bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes In Prothrombin And Activated Partial Thromboplastin Time During Replacement Therapy With Human Recombinant Growth Hormone In Growth Hormone Deficient Adults
Authors: Kamel Y S
Published: October 2020

Introduction/Objective

The aim of this study was to investigate the effects of GH administration on basic coagulation parameters: PT, aPTT and fibrinogen concentrations in adult GHD patients before and during one year of GH replacement.

Methods

Twenty-one adult patients with severe GHD (mean age +/- SE: 38.6 +/- 2.8 years) were included in this hospital based, prospective, interventional study. All patients were treated with rhGH for 12 months (GH dose: 0.4 mg/day for male and 0.6 mg/day for female patients). IGF-1 concentrations were determined using RIA-INEP kits. Basic coagulation tests, i.e. aPTT and fibrinogen concentrations, were measured before and after 3, 6 and 12 months of treatment with rhGH. Control values were obtained from fourteen “healthy” subjects matched by age, sex and body mass index (BMI).

Results

At baseline, we observed no significant differences in PT, aPTT and fibrinogen values between GHD and healthy subjects. IGF-1 concentrations increased significantly within 3 months of GH therapy (8.2 +/- 1.5 vs. 24.2 +/- 2.9 nmol/l, p <0.05) and remained stable thereafter. A significant increase in PT values, which was more pronounced in female subjects, was noted after 6 and 12 months of treatment with GH. aPTT values increased significantly after 12 months of treatment only in male patients (28.8 +/- 4.6 vs. 39.7 +/- 2.1 s.; p <0.05). No significant changes in fibrinogen concentrations were found during the study.

Conclusion

Twelve months of GH replacement therapy led to a significant increase in PT and aPTT values in adult GHD patients, while fibrinogen concentrations did not change. Changes in PT were more pronounced in female GHD patients, while an increase in aPTT values was observed only in male patients with GHD. The clinical significance of these changes needs further evaluation.
Plasmablastic Myeloma Versus Plasmablastic Lymphoma; Is MYC Rearrangement Helpful Towards A Precise Diagnosis?
Authors: Khedr M , Yusuf Y , Aftab L
Published: October 2020

Introduction/Objective

Plasmablastic myeloma (PBM) is a rare and aggressive plasma cell neoplasm. Differentiating PBM from plasmablastic lymphoma (PBL) represents a diagnostic challenge, as both diseases have overlapping cytomorphologic and immunophenotypic features. Genetic mutations in MYC occur in a majority of PBL cases but rarely in PBM, thus can theoretically be used to differentiate between both neoplasms.

Methods

We report a case of a 53-year-old female who presented with a rapidly growing mass in her right mandible. Biopsy revealed circumscribed nodules of immunoblastic cells with moderate cytoplasm, large vesicular nuclei and large prominent nucleoli. Apoptotic debris and brisk mitoses were present. Molecular testing revealed a C-MYC rearrangement. The location of the neoplasm and the above described morphological features were suggestive of PBL, especially with a positive C-MYC rearrangement. The neoplastic cells were positive for CD138, MUM1,CD56 and kappa; and negative for CD45, CD20, PAX5, CD3, CD5, CD30, EBER-ISH, HHV8, ALK-1, Lambda, EMA, CD21, CD23, pancytokeratin, CK20, CK7, Cam5.2, chromogranin, synaptophysin, HMB45, S100, P16, P40. MIB-1 showed high positivity, approximately 95%.

Results

Patient underwent further diagnostic work up, her HIV antibodies result were negative however, she was found to be anemic (Hemoglobin 6.6 g/dl; reference range 12-16 g/dl) and hypercalcemic (Calcium 12.3 mg/dl; reference range 8.5-10.5 mg/dl). PET scan revealed multiple hypermetabolic lytic bone lesions. The bone marrow biopsy showed 80% cellularity with extensive involvement by atypical plasmacytic cells forming large clusters. The patient’s final diagnosis was PBM.

Conclusion

Differentiating PBM from PBL is essential as treatment is different. Although MYC rearrangement in PBM is not common, it has been demonstrated and therefore should not be used to exclude this diagnosis. Here, we highlight the importance of correlating detailed clinical, radiological, laboratory, histological and genetics data for reaching the final diagnosis.
Evaluation of BRCA1 and BRCA2 Protein Dysfunction in Breast Cancer Cells among Women in Osun State, Southwest Nigeria
Authors: Iyiola S , Komolafe A , Samuel A , Onifade J A , Enweani I , Ngokere A
Published: October 2020

Introduction/Objective

Breast cancer among Nigeria women had been found to occur at a much younger age compared with their Caucasian age groups. BRCA1 and BRCA2 were suspected to responsible for breast cancers at a young age, therefore this work examined the BRCA1 and BRCA2 dysfunction among women suffering from breast cancer in Osun State, Nigeria.

Methods

This cross-sectional study was carried out at the Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife and Ladoke Akintola University Teaching Hospital, Osogbo, Nigeria. The request cards and tissue blocks were sorted from the year 2014 to 2017. The breast tissue blocks were sectioned, stained with H&E. A representative tissue block was selected for each patient. Sections obtained from the blocks were stained with BRCA 1 and BRCA 2 antibody using a diaminobenzidine horseradish peroxidase technique. The cells were semi-quantitatively scored as percentage of tumour cells stained brown. Score 0-5% were taken as negative as proposed by Karuna et al., 2013.

The value obtained was tabulated against the age of the patient.

Results

Out of 240 breast cancer patients sampled 16(6.7%), 32(13.3%), 85(35.4%), 43(17.9%), 64(26.7%) patients were between ages 21-30, 31-40, 41-50, 51-60 and 60+ years respectively. 54(22.5%) showed loss of BRCA 1 staining with only 1(0.4%) patient between age 21-40 years while 18(7.5%), 16(6.67), 19(7.9) patients between age 41-50, 51-60 and 60+ years respectively. 82(34.2%) showed loss of BRCA 2 staining; 7(2.9%), 12(5%), 31(12.9%), 15(6.25%),17(5.8%) patients for age between 21-30, 31-40, 41-50, 51-60 and 60+ years respectively. Among women aged 50 years and below, BRCA 1 and BRCA 2 dysfunctions were responsible for 14.3% and 37.6% of breast cancers respectively.

Conclusion

Increase in age increases the rate of BRCA 1 dysfunction while BRCA 2 dysfunction is not more associated to with any age. BRCA1 and BRCA2 are responsible for more than thirty percent of breast cancers among women less than 50 years of age in Osun state.
TRUU-Lab: Methods for Optimizing Test Names for Understanding and Utilization
Authors: Wang J , Garnett E , Singh I , Bierl C , Jackson B
Published: October 2020

Introduction/Objective

Poor understandability of laboratory test names increases the risk for inappropriate test utilization and medical errors. Yet, human understandability has not been a major consideration in existing laboratory test names or naming guidelines. TRUU-Lab (Test Renaming for Understanding and Utilization for Laboratory Test Names) is a national initiative that now has more than 45 members representing more than 20 academic and industry organizations, the CDC, and the FDA. The goals of the initiative include: 1) Identify root causes and challenges in understanding and using laboratory test names; 2) Share resources related to potential solutions; 3) Develop consensus guidelines for laboratory test naming; 4) Establish consensus names for existing laboratory tests; and 5) Promote the adoption and implementation of consensus laboratory test names.

Methods

We previously addressed the first two goals of this initiative by identifying problematic test names and features of test names that contribute to misutilization. We also identified the advantages and limitations of current test naming guidelines and previous standardization efforts. This current study addresses goals 3 and 4. We developed an iterative process of guideline development. This process includes collecting feedback on consensus names to improve guidelines, which then informs the improvement of the consensus names.

Results

By analyzing test name characteristics, we found that the requirements for understandability vary with respect to the clinical scenario and provider background. We have used these results to design a 30-min long survey to test candidate names. The survey will be distributed through the Brand Institute, which offers expertise in pharmaceutical name and brand identity development. This pilot survey will be sent to primary care providers to assesses intuitive name preferences given a short and specific prompt. The second phase will take place in a simulated electronic medical record environment to present clinical scenarios where physicians will select an appropriate test.

Conclusion

We expect that results from survey studies will directly inform the development of TRUU-Lab naming guidelines, in turn permitting development of better-optimized laboratory test names. This process represents a new strategy for the intentional design of laboratory test names that are understandable and promote correct provider utilization.
Gastroblastoma: Cytologic Findings with Resection and Molecular Correlation
Authors: Reardon J D , Hatfield B S , Kraft A O , Smith S C
Published: October 2020

Casestudy

Gastroblastoma is a rare tumor with biphasic components showing epithelial and mesenchymal differentiation. To date, <15 cases have been reported, with molecular confirmation of the recently identified MALAT1-GLI1 translocations only in a subset. Aspiration cytologic and small biopsy findings have not yet been reported. We present a case of gastroblastoma, arising in a 22-year-old female.

Results

A CT scan was performed, showing a 7 cm heterogeneous mass in the distal stomach and pancreas, clinically suspected to represent at gastrointestinal stromal tumor (GIST). She underwent two preoperative samples, including endoscopic ultrasound guided-fine needle aspiration and core biopsy, followed by a distal gastrectomy. Diff- Quik stained touch preparations performed on the core needle biopsy during rapid on-site evaluation showed a hypercellular neoplasm composed of large, three-dimensional aggregates of neoplastic cells in a background of numerous isolated single cells and bare nuclei. The neoplastic cells were bland with spindled to epithelioid nuclei, occasional nuclear grooves, and small nucleoli. Immunostains were only helpful in excluding GIST (CD117 and DOG1 negative). Distal gastrectomy showed a nodular/plexiform tumor with variably epithelioid to spindle cell cytology and solid to focally myxoid/microcystic architecture. Pancytokeratins CAM5.2 (patchy) and AE1/AE3 (very focal) were positive, with negative S100, SMA, Desmin, Melan-A, Inhibin, Calretinin, and Synaptophysin. Based on the age, location, histology and immunophenotype, gastroblastoma was suspected, and multiplex NGS-based fusion sequencing identified a MALAT1-GLI1 fusion. Staging studies were negative for metastasis at presentation.

Conclusion

Based on this experience, we recommend consideration of gastroblastoma for a gastric tumor in a young patient, especially if encountering a cytologic sample showing non-pleomorphic epithelioid and spindle cell cytology. Lack of expression of GIST, smooth muscle, neuroendocrine, and neural sheath-associated markers should particularly raise consideration of this rare neoplasm. While in this case molecular studies clinched the diagnosis upon resection, increasingly used GLI1 immunostain may be of use prospectively for diagnosis of limited samples.
Validation/Verification of Abbott RealTime SARS-CoV-2 Assay on the Abbott m2000 System: The Veteran Affairs Medical Center (VAMC) Experience
Authors: Petersen J M , Dalal S , Jhala D
Published: October 2020

Introduction/Objective

The extraordinary circumstances of the highly contagious SARS-CoV-2 pandemic have led the FDA to approve diagnostic assays with emergency use authorizations (EUA). One of these assays is the Abbott RealTime SARS-CoV-2 assay (Abbott Park, Ill.). However, the literature is sparse on the validation of EUA assays for SARS-CoV-2 assays for this crisis; therefore, we present the Veteran Affairs Medical Center (VAMC) experience in validating/verifying this test for clinical use.

Methods

Validation/verification was performed in three parts as part of quality assurance/quality improvement; 1) sample/patient correlation, 2) precision, and 3) validation/verification of accuracy at the lower limit of detection (LOD). The results from these studies was compiled, reviewed by the laboratory, and after performance was deemed satisfactory, the test would be put for clinical use.

Results

For the sample/patient correlation, a total of 68 known positive and 59 known negative samples were run; these included 56 positive contrived samples or controls, 12 known positive patient samples, 31 negative contrived or controls, and 28 known negative patient samples. All results from the assay were as expected with 100% positive and negative percent agreement except for one sample that was quantity not sufficient for testing. The precision study with 4 known positive and 4 known negative samples run once per day for 5 days yielded perfect 100% precision for both the positive and negative samples. Replicates to determine accuracy at the lower LOD (100 virus copies/ml per instructions for use of the assay) demonstrated accuracy even with dilutions down to 50 virus copies/ml. For this third step, 3 replicates each had been performed at 1000, 500, 250, 70, 60 and 50 virus copies/ml. As 100 virus copies/ml was the provided manufacturer LOD, 7 replicates were performed at 100 virus copies/ml.

Conclusion

The validation/verification indicated that the Abbott RealTime SARS-CoV-2 assay performed with expectations including with real patient samples and could be put into clinical use at the VAMC. After this validation/verification, the assay has been very successfully used for in-house testing for SARS-CoV-2. In fact, the validation demonstrated an LOD as low as 50 virus copies/ml, suggesting the assay may be even more sensitive to low levels of viremia than is stated in the EUA.
Navigating the Diagnostics of COVID-19
Authors: Sanyaolu A , Okorie C , Marinkovic A , Ayodele O , Abbasi A , Prakash S , Ahmed M , Kayode D , Jaferi U , Haider N
Published: October 2020

Introduction/Objective

The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Hubei province, China in December 2019 and has spread worldwide at an alarming rate. With millions of individuals infected and over two hundred thousand deaths, the necessity to develop fast and efficient diagnostic methods is of high importance. Diagnostic modalities rely on a combination of epidemiology, clinical presentation, laboratory examination, and appropriate imaging to diagnose and distinguish SARS-CoV-2 from other pulmonary infections. The purpose of this paper is to report on currently available diagnostic screening methods for patients infected with SARS-CoV-2 to guide frontline healthcare workers involved with COVID-19 patient care.

Methods

An electronic literature search was performed for peer-reviewed articles published from January 1, 2020, until April 26, 2020. Articles were then reviewed and included based on the applicability to the topic.

Results

The preferred diagnostic approach is reverse transcription of the virus’ RNA followed by PCR amplification (RT-PCR). This method recognizes the gene-specific primers to target various viral protein genes, such as the envelope protein gene or the nucleocapsid protein gene, which enables this test to be both sensitive and specific toward SARS-CoV-2. However, this method has been proven to be time-consuming taking hours-to-days for the results. In order to improve the speed and efficiency of diagnostics, newer rapid diagnostic serological tests are being developed for testing SARS-CoV-2, each with its own unique advantages and disadvantages. They could potentially be used as triage tests to rapidly identify patients who are very likely to have COVID-19 in combination with other accurate diagnostic methods.

Conclusion

Therefore, a combination of diagnostic testing used in a timely manner may be beneficial for the rapid and accurate detection of SARS-CoV-2. This was evident in cases where despite initial negative RT-PCR tests for various patients, who later demonstrate chest CT scans with various degrees of consolidation and ground-glass opacity. Thus establishing the need for radiology diagnosis to be complementary to RT-PCR for COVID-19 patients. Hopefully, the continuous development and use of rapid diagnostic tests and the implementation of public health measures will help control the spread of the disease.
Detecting Lung Cancer Stages Earlier By Appropriate Markers Rather Than Biopsy And Other Techniques
Authors: Addissouky T A , Khalil A A
Published: October 2020

Introduction/Objective

Early detection of lung cancer stages is deeply under consideration of scientists. By day, high rate of mortality might be caused by cancer of lung over the world. The biopsy is still the golden standard as a histological predictor to determine lung cancer worldwide. However, a biopsy has various complications and hardness especially in collecting tissue samples. Therefore, detecting appropriate tools to determine the early stages of lung cancer is urgently needed. Some biomarkers levels have been determined in patient’s serum. The correlation between studied biomarkers and lung cancer has been studied by current research to avoid biopsy and other techniques.

Methods

The various biomarkers such as (CEA, SCCA, CYFRA21-1, ProGRP, Prolactin and CKAP4) were measured and calculated in 379 infected cases with lung cancer. Also, the same parameters were determined in 113 healthy persons as controls. Alternative markers’ levels were determined by using ELISA technique. Noninvasive markers were approved by comparison with CT chest scan and Biopsy techniques.

Results

Our research has indicated that Some of the studied biomarkers such as cytoskeleton-associated protein 4 (CKAP4), pro-gastrin-releasing peptide (ProGRP) and Prolactin (PRL) have high sensitivity from 77.05% to 96.72% and accuracy from 89.71% to 97.79% as well as their cut off which approved the aim of this study. However, other indicators (CEA, SCCA and CYFRA21-1) have low sensitivity from 62.49 % to 87.31% and accuracy between 71.27 % and 88.43 %. Meanwhile, CT scan has high sensitivity around 83% with specificity about 71%.

Conclusion

Alternative biomarkers (CEA, SCCA, CYFRA21-1, ProGRP, Prolactin and CKAP4) are considered as prospective markers to differentiate healthy individuals from lung cancer disease by their significant results in early stages detection. Thence, if serum CEA, SCCA, CYFRA21-1, ProGRP, Prolactin and CKAP4 are measured together, it would be the precise criterion of early levels of lung cancer rather than the lung biopsy definitely. However, further researches are needed to prove more reliable noninvasive markers of lung cancer.
Genomic Analysis Identifies Rare ALK Positive Cases In The TCGA Database
Authors: Patil A R , Dabrowski D S , Cotelingam J , Veillon D , Ong M , Dela Cruz N , Wei E , Tirupathi R , Ganti N , Vanga P , Gundale A
Published: October 2020

Introduction/Objective

The anaplastic lymphoma kinase (ALK) gene is a receptor tyrosine kinase gene located in the 2p23.2 region. Normally, dimerization of ALK receptor by binding to its ligand activates the ALK receptor by autophosphorylation of c-termius and activates downstream PI3K, MAPK and JAK3 pathways. The ALK gene is abnormally hyperactivated by fusion of the 3’ half containing the kinase domain with 5’ portion of other genes, resulting in the ligand independent dimerization and activation of the ALK receptor. The tumors harboring these translocations are termed as ALK-positive tumors and can be treated with ALK inhibitors.

Methods

We analyzed the status of clinically relevant ALK fusion driver mutations in 230 different cancer studies, containing tumors from 79222 different individuals, in The Cancer Genome Atlas database (TCGA) using the cbioportal web browser.

Results

We observed that, as expected ALK-positive mutations are predominantly present in NSCLC, with EML4- ALK being the most common. In addition, we were able to identify ALK positive mutations in colorectal carcinomas, papillary thyroid carcinomas, papillary renal cell carcinomas, sarcomas and invasive ductal carcinomas of the breast. Most important, our analysis identified extremely rare ALK positive cases in salivary duct carcinomas, urothelial carcinomas, cutaneous melanomas and prostatic adenocarcinomas.

Conclusion

Our analysis identified ALK positive cases were predominant in adenocarcinoma of lung with EML4-ALK being the most common ALK positive mutation, which is also consistent with the literature. However, the ALK positive mutations were at a lower prevalence rate than that described in the literature. We attribute the lower prevalence rate to underrepresentation of the Asian population in the TCGA database. In addition, we identified extremely rare ALK positive cases in salivary duct carcinomas, melanomas and prostate cancers, thus highlighting the need for testing for these mutations in these cancers.
Prometastatic CXCR4 and Histone Methyltransferase EZH2 are Upregulated in SMARCB1/INI1-deficient and TP53-mutated Metastatic Poorly Differentiated Chordoma to the Liver
Authors: Murzabdillaeva A , Elzamly S , Brown R , Buryanek J , Jafri S , Rowe J
Published: October 2020

Introduction/Objective

Chordoma is a rare tumor most commonly arising in the sacrococcygeal region from notochord remnants. Usually, these tumors are locally invasive and recurrent, but do not have the capability to metastasize. A newly described aggressive variant called poorly differentiated chordoma is different than conventional chordoma in that it does not have the well-differentiated histologic appearance of conventional chordoma and also exhibits loss of SMARCB1/INI1.

Methods

Herein, we describe a case of poorly differentiated chordoma with SMARCB1/INI1 loss, concurrent TP53 mutation and Rb1 loss.

Results

The patient is a 55-year-old man with a history of a previously resected sacrococcygeal chordoma, who was found to have new hepatic, lung, and adrenal lesions. Biopsy of the liver showed sheets of malignant epithelioid cells with vacuolated cytoplasm, areas of necrosis, and up to 5 mitoses in one high power field. No physaliferous features or matrix material were seen. After an extensive panel of immunohistochemical markers, the origin of the metastatic tumor could not be determined and the tumor was only positive for Cam5.2, EMA, and CD56. Brachyury was performed due to the patient’s previous history and was positive. Genomic testing showed a SMARCB1 mutation, a TP53 mutation, and RB1 loss. Additional markers were performed and the tumor showed a Ki-67 proliferation index of approximately 80%, mutant p53 protein, loss of INI1, and strong expression of prometastatic CXCR4 and the histone methyltransferase EZH2. The most recent follow-up of the patient showed that the patient was receiving palliative care.

Conclusion

Poorly differentiated chordoma is a highly aggressive variant of chordoma with few cases reported. This case of SMARCB1/INI-deficient, poorly differentiated chordoma also showed concurrent TP53 mutation and loss of RB1, which resulted in malignant transformation with loss of differentiation, cell cycle progression, up-regulation of prometastatic CXCR4 and the histone methyltransferase EZH2 causing aggressive behavior and metastasis.
In-Silico Screening: Accurately Predicting Results of the Direct Antiglobulin Test using Commonly Available Lab Data
Authors: Cardillo A , Syposs C , Refaai M
Published: October 2020

Introduction/Objective

The Direct Antiglobulin Test (DAT) is a useful screening test to determine whether a patient’s red blood cells have been sensitized to immunoglobulin or complement. Like the majority of screening tests, the DAT compromises specificity for sensitivity in order to quickly assess for hemolysis and its dangerous sequelae. Because of the high sensitivity of the DAT, improper ordering of this test can confuse the clinical picture at best and result in misdiagnosis at worst. Pre-tests for ruling-out disease have proven effective in limiting test ordering, such as the Pulmonary Embolism Rule-out Criteria (“PERC rule”) for limiting the use of D-dimers. A similar pre-test could prove useful in DATs. We use “in silico testing” – testing via computer simulation – to predict the likelihood of any DAT being positive, given common patient attributes and laboratory values.

Methods

A three-layer deep-learning artificial neural network (ANN) was created using Python and the machine learning framework Keras. The ANN was compiled to maximize specificity while retaining 100% sensitivity. Input variables to the model were patient sex and age, along with most recent lab values for hemoglobin, hematocrit, white blood cell count, platelet count, total bilirubin, direct bilirubin, and haptoglobin, where available. The output of the ANN was a binary variable: “ruled-out” versus “further testing necessary”. The ANN was trained on all positive (n=30) and negative (n=63) DATs performed on November 2019 through March 2020, with a final total of ninety-three patients. A 10-fold cross-validation of the entire dataset was used to measure performance.

Results

The ANN was able to maximize specificity to 83% while retaining 100% sensitivity. A ROC curve of the model shows performance well above that of the no-discrimination line.

Conclusion

“In-silico testing” can accurately screen the likelihood of a positive result for a labor and time-intensive test, such as the DAT, before the actual test is performed. This has the potential to reduce unnecessary testing if validated in clinical practice. Analogous to their clinical counterpart “the PERC rule,” computer models that maximize specificity while retaining 100% sensitivity could achieve more effective test utilization and more informative results.
In-House Viral Transport Medium (VTM) Manufacture in the Time of Shortage, Supply and Crisis of COVID-19 at Veteran Affairs Medical Center (VAMC)
Authors: Petersen J M , Dalal S , Jhala D
Published: October 2020

Introduction/Objective

With the outbreak of COVID-19 caused by SARS-CoV-2, there have been challenges in the maintenance of adequate supplies both in terms of PPE and for testing. The shortage of commercial VTM for the transport of specimens for PCR testing has created a situation in which laboratories would need to manufacture their own in-house VTM as commonly used commercial VTM is unavailable. However, there is sparse literature on the emergency manufacture of VTM. Here, we describe the VAMC experience in manufacturing/quality control on its own VTM.

Results

VTM was manufactured by pathology and laboratory medicine using strict aseptic technique with Hanks Balanced Salt Solution (HBSS) 500 ml bottle with phenol red, sterile heat-inactivated fetal bovine serum (FBS) gentamicin sulfate (50 mg/mL) and amphotericin B (250 ug/ml). First, 50 ml of amphotericin B and 50 ml of gentamicin sulfate were mixed. Then 10 ml of FBS was mixed with the HBSS bottle and then 2 ml of the gentamicin/amphotericin B mixture was also mixed into the HBSS bottle. 3 ml aliquots were made from this mixture to constitute individual tubes of VTM for clinical use. Sterility for each batch (after 24-hour incubation at 37o C in the CO2 incubator) was assessed visually and by culture on a blood agar, chocolate agar, and thioglycolate mediums. An efficacy check was performed for each batch by spiking positive and negative controls into the VTM aliquots; RT-PCR for SARS-CoV-2 was executed to verify the medium did not degrade viral RNA and produced expected results for room temperature, refrigerated, and frozen samples. Previously manufactured VTM without phenol red also underwent sterility and efficacy checks.

Results

VTM was successfully manufactured in-house, allowing testing to continue despite the shortage. Sterility and efficacy checks on all lots and bottles from which the VTM aliquots were made passed with no growth detected and efficacy passing with all expected positives and negatives resulting as expected.

Conclusion

To the author’s knowledge, this represents the first published abstract on VTM manufacture in this most unprecedented crisis involving COVID-19. In this national emergency with corresponding shortage of testing supplies including commercial VTM, the in-house manufacture of VTM is both feasible and prudent to ensure continuity of testing and quality patient/laboratory care.
Do Deeper Levels of Cervical Biopsies Preceded by a Pap Smear Diagnosis of LSIL, ASCUS, or NILM/HPV+ Increase the Yield of Identifying Clinically Significant Lesions?
Authors: Manjee K G , Watkin W G
Published: October 2020

Introduction/Objective

Cervical biopsy is performed following an abnormal pap smear or positive HPV testing in an attempt to uncover clinically significant lesions [HSIL/invasive carcinoma (HSIL+)]. An excisional procedure is considered if biopsy confirms HSIL+. When preceded by pap smear of LSIL, ASCUS, NILM/HPV+ or persistent HPV, continued surveillance is recommended for biopsies showing no SIL or LSIL. In our laboratory, cervical biopsies are routinely sectioned at 3 levels. Deeper levels are often ordered when initial sections are non-diagnostic. p16 immunohistochemistry, with or without deeper levels, is often ordered to confirm HSIL, or to differentiate HSIL from mimics. In this study, we examine whether and in what clinical situations does obtaining additional levels uncover clinically significant lesions.

Methods

430 cervical biopsies between January-May 2018, with recent cytology of LSIL, ASCUS or NILM/HPV+ were identified in the pathology database. HPV status (if known), final biopsy diagnosis and past history of LSIL/HSIL were recorded. For each biopsy, orders for additional levels and/or p16 immunohistochemistry were recorded resulting in 4 categories: C1-no additional levels or p16, C2-deeper only, C3-deeper+p16 and C4-p16 only. Final diagnoses were divided into HSIL+, LSIL and no SIL.

Results

There was no significant difference in prior history of LSIL/HSIL and HPV status between all categories. Biopsy results were as follows:

HSIL+: 11/222 (5%) C1; 1/78 (1%) C2; 7/43 (16%) C3; 15/87 (17%) C4

LSIL: 91/222 (41%) C1; 7/78 (9%) C2; 16/43 (37%) C3; 35/87 (40%) C4

No SIL: 120/222 (54%) C1; 70/78 (90%) C2; 20/43 (46%) C3; 37/87 (42%) C4

The average number of additional levels in C2 and C3 was 3.8 and 1.8, respectively.

Conclusion

Deeper levels alone did not enhance the detection of HSIL+. Almost all LSIL/HSIL were detected when initial levels were diagnostic or suspicious and supported by p16 immunohistochemistry. 3 levels are adequate to detect clinically significant lesions.
Sero-Epidemiology And Pattern Of Transfusion-Transmissible Infectious Diseases Among Family Replacement And Voluntary Blood Donors In Lagos University Teaching Hospital (2018-2019), South-West Nigeria
Authors: Otokiti O E
Published: October 2020

Introduction/Objective

Despite innovations and giant strides achieved in medicine, blood transfusion has continually remained an integral aspect of patient care and management. Currently, blood and blood products are part of the World Health Organisation (WHO) model list of Essential Medicine (EML). However, despite being a ‘life saver’, potential risks of transfusion of fatal infections (TTI) are associated with its use, hence this study to evaluate the trend of TTI in blood donors.

Methods

In this study, 21,464 donors were screened for HIV, HBV, HCV and Syphilis between 2018 and 2019 via 4 th generation ELISA. Retrospective data was gotten from records. The results were read using a spectrophotometer.

Optical Density was calculated for positive and negative controls and only results from runs in which controls had passed were used and released.

Results

Of the 21,464donors tested, 3818 (17%) were voluntary blood donors (VBD) and 17,646 (83%) were family replacement donors (FRP). Total number of TTI was 1928 (0.1%) of units donated. Of the screened units positive for TTI, HBV accounted for the highest prevalence 1031 (54%), HCV 498 (26%), HIV 246 (13%) and Syphilis 147 (8%). A much higher incidence of TTI sero-positivity was observed in FRP (85%) as compared with voluntary blood donors (15%). Cumulative discard rate from TTI was approximately 0.1%.

Conclusion

Our results in this study showed that FRP are more likely to transmit TTI than VBD. Blood transfusion services should work more on replacing family replacement donors with voluntary donors. This can be achieved by reinforcing the culture of voluntary blood donation through the media, secondary and higher institutions as well as through advocacy. Indeed the WHO recommends 100% voluntary blood donations for all nations.
A Structured Approach to Evaluating Life-Course Hypotheses: Moving Beyond Analyses of Exposed Versus Unexposed in the -Omics Context
Authors: Zhu Yiwen , Simpkin Andrew J , Suderman Matthew J , Lussier Alexandre A , Walton Esther , Dunn Erin C , Smith Andrew D A C
Published: October 2020

The structured life-course modeling approach (SLCMA) is a theory-driven analytical method that empirically compares multiple prespecified life-course hypotheses characterizing time-dependent exposure-outcome relationships to determine which theory best fits the observed data. In this study, we performed simulations and empirical analyses to evaluate the performance of the SLCMA when applied to genomewide DNA methylation (DNAm). Using simulations (n = 700), we compared 5 statistical inference tests used with SLCMA, assessing the familywise error rate, statistical power, and confidence interval coverage to determine whether inference based on these tests was valid in the presence of substantial multiple testing and small effects—2 hallmark challenges of inference from -omics data. In the empirical analyses (n = 703), we evaluated the time-dependent relationship between childhood abuse and genomewide DNAm. In simulations, selective inference and the max-|t|-test performed best: Both controlled the familywise error rate and yielded moderate statistical power. Empirical analyses using SLCMA revealed time-dependent effects of childhood abuse on DNAm. Our findings show that SLCMA, applied and interpreted appropriately, can be used in high-throughput settings to examine time-dependent effects underlying exposure-outcome relationships over the life course. We provide recommendations for applying the SLCMA in -omics settings and encourage researchers to move beyond analyses of exposed versus unexposed individuals.
Highly accurate diagnosis of papillary thyroid carcinomas based on personalized pathways coupled with machine learning
Authors: Park Kyoung Sik , Kim Seong Hoon , Oh Jung Hun , Kim Sung Young
Published: October 2020

Thyroid nodules are neoplasms commonly found among adults, with papillary thyroid carcinoma (PTC) being the most prevalent malignancy. However, current diagnostic methods often subject patients to unnecessary surgical burden. In this study, we developed and validated an automated, highly accurate multi-study-derived diagnostic model for PTCs using personalized biological pathways coupled with a sophisticated machine learning algorithm. Surprisingly, the algorithm achieved near-perfect performance in discriminating PTCs from non-tumoral thyroid samples with an overall cross-study-validated area under the receiver operating characteristic curve (AUROC) of 0.999 (95% confidence interval [CI]: 0.995–1) and a Brier score of 0.013 on three independent development cohorts. In addition, the algorithm showed excellent generalizability and transferability on two large-scale external blind PTC cohorts consisting of The Cancer Genome Atlas (TCGA), which is the largest genomic PTC cohort studied to date, and the post-Chernobyl cohort, which includes PTCs reported after exposure to radiation from the Chernobyl accident. When applied to the TCGA cohort, the model yielded an AUROC of 0.969 (95% CI: 0.950–0.987) and a Brier score of 0.109. On the post-Chernobyl cohort, it yielded an AUROC of 0.962 (95% CI: 0.918–1) and a Brier score of 0.073. This algorithm also is robust against other various types of clinical scenarios, discriminating malignant from benign lesions as well as clinically aggressive thyroid cancer with poor prognosis from indolent ones. Furthermore, we discovered novel pathway alterations and prognostic signatures for PTC, which can provide directions for follow-up studies.
Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach
Authors: Alam Aftab , Khan Arbaaz , Imam Nikhat , Siddiqui Mohd Faizan , Waseem Mohd , Malik Md Zubbair , Ishrat Romana
Published: October 2020

The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.
CATH functional families predict functional sites in proteins
Authors: Das Sayoni , Scholes Harry M , Sen Neeladri , Orengo Christine
Published: October 2020

Motivation

Identification of functional sites in proteins is essential for functional characterization, variant interpretation and drug design. Several methods are available for predicting either a generic functional site, or specific types of functional site. Here, we present FunSite, a machine learning predictor that identifies catalytic, ligand-binding and protein–protein interaction functional sites using features derived from protein sequence and structure, and evolutionary data from CATH functional families (FunFams).

Results

FunSite’s prediction performance was rigorously benchmarked using cross-validation and a holdout dataset. FunSite outperformed other publicly available functional site prediction methods. We show that conserved residues in FunFams are enriched in functional sites. We found FunSite’s performance depends greatly on the quality of functional site annotations and the information content of FunFams in the training data. Finally, we analyze which structural and evolutionary features are most predictive for functional sites.

Availabilityand implementation

https://github.com/UCL/cath-funsite-predictor.

Supplementary information

Supplementary data are available at Bioinformatics online.
PathExt: a general framework for path-based mining of omics-integrated biological networks
Authors: Sambaturu Narmada , Pusadkar Vaidehi , Hannenhalli Sridhar , Chandra Nagasuma
Published: October 2020

Motivation

Transcriptomes are routinely used to prioritize genes underlying specific phenotypes. Current approaches largely focus on differentially expressed genes (DEGs), despite the recognition that phenotypes emerge via a network of interactions between genes and proteins, many of which may not be differentially expressed. Furthermore, many practical applications lack sufficient samples or an appropriate control to robustly identify statistically significant DEGs.

Results

We provide a computational tool—PathExt, which, in contrast to differential genes, identifies differentially active paths when a control is available, and most active paths otherwise, in an omics-integrated biological network. The sub-network comprising such paths, referred to as the TopNet, captures the most relevant genes and processes underlying the specific biological context. The TopNet forms a well-connected graph, reflecting the tight orchestration in biological systems. Two key advantages of PathExt are (i) it can extract characteristic genes and pathways even when only a single sample is available, and (ii) it can be used to study a system even in the absence of an appropriate control. We demonstrate the utility of PathExt via two diverse sets of case studies, to characterize (i) Mycobacterium tuberculosis response upon exposure to 18 antibacterial drugs where only one transcriptomic sample is available for each exposure; and (ii) tissue-relevant genes and processes using transcriptomic data for 39 human tissues. Overall, PathExt is a general tool for prioritizing context-relevant genes in any omics-integrated biological network for any condition(s) of interest, even with a single sample or in the absence of appropriate controls.

Availabilityand implementation

The source code for PathExt is available at https://github.com/NarmadaSambaturu/PathExt.

Supplementary information

Supplementary data are available at Bioinformatics online.
RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures
Authors: Becquey Louis , Angel Eric , Tahi Fariza
Published: October 2020

Motivation

Applied research in machine learning progresses faster when a clean dataset is available and ready to use. Several datasets have been proposed and released over the years for specific tasks such as image classification, speech-recognition and more recently for protein structure prediction. However, for the fundamental problem of RNA structure prediction, information is spread between several databases depending on the level we are interested in: sequence, secondary structure, 3D structure or interactions with other macromolecules. In order to speed-up advances in machine-learning based approaches for RNA secondary and/or 3D structure prediction, a dataset integrating all this information is required, to avoid spending time on data gathering and cleaning.

Results

Here, we propose the first attempt of a standardized and automatically generated dataset dedicated to RNA combining together: RNA sequences, homology information (under the form of position-specific scoring matrices) and information derived by annotation of available 3D structures (including secondary structure, canonical and non-canonical interactions and backbone torsion angles). The data are retrieved from public databases PDB, Rfam and SILVA. The paper describes the procedure to build such dataset and the RNA structure descriptors we provide. Some statistical descriptions of the resulting dataset are also provided.

Availability and implementation

The dataset is updated every month and available online (in flat-text file format) on the EvryRNA software platform (https://evryrna.ibisc.univ-evry.fr/evryrna/rnanet). An efficient parallel pipeline to build the dataset is also provided for easy reproduction or modification.

Supplementary information

Supplementary data are available at Bioinformatics online.
Glans inflation morphology and female cloaca copulatory interactions of the male American alligator phallus†
Authors: Moore Brandon C , Brennan Patricia L R , Francis Rachel , Penland Samuel , Shiavone Kelsie , Wayne Kathryn , Woodward Allan R , Does Mark D , Kim Dong Kyu , Kelly Diane A
Published: October 2020

The phallic glans of the American alligator (Alligator mississippiensis) is the distal termination of the semen-conducting sulcus spermaticus and during copulation has the closest, most intimate mechanical interactions with the female urodeum, the middle cloacal chamber that contains the opening to the vaginal passages and oviducts. However, the details of this interface leading to insemination and gamete uptake are unclear. Here, we: (1) histologically characterize the underlying tissue types and morphologically quantify the shape changes associated with glans inflation into the copulatory conformation, (2) digitally reconstruct from MRI the 3D shape of functional tissue compartments, and (3) diffusible iodine-based contrast-enhanced computed tomography image the copulatory fit between male phallus and female cloaca. We discuss these results in relation to tissue type material properties, the transfer on intromittent forces, establishing potential copulatory lock, inflated glans volume scaling with body mass/length, the mechanics of semen targeting and insemination, and potential female cryptic choice impacting multiple clutch paternity. In part, this study further clarifies the phallic morphological variation observed among crocodylians and begins to investigate the role(s) these divergent male forms play during copulation interacting with female cloacal forms to increase reproductive success.
Mesenchymal stromal cell-derived extracellular vesicle therapy prevents preeclamptic physiology through intrauterine immunomodulation†
Authors: Taglauer Elizabeth S , Fernandez-Gonzalez Angeles , Willis Gareth R , Reis Monica , Yeung Vincent , Liu Xianlan , Mitsialis S Alex , Kourembanas Stella
Published: October 2020

Human umbilical cord-derived mesenchymal stromal cells (MSCs) are a widely recognized treatment modality for a variety of preclinical disease models and have been transitioned to human clinical trials. We have previously shown in neonatal lung disease that the therapeutic capacity of MSCs is conferred by their secreted extracellular vesicles (MEx), which function primarily through immunomodulation. We hypothesize that MEx have significant therapeutic potential pertinent to immune-mediated gestational diseases. Of particular interest is early-onset preeclampsia, which can be caused by alterations of the maternal intrauterine immune environment. Using a heme-oxygenase-1 null mouse model of pregnancy loss with preeclampsia-like features, we examined the preventative effects of maternal MEx treatment early in pregnancy. Heme oxygenase-1 null females (Hmox1−/−) or wild-type control females were bred in homozygous matings followed by evaluation of maternal and fetal parameters. A single dose of MEx was administered intravenously on gestational day (GD)1 to Hmox1−/− females (Hmox1−/− MEx). Compared with untreated Hmox1−/− females, Hmox1−/− MEx-treated pregnancies showed significant improvement in fetal loss, intrauterine growth restriction, placental spiral artery modification, and maternal preeclamptic stigmata. Biodistribution studies demonstrated that MEx localize to a subset of cells in the preimplantation uterus. Further, mass cytometric (CyTOF) evaluation of utero-placental leukocytes in Hmox1−/− MEx versus untreated pregnancies showed alteration in the abundance, surface marker repertoire, and cytokine profiles of multiple immune populations. Our data demonstrate the therapeutic potential of MEx to optimize the intrauterine immune environment and prevent maternal and fetal sequelae of preeclamptic disease.