Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering.

A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence's 3D chaos game representation can be used to compare DNA sequences without prior alignment and without truncating or padding any of the sequences. Two proposed methods inspired by shape-similarity comparison techniques show that this form of encoding can perform as well as alignment-based techniques for building phylogenetic trees. The first method uses the volume overlap of intersecting spheres and the second uses shape signatures by summarizing the coordinates, oriented angles, and oriented distances of the 3D chaos game trajectory. The methods are tested using: (1) the first exon of the beta-globin gene for 11 species, (2) mitochondrial DNA from four groups of primates, and (3) a set of synthetic DNA sequences. Simulations show that the proposed methods produce distances that reflect the number of mutation events; additionally, on average, distances resulting from deletion mutations are comparable to those produced by substitution mutations.

Myeloid bodies is not an uncommon ultrastructural finding.

The presence of myeloid bodies (MBs) is classically associated with Fabry disease (FD). However, MBs are also identified in patients without clinical evidence of FD. We attempt to further understand the clinicopathologic significance of incidental MBs in those without FD. Among the 4400 renal biopsies accessioned at the University of Rochester Medical Center from 2010 to 2021, we identified 32 cases showing MBs, 6 of which had FD. Medications were compared between a non-FG and a control-group of randomly selected cases without MBs (non-MBs). Both Fabry-group (FG) and non-Fabry-group (non-FG) were predominantly middle-aged (mean 48 years vs 56, respectively). Non-FG had slight female predominance (1:4), while all in FG were female. The majority of both non-FG and non-MBs cohort were on the same medications reported to cause phospholipidosis except sertraline and hydralazine (p = .04), which were more frequent in non-FG. Ultrastructurally, non-FG tended to show focal MBs in predominantly podocytes, while FG showed more extensive MBs in not only podocytes but also parietal, tubular, endothelial, and myocyte cells (p = .03). In addition, half of FG had another superimposed renal disease including kappa-light chain deposition disease, thin-basement membrane nephropathy, and lithium-related changes. MBs are encountered not only in FD but in other settings including CADs, toxins, and other inheritable diseases. Although secondary causes of MBs typically show less extensive involvement compared to FD, these features overlap. Given the challenges in diagnosing female carriers, the finding of MBs, though not specific to FD, may be the only clue that leads to further work-up and timely diagnosis, underscoring the importance of considering FD among other etiologies in differential diagnosis.

Subepithelial deposits with microspherular structures in membranous glomerulonephritis.

Rare cases of membranous glomerulopathy (MGN) with subepithelial deposits consisting of microspherular structures identified by electron microscopy have been described in the literature as either MGN with spherules or podocyte infolding glomerulopathy (PIG). The paucity of available studies shows a strong association with underlying autoimmune disease. To further understand the significance of subepithelial microspherular deposits, we retrospectively identified native kidney biopsies from 10 patients diagnosed as MGN with subepithelial microspherular structures identified by ultrastructural examination at the University of Rochester Medical Center (URMC) during an 11-year period. The majority were Caucasian (80%) with a mean age of 51.3 (±12.9) years. 50% had an autoimmune disorder, of which 80% were SLE. Two SLE cases had concomitant rheumatoid arthritis and Sjogren's syndrome. One additional case had antiphospholipid syndrome and showed lupus-like features on biopsy. 40% were idiopathic and negative for PLA2R, NELL1, and THSD7A. MGN with subepithelial microspherular structures is frequently associated with an underlying autoimmune disease. The majority are negative for markers of primary MGN (PLA2R, THSD7A, and NELL1) and show features suggestive of secondary MGN.

The spectrum of renal diseases with lupus-like features: a single-center study.

BACKGROUND: A subset of patients without overt systemic lupus erythematosus (SLE) present with biopsy findings typically seen in lupus nephritis (LN). Although a minority eventually develops SLE, many do not. It remains unclear how to classify or treat these patients. Our study attempted to further understand the clinical and pathological characteristics of cases with lupus-like nephritis (LLN). METHODS: Among 2700 native kidney biopsies interpreted at University of Rochester Medical Center (URMC) from 2010 to 2019, we identified 27 patients with biopsies showing lupus-like features (LL-fx) and 96 with LN. Of those with LL-fx, 17 were idiopathic LLN and 10 were associated with a secondary etiology (e.g., infection/drugs). RESULTS: At the time of biopsy, the LLN-group tended to be slightly older (44 vs. 35), male (58.8 vs. 17.7%, p = .041), and Caucasian (47.0 vs. 28.1%, p = .005). Chronic kidney disease was the most common biopsy indication in LLN (21.4 vs. 2.8%, p = .001). Both LN and LLN presented with nephrotic-range proteinuria (mean 5.73 vs. 4.40 g/d), and elevated serum creatinine (mean 1.66 vs. 1.47 mg/dL). Tubuloreticular inclusions (TRIs; p < .001) and fibrous crescents (p = .04) were more often seen in LN, while more tubulointerstitial scarring was seen in LLN (p = .011). At mean follow-up of 1684 d (range: 31-4323), none of the LLN patients developed ESRD. A subset of both LN and cases with LL-fx overlapped with other autoimmune diseases. CONCLUSIONS: Lupus-like pathologic features are seen in a wide array of disease processes. The findings suggest that LLN may be a manifestation of an autoimmune process that overlaps with SLE.

Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy.

PURPOSE: We aimed to validate GEMCaP (Genomic Evaluators of Metastatic Cancer of the Prostate) as a novel copy number signature predictive of prostate cancer recurrence. MATERIALS AND METHODS: We randomly selected patients who underwent radical prostatectomy at Cleveland Clinic or University of Rochester from 2000 to 2005. DNA isolated from the cancer region was extracted and subjected to high resolution array comparative genomic hybridization. A high GEMCaP score was defined as 20% or greater of genomic loci showing copy number gain or loss in a given tumor. Cox regression was used to evaluate associations between the GEMCaP score and the risk of biochemical recurrence. RESULTS: We report results in 140 patients. Overall 38% of patients experienced recurrence with a median time to recurrence of 45 months. Based on the CAPRA-S (Cancer of the Prostate Risk Assessment Post-Surgical) score 39% of the patients were at low risk, 42% were at intermediate risk and 19% were at high risk. The GEMCaP score was high (20% or greater) in 31% of the cohort. A high GEMCaP score was associated with a higher risk of biochemical recurrence (HR 2.69, 95% CI 1.51-4.77) and it remained associated after adjusting for CAPRA-S score and age (HR 1.94, 95% CI 1.06-3.56). The C-index of GEMCaP alone was 0.64, which improved when combined with the CAPRA-S score and patient age (C-index = 0.75). CONCLUSIONS: A high GEMCaP score was associated with biochemical recurrence in 2 external cohorts. This remained true after adjusting for clinical and pathological factors. The GEMCaP biomarker could be an efficient and effective clinical risk assessment tool to identify patients with prostate cancer for early adjuvant therapy.

Copper Ion Binding Site in ß-Amyloid Peptide.

ß-Amyloid aggregates in the brain play critical roles in Alzheimer's disease, a chronic neurodegenerative condition. Amyloid-associated metal ions, particularly zinc and copper ions, have been implicated in disease pathogenesis. Despite the importance of such ions, the binding sites on the ß-amyloid peptide remain poorly understood. In this study, we use scanning tunneling microscopy, circular dichroism, and surface-enhanced Raman spectroscopy to probe the interactions between Cu2+ ions and a key ß-amyloid peptide fragment, consisting of the first 16 amino acids, and define the copper-peptide binding site. We observe that in the presence of Cu2+, this peptide fragment forms ß-sheets, not seen without the metal ion. By imaging with scanning tunneling microscopy, we are able to identify the binding site, which involves two histidine residues, His13 and His14. We conclude that the binding of copper to these residues creates an interstrand histidine brace, which enables the formation of ß-sheets.

Hexagons to Ribbons: Flipping Cyanide on Au{111}.

Cyanide monolayers on Au{111} restructure from a hexagonal close-packed lattice to a mixed-orientation "ribbon" structure through thermal annealing. The new surface structure loses most of the observed surface features characterizing the initial as-adsorbed system with "ribbon" domain boundaries isolating rotationally offset surface regions where the orientation is guided by the underlying gold lattice. A blue shift to higher frequencies of the CN vibration to 2235 cm-1 with respect to the as-adsorbed CN/Au{111} vibration at 2146 cm-1 is observed. In addition, a new low-frequency mode is observed at 145 cm-1, suggesting a chemical environment change similar to gold-cyanide crystallization. We discuss this new structure with respect to a mixed cyanide/isocyanide monolayer and propose a bonding scheme consisting of Au-CN and Au-NC bound molecules that are oriented normal to the Au{111} surface.

Cytologic Assessment of the Supernatants of Formalin Solution Following Histologic Examination of Transurethral Biopsy/Resection Specimens.

CONTEXT.­: Urothelial denudation seen in transurethral biopsy specimens may occasionally indicate the presence of discohesive high-grade urothelial carcinoma (HGUC). OBJECTIVE.­: To determine if denuded urothelial cells can be detected in the supernatants of formalin solution collected from the containers of transurethral biopsy/resection specimens after the entire tissue was submitted for histologic examination. DESIGN.­: We assessed the formalin supernatants by processing for cell block (n = 43) or ThinPrep smear (n = 57). RESULTS.­: In the cell block cohort, only 2 of 43 cases (5%) (1 pTa HGUC, 1 pT1 HGUC) showed rare urothelial cells. By contrast, in the ThinPrep method, the smear was satisfactory for evaluation in 52 of 57 cases (91%). The cytologic diagnosis of HGUC was made in the smears from 7 of 12 (58%) pTa/pT1 cases and 6 of 9 (67%) pTis cases. Remarkably, HGUC cells were detected in 2 of 5 cases (40%) with histologic diagnosis of urothelial atypia suspicious for but not diagnostic of urothelial carcinoma in situ. Additionally, in 31 cases exhibiting urothelial denudation without definitive cancer on hematoxylin-eosin-stained slides, HGUC cells (2 of 31; 6%), atypical urothelial cells (5 of 31; 16%), or benign-appearing urothelial cells (20 of 31; 65%) were present, and only 4 of 31 (13%) were unsatisfactory. CONCLUSIONS.­: Cytologic examination of ThinPrep smears from the formalin supernatants even following submission of the entire transurethral biopsy/resection specimens for histologic examination is useful for assessing denuded urothelial cells. This technique can particularly be applied to nonneoplastic cases showing extensive urothelial denudation to detect possible malignant cells and/or indeterminate cases to assist to make a more definitive diagnosis.

The Clinicopathologic Spectrum of Membranous Nephropathy with Lupus-Like Features.

INTRODUCTION: The pathologic features of membranous lupus nephritis (MLN) are occasionally encountered in secondary membranous nephropathy (sMN) without overt clinical evidence of systemic lupus erythematosus. Moreover, some sMN with lupus-like features (lupus-like membranous nephropathy [LL-MN]) have a clinical presentation more typical of primary membranous nephropathy (pMN). Based on the confounding clinical and pathologic presentation, it is unclear how to categorize and treat these patients. METHODS: We performed immunohistochemical staining for recently discovered target antigens associated with MN -NELL-1, THSD7A, and EXT1/2 and compared the clinicopathologic presentation of patients with LL-MN to those with pMN and MLN. RESULTS: From 2015 to 2020, there were 21 patients with MLN and 99 with MN, of which 59% were diagnosed pMN and 41% sMN. 44% of sMN patients showed lupus-like features (LL-fx). All LL-MN patients were negative for PLA2R and NELL1, but 12% were positive for EXT1/2. 50% of LL-MN patients had an identifiable systemic disease, of which 56% were autoimmune disease (AD) and 44% infection. Compared to pMN, LL-MN had a higher incidence of underlying AD (p = 0.02). Within pMN, 24% also had LL-fx (LL-pMN), and all but 1 were PLA2R- (78%) or NELL1-positive (15%). Only 5% of pMN patients had an AD, 66% of which showed LL-fx. Most idiopathic LL-MN were treated and behaved clinically similarly to pMN. There were no differences in outcome in terms of progression toward end-stage renal disease or mortality between LL-MN versus pMN and MLN. CONCLUSION: LL-MN appears to have a significant association with underlying AD and has a subset showing EXT1/2 positivity, whereas most LL-pMN and idiopathic LL-MN likely represent an atypical pathologic presentation of pMN.

Extraction of Hidden Science from Nanoscale Images.

Scanning probe microscopies and spectroscopies enable investigation of surfaces and even buried interfaces down to the scale of chemical-bonding interactions, and this capability has been enhanced with the support of computational algorithms for data acquisition and image processing to explore physical, chemical, and biological phenomena. Here, we describe how scanning probe techniques have been enhanced by some of these recent algorithmic improvements. One improvement to the data acquisition algorithm is to advance beyond a simple rastering framework by using spirals at constant angular velocity then switching to constant linear velocity, which limits the piezo creep and hysteresis issues seen in traditional acquisition methods. One can also use image-processing techniques to model the distortions that appear from tip motion effects and to make corrections to these images. Another image-processing algorithm we discuss enables researchers to segment images by domains and subdomains, thereby highlighting reactive and interesting disordered sites at domain boundaries. Lastly, we discuss algorithms used to examine the dipole direction of individual molecules and surface domains, hydrogen bonding interactions, and molecular tilt. The computational algorithms used for scanning probe techniques are still improving rapidly and are incorporating machine learning at the next level of iteration. That said, the algorithms are not yet able to perform live adjustments during data recording that could enhance the microscopy and spectroscopic imaging methods significantly.

Copy number and gene expression differences between African American and Caucasian American prostate cancer.

BACKGROUND: The goal of our study was to investigate the molecular underpinnings associated with the relatively aggressive clinical behavior of prostate cancer (PCa) in African American (AA) compared to Caucasian American (CA) patients using a genome-wide approach. METHODS: AA and CA patients treated with radical prostatectomy (RP) were frequency matched for age at RP, Gleason grade, and tumor stage. Array-CGH (BAC SpectralChip2600) was used to identify genomic regions with significantly different DNA copy number between the groups. Gene expression profiling of the same set of tumors was also evaluated using Affymetrix HG-U133 Plus 2.0 arrays. Concordance between copy number alteration and gene expression was examined. A second aCGH analysis was performed in a larger validation cohort using an oligo-based platform (Agilent 244K). RESULTS: BAC-based array identified 27 chromosomal regions with significantly different copy number changes between the AA and CA tumors in the first cohort (Fisher's exact test, P < 0.05). Copy number alterations in these 27 regions were also significantly associated with gene expression changes. aCGH performed in a larger, independent cohort of AA and CA tumors validated 4 of the 27 (15%) most significantly altered regions from the initial analysis (3q26, 5p15-p14, 14q32, and 16p11). Functional annotation of overlapping genes within the 4 validated regions of AA/CA DNA copy number changes revealed significant enrichment of genes related to immune response. CONCLUSIONS: Our data reveal molecular alterations at the level of gene expression and DNA copy number that are specific to African American and Caucasian prostate cancer and may be related to underlying differences in immune response.

The Empirical Watershed Wavelet.

The empirical wavelet transform is an adaptive multi-resolution analysis tool based on the idea of building filters on a data-driven partition of the Fourier domain. However, existing 2D extensions are constrained by the shape of the detected partitioning. In this paper, we provide theoretical results that permits us to build 2D empirical wavelet filters based on an arbitrary partitioning of the frequency domain. We also propose an algorithm to detect such partitioning from an image spectrum by combining a scale-space representation to estimate the position of dominant harmonic modes and a watershed transform to find the boundaries of the different supports making the expected partition. This whole process allows us to define the empirical watershed wavelet transform. We illustrate the effectiveness and the advantages of such adaptive transform, first visually on toy images, and next on both unsupervised texture segmentation and image deconvolution applications.

Sonographic Evaluation of Genitourinary Inflammatory Pseudotumors and Its Mimics.

ABSTRACT: Inflammatory pseudotumor is a relatively rare, nonneoplastic lesion composed of inflammatory cells and myofibroblastic spindle cells that can be identified on sonographic evaluation of the genitourinary system. These lesions are thought to be an inflammatory response to insults such as surgery, trauma, infection, or malignancy. Such lesions need to be distinguished from true neoplasms and other benign lesions, including inflammatory responses and infectious processes. Identification of inflammatory pseudotumors and its mimics is important for radiologists to guide patient treatment and follow-up. This pictorial essay presents sonographic features of inflammatory pseudotumors of the genitourinary tract and its mimics with cross-sectional imaging and histopathology, where available.

Progressive Gorham disease of the forearm.

Gorham's-Stout disease is a rare but potentially debilitating disease consisting of massive bone osteolysis and bone resorption associated with vascular proliferation and increased osteoclastic activity. Although it can present in a wide variety of forms, it typically involves bones formed by intramembranous ossification such as the skull, pelvis, and scapula. It can occur spontaneously or after trauma. Most cases are monofocal and resolved spontaneously, although there are reports of multifocal and rapidly progressing disease. It typically presents as disuse muscle atrophy or pathologic fracture during the second through fourth decades of life, yet it has also been reported in childhood and in the elderly. The etiology of Gorham's disease remains to be fully elucidated. Gorham attributed the origin of the disease to uncontrolled proliferation of small vessels eating away bone tissue. Other authors attribute the cause of the disease to increased osteoclastic activity mediated by elevated cytokine levels and increased osteoclastic differentiation. Treatment is not established and focuses at stopping osteoclastic activity and angiogenic proliferation. Radiation therapy, chemotherapy, bone grafting, and antiresorptives medications have all been used with different degrees of success. In an effort to further characterize this elusive disease, we report on an unusual presentation of a patient with Gorham's disease of the radius spreading to the ulna and then the proximal humerus with a 13-year follow-up. To our knowledge this is the first report in the literature of a saltatory type of Gorham's disease spreading from bone to bone across a joint.

Testicular Microlithiasis in the Setting of Primary Extragonadal Germ Cell Tumor: A Case Series.

The clinical significance of testicular microlithiasis (TM) in patients with primary extragonadal germ cell tumor (EGCT) is not well understood. When EGCT is suspected, sonographic and physical examination of the testicles should be performed to evaluate for testicular lesion or atrophy; negative testicular ultrasound with current technology virtually excludes the possibility of occult primary lesion. Although EGCTs are known to be associated with elevated level of serum tumor markers, the utility of tumor markers in the presence of TM is not well understood. Current guidelines for TM follow-up and management do not include any potential correlation between TM and primary EGCT, an association that should be addressed on future updates.

Cautery artifact understages urothelial cancer at initial transurethral resection of large bladder tumours.

INTRODUCTION: We sought to determine how frequently cautery (thermal) artifact precludes an accurate determination of stage at initial transurethral resection of bladder tumour (TURBT) of large bladder tumours. METHODS: We queried our institution's billing data to identify patients who underwent TURBT for large bladder tumours >5cm (CPT 52240) by two urologists at an academic centre from January 2009 through April 2013. Only patients who underwent initial-staging TURBT for urothelial cancer were included. Pathological reports were reviewed for stage, number of separate pathological specimens per TURBT, and presence of cautery artifact. Operative reports were reviewed for whether additional cold cup biopsies were taken of other suspicious areas of the bladder, resident involvement, and type of electrocautery. RESULTS: We identified 119 patients who underwent initial staging TURBT for large tumours. Cautery artifact interfered with accurate staging in 7/119 (6%) of cases. Of these, six patients underwent restaging TURBT, with 50% percent experiencing upstaging to T2 disease. Tumour size, tumour grade, whether additional cold cup biopsies were taken, number of separate pathological specimens sent, and resident involvement were not associated with cautery artifact (all p>0.05). Bipolar resection had a higher rate of cautery artifact 5/42 (12%), compared to monopolar resection 2/77 (2.6%) approaching significance (p=0.095). CONCLUSIONS: Cautery artifact may delay accurate staging at initial TURBT for large tumours by understaging up to 6% of patients.

Mapping Buried Hydrogen-Bonding Networks.

We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-N-nonylpropionamide on Au{111}. The contributing interactions include the buried S-Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder.

A Regularization Approach to Blind Deblurring and Denoising of QR Barcodes.

QR bar codes are prototypical images for which part of the image is a priori known (required patterns). Open source bar code readers, such as ZBar, are readily available. We exploit both these facts to provide and assess purely regularization-based methods for blind deblurring of QR bar codes in the presence of noise.

Defect-Tolerant Aligned Dipoles within Two-Dimensional Plastic Lattices.

Carboranethiol molecules self-assemble into upright molecular monolayers on Au{111} with aligned dipoles in two dimensions. The positions and offsets of each molecule's geometric apex and local dipole moment are measured and correlated with sub-Ångström precision. Juxtaposing simultaneously acquired images, we observe monodirectional offsets between the molecular apexes and dipole extrema. We determine dipole orientations using efficient new image analysis techniques and find aligned dipoles to be highly defect tolerant, crossing molecular domain boundaries and substrate step edges. The alignment observed, consistent with Monte Carlo simulations, forms through favorable intermolecular dipole-dipole interactions.

A case series of transformation of teratoma to primitive neuroectodermal tumor: evolving management of a rare malignancy.

Primitive neuroectodermal tumor (PNET) is a pathologic diagnosis that encompasses several different tumor types, including central nervous system tumors and Ewing's sarcomas. Teratoma, a common element of germ cell tumor (GCT), has the ability to transform to malignant PNET in a small number of patients. Making a definitive diagnosis of PNET is difficult given its deviation from elements of GCT and its non-specific pathologic findings. Establishing the diagnosis is crucial as PNETs respond poorly to standard platinum-based chemotherapy used for treatment of GCT. Primary treatment for PNET is surgical, though this is often not feasible in many patients due to extensive disease at diagnosis. As an alternative, chemotherapy regimens traditionally used for Ewing's sarcoma, such as vincristine, doxorubicin and cyclophosphamide alternating with ifosfamide and etoposide, have shown limited efficacy in the neoadjuvant, adjuvant, and palliative settings. Future research should delineate the genetic underpinnings of PNET and develop therapeutic options accordingly.