93% (87–97%) by Wisepill, 100% (99–100%) by unannounced pill count, 100% (100–100%) by self-report, and 92% (79–98%) by prior standard electronic monitoring. Four individuals developed transient, low-level viremia. After overcoming technical challenges, real-time adherence monitoring is feasible for resource-limited settings and may detect suboptimal adherence prior to viral rebound.     

Extracting timing and status descriptors for colonoscopy testing from electronic medical records

Colorectal cancer (CRC) screening rates are low despite confirmed benefits. The authors investigated the use of natural language processing (NLP) to identify previous colonoscopy screening in electronic records from a random sample of 200 patients at least 50 years old. The authors developed algorithms to recognize temporal expressions and ‘status indicators’, such as ‘patient refused’, or ‘test scheduled’. The new methods were added to the existing KnowledgeMap concept identifier system, and the resulting system was used to parse electronic medical records (EMR) to detect completed colonoscopies. Using as the ‘gold standard’ expert physicians'' manual review of EMR notes, the system identified timing references with a recall of 0.91 and precision of 0.95, colonoscopy status indicators with a recall of 0.82 and precision of 0.95, and references to actually completed colonoscopies with recall of 0.93 and precision of 0.95. The system was superior to using colonoscopy billing codes alone. Health services researchers and clinicians may find NLP a useful adjunct to traditional methods to detect CRC screening status. Further investigations must validate extension of NLP approaches for other types of CRC screening applications.Colorectal cancer (CRC) is the third most common cancer found in men and women in the USA, and is the second leading cause of cancer deaths.¹ Screening for CRC is recommended for average-risk individuals aged 50 years and older.² Current screening rates, however, are suboptimal; recent national studies report that only 40–60% of eligible patients receive proper screening.^{1 3}Whereas computerized decision support tools have the potential to improve CRC screening rates, the critical challenge is to identify quickly and accurately patients in need of screening. Current methods for determining CRC screening status (patient self-report, physician report, billing data, and manual chart abstraction) are time-consuming, expensive, and often inaccurate. Studies have shown that billing data underestimated CRC screening rates.⁴ Manual chart abstraction is expensive, and references to completed CRC screening tests are often located within the text of clinic notes, making them difficult to find. An Institute of Medicine report highlighted the need for automated data collection systems that could process natural language clinical texts to address challenges such as these.⁵This study investigated the use of a natural language processing (NLP) system to detect the timing and receipt of colonoscopies, the most commonly recommended CRC screening test at many institutions, including the study institution. The authors developed new algorithms to detect the timing and status of colonoscopy references within Vanderbilt Medical Center electronic medical record (EMR) system documents. Vanderbilt''s EMR comprises an integrated longitudinal system that receives data from more than 100 diverse sources such as laboratory and radiology reports, typed and dictated notes, interdisciplinary clinician-maintained problem lists, and inter- and intra-office messaging records.     

Multiples in dermatology: markers for special considerations in diagnosis, therapy, and prognosis

Multiples of certain cutaneous lesions should alert the clinician to a wider differential diagnosis and possible systemic associations although the individual skin lesion is often benign in nature and banal in appearance. This article focuses on such findings in selected multiple cutaneous lesions that may be classified according to the primary cutaneous feature as vascular, pigmentary, nevoid hamartomas, and tumors/neoplastic conditions. The clinical presentation of each entity and its significance, appropriate diagnostic evaluation, therapeutic and prognostic considerations and pertinent differential diagnoses will be reviewed.