PAT-GEOM: A Software Package for the Analysis of Animal Patterns

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Data Accessibility: The PAT-GEOM software package and its User Guide are available from the first author’s personal website (www.ianzwchan.com/my-research/pat-geom) or the Zenodo repository, https://doi.org/10.5281/zenodo.1834035 (for the software package; Chan, Stevens & Todd, 2018a) and https://doi.org/10.5281/zenodo.1835291 (for the User Guide; Chan, Stevens & Todd, 2018b). Datasets and R code are also available from Zenodo, https://doi.org/10.5281/zenodo.1831671 (Chan, Stevens & Todd, 2018c).1. Colour patterns often influence how animals interact with one another, but the ability 21 of researchers to quantify pattern per se is hampered by a lack of easily-accessible and user-friendly measurement software packages. 2. We address this issue by releasing PAT-GEOM, a free software package for use within ImageJ that allows users to measure seven properties of a pattern: (1) the shape of its markings, (2) the directionality in the shape of its markings, (3) the size of its markings, (4) the contrast of the pattern, (5) the distribution of its markings, (6) the directionality in the distribution of its markings, and (7) the randomness of the pattern. 3. We provide examples of how PAT-GEOM may be used, such as to visualise the ‘average pattern’ of a population of animals, or to compare the patterns on two animals. Using data from two case studies, we also demonstrate PAT-GEOM’s ability to identify the specific aspects of an organism’s pattern that match its background and to design artificial prey items that accurately resemble their model organism for use in predation experiments. 4. PAT-GEOM collates the tools to measure these seven diverse properties of animal colour patterns into one convenient, easy-to-use package. It can be employed in a wide range of studies on topics such as aposematism, camouflage and mimicry, and also has the potential to be applied to other research fields such as landscape ecology, botany and cellular biology.Singapore Ministry of Educatio

Tumors Metastatic to Thyroid Neoplasms: A Case Report and Review of the Literature

Metastasis into a thyroid neoplasm—tumor-to-tumor metastasis—is exceedingly rare. We describe the 28th documented case of a tumor metastatic to a thyroid neoplasm and review the literature on tumor-to-tumor metastasis involving a thyroid neoplasm as recipient. All cases showed a recipient thyroid neoplasm with an abrupt transition to a morphologically distinct neoplasm. Metastasis into primary thyroid neoplasm was synchronous in 33% of cases and metachronous in 67%. Follicular adenoma was the most common recipient thyroid neoplasm overall (16/28), and papillary thyroid carcinoma was the most common malignant recipient neoplasm (9/28). Of the 9 recipient papillary carcinomas, 6 were follicular variants. Renal cell carcinoma was the most common neoplasm to metastasize to a primary thyroid neoplasm (9/28), followed by lung (6/28), breast (5/28), and colon (3/28) carcinoma. Tumor-to-tumor metastasis should be considered whenever a dimorphic pattern is encountered in a thyroid tumor

Poorly Differentiated Squamous Cell Carcinoma Arising in Tattooed Skin

Introduction. Tattoos have increasingly become accepted by mainstream Western society. As a result, the incidence of tattoo-associated dermatoses is on the rise. The presence of a poorly differentiated squamous cell carcinoma in an old tattooed skin is of interest as it has not been previously documented. Case Presentation. A 79-year-old white homeless man of European descent presented to the dermatology clinic with a painless raised nodule on his left forearm arising in a tattooed area. A biopsy of the lesion revealed a poorly differentiated squamous cell carcinoma infiltrating into a tattoo. The lesion was completely excised and the patient remains disease-free one year later. Conclusion. All previous reports of squamous cell carcinomas arising in tattoos have been well-differentiated low-grade type or keratoacanthoma-type and are considered to be coincidental rather than related to any carcinogenic effect of the tattoo pigments. Tattoo-associated poorly differentiated invasive carcinoma appears to be extremely rare

Neoadjuvant treatment of Dermatofibrosarcoma Protuberans of pancreas with Imatinib: case report and systematic review of literature

Abstract Dermatofibrosarcoma Protuberans (DFSP) is a rare skin tumor, characterized by frequent local recurrence but is seldom metastatic. It is histologically characterized by storiform arrangement of spindle cells. Cytogenetically, most tumors are characterized by translocation 17:22 leading to overexpression of tyrosine kinase PDGFB which can be targeted with tyrosine kinase inhibitor, Imatinib. We describe the first case of unresectable pancreatic metastases from DFSP treated with neoadjuvant Imatinib and subsequently R0 metastectomy. Additionally, a comprehensive systematic review of DFSP pancreatic metastases and the current published data on the use of Imatinib in DFSP is summarized.Peer Reviewe

Three-Dimensional Reconstructions of Tadpole Chondrocrania from Histological Sections

Reconstructing three dimensional structures (3DR) from histological sections has always been difficult but is becoming more accessible with the assistance of digital imaging. We sought to assemble a low cost system using readily available hardware and software to generate 3DR for a study of tadpole chondrocrania. We found that a combination of RGB camera, stereomicroscope, and Apple Macintosh PowerPC computers running NIH Image, Object Image, Rotater. and SURFdriver software provided acceptable reconstructions. These are limited in quality primarily by the distortions arising from histological protocols rather than hardware or software

A dynamical framework for the origin of the diagonal South Pacific and South Atlantic convergence zones

The South Pacific Convergence Zone (SPCZ) and South Atlantic Convergence Zone (SACZ) are diagonal bands of precipitation that extend from the equator southeastward into the Southern Hemisphere over the western Pacific and Atlantic Oceans, respectively. With mean precipitation rates over 5 mm day−1, they are a major component of the tropical and global climate in austral summer. However, their basic formation mechanism is not fully understood. Here, a conceptual framework for the diagonal convergence zones is developed, based on calculations of the vorticity budget from reanalysis and Rossby wave theory. Wave trains propagate eastward along the Southern Hemisphere subtropical jet, with initially quasi-circular vorticity centres. In the zonally sheared environment on the equatorward flank of the jet, these vorticity centres become elongated and develop a northwest-southeast tilt. Ray tracing diagnostics in a non-divergent, barotropic Rossby wave framework then explain the observed equatorward propagation of these diagonal vorticity structures toward the westerly ducts over the equatorial Pacific and Atlantic. The baroclinic component of these circulations leads to destabilisation and ascent ahead of the cyclonic vorticity anomaly in the wave, triggering deep convection because of the high sea surface temperatures in this region. Latent heat release then forces additional ascent and strong upper-tropospheric divergence, with an associated anticyclonic vorticity tendency. A vorticity budget shows that this cancels out the advective cyclonic vorticity tendency in the wave train over the SPCZ, and dissipates the wave within a day. The mean SPCZ is consequently comprised of the sum of these pulses of diagonal bands of precipitation. Similar mechanisms also operate in the SACZ. However, the vorticity anomalies in the wave trains are stronger, and the precipitation and negative feedback from the divergence and anticyclonic vorticity tendency are weaker, resulting in continued propagation of the wave and a more diffuse diagonal convergence zone

Identification of Two Independent Risk Factors for Lupus within the MHC in United Kingdom Families

The association of the major histocompatibility complex (MHC) with SLE is well established yet the causal variants arising from this region remain to be identified, largely due to inadequate study design and the strong linkage disequilibrium demonstrated by genes across this locus. The majority of studies thus far have identified strong association with classical class II alleles, in particular HLA-DRB1*0301 and HLA-DRB1*1501. Additional associations have been reported with class III alleles; specifically, complement C4 null alleles and a tumor necrosis factor promoter SNP (TNF-308G/A). However, the relative effects of these class II and class III variants have not been determined. We have thus used a family-based approach to map association signals across the MHC class II and class III regions in a cohort of 314 complete United Kingdom Caucasian SLE trios by typing tagging SNPs together with classical typing of the HLA-DRB1 locus. Using TDT and conditional regression analyses, we have demonstrated the presence of two distinct and independent association signals in SLE: HLA-DRB1*0301 (nominal p = 4.9 × 10−8, permuted p < 0.0001, OR = 2.3) and the T allele of SNP rs419788 (nominal p = 4.3 × 10−8, permuted p < 0.0001, OR = 2.0) in intron 6 of the class III region gene SKIV2L. Assessment of genotypic risk demonstrates a likely dominant model of inheritance for HLA-DRB1*0301, while rs419788-T confers susceptibility in an additive manner. Furthermore, by comparing transmitted and untransmitted parental chromosomes, we have delimited our class II signal to a 180 kb region encompassing the alleles HLA-DRB1*0301-HLA-DQA1*0501-HLA-DQB1*0201 alone. Our class III signal importantly excludes independent association at the TNF promoter polymorphism, TNF-308G/A, in our SLE cohort and provides a potentially novel locus for future genetic and functional studies