Modular Breath Analyzer (MBA): Introduction of a Breath Analyzer Platform Based on an Innovative and Unique, Modular eNose Concept for Breath Diagnostics and Utilization of Calibration Transfer Methods in Breath Analysis Studies
Exhaled breath analysis for early disease detection may provide a convenient method for painless and non-invasive diagnosis. In this work, a novel, compact and easy-to-use breath analyzer platform with a modular sensing chamber and direct breath sampling unit is presented. The developed analyzer system comprises a compact, low volume, temperature-controlled sensing chamber in three modules that can host any type of resistive gas sensor arrays. Furthermore, in this study three modular breath analyzers are explicitly tested for reproducibility in a real-life breath analysis experiment with several calibration transfer (CT) techniques using transfer samples from the experiment. The experiment …
An Overview of the Application of Deep Learning in Short Read Sequence Classification
AbstractAdvances in sequencing technology have led to an ever increasing amount of available short read sequencing data. This has, consequently, exacerbated the need for efficient and precise classification tools that can be used in the analysis of this data. As it stands, recent years have shown that massive leaps in performance can be achieved when it comes to approaches that are based in heuristics, and alongside these improvements there has been an ever increasing interest in applying deep learning techniques to revolutionize this classification task. We attempt to gather up these approaches and to evaluate their performance in a reproducible fashion to get a better perspective on the c…
Does Family History of Cancer Influence Undergoing Screening and Gastrointestinal Investigations?
Background and Aims: Although a family history of cancer (FHC) can modify the lifestyle and attitudes towards participation in cancer screening programs, studies on this relationship show mixed results and vary across populations. The objectives of the study were to compare sociodemographic characteristics, history of gastrointestinal (GI) investigations and Helicobacter pylori eradication, and modifiable cancer risk factors between those with FHC and those with no FHC (NFHC), and to investigate the association between FHC and a history of GI investigations.
 Methods: A total of 3,455 questionnaires from the pilot study of the “Helicobacter pylori eradication and pepsinogen testing for…
Multicentric randomised study ofHelicobacter pylorieradication and pepsinogen testing for prevention of gastric cancer mortality: the GISTAR study
IntroductionPopulation-based eradication ofHelicobacter pylorihas been suggested to be cost-effective and is recommended by international guidelines. However, the potential adverse effects of widespread antibiotic use that this would entail have not been sufficiently studied. An alternative way to decrease gastric cancer mortality is by non-invasive search for precancerous lesions, in particular gastric atrophy; pepsinogen tests are the best currently available alternative. The primary objective of GISTAR is to determine whetherH pylorieradication combined with pepsinogen testing reduces mortality from gastric cancer among 40–64-year-old individuals. The secondary objectives include evaluat…
Class Decomposition for Gastric Cancer Detection from Breath
Pepsinogen testing for evaluation of the success of Helicobacter pylori eradication at 4 weeks after completion of therapy.
Background and objective: Pepsinogen levels in plasma are increased by inflammation in the gastric mucosa, including inflammation resulting from Helicobacter pylori infection. A decrease in pepsinogen II level has been suggested as a reliable marker to confirm the successful eradication of infection. The aim of our study was to evaluate the potential role of pepsinogens I and II, gastrin-17 and H. pylori antibodies in confirming successful eradication. Material and methods: Altogether 42 patients (25 women, 17 men), mean age 45 years (range 23–74), were enrolled. Pepsinogens I and II, gastrin-17 and H. pylori IgG antibodies were measured in plasma samples using an ELISA test (Biohit, Oyj., …
The Riga East University Hospital Stroke Registry—An Analysis of 4915 Consecutive Patients with Acute Stroke
Background and Objectives: A hospital-based stroke registry is a useful tool for systematic analyses of the epidemiology, clinical characteristics, and natural course of stroke. Analyses of stroke registry data can provide information that can be used by health services to improve the quality of care for patients with this disease. Materials and Methods: Data were collected from the Riga East University Hospital (REUH) Stroke Registry in order to evaluate the etiology, risk factors, clinical manifestations, treatment, functional outcomes, and other relevant data for acute stroke during the period 2016–2020. Results: During a five-year period, 4915 patients (3039 females and 1876 males) with…
Screening for gastric cancer using exhaled breath samples.
Abstract Background The aim was to derive a breath-based classifier for gastric cancer using a nanomaterial-based sensor array, and to validate it in a large screening population. Methods A new training algorithm for the diagnosis of gastric cancer was derived from previous breath samples from patients with gastric cancer and healthy controls in a clinical setting, and validated in a blinded manner in a screening population. Results The training algorithm was derived using breath samples from 99 patients with gastric cancer and 342 healthy controls, and validated in a population of 726 people. The calculated training set algorithm had 82 per cent sensitivity, 78 per cent specificity and 79 …
Sociodemographic, Lifestyle and Medical Factors Associated with Helicobacter Pylori Infection
Background and Aims: The prevalence of Helicobacter pylori (H. pylori) infection is higher in developing countries and is often linked to lower socioeconomic status. Few studies have investigated the association between H. pylori and individual level characteristics in Europe, where several countries have a high prevalence of H. pylori infection. The study aimed to identify risk factors for H. pylori infection among adults in a large clinical trial in Latvia.
 Methods: 1,855 participants (40-64 years) of the “Multicenter randomized study of H. pylori eradication and pepsinogen testing for prevention of gastric cancer mortality” (GISTAR study) in Latvia tested for H. pylori IgG antibodi…
Low Prevalence of Celiac Disease among Patients with Functional Gastrointestinal Disorders in Latvia.
Background and Aims: Studies suggest that the prevalence of celiac disease (CD) is increased in individuals with functional gastrointestinal disorders (FGIDs), in particular, irritable bowel syndrome (IBS); however, the evidence is conflicting. We aimed to analyze the prevalence of CD in patients with FGIDs in Latvia.
 Methods: This retrospective study included patients with FGIDs, referred for a gastroenterologist consultation in a secondary gastroenterology practice unit. Patients were divided into three groups – patients only with IBS (IBS group), patients only with functional dyspepsia (FD) (FD group), patients with mixed symptoms IBS and FD (Mixed group). Patient levels of tissue …
Constructing Interpretable Classifiers to Diagnose Gastric Cancer Based on Breath Tests
Quick, inexpensive and accurate diagnosis of gastric cancer is a necessity, but at this moment the available methods do not hold up. One of the most promising possibilities is breath test analysis, which is quick, relatively inexpensive and comfortable to the person tested. However, this method has not yet been well explored. Therefore in this article the authors propose using transparent classification models to explain diagnostic patterns and knowledge, which is acquired in the process. The models are induced using decision tree classification algorithms and RIPPER algorithm for decision rule induction. The accuracy of these models is compared to neural network accuracy.
Prevalence and Potential Risk Factors of Helicobacter pylori Infection among Asymptomatic Individuals in Kazakhstan
Background: Helicobacter pylori (H. pylori) infection is associated with several risk factors such as demographic, socioeconomic status and personal habits, which vary in different populations. This is the most up-to-date data on H. pylori prevalence and potential risk factors for H. pylori infection among asymptomatic middle-aged individuals in Kazakhstan. Methods: Apparently healthy individuals aged 40 to 64, who took part in the health control in the outpatient clinic, were invited to participate in the study; answered a questionnaire, donated a blood sample. The antibodies to H. pylori were analysed by latex agglutination method. The baseline characteristics of study subjects with or wi…
Repeatability Study on a Classifier for Gastric Cancer Detection from Breath Sensor Data
The SNIFFPHONE device is a portable multichannel gas sensor, aiming to detect gastric cancer (GC) from breath samples. It employs gold nanoparticle (GNP) sensors reacting to volatile organic compounds (VOCs) in the exhaled breath, a non-invasive technique to support early diagnosis. This study evaluates the repeatability of the SNIFFPHONE classification result for measurements conducted on healthy subjects over a short period of time of less than 10 minutes. Due to the portable nature of the device, repeatability is studied with respect to varying measurement location. We find the classification results repeatable with a statistically significant 81 % Pearson correlation coefficient, even t…
How do international gastric cancer prevention guidelines influence clinical practice globally?
Clinical guidelines recommend particular approaches, including 'screen-and-treat' strategy for Helicobacter pylori, to prevent gastric cancer. However, little of this is implemented in clinical practice. The aim of the study was to identify barriers to implementation of international guidelines. A web-based questionnaire distributed globally to specialists in the field. Altogether 886 responses from 75 countries were received. Of the responders, 570 (64%) were men of mean age 47 years. There were 606 gastroenterologists and 65 epidemiologists among the responders. Altogether, 79.8% of the responders disagreed that the burden of gastric cancer is a diminishing problem. 'Screen-and-treat' str…
Overview on SNIFFPHONE:A portable device for disease diagnosis
We present SNIFFPHONE, a handy and easy-To-use device that allows the non-invasive detection of gastric diseases. It analyzes the user's exhaled breath using specifically developed gas sensors. The device is coupled to a smartphone, which governs the breath analysis process, sends the data measurements to an external data analysis server, and finally gives feedback to the user. In this work, we describe the SNIFFPHONE device and the general platform under development.
Modular Point-of-Care Breath Analyzer and Shape Taxonomy-Based Machine Learning for Gastric Cancer Detection
Background: Gastric cancer is one of the deadliest malignant diseases, and the non-invasive screening and diagnostics options for it are limited. In this article, we present a multi-modular device for breath analysis coupled with a machine learning approach for the detection of cancer-specific breath from the shapes of sensor response curves (taxonomies of clusters). Methods: We analyzed the breaths of 54 gastric cancer patients and 85 control group participants. The analysis was carried out using a breath analyzer with gold nanoparticle and metal oxide sensors. The response of the sensors was analyzed on the basis of the curve shapes and other features commonly used for comparison. These f…
Variability of Classification Results in Data with High Dimensionality and Small Sample Size
The study focuses on the analysis of biological data containing information on the number of genome sequences of intestinal microbiome bacteria before and after antibiotic use. The data have high dimensionality (bacterial taxa) and a small number of records, which is typical of bioinformatics data. Classification models induced on data sets like this usually are not stable and the accuracy metrics have high variance. The aim of the study is to create a preprocessing workflow and a classification model that can perform the most accurate classification of the microbiome into groups before and after the use of antibiotics and lessen the variability of accuracy measures of the classifier. To ev…
Non-contact breath sampling for sensor-based breath analysis
Breath analysis holds great promise for real-time and non-invasive medical diagnosis. Thus, there is a considerable need for simple-in-use and portable analyzers for rapid detection of breath indicators for different diseases in their early stages. Sensor technology meets all of these demands. However, miniaturized breath analyzers require adequate breath sampling methods. In this context, we propose non-contact sampling; namely the collection of breath samples by exhalation from a distance into a miniaturized collector without bringing the mouth into direct contact with the analyzing device. To evaluate this approach different breathing maneuvers have been tested in a real-time regime on a…
Pepsinogen Test for the Evaluation of Precancerous Changes in Gastric Mucosa: a Population-Based Study
Aims: The aim of the study was to evaluate the rationale of blood pepsinogen (PG) testing in population based screening settings.Methods: Participants from a cross-sectional population-based study of cardiovascular risk factors in Latvia were invited to participate in the current study. Pepsinogen I and II were measured in blood samples taken during the initial study and at follow-up; upper gastrointestinal endoscopy was performed. There were three groups of patients: with moderately decreased (PG I< 70 ng/ml and PG I/PG II ratio < 3), with strongly decreased (PG I< 30 ng/ml and PG I/PG II ratio < 2), and with normal PG level. Biopsy with H. pylori detection was performed (updat…
Clinicopathological characteristics of Epstein-Barr virus-positive gastric cancer in Latvia
Objective Epstein-Barr virus (EBV)-associated gastric cancer has been proposed to be a distinct gastric cancer molecular subtype. The prognostic significance of EBV infection in gastric cancer remains unclear and needs further investigation. Our study aimed to analyze EBV-positive and EBV-negative gastric cancer patients regarding their personal and tumor-related characteristics, and compare their overall survival. Methods Gastric cancer patients consecutively treated at the Riga East University Hospital during 2009-2016 were identified retrospectively. Tumor EBV status was determined by in-situ hybridization for EBV-encoded RNA (EBER). Information about clinicopathological characteristics …
Detection of gastric atrophy by circulating pepsinogens: A comparison of three assays.
Background Circulating levels of pepsinogens have been used in high gastric cancer-risk Asian and European populations to triage endoscopic evaluation for more severe pathology. There are different analytic methods with uncertain correlations. We therefore compared diagnostic performance of three commonly used pepsinogen assays to detect histologically confirmed gastric atrophy. Methods We tested plasma samples from adult patients with (n=50) and without (n=755) moderate or severe gastric corpus atrophy, as determined histologically by consensus of three expert pathologists. A single laboratory measured pepsinogens I (PgI) and II (PgII) using commercially available assays: two ELISA assays …
Prevalence of Atrophic Gastritis in Kazakhstan and the Accuracy of Pepsinogen Tests to Detect Gastric Mucosal Atrophy
Background Atrophic gastritis is considered precursor condition for gastric cancer. There is so far limited evidence on the performance of pepsinogens for atrophy detection in Central Asia. The aim of our study was to detect the prevalence of atrophic gastritis in the asymptomatic adult population in Kazakhstan as well as address the accuracy of pepsinogen testing in atrophy detection. Methods Healthy individuals aged 40-64 were included. Upper endoscopy and pepsinogens (PG) evaluation were performed. PG were analysed in plasma by latex agglutination. Cut off values were used to define decreased PG values (PGR ≤ 3 and PG I ≤ 70 ng/mL); severely decreased PG values (PGR ≤ 2 and PG I ≤ 30 ng/…
Sensing gastric cancer via point‐of‐care sensor breath analyzer
Background Detection of disease by means of volatile organic compounds from breath samples using sensors is an attractive approach to fast, noninvasive and inexpensive diagnostics. However, these techniques are still limited to applications within the laboratory settings. Here, we report on the development and use of a fast, portable, and IoT-connected point-of-care device (so-called, SniffPhone) to detect and classify gastric cancer to potentially provide new qualitative solutions for cancer screening. Methods A validation study of patients with gastric cancer, patients with high-risk precancerous gastric lesions, and controls was conducted with 2 SniffPhone devices. Linear discriminant an…
Associations of diet and lifestyle factors with common volatile organic compounds in exhaled breath of average-risk individuals.
Background Detection of diseases via exhaled breath remains an attractive idea despite persisting gaps in understanding the origin of volatile organic compounds (VOCs) and their relationship with the disease of interest. Data on factors potentially influencing the results of breath analysis remain rather sparse and often controversial. In this study, we aimed to investigate the associations of common VOCs in exhaled breath of average-risk individuals with socio-demographic and lifestyle factors, medical conditions as well as diet. Methods Alveolar breath samples of 1447 men and women were collected in the morning after fasting and were analyzed using gas-chromatography linked with mass-spec…
Comparison of the yield from two faecal immunochemical tests at identical cutoff concentrations – a randomized trial in Latvia
OBJECTIVE We have compared the performance of two faecal immunochemical tests (FIT) in an average-risk population. MATERIALS AND METHODS Altogether, 10 000 individuals aged 50-74 were selected randomly from the population of Latvia in 2011 and assigned randomly either to OC-Sensor or to FOB Gold single-time testing. Positivity of the test, frequency of colonic lesions, number needed to screen (NNscreen) and scope for the detection of an advanced neoplasm (cancer and advanced adenoma) were compared between the tests using the same cutoff concentrations in µg/g faeces. Confidence intervals (CIs) at 95% were calculated. RESULTS Positivity with the cutoff set at 10 µg/g faeces was 12.8% (95% CI…