Computational and Mathematical Methods in Medicine

Os resultados laboratoriais que mostram inflamacao e lesao hepatica indiretamente suportam a possibilidade de transmissao vertical. Embora a infeccao no momento do parto nao possa ser descartada, os anticorpos IgM geralmente nao aparecem ate 3 a 7 dias apos a infeccao.

Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn. JAMA, March (online).

Summary Background Previous studies on the pneumonia outbreak caused by the 2019 novel coronavirus disease (COVID-19) were based on information from the general population. Limited data are available for pregnant women with COVID-19 pneumonia. This study aimed to evaluate the clinical characteristics of COVID-19 in pregnancy and the intrauterine vertical transmission potential of COVID-19 infection. Methods Clinical records, laboratory results, and chest CT scans were retrospectively reviewed for nine pregnant women with laboratory-confirmed COVID-19 pneumonia (ie, with maternal throat swab samples that were positive for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) who were admitted to Zhongnan Hospital of Wuhan University, Wuhan, China, from Jan 20 to Jan 31, 2020. Evidence of intrauterine vertical transmission was assessed by testing for the presence of SARS-CoV-2 in amniotic fluid, cord blood, and neonatal throat swab samples. Breastmilk samples were also collected and tested from patients after the first lactation. Findings All nine patients had a caesarean section in their third trimester. Seven patients presented with a fever. Other symptoms, including cough (in four of nine patients), myalgia (in three), sore throat (in two), and malaise (in two), were also observed. Fetal distress was monitored in two cases. Five of nine patients had lymphopenia ( Interpretation The clinical characteristics of COVID-19 pneumonia in pregnant women were similar to those reported for non-pregnant adult patients who developed COVID-19 pneumonia. Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy. Funding Hubei Science and Technology Plan, Wuhan University Medical Development Plan.

Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records

High throughput sequencing technologies have become essential in studies on genomics, epigenomics, and transcriptomics. Although sequencing information has traditionally been elucidated using a low throughput technique called Sanger sequencing, high throughput sequencing technologies are capable of sequencing multiple DNA molecules in parallel, enabling hundreds of millions of DNA molecules to be sequenced at a time. This advantage allows high throughput sequencing to be used to create large data sets, generating more comprehensive insights into the cellular genomic and transcriptomic signatures of various diseases and developmental stages. Within high throughput sequencing technologies, whole exome sequencing can be used to identify novel variants and other mutations that may underlie many genetic cardiac disorders, whereas RNA sequencing can be used to analyze how the transcriptome changes. Chromatin immunoprecipitation sequencing and methylation sequencing can be used to identify epigenetic changes, whereas ribosome sequencing can be used to determine which mRNA transcripts are actively being translated. In this review, we will outline the differences in various sequencing modalities and examine the main sequencing platforms on the market in terms of their relative read depths, speeds, and costs. Finally, we will discuss the development of future sequencing platforms and how these new technologies may improve on current sequencing platforms. Ultimately, these sequencing technologies will be instrumental in further delineating how the cardiovascular system develops and how perturbations in DNA and RNA can lead to cardiovascular disease.

Overview of High Throughput Sequencing Technologies to Elucidate Molecular Pathways in Cardiovascular Diseases

Pregnancy causes dramatic physiological changes in the expectant mother. The placenta, mostly foetal in origin, invades maternal uterine tissue early in pregnancy and unleashes a barrage of hormones and other factors. This foetal ‘invasion’ profoundly reprogrammes maternal physiology, affecting nearly every organ, including the heart and its metabolism. We briefly review here maternal systemic metabolic changes during pregnancy and cardiac metabolism in general. We then discuss changes in cardiac haemodynamic during pregnancy and review what is known about maternal cardiac metabolism during pregnancy. Lastly, we discuss cardiac diseases during pregnancy, including peripartum cardiomyopathy, and the potential contribution of aberrant cardiac metabolism to disease aetiology.

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Maternal cardiac metabolism in pregnancy

Result: The commonest histopathological diagnosis was secretory endometrium 571 (24.9%), followed by proliferative endometrium 498 (21.7%), endometrial polyp 227 (9.9%), disordered proliferative endometrium 200 (8.7%), simple cystic hyperplasia 160 (7%), chronic endometritis 134 (5.8%), inactive endometrium 126 (5.5%), atrophic endometrium 70 (3.1%), uterine malignancies 41 (1.8%), complex hyperplasia without atypia 33 (1.4%) and finally complex hyperplasia with atypia 15 (0.7%). Two hundred twenty (9.6%) revealed no endometrial tissue and were considered insufficient for diagnosis. Uterine malignancies and complex hyperplasia with atypia were more common in the age group of 52 years and older, 3.3% and 1.2% respectively. Conclusion: The present study revealed that secretory and proliferative endometrium are the most common endometrial histopathological patterns identified in endometrial samples obtained for abnormal uterine bleeding in our region.

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Histopathological Pattern of Endometrial Sampling Performed for Abnormal Uterine Bleeding

Objective: To study the prevalence, pattern of distribution, and the outcome of different types of kidney and urinary tract anomalies (CAKUT) diagnosed during the antenatal period. The second objective is to test the accuracy of antenatal diagnosis of CAKUT. Materials and Methods: In a cross-sectional hospital-based study, all cases diagnosed antenatally with urinary tract anomalies at King Abdulaziz University Hospital (KAUH), Jeddah, Kingdom of Saudi Arabia, were studied. The prevalence, pattern of distribution, and immediate postnatal outcomes, in addition to the accuracy of antenatal diagnosis, of those cases are reported. Results: One hundred and forty-one cases of urinary tract anomalies were antenatally diagnosed; postnatal diagnosis was confirmed in 128 cases (90.1%). The prevalence of CAKUT in our population is 3.26 per 1000 births. The most common abnormalities detected were hydronephrosis, polycystic kidney disease, multicystic dysplastic kidney, and renal agenesis, in descending order of frequency. The perinatal mortality rate among fetuses with CAKUT is 310 per 1000, the majority of these cases (90%) occurred in cases with renal parenchyma involvement. Conclusions: The prevalence of different types of CAKUT is higher than that reported in developed countries. Urinary tract anomalies can be accurately diagnosed and classified in the antenatal period using ultrasonography imaging. Antenatal diagnosis is a helpful tool in planning immediate postnatal care and deciding the place for delivery. This might prevent or slow renal function deterioration and help in early identification of patients who need early surgical intervention.

Antenatal diagnosis, prevalence and outcome of congenital anomalies of the kidney and urinary tract in Saudi Arabia.

Objective: To identify and categorize various pathological changes seen in testicular biopsies of males with infertility and to compare the results with data from other local and international studies. Materials and Methods: All testicular biopsies from males with infertility received by the Pathology Department of King AbdulAziz University Hospital, Jeddah, in the period from January 2004 until May 2010 are reviewed and histopathologically classified into seven categories as follows : Normal spermatogenesis, hypospermatogenesis, germ cell maturation arrest (GCMA), Sertoli cell only syndrome, seminiferous tubule hyalinization, mixed and discordant patterns. Results: One hundred testicular biopsies were identified in the computerized records of the Department of Pathology of King AbdulAziz University Hospital in the studied period. The age ranged from 22 to 70 years with a mean age of 24.5 years. The histopathological patterns were as follows: 14 (14%) cases were reported as normal spermatogenesis;(29, 29%) cases as hypospermatogesis; and 12 (12%) cases were reported as GCMA, mostly at the level of primary spermatocytes. The Sertoli cell only syndrome and the seminiferous tubule hyalinization categories were each reported in 16 cases (16%). Nine cases (9%) showed a mixed pattern. Discordant pattern was seen in 5 (5%) cases. Conclusion: Our study showed that hypospermatogenesis is the commonest pattern in testicular biopsies taken from males with infertility in our region. This study supports the recommendation of bilateral testicular biopsies when investigating male infertility.

Histopathological patterns of testicular biopsy in male infertility: A retrospective study from a tertiary care center in the western part of Saudi Arabia

OBJECTIVES 
To identify the different histopathological types of ovarian neoplasms and their age distribution.
 METHODS 
This is a retrospective study were ovarian neoplasms received by the Pathology Department of King Abdulaziz University, Jeddah, Saudi Arabia between January 1995 and December 2010 were reviewed and their frequencies in different age groups were calculated.
 RESULTS 
Out of 618 ovarian specimens studied, 382 (61.8%) were ovarian neoplasms while 38.2% were non-neoplastic functional cysts. Benign neoplasms (n=278; 72.8%) were more common than borderline (n=20; 5.2%) and malignant ones (n=84; 22%) in all age groups. Surface epithelial neoplasms were the most common (61%) followed by germ cell (28%), gender cord stromal (7.6%) and metastatic tumors (3.4%). The most common benign neoplasm was serous cystadenoma (44.6%) and the most common malignant was serous cystadenocarcinoma (33.3%). The most common ovarian neoplasm below the age of 20 years was surface epithelial tumors (n=24) followed by germ cell tumor (16 cases). Benign neoplasms (n=213) were more common than malignant ones (n=42) in the age group from 20-51 years. Malignant ovarian neoplasms (35 out of the 71) were more common than benign (34 cases) in the age above 52.
 CONCLUSIONS 
Benign ovarian neoplasms are more common than malignant ones. The most common benign ovarian neoplasm is serous cystadenoma and the commonest malignant neoplasm is serous cystadenocarcinoma. The prevalence of malignant ovarian neoplasms increases with increasing age.

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Histopathological pattern of ovarian neoplasms and their age distribution in the western region of Saudi Arabia.

GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O-linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1. Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases.

/pdf/first-comprehensive-in-silico-analysis-of-the-functional-and-3o843kwx4f.pdf

Nabeel S. Bondagji

Papers

Histopathological Pattern of Endometrial Sampling Performed for Abnormal Uterine Bleeding

Antenatal diagnosis, prevalence and outcome of congenital anomalies of the kidney and urinary tract in Saudi Arabia.

Histopathological patterns of testicular biopsy in male infertility: A retrospective study from a tertiary care center in the western part of Saudi Arabia

Histopathological pattern of ovarian neoplasms and their age distribution in the western region of Saudi Arabia.

First Comprehensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human GalNAc-T1 Gene