SlicerSALT: Shape AnaLysis Toolbox

SlicerSALT is an open-source platform for disseminating state-of-the-art methods for performing statistical shape analysis. These methods are developed as 3D Slicer extensions to take advantage of its powerful underlying libraries. SlicerSALT itself is a heavily customized 3D Slicer package that is designed to be easy to use for shape analysis researchers. The packaged methods include powerful techniques for creating and visualizing shape representations as well as performing various types of analysis.

Automatic quantification framework to detect cracks in teeth

Studies show that cracked teeth are the third most common cause for tooth loss in industrialized countries. If detected early and accurately, patients can retain their teeth for a longer time. Most cracks are not detected early because of the discontinuous symptoms and lack of good diagnostic tools. Currently used imaging modalities like Cone Beam Computed Tomography (CBCT) and intraoral radiography often have low sensitivity and do not show cracks clearly. This paper introduces a novel method that can detect, quantify, and localize cracks automatically in high resolution CBCT (hr-CBCT) scans of teeth using steerable wavelets and learning methods. These initial results were created using hr-CBCT scans of a set of healthy teeth and of teeth with simulated longitudinal cracks. The cracks were simulated using multiple orientations. The crack detection was trained on the most significant wavelet coefficients at each scale using a bagged classifier of Support Vector Machines. Our results show high discriminative specificity and sensitivity of this method. The framework aims to be automatic, reproducible, and open-source. Future work will focus on the clinical validation of the proposed techniques on different types of cracks ex-vivo. We believe that this work will ultimately lead to improved tracking and detection of cracks allowing for longer lasting healthy teeth.

Seven additional families with spondylocarpotarsal synostosis syndrome with novel biallelic deleterious variants in FLNB

The location and/or type of variants in FLNB result in a spectrum of osteochondrodysplasias ranging from mild forms, like spondylocarpotarsal synostosis syndrome and Larsen syndrome, to severe perinatal lethal forms, such as atelosteogenesis I and III and Boomerang dysplasia. Spondylocarpotarsal synostosis syndrome is characterized by disproportionate short stature, vertebral anomalies and fusion of carpal and tarsal bones. Biallelic loss-of-function variants in FLNB are known to cause spondylocarpotarsal synostosis syndrome and 9 families and 9 pathogenic variants have been reported so far. We report clinical features of 10 additional patients from 7 families with spondylocarpotarsal synostosis syndrome due to 7 novel deleterious variants in FLNB, thus expanding the clinical and molecular repertoire of spondylocarpotarsal synostosis syndrome. Our report validates key clinical (fused thoracic vertebrae and carpal and tarsal coalition) and molecular (truncating variants in FLNB) characteristics of this condition.

Alpha galactosidase A activity in Parkinson's disease

Glucocerebrosidase (GCase, deficient in Gaucher disease) enzymatic activity measured in dried blood spots of Parkinson's Disease (PD) cases is within healthy range but reduced compared to controls. It is not known whether activities of additional lysosomal enzymes are reduced in dried blood spots in PD. To test whether reduction in lysosomal enzymatic activity in PD is specific to GCase, we measured GCase, acid sphingomyelinase (deficient in Niemann-Pick disease types A and B), alpha galactosidase A (deficient in Fabry), acid alpha-glucosidase (deficient in Pompe) and galactosylceramidase (deficient in Krabbe) enzymatic activities in dried blood spots of PD patients (n = 648) and controls (n = 317) recruited from Columbia University. Full sequencing of glucocerebrosidase (GBA) and the LRRK2 G2019S mutation was performed. Enzymatic activities were compared between PD cases and controls using t-test and regression models adjusted for age, gender, and GBA and LRRK2 G2019S mutation status. Alpha galactosidase A activity was lower in PD cases compared to controls both when only non-carriers were included (excluding all GBA and LRRK2 G2019S carriers and PD cases with age-at-onset below 40) [2.85 μmol/l/h versus 3.12 μmol/l/h, p = 0.018; after controlling for batch effect, p = 0.006 (468 PD cases and 296 controls)], and when including the entire cohort (2.89 μmol/l/h versus 3.10 μmol/l/h, p = 0.040; after controlling for batch effect, p = 0.011). Because the alpha galactosidase A gene is X-linked, we stratified the analyses by sex. Among women who were non-carriers of GBA and LRRK2 G2019S mutations (PD, n = 155; control, n = 194), alpha galactosidase A activity was lower in PD compared to controls (2.77 μmol/l/h versus 3.10 μmol/l/h, p = 0.044; after controlling for a batch effect, p = 0.001). The enzymatic activity of acid sphingomyelinase, acid alpha-glucosidase and galactosylceramidase was not significantly different between PD and controls. In non-carriers, most lysosomal enzyme activities were correlated, with the strongest association in GCase, acid alpha-glucosidase, and alpha galactosidase A (Pearson correlation coefficient between 0.382 and 0.532). In a regression model with all five enzymes among non-carriers (adjusted for sex and age), higher alpha galactosidase A activity was associated with lower odds of PD status (OR = 0.54; 95% CI:0.31-0.95; p = 0.032). When LRRK2 G2019S PD carriers (n = 37) were compared to non-carriers with PD, carriers had higher GCase, acid sphingomyelinase and alpha galactosidase A activity. We conclude that alpha galactosidase A may have a potential independent role in PD, in addition to GCase.

Role of Central Corneal Thickness on Baseline Parameters and Progression of Visual Fields in Open Angle Glaucoma

Purpose

To evaluate the relationship of central corneal thickness (CCT) to baseline visual field parameters and visual field progression in patients with primary open-angle glaucoma (POAG).

Methods

Charts of consecutive patients with POAG were reviewed to obtain visual field data. Visual field was measured by standard threshold static perimetry. Variables analyzed included mean deviation (MD) and pattern standard deviation (PSD).

Results

A total of 121 eyes examined over 4 years were evaluated. A significant negative relationship between CCT and PSD (correlation coefficient: −0.02, p<0.05) was found. Analyses comparing CCT to change in PSD and MD (visual field progression) were statistically not significant.

Conclusions

Patients with thinner corneas initially present with a greater visual field defect, indicating that thin corneas may contribute to advanced glaucomatous damage at the time of diagnosis. However, CCT does not seem to be a significant risk factor for progression of the disease.

Neurenteric cyst of the conus medullaris

Background:

Neurenteric cysts (NECs) are rare developmental malformations of the central nervous system (CNS) which originate as benign congenital lesions. They originate from developmental foregut precursors, and are presumed to be the result of abnormal partitioning of the embryonic notochord plate. Such NECs predominantly arise in the cervical region in patients around 6 years of age or in their twenties or thirties. Notably, NECs of the conus medullaris are exceedingly rare, especially in patients of advanced age.

Case Description:

A 70-year-old male presented with bilateral upper thigh and leg pain of over 20 years duration. His pain worsened over the past 3 years, and he sought surgical management. Although his neurological exam was normal, the lumbar magnetic resonance imaging revealed an intradural, nonenhancing, thin-walled, cystic lesion at L1/conus medullaris. The lesion was successfully resected without any adverse sequelae.

Conclusions:

NECs are rare congenital legions that involve the spine. Here, an L1 intradural extramedullay neuroenteric cyst of the conus medullaris was resected without complications.

Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions

Mechanisms driving acute food allergic reactions have not been fully characterized. We profile the dynamic transcriptome of acute peanut allergic reactions using serial peripheral blood samples obtained from 19 children before, during, and after randomized, double-blind, placebo-controlled oral challenges to peanut. We identify genes with changes in expression triggered by peanut, but not placebo, during acute peanut allergic reactions. Network analysis reveals that these genes comprise coexpression networks for acute-phase response and pro-inflammatory processes. Key driver analysis identifies six genes (LTB4R, PADI4, IL1R2, PPP1R3D, KLHL2, and ECHDC3) predicted to causally modulate the state of coregulated networks in response to peanut. Leukocyte deconvolution analysis identifies changes in neutrophil, naive CD4+ T cell, and macrophage populations during peanut challenge. Analyses in 21 additional peanut allergic subjects replicate major findings. These results highlight key genes, biological processes, and cell types that can be targeted for mechanistic study and therapeutic targeting of peanut allergy.

Robust head CT image registration pipeline for craniosynostosis skull correction surgery

Craniosynostosis is a congenital malformation of the infant skull typically treated via corrective surgery. To accurately quantify the extent of deformation and identify the optimal correction strategy, the patient-specific skull model extracted from a pre-surgical computed tomography (CT) image needs to be registered to an atlas of head CT images representative of normal subjects. Here, the authors present a robust multi-stage, multi-resolution registration pipeline to map a patient-specific CT image to the atlas space of normal CT images. The proposed registration pipeline first performs an initial optimisation at very low resolution to yield a good initial alignment that is subsequently refined at high resolution. They demonstrate the robustness of the proposed method by evaluating its performance on 560 head CT images of 320 normal subjects and 240 craniosynostosis patients and show a success rate of 92.8 and 94.2%, respectively. Their method achieved a mean surface-to-surface distance between the patient and template skull of <2.5 mm in the targeted skull region across both the normal subjects and patients.

Post-prophylaxis Toxoplasma chorioretinitis following donor-recipient mismatched liver transplantation

Toxoplasmosis may be transferred by organ transplantation. The most common clinical presentation is with multisystem disease, although isolated ocular toxoplasmosis has been described. Many centers have suggested that universal use of co-trimoxazole prophylaxis obviates the need for specific Toxoplasma testing. We report a case of donor-acquired ocular toxoplasmosis after liver transplantation despite co-trimoxazole prophylaxis. The diagnosis was confirmed by Toxoplasma polymerase chain reaction assay in conjunction with seroconversion. The fact that the infection was donor acquired was confirmed by serological mismatch and the absence of sporozoite-specific antigen antibody in the recipient.

Second family provides further evidence for causation of Steel syndrome by biallelic mutations in COL27A1

Steel syndrome is a rare disorder of the skeleton characterized by facial dysmorphism, short stature, carpal coalition, dislocated radial heads, bilateral hip dislocation and vertical talus. Homozygous variants in COL27A1 were reported in an extending family from Puerto Rico. Here, we report a 5-year-old girl from a non-consanguineous family with facial dysmorphism, short stature, carpal coalition, dislocation of radial heads, bilateral hip dislocation, scoliosis and vertical talus. Exome sequencing identified 2 novel compound heterozygous variants c.521_528del (p.(Cys174Serfs*34)) and c.2119C>T (p.(Arg707*)) in COL27A1 in this child and the parents were heterozygous carriers. We hence report the second molecularly proven case of Steel syndrome and the first case to be reported among non-Puerto Rican population. Our report further validates the role of COL27A1 mutations in causation of Steel syndrome.

Young onset colorectal cancer: How does it differ from its older counterpart?

BACKGROUND

Colorectal cancer in the young has been a debated topic in literature with conflicting reports as to its pattern of occurrence and survival as compared to the older age group.

MATERIALS AND METHODS

Retrospective study to analyze the clinicopathological characteristics, treatment modalities and survival of sporadic young-onset colorectal cancer (YOCR) patients (<40 years) and compare them with the older group (>40 years).

RESULTS

Of 172 patients managed, 72 (42%) were in the YOCR group. Among 72 patients, six were excluded because of hereditary syndromes. Incontinence (P = 0.02) and obstruction at time of presentation (P = 0.03) was significantly more common in the YOCR group. Left sided disease was more common in YOCR group (47/66) compared to the older group (65/100), but the difference was not statistically significant (P = 0.45). The proportion of rectal cancers was significantly more in the YOCR group (39/47) compared to the older group (39/65) (P = 0.01). Significant difference in resectability was noted in the left sided (YOCR 26/47 vs. older 49/65 P = 0.04) and the rectal cancers (YOCR 18/39 vs. Older 29/39 P = 0.02). The survival was similar among the two groups.

CONCLUSIONS

Sporadic colorectal cancers in the young are more advanced and less resectable when compared to older population. Genetic studies are needed to elaborate the reasons for left sided predominance and aggressiveness of sporadic colorectal cancers in the younger subgroups.

Characterization of a biologically derived rabbit tracheal scaffold

There is a clinical need to provide replacement tracheal tissue for the pediatric population affected by congenital defects, as current surgical solutions are not universally applicable. A potential solution is to use tissue engineered scaffold as the framework for regenerating autologous tissue. Rabbit trachea were used and different detergents (Triton x-100 and sodium deoxycholate) and enzymes (DNAse/RNAse) investigated to create a decellularization protocol. Each reagent was initially tested individually and the outcome used to design a combined protocol. At each stage the resultant scaffold was assessed histologically, molecularly for acellularity and matrix preservation. Immunogenicity of the final scaffold was assessed by implantation into a rat model for 4 weeks. Both enzymes and detergents were required to produce a completely acellular (DNA content 42.78 ng/mg) scaffold with preserved collagen and elastin however, GAG content were reduced (8.78 ± 1.35 vs. 5.5 ± 4.8). Following in vivo implantation the scaffold elicited minimal immune response and showed significant cellular infiltration and vasculogenesis. The luminal aspect of the implanted scaffold showed infiltration of host derived cells, which were positive for pan cytokeratin. It is possible to create biologically derived biocompatible scaffolds to address specific pediatric clinical problems. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 2126-2135, 2017.