Automated Landmarking via Multiple Templates

Geometric morphometrics based on landmark data has been increasingly used in biomedical and biological researchers for quantifying complex phenotypes. However, manual landmarking can be laborious and subject to intra and interobserver errors. This has motivated the development of automated landmarking methods. We have recently introduced ALPACA (Automated Landmarking through Point cloud Alignment and Correspondence), a fast method to automatically annotate landmarks via use of a landmark template as part of the SlicerMorph toolkit. Yet, using a single template may not consistently perform well for large study samples, especially when the sample consists of specimen with highly variable morphology, as it is common evolutionary studies. In this study, we introduce a variation on our ALPACA pipeline that supports multiple specimen templates, which we call MALPACA. We show that MALPACA outperforms ALPACA consistently by testing on two different datasets. We also introduce a method of choosing the templates that can be used in conjunction with MALPACA, when no prior information is available. This K-means method uses an approximation of the total morphological variation in the dataset to suggest samples within the population to be used as landmark templates. While we advise investigators to pay careful attention to the template selection process in any of the template-based automated landmarking approaches, our analyses show that the introduced K-means based method of templates selection is better than randomly choosing the templates. In summary, MALPACA can accommodate larger morphological disparity commonly found in evolutionary studies with performance comparable to human observer.

Predictive role of serum rheumatoid factor in different disease pattern of psoriasis and psoriatic arthritis

Background Psoriasis is a multisystem inflammatory disorder with variable morphology, clinical pattern and multiple comorbidities. Interplay between genetic and environmental factors leading to an aberrant immune response in the skin may contribute to disease development. The assessment for risk factors, signs, and symptoms of potential comorbid diseases is an important component of patient management. The aim of this study is to determine rheumatoid factors (RF) positivity and its levels in psoriasis patients, and describe its relationship with the demographic and clinical characteristics, comorbidities, and disease patterns of psoriasis. Results Rheumatoid factor was positive in psoriatic patients more than control,30% of patients had positive rheumatoid factor while only 10% of control had positive results. Rheumatoid factor level was 63.8 ± 186.7 IU/ml in psoriasis vs. 9.3 ± 12.3 in control. Thirty percent of psoriasis patients have positive rheumatoid factor vs. 10% of control. There was no significant statistical difference between psoriasis patients with or without arthritis as regard rheumatoid factor positivity and titer; rheumatoid factor was positive in 20% in psoriatic patients with arthritis vs. 26% in psoriatic patients without arthritis. In psoriatic patients, the status of rheumatoid factor did not relate to disease severity, onset, course, site of affection, presence of scalp, nail affection, and presence of dactylitis (p value>0.5). Conclusion Psoriasis was associated with higher seropositivity of RF compared to age-matched non-psoriatic healthy controls. Occurrence and level of rheumatoid factor were not associated with severity or clinical pattern of psoriasis.

Segmentation and Automatic Identification of Vasculature in Coronary Angiograms

Coronary angiography is the “gold standard” for the diagnosis of coronary heart disease, of which vessel segmentation and identification technologies are paid much attention to. However, because of the characteristics of coronary angiograms, such as the complex and variable morphology of coronary artery structure and the noise caused by various factors, there are many difficulties in these studies. To conquer these problems, we design a preprocessing scheme including block-matching and 3D filtering, unsharp masking, contrast-limited adaptive histogram equalization, and multiscale image enhancement to improve the quality of the image and enhance the vascular structure. To achieve vessel segmentation, we use the C-V model to extract the vascular contour. Finally, we propose an improved adaptive tracking algorithm to realize automatic identification of the vascular skeleton. According to our experiments, the vascular structures can be successfully highlighted and the background is restrained by the preprocessing scheme, the continuous contour of the vessel is extracted accurately by the C-V model, and it is verified that the proposed tracking method has higher accuracy and stronger robustness compared with the existing adaptive tracking method.

Morphology, Formation, and Activity of Three Different Pockmark Systems in Peri-Alpine Lake Thun, Switzerland

Pockmarks are crater-like depressions formed by upward fluid flow (gas and/or liquid) through the unconsolidated sediment column on the floor of oceans and lakes. While pockmarks are well described in the marine realm, they have essentially been overlooked in lacustrine settings, likely due to a lack in economic interest to apply high-resolution hydroacoustic techniques in lakes. A swath-bathymetry survey on Lake Thun, Switzerland, revealed the existence of three pockmark systems. One pockmark (110 m in diameter) was discovered near a big karst system at Beatenberg at a water depth of ~217 m. Its activity is probably associated with episodic groundwater seepage induced by earthquakes, floods and snowmelt. At another site, Daerligen, we detected at ~60 m water depth the presence of multiple smaller pockmarks (~1.5 to 10 m in diameter) that seem to be active, continuously liberating CH4 gas by bubble ebullition. The CH4 displayed a biogenic carbon isotopic signature, however, the exact origin of the gas remains unknown. The third site, Tannmoos (~35 m water depth), comprises two large pockmarks (20–43 m in diameter) connected to a karst system in gypsum-carrying bedrock. One of these pockmarks is constituted of several unit pockmarks (e.g., sub-pockmarks; 0.3 to 0.8 m in diameter). While strong evidence is still lacking, we suggest that groundwater discharge occasionally occurs through these unit pockmarks during periods of intense precipitation. Hence, this study reveals the existence of three pockmark systems of variable morphology and mechanisms of formation within the same lake, reflecting different hydrological and biogeochemical regimes. Moreover, it underscores the potential importance of pockmarks in influencing hydrological and CH4 budgets in lakes. Clearly more work on quantifying seasonal fluxes of groundwater and CH4 release via lacustrine pockmarks is required, and it needs to be seen whether the observations made in Lake Thun are universal and apply also to many other lacustrine environments worldwide.

Immunohistochemical evaluation of suspected oral malignant melanoma in cats

Oral malignant melanoma (OMM) is considered the third most common oral malignant neoplasm in cats, but its variable morphology and frequent lack of melanin pigment make it a diagnostic challenge. Twenty-two cases of cats with malignant oral neoplasms that were diagnosed as OMM or listed OMM as a suspected differential diagnosis on the biopsy report were examined using an immunohistochemistry (IHC) panel for S100, melan-A, PNL2, laminin, CD34, and pan-cytokeratin. Although OMM was suspected ( n = 14) or previously diagnosed ( n = 8), only 2 cases were immunohistochemically confirmed as OMM. Seven cases were classified as soft tissue sarcoma based on positive expression of CD34 or laminin, and one was classified as carcinoma based on positive expression of pan-cytokeratin. The majority of cases ( n = 12) were categorized as unclassified malignant neoplasms because they did not express melan-A, PNL2, laminin, CD34, or pan-cytokeratin; however, a proportion of these did express S100 ( n = 7). Long-term prognosis of all 22 cats was poor, with a median survival time of 87 days (range = 2–249 days). Cases with longer survival times (>100 days) were treated with surgery, radiation therapy, or a combination. For feline oral malignant neoplasms thought to be OMM, routine use of IHC is required for an accurate diagnosis.

Surface Texturing of Polyethylene Terephthalate Induced by Excimer Laser in Silver Nanoparticle Colloids

We report on a novel technique of surface texturing of polyethylene terephthalate (PET) foil in the presence of silver nanoparticles (AgNPs). This approach provides a variable surface morphology of PET evenly decorated with AgNPs. Surface texturing occurred in silver nanoparticle colloids of different concentrations under the action of pulse excimer laser. Surface morphology of PET immobilized with AgNPs was observed by AFM and FEGSEM. Atomic concentration of silver was determined by XPS. A presented concentration-controlled procedure of surface texturing of PET in the presence of silver colloids leads to a highly nanoparticle-enriched polymer surface with a variable morphology and uniform nanoparticle distribution.

A Microcomputed Tomographic Evaluation of Root Canal Morphology of Maxillary Second Premolars in a Pakistani Cohort

This study aimed to investigate variations in the root canal morphology of maxillary second premolar (MSP) teeth using microcomputed tomography (micro-CT). Sixty (N = 60) human extracted MSPs were collected and prepared for micro-CT scanning. The duration for scanning a single sample ranged between 30 and 40 min and a three-dimensional (3-D) image was obtained for all the MSPs. The images were evaluated by a single observer who recorded the canal morphology type, number of roots, canal orifices, apical foramina(s), apical delta(s), and accessory canals. The root canal configuration was categorized in agreement with Vertucci’s classification, and any configuration not in agreement with Vertucci’s classification was reported as an “additional canal configuration”. Descriptive statistics (such as mean percentages) were calculated using SPSS software. The most common types agreeing with Vertucci’s classification (in order of highest to lowest incidence) were types I, III, V, VII, II, and VI. The teeth also exhibited four additional configurations that were different from Vertucci’s classification: types 2-3, 1-2-3, 2-1-2-1, and 1-2-1-3. A single root was found in 96.7% and the majority of the samples demonstrated two canals (73.3%). Further, 80% of the teeth showed one canal orifice. The number of apical foramina’s in the teeth was variable, with 56.7% having solitary apical foramen. The accessory canal was found in 33.3%, and apical delta was found in only 20% of the samples. Variable morphology of the MSPs was detected in our study. The canal configuration most prevalent was type 1; however, the results also revealed some additional canal types.

Immunohistochemical characterization of mesothelioma in 6 large felids

Mesothelioma has been reported frequently in large felids. These neoplasms present a diagnostic challenge given their highly variable morphology that mimics carcinomas or sarcomas at different locations. Our goal was to characterize mesotheliomas morphologically and immunohistochemically to determine if a panel of antibodies could be used to more accurately support the diagnosis of these neoplasms in large felids. Mesotheliomas from 6 large felids, including 4 clouded leopards, 1 Bengal tiger, and 1 cheetah, were immunohistochemically labeled for vimentin, E-cadherin, pancytokeratin, Wilms tumor 1 (WT1), MUC-1, and calretinin. The mesotheliomas of the 4 clouded leopards and the tiger were of the epithelial subtype; the mesothelioma from the cheetah was biphasic. All 6 mesotheliomas had strong immunohistochemical labeling for vimentin, E-cadherin, and pancytokeratin. All cases had cytoplasmic labeling for WT1, and 2 also had nuclear labeling. The 3 mesotheliomas with distinct papillary fronds were weakly positive for MUC-1. These and one other epithelial mesothelioma were also positive for calretinin. Our study demonstrates that the morphologic and immunohistochemical phenotypes of mesothelioma that have been identified in humans and domestic species can occur in large felids, and a panel of pancytokeratin, vimentin, WT1, and calretinin can be utilized to support the diagnosis of these neoplasms.

BCOR-CCNB3 Sarcoma with Prominent Rhabdoid Cells Mimicking Rhabdomyoblasts: Expanding the Morphologic spectrum of BCOR-CCNB3 Sarcoma

BCOR-CCNB3 sarcoma (BCS) is a rare recently defined undifferentiated sarcoma that predominantly affects children and young adults. The diagnosis of this tumor is difficult due to the highly variable morphology and nonspecific immunophenotype. Emerging data suggest that patients with BCS show response to Ewing sarcoma-based treatment regimen, thus correct diagnosis is of clinical relevance. In this study, we report a case of BCS arising from the big toe of a 15-year-old male patient. The tumor had a prominent population of rhabdoid cells with bright eosinophilic cytoplasm mimicking rhabdomyosarcoma. The tumor cells were focally positive for desmin and myogenin, and negative for CD99. Next-generation sequencing showed the presence of BCOR-CCNB3 gene fusion. BCS with prominent rhabdoid cells has not been described before. This study further expands the morphologic spectrum of BCS.