scholarly journals mRBioM: An Algorithm for the Identification of Potential mRNA Biomarkers From Complete Transcriptomic Profiles of Gastric Adenocarcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Changlong Dong ◽  
Nini Rao ◽  
Wenju Du ◽  
Fenglin Gao ◽  
Xiaoqin Lv ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Gastric Adenocarcinoma ◽  
Colon Adenocarcinoma ◽  
Interaction Network ◽  
High Specificity ◽  
Classification Performance ◽  
Related Factors ◽  
Total Information ◽  
Specificity And Sensitivity ◽  
Information Amount

PurposeIn this work, an algorithm named mRBioM was developed for the identification of potential mRNA biomarkers (PmBs) from complete transcriptomic RNA profiles of gastric adenocarcinoma (GA).MethodsmRBioM initially extracts differentially expressed (DE) RNAs (mRNAs, miRNAs, and lncRNAs). Next, mRBioM calculates the total information amount of each DE mRNA based on the coexpression network, including three types of RNAs and the protein-protein interaction network encoded by DE mRNAs. Finally, PmBs were identified according to the variation trend of total information amount of all DE mRNAs. Four PmB-based classifiers without learning and with learning were designed to discriminate the sample types to confirm the reliability of PmBs identified by mRBioM. PmB-based survival analysis was performed. Finally, three other cancer datasets were used to confirm the generalization ability of mRBioM.ResultsmRBioM identified 55 PmBs (41 upregulated and 14 downregulated) related to GA. The list included thirteen PmBs that have been verified as biomarkers or potential therapeutic targets of gastric cancer, and some PmBs were newly identified. Most PmBs were primarily enriched in the pathways closely related to the occurrence and development of gastric cancer. Cancer-related factors without learning achieved sensitivity, specificity, and accuracy of 0.90, 1, and 0.90, respectively, in the classification of the GA and control samples. Average accuracy, sensitivity, and specificity of the three classifiers with machine learning ranged within 0.94–0.98, 0.94–0.97, and 0.97–1, respectively. The prognostic risk score model constructed by 4 PmBs was able to correctly and significantly (∗∗∗p < 0.001) classify 269 GA patients into the high-risk (n = 134) and low-risk (n = 135) groups. GA equivalent classification performance was achieved using the complete transcriptomic RNA profiles of colon adenocarcinoma, lung adenocarcinoma, and hepatocellular carcinoma using PmBs identified by mRBioM.ConclusionsGA-related PmBs have high specificity and sensitivity and strong prognostic risk prediction. MRBioM has also good generalization. These PmBs may have good application prospects for early diagnosis of GA and may help to elucidate the mechanism governing the occurrence and development of GA. Additionally, mRBioM is expected to be applied for the identification of other cancer-related biomarkers.

In1-ghrelin splicing variant as a key element in the pathophysiological association between obesity and prostate cancer

2021 ◽  
Author(s):  
Juan M Jiménez-Vacas ◽  
Antonio J Montero-Hidalgo ◽  
Enrique Gómez-Gómez ◽  
Antonio C Fuentes-Fayos ◽  
Francisco Ruiz-Pino ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
High Specificity ◽  
Metabolic Status ◽  
Grey Zone ◽  
Clinical Value ◽  
Related Factors ◽  
Clinical Model ◽  
Non Invasive ◽  
Splicing Variant ◽  
Specificity And Sensitivity

Abstract Context Recent studies emphasize the importance of considering the metabolic status to develop personalized medicine approaches. This is especially relevant in prostate cancer (PCa), wherein the diagnostic capability of PSA dramatically drops when considering patients with PSA levels ranging 3-10 ng/mL, the so-called “grey-zone”. Hence, additional non-invasive diagnostic and/or prognostic PCa biomarkers are urgently needed, especially in the metabolic-status context. Objective To assess the potential relation of urine In1-ghrelin (a ghrelin splicing variant) levels with metabolic-related/pathological conditions (e.g. obesity/diabetes/BMI/insulin-glucose levels), and to define its potential clinical value in PCa (diagnostic/prognostic capacity) and relationship with PCa-risk in patients with PSA in the grey-zone. Methods Urine In1-ghrelin levels were measured by radioimmunoassay in a clinically/metabolically/pathologically well-characterized cohort of patients without (n=397) or with (n=213) PCa with PSA in the grey-zone. Results Key obesity-related factors associated with PCa-risk (BMI/diabetes/glucose/insulin) were strongly correlated to In1-ghrelin levels. Importantly, In1-ghrelin levels were higher in PCa patients compared to control patients (with suspect of PCa but negative-biopsy). Moreover, high In1-ghrelin levels were associated with increased PCa-risk and linked to PCa-aggressiveness (e.g. tumour-stage/lymphovascular-invasion). In1-ghrelin levels added significant diagnostic value to a clinical model consisting of age, suspicious-DRE, previous-biopsy, and PSA levels. Furthermore, a multivariate model consisting of clinical and metabolic variables, including In1-ghrelin levels, showed high specificity and sensitivity to diagnose PCa (AUC=0.740). Conclusions Urine In1-ghrelin levels are associated with obesity-related factors and PCa risk/aggressiveness, and could represent a novel and valuable non-invasive PCa biomarker, as well as a potential link in the pathophysiological relationship between obesity and PCa.

scholarly journals Concurrent and Convergent Validity of a Single, Brief Question for Physical Activity Assessment

2020 ◽  
Vol 17 (6) ◽  
pp. 1989 ◽  
Author(s):  
Antonio Moreno-Llamas ◽  
Jesús García-Mayor ◽  
Ernesto De la Cruz-Sánchez
Keyword(s):  
Physical Activity ◽  
Convergent Validity ◽  
High Specificity ◽  
Cost Effective ◽  
Classification Performance ◽  
Short Version ◽  
Operating Characteristics ◽  
Time Saving ◽  
Physically Active ◽  
Specificity And Sensitivity

An extensive number of self-reported methods for physical activity (PA) measurement are available, including short and long recall questionnaires ranging from a few to tens of questions. Due to the fact that simple, time-saving methods could be more practical and desirable for use in a busy clinical context, as well as in public health surveys, we evaluated how a single-item question might be a useful and cost-effective method for assessing compliance with PA guidelines. Using multiple receiver operating characteristics (ROC), we assessed the classification performance of a single brief question, employing the short version of the International Physical Activity Questionnaire as criterion instrument, in a total of 55,950 people (30,601 women and 25,349 men). Both those who practice PA almost daily and a few times a week presented an upper threshold (1042.5 metabolic equivalent minutes (MET) minutes/week) to the established compliance PA guidelines (600 MET minutes/week) with high specificity and sensitivity, using a sedentary group as reference. Otherwise, the occasionally physically active group did not reach the minimum (349.5 MET minutes/week) and obtained a poorer classification performance. A single brief question is a pragmatic and alternative method for assessment of compliance with PA guidelines.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

2020 ◽  
Vol 20 (10) ◽  
pp. 831-840
Author(s):  
Weibin Li
Keyword(s):  
Pathogenic Bacteria ◽  
Genetic Diagnosis ◽  
Bloodstream Infections ◽  
High Specificity ◽  
Peptide Sequence ◽  
High Morbidity ◽  
Specificity And Sensitivity ◽  
Prospective Application ◽  
Small Molecule Therapeutics

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

scholarly journals Clinicopathological and Endoscopic Features of Raspberry-Shaped Gastric Cancer in Helicobacter pylori-Uninfected Patients

Digestion ◽  
2020 ◽  
pp. 1-8
Author(s):  
Noboru Yatagai ◽  
Hiroya Ueyama ◽  
Muneo Ikemura ◽  
Ryota Uchida ◽  
Hisanori Utsunomiya ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Gastric Adenocarcinoma ◽  
Submucosal Tumor ◽  
Clinicopathological Characteristics ◽  
Fundic Gland ◽  
Histopathological Classification ◽  
Histological Characteristics ◽  
Greater Curvature ◽  
H Pylori ◽  
Tumor Shape

<b><i>Background:</i></b> Gastric adenocarcinoma of foveolar type (GA-FV) is a raspberry-shaped gastric cancer (RSGC) and garners much attention as <i>H. pylori</i> (<i>Hp</i>)-uninfected gastric cancer. However, the classification and clinicopathological and endoscopic features of RSGCs in <i>Hp</i>-uninfected patients are poorly defined. We designed a new histopathological classification of RSGC and compared them via endoscopic and clinicopathological characteristics. <b><i>Summary:</i></b> From 996 patients with early gastric cancers resected by endoscopy in our hospital, we studied 24 RSGC lesions from 21 (2.4%) <i>Hp</i>-uninfected patients. RSGCs were classified into 3 histological types as follows: GA-FV (<i>n</i> = 19), gastric adenocarcinoma of fundic gland type (GA-FG, <i>n</i> = 2), and gastric adenocarcinoma of fundic gland mucosa type (GA-FGM, <i>n</i> = 3). Most of the lesions were found at the greater curvature of the upper or middle third of the stomach. GA-FV lesions were homogeneously reddish and frequently accompanied with a whitish area around the tumor and an irregular microvascular (MV) pattern; these features were confirmed histopathologically by the presence of homogeneous neoplastic foveolar epithelium with foveolar hyperplasia around the tumors. GA-FG lesions might be heterogeneously reddish with a submucosal tumor shape and regular MV pattern; these were confirmed by the presence of covered or mixed nonneoplastic epithelium on deeper regions of tumors. GA-FGM lesions might be homogeneously reddish and occasionally had a submucosal tumor shape and irregular MV pattern; these were confirmed by the presence of homogeneous neoplastic foveolar epithelium on deeper regions of the tumors. <b><i>Key Messages:</i></b> RSGCs in <i>Hp</i>-uninfected patients are classified into 3 histopathological types. For accurate diagnosis of RSGCs, it may be necessary to fully understand endoscopic features of these lesions based on these histological characteristics and to take a precise biopsy.

scholarly journals SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mikail Dogan ◽  
Lina Kozhaya ◽  
Lindsey Placek ◽  
Courtney Gunter ◽  
Mesut Yigit ◽  
...  
Keyword(s):  
Specific Antibody ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
High Specificity ◽  
Spike Protein ◽  
Humoral Immune ◽  
Specificity And Sensitivity ◽  
Wide Range ◽  
Specific Igg ◽  
Negative Controls

AbstractDevelopment of antibody protection during SARS-CoV-2 infection is a pressing question for public health and for vaccine development. We developed highly sensitive SARS-CoV-2-specific antibody and neutralization assays. SARS-CoV-2 Spike protein or Nucleocapsid protein specific IgG antibodies at titers more than 1:100,000 were detectable in all PCR+ subjects (n = 115) and were absent in the negative controls. Other isotype antibodies (IgA, IgG1-4) were also detected. SARS-CoV-2 neutralization was determined in COVID-19 and convalescent plasma at up to 10,000-fold dilution, using Spike protein pseudotyped lentiviruses, which were also blocked by neutralizing antibodies (NAbs). Hospitalized patients had up to 3000-fold higher antibody and neutralization titers compared to outpatients or convalescent plasma donors. Interestingly, some COVID-19 patients also possessed NAbs against SARS-CoV Spike protein pseudovirus. Together these results demonstrate the high specificity and sensitivity of our assays, which may impact understanding the quality or duration of the antibody response during COVID-19 and in determining the effectiveness of potential vaccines.

scholarly journals Highly Sensitive Fluorescent Detection of Acetylcholine Based on the Enhanced Peroxidase-Like Activity of Histidine Coated Magnetic Nanoparticles

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1207
Author(s):  
Hong Jae Cheon ◽  
Quynh Huong Nguyen ◽  
Moon Il Kim
Keyword(s):  
Magnetic Nanoparticles ◽  
High Sensitivity ◽  
High Specificity ◽  
Choline Oxidase ◽  
Fluorescent Detection ◽  
One Pot ◽  
Site Structure ◽  
Specificity And Sensitivity ◽  
Highly Sensitive ◽  
Peroxidase Mimics

Inspired by the active site structure of natural horseradish peroxidase having iron as a pivotal element with coordinated histidine residues, we have developed histidine coated magnetic nanoparticles (His@MNPs) with relatively uniform and small sizes (less than 10 nm) through one-pot heat treatment. In comparison to pristine MNPs and other amino acid coated MNPs, His@MNPs exhibited a considerably enhanced peroxidase-imitating activity, approaching 10-fold higher in catalytic reactions. With the high activity, His@MNPs then were exploited to detect the important neurotransmitter acetylcholine. By coupling choline oxidase and acetylcholine esterase with His@MNPs as peroxidase mimics, target choline and acetylcholine were successfully detected via fluorescent mode with high specificity and sensitivity with the limits of detection down to 200 and 100 nM, respectively. The diagnostic capability of the method is demonstrated by analyzing acetylcholine in human blood serum. This study thus demonstrates the potential of utilizing His@MNPs as peroxidase-mimicking nanozymes for detecting important biological and clinical targets with high sensitivity and reliability.

scholarly journals Prognosis after surgery for gastric adenocarcinoma in the Swedish Gastric Cancer Surgery Study (SWEGASS)

2021 ◽  
pp. 1-8
Author(s):  
Johannes Asplund ◽  
Eivind Gottlieb-Vedi ◽  
Wilhelm Leijonmarck ◽  
Fredrik Mattsson ◽  
Jesper Lagergren
Keyword(s):  
Gastric Cancer ◽  
Gastric Adenocarcinoma ◽  
Cancer Surgery ◽  
Gastric Cancer Surgery

scholarly journals Serum MicroRNA Signature as a Diagnostic and Therapeutic Marker in Patients with Psoriatic Arthritis

2020 ◽  
Vol 47 (12) ◽  
pp. 1760-1767
Author(s):  
Sarah M. Wade ◽  
Trudy McGarry ◽  
Siobhan C. Wade ◽  
Ursula Fearon ◽  
Douglas J. Veale
Keyword(s):  
Psoriatic Arthritis ◽  
Characteristic Curve ◽  
High Specificity ◽  
Serum Samples ◽  
Rna Molecules ◽  
Serum Mirna ◽  
Serum Microrna ◽  
Specificity And Sensitivity ◽  
European League Against Rheumatism ◽  
Noninvasive Markers

ObjectiveMicroRNA (miRNA) are small endogenous regulatory RNA molecules that have emerged as potential therapeutic targets and biomarkers in autoimmunity. Here, we investigated serum miRNA levels in patients with psoriatic arthritis (PsA) and further assessed a serum miRNA signature in therapeutic responder versus nonresponder PsA patients.MethodsSerum samples were collected from healthy controls (HC; n = 20) and PsA patients (n = 31), and clinical demographics were obtained. To examine circulatory miRNA in serum from HC and PsA patients, a focused immunology miRNA panel was analyzed utilizing a miRNA Fireplex assay (FirePlex Bioworks Inc.). MiRNA expression was further assessed in responders versus nonresponders according to the European League Against Rheumatism response criteria.ResultsSix miRNA (miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, miR-26a-5p, and miR-21-5p) were significantly higher in PsA compared to HC (all P < 0.05), with high specificity and sensitivity determined by receiver-operating characteristic curve analysis. Analysis of responder versus nonresponders demonstrated higher baseline levels of miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, and miR-26a-5p were associated with therapeutic response.ConclusionThis study identified a 6-serum microRNA signature that could be attractive candidates as noninvasive markers for PsA and may help to elucidate the disease pathogenesis.

scholarly journals Validity of the International Prostate Symptoms Score in predicting urinary retention after joint replacement

2019 ◽  
Vol 27 (3) ◽  
pp. 230949901986867 ◽  
Author(s):  
Alasdair JA Santini ◽  
Chetan A Jakaraddi ◽  
Fotis Polydoros ◽  
Sree Metikala
Keyword(s):  
Urinary Tract ◽  
Urinary Retention ◽  
Preoperative Evaluation ◽  
Age Groups ◽  
High Specificity ◽  
Logistic Regression Models ◽  
Prosthetic Joints ◽  
Specificity And Sensitivity ◽  
Urinary Tract Symptoms ◽  
Risk Patients

Postoperative urinary retention necessitating catheterization after major lower limb arthroplasty surgery adds to the patients’ postoperative discomfort and increases the risk of urinary tract infection with potential risk of transient bacteraemia and seeding of infection to prosthetic joints. Preoperative evaluation of patients with lower urinary tract symptoms may help to identify at-risk patients and the International Prostate Symptoms Score (IPSS) has been used as a screening tool to quantify the severity of symptoms in males. A prospective cohort of 303 patients undergoing total hip or knee arthroplasty was evaluated using the IPSS. Patients were categorized into three symptom groups (mild, moderate and severe based on scores of 0–7, 8–18 and greater than 18, respectively) and four age groups (<50 years, 51–60 years, 61–70 years and greater than 70 years). Twenty-six patients (8.6%) developed urinary retention and were catheterized postoperatively; of these, 16 were male and 10 were female. Statistical analysis using logistic regression models showed significant association between severe IPSS scores (>18) and urinary retention requiring catheterization in both males and females with both high specificity and sensitivity in the test in predicting postoperative catheterization. Hence, this test is a valid preoperative screen in predicting postoperative catheterization.

scholarly journals Effects of exposure of honey bee colonies to neonicotinoid seed–treated maize crops

2013 ◽  
Vol 57 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Krystyna Pohorecka ◽  
Piotr Skubida ◽  
Piotr Semkiw ◽  
Artur Miszczak ◽  
Dariusz Teper ◽  
...  
Keyword(s):  
Zea Mays ◽  
Honey Bee ◽  
High Specificity ◽  
Negative Effects ◽  
Term Survival ◽  
Pollen Loads ◽  
Modified Quechers ◽  
Specificity And Sensitivity ◽  
Bee Colonies

Abstract The effects to honeybee colonies (Apis mellifera L.) during and after exposure to flowering maize (Zea mays L.), grown from seeds coated with clothianidin and imidacloprid was assessed in field-realistic conditions. The experimental maize crops were adjacent to the other flowering agriculture plants. Honey bee colonies were placed in three differently protected maize fields throughout the blooming period, and thereafter they were transferred to a stationary apiary. Samples of pollen loads, bee bread, and adult bees were collected and analyzed for neonicotinoid residues. To ensure high specificity and sensitivity of detection of the analyzed pesticides, a modified QuEChERS extraction method and liquid chromatography coupled with tandem mass spectrometry were used. Clothianidin was detected only in the samples of pollen loads. Their residue levels ranged from 10.0 to 41.0 ng/g (average 27.0 ng/g). Imidacloprid was found in no investigated sample. No negative effects of neonicotinoid seed-treated maize on the development and long-term survival of honey bee colonies were observed. The low proportion of Zea mays pollen in total bee-collected pollen during the maize flowering period was noted. The findings suggest that maize plants are less attractive forage for honey bees than phacelia (Phacelia tanacetifolia Benth.), buckwheat (Fagopyrum Mill.), white clover (Trifolium repens L.), goldenrod (Solidago L.), and vegetation from Brassicaceae family. The results indicate a possibility of reducing the risk of bees being exposed to the toxic effect of insecticidal dusts dispersed during maize sowing by seeding, in the areas surrounding maize crops, plants that bloom later in the year.

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