Draft genomes of 10 isolates collected in Sudan in 2019.

This report presents the first genomes from positive cases of cholera in Sudan. Genomic analysis of 10 isolates, profiled as serogroup O1, reveals evidence of antimicrobial resistance genes and a 139-kb IncC plasmid with 99.74% identity to the multidrug-resistant plasmid pCNRVC190243 previously reported in Yemen and Lebanon.

A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

Background: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings.

Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting.

Background: Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding.

Statistical Investigation of High Culture Contamination Rates in Mycobacteriology Laboratory.

Background: Culture of remains the gold standard in mycobacteriology laboratories, constrained by the very high risk of contamination; therefore, contamination rate is an important key performance indicator (KPI) for laboratory monitoring and evaluation processes.

Aim: This study aimed to investigate the factors that contribute to elevated contamination rates in the Sudan National Tuberculosis Reference Laboratory.

Method: A laboratory-based retrospective study was applied; a TB culture register-book was carefully reviewed and data from 2 January 2019 to 31 December 2019 were entered, cleaned, and analyzed using IBM SPSS 20.

Very poor practices regarding breast cancer screening among Sudanese female workers at a secondary-level hospital: a cross-sectional study.

Introduction: breast cancer (BC) mortality and morbidity burden in African countries is higher compared to western countries due to late diagnosis produced by deficient screening. We aimed to assess the level of knowledge, attitude and practice regarding breast cancer screening among Sudanese female workers at a secondary-level hospital.

Methods: this is a cross-sectional study carried out at the largest governmental hospital of Ad-Damazin City (capital of Blue Nile State, south-eastern Sudan) in 2018.

Long-term outcome of novel combined surgical-injection treatment (COSIT) for large hepatocellular carcinoma: Stage 2A IDEAL prospective case series.

Background: Large hepatocellular carcinoma (HCC) treatment options have obvious limitations. Our trial comprises ipsilateral hepatic artery ligation and extrahepatic collaterals division (HALED, reinforced by percutaneous tumor injection controlling residual HCC arterial supply. We aimed to evaluate the long term safety and feasibility of the Combined Surgical and Injection of alcohol Treatment (COSIT) as a novel therapy for the large HCC.

Ancestry-associated transcriptomic profiles of breast cancer in patients of African, Arab, and European ancestry.

Breast cancer largely dominates the global cancer burden statistics; however, there are striking disparities in mortality rates across countries. While socioeconomic factors contribute to population-based differences in mortality, they do not fully explain disparity among women of African ancestry (AA) and Arab ancestry (ArA) compared to women of European ancestry (EA). In this study, we sought to identify molecular differences that could provide insight into the biology of ancestry-associated disparities in clinical outcomes.

Vitamin D level and its determinants among Sudanese Women: Does it matter in a sunshine African Country?

Background: Vitamin D deficiency is a worldwide concern. The aim of the current study was to determine the vitamin D level and its contributing factors in Sudanese women.

Methods: In this cross-sectional study, 251 Sudanese women attending Family Health Centers in Khartoum, Sudan were interviewed.

Serum vitamin D level, sun-exposed area, dietary factors, and physical activity as predictors of invasive breast cancer risk among Sudanese women: A case-control study.

Background: The role of vitamin D in the development, progression, and prognosis of breast cancer, though widely studied worldwide, has been inconclusive. This study intended to assess the role of some factors (including serum vitamin D level, sun-exposed area, dietary factors, and physical activity) as predictors of the development of invasive breast cancer (IBC) among Sudanese women.

Methods: A case-control study was conducted on 200 Sudanese women (100 with newly diagnosed IBC and 100 matched healthy females).

Epstein-Barr virus (EBV) status in colorectal cancer: a mini review.

Epstein-Barr virus (EBV) is a well-characterized oncovirus, associated with several malignancies. The complex and heterogeneous nature of colorectal cancer (CRC) has led to many epidemiological causal associations with CRC. However, a direct causal link between microbial infections and CRC has not been established yet.

Comparison of Receptor-Defined Breast Cancer Subtypes Between German and Sudanese Women: A Facility-Based Cohort Study.

Purpose: The objective of this study was to compare tumor characteristics, biomarkers, and surrogate subtypes of breast cancer between Sudanese and German women.

Methods: Tumor characteristics and immunohistochemistry markers (estrogen receptor [ER], progesterone receptor [PR], and human epidermal growth factor receptor 2 [HER2]) were collected from the routine assessment of consecutive patients with invasive breast cancer diagnosed from 2010 to 2015 (Gezira University Pathology Laboratory, Gezira, Sudan) and from 1999 to 2013 (Breast Centre, Martin-Luther-University, Halle, Germany).

Results: A total of 2,492 patients (German [n = 1,932] and Sudanese [n = 560]) were included.

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification.

The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB).

Immunohistochemistry defined subtypes of breast cancer in 678 Sudanese and Eritrean women; hospitals based case series.

Background: Breast cancer is the most common malignancy accounting for 25% of all cancers in females. In Africa, breast cancer prevalence and mortality are steadily increasing. Knowledge of hormone receptors and human epidermal growth factor receptor-2 (HER-2) expressions are vital for breast cancer management plans and decision making.

Introduction of p16 as a surrogate biomarker for HPV in women with invasive cervical cancer in Sudan.

Background: Cervical cancer is the fourth most common cancer in women worldwide with highest incidence reported in Eastern Africa in 2012. The primary goal of this study was to study the expression of p16 in squamous cell carcinoma (SCC) of the cervix by immunohistochemistry (IHC) and determine relation with clinico-pathological parameters. This study further explored the correlation of p16 immunostaining with another proliferation marker, Ki-67 and to study if human papillomavirus (HPV) IHC can be used as a marker for detection of virus in high-grade dysplasia.

Assessing Tumor-Infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method from the International Immuno-Oncology Biomarkers Working Group: Part 2: TILs in Melanoma, Gastrointestinal Tract Carcinomas, Non-Small Cell Lung Carcinoma and Mesothelioma, Endometrial and Ovarian Carcinomas, Squamous Cell Carcinoma of the Head and Neck, Genitourinary Carcinomas, and Primary Brain Tumors.

Assessment of the immune response to tumors is growing in importance as the prognostic implications of this response are increasingly recognized, and as immunotherapies are evaluated and implemented in different tumor types. However, many different approaches can be used to assess and describe the immune response, which limits efforts at implementation as a routine clinical biomarker. In part 1 of this review, we have proposed a standardized methodology to assess tumor-infiltrating lymphocytes (TILs) in solid tumors, based on the International Immuno-Oncology Biomarkers Working Group guidelines for invasive breast carcinoma.

Assessing Tumor-infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method From the International Immunooncology Biomarkers Working Group: Part 1: Assessing the Host Immune Response, TILs in Invasive Breast Carcinoma and Ductal Carcinoma In Situ, Metastatic Tumor Deposits and Areas for Further Research.

Assessment of tumor-infiltrating lymphocytes (TILs) in histopathologic specimens can provide important prognostic information in diverse solid tumor types, and may also be of value in predicting response to treatments. However, implementation as a routine clinical biomarker has not yet been achieved. As successful use of immune checkpoint inhibitors and other forms of immunotherapy become a clinical reality, the need for widely applicable, accessible, and reliable immunooncology biomarkers is clear.

Standardized evaluation of tumor-infiltrating lymphocytes in breast cancer: results of the ring studies of the international immuno-oncology biomarker working group.

Multiple independent studies have shown that tumor-infiltrating lymphocytes (TIL) are prognostic in breast cancer with potential relevance for response to immune-checkpoint inhibitor therapy. Although many groups are currently evaluating TIL, there is no standardized system for diagnostic applications. This study reports the results of two ring studies investigating TIL conducted by the International Working Group on Immuno-oncology Biomarkers.

TNRC9 downregulates BRCA1 expression and promotes breast cancer aggressiveness.

Although the linkage between germline mutations of BRCA1 and hereditary breast/ovarian cancers is well established, recent evidence suggests that altered expression of wild-type BRCA1 might contribute to the sporadic forms of breast cancer. The breast cancer gene trinucleotide-repeat-containing 9 (TNRC9; TOX3) has been associated with disease susceptibility but its function is undetermined. Here, we report that TNRC9 is often amplified and overexpressed in breast cancer, particularly in advanced breast cancer.

Risk factors for atherosclerosis and the development of preatherosclerotic intimal hyperplasia.

Background: Intimal hyperplasia or thickening is considered to be the precursor lesion for atherosclerosis in humans; however, the factors governing its formation are unclear. To gain insight into the etiology of preatherosclerotic intimal hyperplasia, we correlated traditional risk factors for atherosclerosis with the intimal hyperplasia in an atherosclerosis-resistant vessel, the internal thoracic artery.

Methods: Paired internal thoracic arteries were obtained from 89 autopsies.

Regulation of protein kinase CK1alphaLS by dephosphorylation in response to hydrogen peroxide.

Low levels of hydrogen peroxide (H(2)O(2)) are mitogenic to mammalian cells and stimulate the hyperphosphorylation of heterogeneous nuclear ribonucleoprotein C (hnRNP-C) by protein kinase CK1alpha. However, the mechanisms by which CK1alpha is regulated have been unclear. Here it is demonstrated that low levels of H(2)O(2) stimulate the rapid dephosphorylation of CK1alphaLS, a nuclear splice form of CK1alpha.

In vivo 18F-fluorodeoxyglucose positron emission tomography imaging provides a noninvasive measure of carotid plaque inflammation in patients.

Objectives: Given the importance of inflammation in atherosclerosis, we sought to determine if atherosclerotic plaque inflammation could be measured noninvasively in humans using positron emission tomography (PET).

Background: Earlier PET studies using fluorodeoxyglucose (FDG) demonstrated increased FDG uptake in atherosclerotic plaques. Here we tested the ability of FDG-PET to measure carotid plaque inflammation in patients who subsequently underwent carotid endarterectomy (CEA).

Analysis of intimal proteoglycans in atherosclerosis-prone and atherosclerosis-resistant human arteries by mass spectrometry.

The propensity to develop atherosclerosis varies markedly among different sites in the human vasculature. To determine a possible cause for such differences in atherosclerosis susceptibility, a proteomics-based approach was used to assess the extracellular proteoglycan core protein composition of intimal hyperplasia from both the atherosclerosis-prone internal carotid artery and the atherosclerosis-resistant internal thoracic artery. The intimal proteoglycan composition in these preatherosclerotic lesions was found to be more complex than previously appreciated with up to eight distinct core proteins present, including the large extracellular proteoglycans versican and aggrecan, the basement membrane proteoglycan perlecan, the class I small leucine-rich proteoglycans biglycan and decorin, and the class II small leucine-rich proteoglycans lumican, fibromodulin, and prolargin/PRELP (proline arginine-rich end leucine-rich repeat protein).

High prevalence of herpes simplex virus DNA in temporal arteritis biopsy specimens.

Giant cell arteritis (GCA) affecting the cranial arteries is a disease of unknown cause that causes blindness, stroke, and other morbidity. Its sudden onset and segmental distribution are suggestive of diseases that involve viral reactivation, and cranial arteries are known to be innervated by ganglia that harbor herpes simplex virus (HSV). We used a high-sensitivity polymerase chain reaction assay to test for HSV DNA in specimens from 39 consecutive temporal artery biopsies performed for suspected GCA.