Rethinking Embedded Blocks for Machine Learning Applications

The underlying goal of FPGA architecture research is to devise flexible substrates that implement a wide variety of circuits efficiently. Contemporary FPGA architectures have been optimized to support networking, signal processing, and image processing applications through high-precision digital signal processing (DSP) blocks. The recent emergence of machine learning has created a new set of demands characterized by: (1) higher computational density and (2) low precision arithmetic requirements. With the goal of exploring this new design space in a methodical manner, we first propose a problem formulation involving computing nested loops over multiply-accumulate (MAC) operations, which covers many basic linear algebra primitives and standard deep neural network (DNN) kernels. A quantitative methodology for deriving efficient coarse-grained compute block architectures from benchmarks is then proposed together with a family of new embedded blocks, called MLBlocks. An MLBlock instance includes several multiply-accumulate units connected via a flexible routing, where each configuration performs a few parallel dot-products in a systolic array fashion. This architecture is parameterized with support for different data movements, reuse, and precisions, utilizing a columnar arrangement that is compatible with existing FPGA architectures. On synthetic benchmarks, we demonstrate that for 8-bit arithmetic, MLBlocks offer 6× improved performance over the commercial Xilinx DSP48E2 architecture with smaller area and delay; and for time-multiplexed 16-bit arithmetic, achieves 2× higher performance per area with the same area and frequency. All source codes and data, along with documents to reproduce all the results in this article, are available at http://github.com/raminrasoulinezhad/MLBlocks .

Roles of Proliferation and Angiogenesis in Locally Aggressive Biologic Behavior of Ameloblastoma versus Ameloblastic Fibroma

Background: The present study was carried out to evaluate the roles of proliferation and angiogenesis in locally aggressive biologic behavior of ameloblastoma versus ameloblastic fibroma; Methods: 30 formalin-fixed paraffin embedded blocks (15 cases of ameloblastoma & 15 cases of ameloblastic fibroma) were used. To evaluate the proliferation, the tissue sections were stained with AgNORs stain. CD105 was used as immunohistochemical marker of angiogenesis. Quantitative evaluations of AgNORs were performed. The mean vascular density was evaluated as a measure for CD105 protein expression by using image analyzer computer system; Results: The mean number of AgNORs dots per nucleus was significantly higher in ameloblastoma as compared to ameloblastic fibroma. Also, the protein level of CD105 showed positive expression and wide distribution that the mean vascular density was significantly higher in ameloblastoma as compared to ameloblastic fibroma; Conclusion: Quantitative evaluation of AgNORs stain & the mean vascular density utilizing CD105 protein expression may reflect a higher proliferative activity and a more locally aggressive biologic behavior of ameloblastoma when compared to ameloblastic fibroma, that other factors may be involved in biologic behavior of ameloblastic fibroma.

Deeper Sections: Its Frequency and Diagnostic Utility in Histopathology of Noncutaneous Small Biopsy Specimen in a Tertiary Hospital in Nepal

Background. Biopsy is an important tool for accurate diagnosis of disease in histopathology which can be examined at multiple levels during microscopic examination. The initial sections may not be representative of the entire biopsy, which leads to frequent request for deeper sections. This study assessed the frequency and diagnostic utility of deeper sections in noncutaneous small biopsy specimens at a tertiary hospital. Material and Methods. All the formalin fixed noncutaneous small biopsy specimens received were processed for grossing followed by tissue processing and embedding. The paraffin-embedded blocks were cut into 3–5 µm sections, fixed in a glass slide, deparaffinised, and then stained with hematoxylin and eosin (H&E) stain as per the standard protocol. Deeper sections were instructed based on microscopic findings of initial slides. The overall frequency of deeper section, its levels of cutting, tissue survival, and outcome were assessed and interpreted for the final diagnosis. Results. A total of 125 cases (26.9%) from 464 samples received were requested for deeper sections. The most frequent deeper sections were from cervix (72 cases) followed by stomach (18 cases) and endometrium (17 cases). The deeper sections were performed most frequently at 4 levels (17.8%) followed by 5 levels (14.8%) and 6 levels (13.3%). Deeper sections revealed nondiagnostic additional features in 28.2%, while 2.2% showed additional diagnostic features. Likewise, 2.2% had tissue segment loss. The overall mean level showing additional features was 6 levels. Tissue survival increased in 13% cases and 1.5% had decreased survival. The most common reason for requesting deeper section was to enhance sensitivity and diagnostic accuracy of disease. Conclusions. Deeper sections often contribute to final diagnosis. Therefore, deeper sections on biopsies that cannot readily be diagnosed on routine levels are recommended regardless of size of the lesion and there should be uniformity in the practice of deeper sections across the globe.

Contrast-Enhanced Tissue Processing of Fibrillin-Rich Elastic Fibres for 3D Visualization by Volume Scanning Electron Microscopy

Elastic fibres constitute an important component of the extracellular matrix and currently are the subject of intensive study in order to elucidate their assembly, function and involvement in cell–matrix interactions and disease. However, few studies to date have investigated the 3D architecture of the elastic fibre system in bulk tissue. We describe a protocol for preparation of tissue samples, including primary fixation and backscatter electron contrast-enhancement steps, through dehydration into stable resin-embedded blocks for volume electron microscopy. The use of low molecular weight tannic acid and alcoholic lead staining are critical stages in this procedure. Block preparation by ultramicrotomy and evaporative metal coating prior to microscopical examination are also described. We present images acquired from serial block face scanning electron microscopy of cornea and aorta showing target structures clearly differentiated from cells and other matrix components. The processing method imparts high contrast to fibrillin-containing elastic fibres, thus facilitating their segmentation and rendering into 3D reconstructions by image analysis software from large serial image datasets.

IMMUNOHISTOCHEMICAL EXPRESSION OF P16 IN LOW GRADE UROTHELIAL CARCINOMA

Objective: To determine the frequency of Immunohistochemical expression of P16 in low grade urothelial carcinoma patients. Study Design: Cross sectional study. Place and Duration of Study: Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, from May 2018 to Jul 2019. Methodology: A total of 120 formalin-fixed and paraffin embedded blocks from patients having low grade urothelial carcinomawere included in the study and were stainedimmunohistochemically with P16 antibody. Expression of P16 was noted by two independent pathologists and nuclear stain of strong intensity was taken as positive. Results: There were 91 (76%) males and 29 (24%) females with age range from 18-85 years (mean 67.19 ± 11.5 years) female to male ratio was 1:3. P16 stain was positive in (70.8%) and negative in 37 (31%) of low gradeurothelial carcinoma cases. Conclusion: The p-16 is expressed in a significant number of urothelial carcinomas (low grade) and this marker could be used in routine practice for early identification of patients at high risk of progression to advanced stage.

HISTOPATHOLOGICAL SPECTRUM OF NON NEOPLASTIC AND NEOPLASTIC LESIONS OF UTEROCERVIX IN NORTH WEST RAJASTHAN

Background: The female genital tract includes the uterine corpus, cervix, fallopian tubes and ovaries. Women worldwide suffer from gynaecologic and obstetric disorders that require hysterectomy as a treatment option. Hysterectomy is a definite treatment of pelvic pathology including fibroid, abnormal heavy bleeding, chronic pelvic pain, endometriosis, adenomyosis, uterine prolapse, pelvic inflammatory disease and cancer of reproductive organs. Hysterectomy specimens contribute a major component of histopathological work in Pathology laboratories. Methods: This is a prospective study carried out in the Department of Pathology, SPMC, Bikaner for two years from October 2018 to September 2020. All surgically excised hysterectomy specimens received by the department during study period were included in the study. Tissues were fixed and processed as per departmental protocols. Pieces taken from ectocervix, endocervix, uterine canal and fundus. Pieces also taken from any abnormal area. Tissue bits routinely processed 3 to 6 micron thick sections made from paraffin embedded blocks and were stained with H&E stain. Special stains will be done whenever necessary. Results: We included a total of 148 cases of hysterectomies received to our department during the study period in our study. Of total 148 cases, 87.83% hysterectomies were abdominal and 12.16% were vaginal and TAHBSO was the commonest procedure. In myometrium the most common finding was leiomyoma and adenomyosis with 79.73% and 43.92% cases respectively. In cervix, most cases were inflammatory lesions with chronic nonspecific cervicitis was the most common histopathological finding. Two cases (1.37%) of carcinoma cervix were reported. Conclusions: Most of the cases which underwent hysterectomy were for symptomatic untreatable benign conditions and few for malignancies. Majority of the cases were histopathologically consistent with clinical diagnosis. Histopathological examination and its correlative study with preoperative clinical diagnosis is very important. Thus, histopathological examination is still the gold standard test to diagnose and rule out malignancy and must be compulsory for all the surgical specimens. Keywords: Hysterectomy, Uterocervix, Pathology

Prevalence of BRAF V600E Mutation in the Iranian Patients with Hairy Cell Leukemia: A Retrospective Study

Objective: BRAF V600E mutation has several implications in hairy cell leukemia (HCL). The prevalence of This mutation has been investigated in various populations, but not in Iran. In this study, we evaluated the prevalence of BRAF V600E mutation in an Iranian HCL population as well as its association with the patients’ characteristics.Methods: In a retrospective (archival) study, 20 HCL patients with the confirmed immunophenotypic and morphologic diagnosis were included. Paraffin-embedded blocks of bone marrow aspirate were used to investigated BRAF V600E mutation using amplification refractory mutation system (ARMS) PCR. Demographic, clinical, laboratory, and immunophenotypic characteristics of patients were extracted from the patients medical profiles.Result: BRAF V600E mutation was present in 17 (85%) HCL patients and absent in three (15%) patients. The mean age of the patients was 44.76 ± 8.69 years in mutation-positive and 62.33 ± 8.69 in mutation-negative patients. This difference was statistically significant (p=0.013). No significant difference was found between the laboratory indices of the mutation-positive and mutation-negative groups. The clinical, morphologic, and immunophenotypic characteristics of the two groups were also statistically comparable.Conclusion: BRAF V600E mutation is present in the majority of the Iranian HCL patients and is associated with younger age of presentation.

Molecular Investigation of the Human Adenovirus in Retinoblastoma Patients

Background and Aims: Retinoblastoma tumors are the most common intraocular malignancy in childhood, leading to death after two years. The Human Adenovirus (HAdV) infection could be critical in the retinoblastoma pathogenesis due to the virus and retinoblastoma 1 interactions. The objective of the current study was to investigate the possible presence of the HAdV genome in the retinoblastoma patient's tumors. Materials and Methods: In this study, we evaluated the HAdV infection in 96 pathological confirmed retinoblastoma samples. The DNA was extracted from formalin-fixed paraffin-embedded blocks, and the virus infection was assessed using polymerase chain reaction. SPSS version 22 was used for statistical analysis. Results: The mean age ± SD of the retinoblastoma patients was 28.89 ± 17 months. In addition, the demographic evaluation indicated that 43 (46.7%) of patients were female. The retinoblastoma laterality assessment indicates 87 (90.4%) unilateral and 9 (9.4%) bilateral tumors. Growth pattern analysis indicates endophytic 58 (77.3%), exophytic 8 (10.7%), and 9 (12%) of tumors with mix endophytic and exophytic patterns. The polymerase chain reaction results could not found any evidence of HAdV infection in all 96 formalin-fixed paraffin-embedded samples. Conclusions: The study results suggest that there is not any association between HAdV infection and retinoblastoma tumors in studied samples. The HAdV infection may not a concern in retinoblastoma pathogenesis. Further investigations are recommended in this field of study.

High expression of FBP1 and LDHB in fibroadenomas and invasive breast cancers

BACKGROUND: The role of gluconeogenesis in cancer cells as the reverse pathway for glycolysis is not well known. Several studies of gluconeogenesis in cancer cells still show conflicting results. Expression of key enzymes such as FBP1 and LDHB in cancer tissues may explain the role of gluconeogenesis in tumor development. OBJECTIVE: This study aimed to analyze the expression of FBP1 and LDHB in fibroadenomas and invasive cancers of the breast. METHODS: The immunohistochemical staining technique was used to show the expression of FBP1 and LDHB in formalin-fixed, paraffin-embedded blocks of 32 fibroadenomas and 31 invasive breast cancer samples. RESULTS: FBP1 was expressed by the majority of fibroadenoma (68.7%) and invasive breast cancer (71%) samples. LDHB expression in fibroadenomas was significantly higher than in invasive breast cancers (P = 0.029). The expression of these two enzymes was found in lobular, ductal, and NST types of invasive breast cancers, and at low, intermediate, and high grades of malignancy. CONCLUSIONS: High expression of FBP1 and LDHB was found in fibroadenomas and invasive breast cancers. A higher level of LDHB expression was observed in fibroadenomas. These results may indicate the enzymes’ role in the pathogenesis of both breast diseases.