Sample Collection Research Articles

Insights and future directions in studying intestinal microbiota post-transjugular intrahepatic portosystemic shunt for hepatitis B virus-related portal hypertension

The gut microbiota (GM) plays a major role in the progression and treatment response of liver diseases, with diverse compositions based on different etiologies. In China, hepatitis B virus (HBV) infection is the leading cause of cirrhosis and affects the GM composition in patients with cirrhosis-related portal hypertension (PH). However, a few studies have been conducted on GM alterations after transjugular intrahepatic portosystemic shunt (TIPS) in patients with HBV-related PH. A recent study investigated the changes in the GM in these patients after TIPS. This study found an increase in potentially pathogenic bacteria and a decrease in beneficial bacteria post-TIPS, particularly in patients with hepatic encephalopathy (HE), indicating the potential role of the GM in HE prediction and management post-TIPS. Nevertheless, the study had several limitations, including a small sample size, limited follow-up, a single time point for sample collection, and inadequate analysis of the correlation between intestinal flora, HBV infection status, and clinical parameters. Future research should address these limitations by expanding the sample size, prolonging the follow-up duration, collecting samples at multiple time points, and conducting comprehensive analyses to confirm the findings and evaluate the effectiveness of individualized microbiome-based therapies.

Why PNI scientists need to engage in exploratory hypothesis-generating biomarker studies

Multi-omics research is developing rapidly, offering extensive sample analysis options and advanced statistical solutions to identify and understand complex networks of biomarkers. This review encourages groups in the psychoneuroimmunology field with limited experience in omics research to embrace these advances. Cross-sectional studies can leverage existing sample collections to provide unique information that complements longitudinal studies, providing insights into which biological systems may warrant further investigation and building fundamental mechanistic knowledge of biological networks. The understanding of immune-brain interactions should inform ongoing developments in exploratory, hypothesis-generating research. Disregarding psychoneuroimmunological aspects may have led to challenges in some prior biomarker research. Moving forward, a more nuanced perspective on inflammation and psychological comorbidity is needed. The first steps in the conceptualization of an explorative cross-sectional omics study are discussed from a pragmatic perspective, highlighting who we choose to study and what we choose to measure.

Unraveling influenza sentinel surveillance in Pakistan 2008-2024: Epidemiological insights during the pre and post pandemic period of COVID-19.

The coronavirus pandemic has substantially influenced the transmission pattern of other respiratory viruses. However, screening and detecting other respiratory pathogens was unheeded during this time to combat the COVID-19 pandemic. High virulence and re assortment factors intensify the importance of influenza virus surveillance for effective disease management. Therefore, the present surveillance study was designed to determine the influenza positivity rate from 2008-24. This study will provide integral support in depicting a panoramic representation of two respiratory-pandemic periods, 2010-11 and 2019-2021, for influenza and COVID-19 pandemics, respectively. An inferential cross-sectional study was conducted from 2008 to 2024 by collecting influenza surveillance data from twelve sentinel sites in Pakistan. Clinical and demographic data was recorded at sample collection time. Specimens were collected through nasopharyngeal/throat swabs and stored in viral transport medium (VTM) at the sentinel site laboratory at 2-4°C. Viral RNA was isolated from the samples using KingFisher TM Flex Purification System and MagMAX™ Viral/Pathogen Nucleic Acid Extraction Kit. Within 16 years, 78118 samples were tested for influenza, of which 7999 (10.2%) appeared positive. The positivity rate appeared very low in recent years, with only a 3.5% positivity rate observed in 2020. Influenza A strain H1N1pdm09 seemed to be the prominent strain (n=3407, 42.6%), followed by influenza B (n=2125, 26.6%). The positivity of influenza samples was 10.2% and recorded in patients where typical clinical representation of influenza was absent. Fewer samples were reported during the coronavirus pandemic, which might be because influenza screening was hindered and overlooked to combat the SARS-CoV-2 virus, and the patient threshold was very high for COVID-19 virus screening.

A Day Saved is a Life Saved: Direct Antimicrobial Susceptibility Testing from Positively Flagged Blood Culture Bottles and their Concordance with the Routine Method.

Sepsis is a major health problem worldwide and is associated with high morbidity and mortality with every hour delay in initiation of therapy. A conventional method of blood culture and Antimicrobial Susceptibility Testing (AST) takes around 48-72 hours. Empirical antibiotics need to be administered until the sensitivity report is made available. It has been estimated that 20-50% of the empirical antibiotics are inappropriate, resulting in prolonged hospital stays, adverse effects, and emergence of drug resistance. Additionally, this also puts an extra financial burden on both the patients and healthcare settings. Performing direct Antimicrobial Sensitivity Testing (dAST) is an important tool to reduce turn-around time (TAT) by at least 18-24 hours, thus reducing morbidity and mortality among critically ill patients. Direct AST (dAST) was performed from the positively flagged blood culture bottles received between December, 2021 to May, 2022 from Intensive Care Units (ICUs) on Mueller- Hinton Agar (MHA) using four drops of withdrawn blood. dAST was performed for six drugs: Ceftriaxone-30 μg (CTR), Piperacillin/Tazobactam-100/10 μg (PIT), Meropenem-10 μg (MRP), Ciprofloxacin-5 μg (CIP), Aztreonam-30 μg (AT), and Colistin (CL). The zone of inhibition was interpreted as per CLSI M100 ed32, 2022 guidelines. A parallel conventional method was also performed to examine for categorical agreement and disagreement. Identification was carried out using MALDI-TOF MS from the colonies that appeared on the dAST plate on the subsequent day. A total of 162 positively flagged blood culture bottles were included in the study. The majority of the Gram-negative organisms were from Enterobacterales (n=109), followed by Acinetobacter spp. (n=28) and Pseudomonas aeruginosa (n=25). Out of the 972 isolate-antimicrobial combinations, overall Categorical Agreement (CA) was seen in 936 (96.3%), whereas disagreement was observed in 36 with minor error (mE) in 21 (2.2%), major error (ME) in 7 (0.7%), and very major error (VME) in 8 (0.8%) when compared to the routine method. Categorical agreement (CA) of > 99% was seen in ceftriaxone (CTR) and ciprofloxacin (CIP). In comparison, the lowest CA was observed with meropenem (MRP) at 92%. Colistin dAST was performed using the E-strip method, and the result obtained was highly convincing, with an overall disagreement of only 1.2%. Rapid dAST from positively flagged blood culture bottles proved to significantly reduce the TAT from the time of sample collection to the first availability of antimicrobial susceptibility report with excellent categorical agreement of > 95% using the conventional disc diffusion method. Results obtained were within the acceptance criteria set by U. S. Food and Drug Administration (FDA) guidelines of > 90% categorical agreement for a new method. We were able to obtain excellent concordance for colistin using the E-strip method. Performing dAST not only saves a "day", but its proper implementation would save a "life".

Marburg Virus Minigenome Assays.

This chapter describes minigenome systems for Marburg virus (MARV), which reconstitute the viral polymerase complex functions of gene expression and genome replication. Procedures covered herein include passage and seeding of cells, transfection, sample collection, and reporter gene assays.

Assessment of Rapid Antigen Diagnostic Tests at Mass Events: Identifying Optimal Floor Plan Configurations for Enhanced Efficiency

Background/Objectives: The COVID-19 pandemic underscored the urgent need for rapid, efficient testing methods at large-scale events to control virus spread. This study leverages queueing theory to explore how different floor plan configurations affect the efficiency of Rapid Antigen Diagnostic Test (RADT) centers at mass gatherings, aiming to enhance throughput and minimize wait times. Methods: Employing the MAP/PH/c model (Markovian Arrival Process/phase-type service distribution with c servers), this study compared the operational efficiency of RADT centers using U-shaped and straight-line floor plans. The research involved 500 healthy participants, who underwent the RADT process, including queue number issuance, registration, sample collection, sample mixing, and results dissemination. Agile management techniques were implemented to optimize operations. Results: The findings demonstrated that the U-shaped layout was more efficient than the straight-line configuration, reducing the average time from sample collection to results acquisition—1.6 minutes in the U-shaped layout versus 1.8 minutes in the straight-line layout. The efficiency of the U-shaped layout was particularly notable at the results stage, with statistically significant differences (p < 0.05) in reducing congestion and improving resource allocation. Conclusions: The study confirms the feasibility of implementing RADT procedures at mass gatherings and identifies the U-shaped floor plan as the optimal configuration. This layout significantly enhances testing efficiency and effectiveness, suggesting its suitability for future large-scale testing scenarios. The research contributes to optimizing mass testing strategies, vital for public health emergency management during pandemics.

Assessing Pantanal fauna through environmental DNA metabarcoding after the 2020 megafire

The environmental DNA (eDNA) metabarcoding is a methodology that, from environmental samples such as soil, water, air, and others, enables the simultaneous identification of multiple species, thus allowing for large-scale mapping of biological diversity in a specific study area. Due to its non-invasive sampling approach, where species are detected from the traces they leave in the environment, eliminating the need to isolate and capture organisms, eDNA metabarcoding emerges as a valuable tool in conservation strategies. This study aims to explore the use of eDNA methodology for biodiversity monitoring and environmental impact assessment caused by the 2020 megafire in the Pantanal of Brazil, focusing on vertebrates. Environmental samples were collected at two protected areas and their surrounding areas, Taiamã Ecological Station (TES) and Pantanal Matogrossense National Park (PMNP), Mato Grosso, Brazil. We identified in TES, 27 mammals, 56 fishes, 12 birds, 4 amphibians, and 4 reptiles, while in PMNP, 43 mammals, 45 fishes, 126 birds, 19 amphibians, and 11 reptiles. Soil sampling proved to be more efficient compared to water sampling: 26 species were exclusively identified in soil samples, while 9 were attributed to water samples. Here, we demonstrated that the primer 12SV5 only a superior efficacy in identifying mammal and herpetofauna species compared to the other markers used (16Smam and MiBird). Moreover, we confirmed the complementary role of eDNA alongside camera trapping, and its advantage to estimate species richness with a single field expedition. We stress the need to optimize sample collection methods for the target group and to reduce the influence of contamination and water flow. This study highlights the importance of eDNA methodology as a crucial tool for biodiversity monitoring and environmental impact assessment, enabling rapid access to biodiversity and long-term monitoring.

The Liquid Biopsy: A Detailed Review of Evolution, Technologies and Clinical Implications

Liquid biopsy has transformed molecular diagnostics by providing a non-invasive method for disease identification and monitoring, notably in cancer. This study examines the history of liquid biopsy, with an emphasis on the critical role of circulating tumor DNA (ctDNA) and the move from targeted to genome-wide analysis. It emphasizes the value of liquid biopsy in non-invasive diagnosis, patient comfort, real-time monitoring, and individualized treatment solutions. Success stories in early cancer identification across several cancer types highlight the efficiency of liquid biopsy in detecting particular genetic alterations associated with early-stage illness. The paper also examines the use of liquid biopsy for tracking treatment response and finding minimum residual disease, underlining its potential to revolutionize therapy assessment and post-treatment care. However, consistency issues, such as heterogeneity in sample collection, storage, and processing, as well as variations among cancer types, represent substantial barriers to the widespread use of liquid biopsy. Efforts to solve these problems through collaborative projects and standardization ideas are presented, with a focus on data sharing and the advancement of innovative liquid biopsy technologies. Overall, this review gives a thorough overview of liquid biopsy achievements and limitations, emphasizing its promise as a foundation for current diagnostic techniques.

Salivary alpha-amylase: A marker of stress in gynecological residents during a shoulder dystocia simulation scenario.

Salivary alpha-amylase (sAA) has been recently proposed as biomarker of stress responsiveness within the sympathetic nervous system, preferable to cortisol, since limitations related to cortisol measurement (e.g. diurnal and seasonal rhythms, drugs interferences). Several factors, as age, collection device and analytical methods, also influence sAA levels and interpretation. This study aims to assess whether sAA could be useful to evaluate the stress response, also verifying some sources of variability. To identify any sources of sAA variability, saliva samples were collected from eight healthy subjects at five different times (8:00, 10:00, 12:00, 14:00 and 16:00) over five consecutive days using two different collection devices. Saliva was then collected from 35 obstetric residents before and after a simulated shoulder dystocia scenario, one of the most traumatic birth events in the professional life of gynecologists, to assess the stress levels. Samples were analysed throughout two different assays. Heart rate (HR) of residents was also measured before and after simulation scenario. Residents self-collected two saliva samples 10 min apart on a typical day. Overall, sAA levels increased significantly from morning to afternoon. Levels varied between subjects, but no differences were found between days or sampling devices. sAA activity levels in samples from 35 residents were significantly higher than those obtained before the scenario took place (about ten minutes later). These results were confirmed by two different assays. Moreover, a similar trend was observed when HR was considered. No differences were observed between samples collected 10 minutes apart on a typical day. Salivary alpha-amylase activity is a reliable, quick, and efficient marker for stress response, then its measurement will be of potential interest in the field of stress-related disorders. However, it is important to consider the timing of sample collection before introducing sAA in a clinical setting.

A méh- vagy darázscsípés okozta anafilaxiás sokk vizsgálata a triptáz enzim és a méh-, illetve darázsméreg specifikus immunglobulin E szintek vérből történő meghatározása alapján, egyes rendkívüli haláleseti eljárásokban

Aim: Systemic allergic reactions triggered by bee and wasp venom affect approximately 3% of adults, and in severe cases, can lead to anaphylactic reactions and death. The exact cause of extraordinary deaths resulting from insect stings is often not determined in a significant number of cases. The aim of this study is to provide guidance through methodological recommendations to investigate the precise cause of deaths presumably resulting from insect stings, specifically focusing on uncovering the facts and causes of anaphylaxis. Methodology: The study reviews literature related to anaphylaxis caused by insect stings and animal toxins, as well as its immunological background. It seeks to translate the information found in the literature into the realm of official activities related to extraordinary deaths. The study also summarises knowledge about groups of animals in Hungary that are medically significant due to their venom, providing guidance for on-site recognition, search, documentation, and recording of the most common Hymenoptera species with venom capable of frequently inducing anaphylactic reactions. Findings: The key to diagnosing deaths caused by anaphylaxis lies in crime scene investigation. The attending medical doctor must recognise the symptoms of insect stings and ensure the collection of a blood sample for allergological purposes. A special blood collection kit has been assembled for this purpose. The blood sample, which must be stored at 2–8ºC, should be sent to the Semmelweis University Institute of Laboratory Medicine within 2 days. By measuring the level of tryptase enzyme in the blood sample and detecting the presence of specific immunoglobulin E for the venom of the respective bee or wasp species, the cause of the anaphylactic reaction can be confirmed. The crime scene investigation team should also make an effort to locate and secure the potential insect species responsible for the sting. If the forensic entomologist successfully identifies the species, it facilitates the specific IgE allergological examination for the respective venom. Value: In cases of death resulting from insect stings, the cause is often not determined due to lack of proper caution and appropriate methods. The procedural approach recommended in the study establishes the basis for determining the precise cause of death in cases of suspected insect stings.

Gut Microbiota Comparison in Rectal Swabs Versus Stool Samples in Cats with Kidney Stones

To investigate the role of the intestinal bacterial microbiota in the pathogenesis of calcium oxalate nephrolithiasis in cats, a condition characterized by the formation of kidney stones, it is desirable to identify a sample collection method that accurately reflects the microbiota’s composition. The objective of this study was to evaluate the impact of fecal sample collection methods on the intestinal microbiota composition in two cat populations: healthy cats and kidney stone-diseased cats. The study included eighteen cats from the same colony, comprising nine healthy cats and nine cats with spontaneously occurring presumed calcium oxalate kidney stones. Three fecal collection methods were compared: rectal swabs, the collection of fresh stool, and the collection of stool exposed to ambient air for 24 h. The bacterial microbiota was analyzed through the high-resolution sequencing of the V3–V4 region of the 16S rRNA gene. For all cats, within the same individual, a one-way PERMANOVA analysis showed a significant difference between the rectal swabs and fresh stool (p = 0.0003), as well as between the rectal swabs and stool exposed to ambient air for 24 h (p = 0.0003), but no significant difference was identified between the fresh stool and non-fresh stool (p = 0.0651). When comparing the two populations of cats, this study provides seemingly conflicting results. (1) A principal component analysis (PCA) comparison revealed a significant difference in the bacterial composition between the healthy cats and the cats with kidney stones only when the sample was a fresh fecal sample (p = 0.0037). This finding suggests that the intestinal bacteria involved in the pathogenesis of kidney stones in cats are luminal and strictly anaerobic bacteria. Consequently, exposure to ambient air results in a loss of information, preventing the identification of dysbiosis. For clinical studies, non-fresh stool samples provided by owners does not appear suitable for studying the gut microbiota of cats with kidney stones; fresh stool should be favored. (2) Interestingly, the rectal swabs alone highlighted significant differences in the proportion of major phyla between the two populations. These findings highlight the critical importance of carefully selecting fecal collection methods when studying feline gut microbiota. Combining rectal swabs and fresh stool sampling provides complementary insights, offering the most accurate understanding of the gut microbiota composition in the context of feline kidney stone pathogenesis.

Serum Levels of Semaphorin 4C in Breast Cancer – Assessment of Prognostic Value and Potential for Monitoring Surgical Treatment Response

Abstract Introduction. The global burden of breast cancer (BC) has encouraged ceaseless research in exploring novel biomarkers, aiming to optimize BC management and prognosis. Objective. To explore the prognostic value of serum SEMA4C and investigate its potential for monitoring the response to surgical treatment in patients with BC. Materials and methods. Seventy-five (75) pre-treatment patients from the Clinic of Surgery with invasive BC without any initial treatment prior to blood sample collection were included in the study. The enzyme-linked immunosorbent assay (ELISA) method was used to measure serum levels of SEMA4C in human serum. Participants were divided based on pathological stage, nodal involvement and histological grade. Follow-up blood samples of 35 patients who underwent surgery were collected to investigate if SEMA4C could measure the response to surgical treatment. Results. Postoperative serum levels of SEMA4C were significantly lower than preoperative levels (p p < 0.001). Regarding prognostic value, no statistically significant difference was observed in terms of the pathological stage (p = 0.181), lymph node (LN) status (p = 0.752), and histological grade (p = 0.412). Conclusion. According to our study, serum SEMA4C levels did not differ significantly in terms of pathological stage, LN status and histological grade. Notably, postoperative serum levels of SEMA4C were significantly decreased after surgical treatment compared to preoperative values, which underscores the potential of SEMA4C as a putative candidate biomarker for monitoring response to therapy in patients with BC. However, additional research is mandatory to validate the role of SEMA4C in BC.

Real-World Evaluation of Point-of-Care Testing for Hepatitis C Antibodies: Navigating Hepatitis C Elimination Effort.

An HCV elimination program aims to diagnose more than 90% of Chronic HCV cases. We critically evaluated the performance of a point-of-care test (POCT) using an HCV Rapid Antibody Test. PWID from 4 Halfway Houses (HWH) in Singapore were recruited from March 2022 to April 2023. Participants were concurrently screened for HCV via venous blood for anti-HCV serology and using fingerstick capillary whole blood (FSWB) and oral mucosal transudates (OMT) for POCT, which were interpreted by trained personnel. A blinded study team member independently assessed images of POCTs. Of 207 participants, 37.3% were anti-HCV positive. Compared to anti-HCV serology, POCT performance on FSWB and OMT were: Sensitivity 81.8 (73.2-90.4), 74.0 (64.2-83.8), p = 0.014; Specificity 100.0 (100.0-100.0), 98.5 (96.3-100), p = 0.157. Sub-group analysis of strict 30-min pre-test nil-by-mouth instruction in 103 subjects reported Sensitivity 77.5 (64.6-90.4), 77.5 (64.6-90.4) and Specificity 100.0 (100.0-100.0) and 98.4 (95.3-100.0). OMT positivity and false-negative outcomes did not correlate with the sample analytical cutoff index signal distribution of anti-HCV Serology. Inter-class correlation between real-time and imaging readings of POCT for FSWB and OMT at 20 and 40 min were Kappa 0.9666, 0.9674; 0.8803, 0.8940. Proper preparation and patient selection enhance test performance. Differences in oral fluid immunoglobulin secretion, oral pathology, age, and sample collection can affect POCT OMT readings. POCT OMT is promising in serial and self-testing, complementing its convenience in testing.

D-PRISM: a global survey-based study to assess diagnostic and treatment approaches in pneumonia managed in intensive care

BackgroundPneumonia remains a significant global health concern, particularly among those requiring admission to the intensive care unit (ICU). Despite the availability of international guidelines, there remains heterogeneity in clinical management. The D-PRISM study aimed to develop a global overview of how pneumonias (i.e., community-acquired (CAP), hospital-acquired (HAP), and Ventilator-associated pneumonia (VAP)) are diagnosed and treated in the ICU and compare differences in clinical practice worldwide.MethodsThe D-PRISM study was a multinational, survey-based investigation to assess the diagnosis and treatment of pneumonia in the ICU. A self-administered online questionnaire was distributed to intensive care clinicians from 72 countries between September to November 2022. The questionnaire included sections on professional profiles, current clinical practice in diagnosing and managing CAP, HAP, and VAP, and the availability of microbiology diagnostic tests. Multivariable analysis using multiple regression analysis was used to assess the relationship between reported antibiotic duration and organisational variables collected in the study.ResultsA total of 1296 valid responses were collected from ICU clinicians, spread between low-and-middle income (LMIC) and high-income countries (HIC), with LMIC respondents comprising 51% of respondents. There is heterogeneity across the diagnostic processes, including clinical assessment, where 30% (389) did not consider radiological evidence essential to diagnose pneumonia, variable collection of microbiological samples, and use and practice in bronchoscopy. Microbiological diagnostics were least frequently available in low and lower-middle-income nation settings. Modal intended antibiotic treatment duration was 5–7 days for all types of pneumonia. Shorter durations of antibiotic treatment were associated with antimicrobial stewardship (AMS) programs, high national income status, and formal intensive care training.ConclusionsThis study highlighted variations in clinical practice and diagnostic capabilities for pneumonia, particularly issues with access to diagnostic tools in LMICs were identified. There is a clear need for improved adherence to existing guidelines and standardized approaches to diagnosing and treating pneumonia in the ICU.Trial registration As a survey of current practice, this study was not registered. It was reviewed and endorsed by the European Society of Intensive Care Medicine.Graphical abstract

Evaluating Collection Time of Intragastric Fluid During Endoscopy for Point-of-care Test-based Helicobacter pylori Polymerase Chain Reaction.

Objective To evaluate the influence of sample collection time during esophagogastroduodenoscopy (EGD) on the accuracy of a newly approved point-of-care test (POCT)-based polymerase chain reaction kit for detecting Helicobacter pylori and clarithromycin susceptibility in gastric wash fluid. Methods Intragastric fluid was collected at three time points: Collection Time 1 (start of EGD), Collection Time 2 (during EGD), and Collection Time 3 (after indigo carmine spraying). POCT-based quantitative PCR (qPCR) targeting 23S rRNA domain V (2142/2143) was used to quantify H. pylori DNA in the collected fluid at all three time points and compared with qPCR targeting 16S rRNA. Patients Fifty patients with suspected H. pylori infection were consecutively enrolled in this study over a three-month period and underwent EGD. Results In 9 out of 50 EGD cases that were H. pylori-positive, no significant differences in H. pylori DNA content, quantified using POCT-based qPCR targeting 23S rRNA, were observed between the three collection times: 1 vs. 2, p=0.81; 2 vs. 3, p=0.59; 1 vs. 3. Collection Time 2 had the strongest inverse correlation with the urea breath test (r=-0.80, p=0.01) and was the only time-point at which POCT-based qPCR could detect H. pylori in case 15. Conclusion This study suggests that the optimal collection timing for the H. pylori detection POCT kit (within 60 min) using intragastric fluid (with no biopsy) may be during EGD (Collection Time 2). However, our study had a limited sample size, so the findings must be verified through large-scale, multicenter collaboration studies.

Impact of the Seasons on the Evolution of Tomato-infecting Geminivirus and Identification of Plant Reservoirs Harboring Geminivirus in Burkina Faso

Geminiviruses are known as responsible for huge damage to vegetable crops in many tropical, subtropical, and temperate regions. In Burkina Faso, tomato was reported as the most infected vegetable crop with the involvement of several geminivirus species despite its socioeconomic importance. This suggests and underlines the pressing need for additional information on virus population evolution (diversity, prevalence, and host plant reservoirs). Thus, to address this problem, surveys and sample collection were carried out in three localities in Burkina Faso (Goué, Léguéma, and Toussiana). Tomato leaves and those of cultivated and non-cultivated plants around the tomato fields were collected. The total DNA extracted from these samples was subjected to diagnosis based on the polymerase chain reaction (PCR) protocol with or without amplicon sequencing. Results showed that depending on the season and locality, the prevalence of the disease varied from 0 to 53.33% and that of the virus species varied from 0 to 76.67%. The highest prevalence was observed in the dry season. In addition, PepYVMLV was the virus that was widely detected in all three localities in the rainy (18.89%) and dry (52.22%) seasons. The DNA-B molecule associated with this virus was associated with other begomoviruses (ToLCMLV). In addition, out of 200 samples collected in the vicinity of the tomato fields, only 63 were positive based on PCR diagnosis. Amplicon sequencing yielded 63 partial sequences of virus from ten plant species, including six non-cultivated species. Based on phylogenetic analysis, the 63 partial sequences belonged to three phylogenetic groups (the ToLCV group, the PepYVMLV group, and the CLCuGV group). This study allowed a better understanding of the evolution of tomato leaf curl/yellow disease in Burkina Faso and the diversity of plant species serving as reservoirs for involved viruses. This constitutes an important step in the search for adequate control methods.

Community Based Management Of Sustainable Mangrove Ecosystems In Kendari City, Southeast Sulawesi

Mangrove ecosystems are a form of important role in maintaining the stability of the coastal environment that has ecological, physical and economic-social functions so as to provide interaction between people who live in mangrove areas. efforts in managing sustainable mangrove ecosystems in order to provide carrying capacity to all parties so as to identify, analyze, determine the needs and potential of natural resources in mangrove ecosystems. Mangrove ecosystem damage is caused by two things, namely community activities and natural factors so as to prevent degradation, the application of sustainable mangrove ecosystem management is carried out optimally to preserve mangroves. The study aims to determine the observation of ecosystems and community concepts in sustainable mangrove management in Kendari City. This research method uses descriptive quantitative with sampling techniques using cluster sampling and direct observation data collection. The results of this study indicate that the results of observations from two areas in Kendari City, namely mangroves in the Nambo area with observations of natural / bio and physical environment score range 23 is quite fulfilling for mangrove management while mangroves in the Bungkutoko area score range 37 is very fulfilling said to be sustainable for mangrove management and the results of the questionnaire statement regarding the concept of management descriptively shows community-based sustainable ecosystem management strongly agrees to be well implemented and can be said to be sustainable in mangrove ecosystem management Kendari City Southeast Sulawesi.

Fourier Transform Infrared (FTIR) Spectroscopy as a Tool to Characterize Exercise and Physical Activity: A Systematic Review.

Over the past few decades, the scientific community has recognized the impact of physical activity on health and performance. In parallel, researchers have been actively exploring novel methodologies to analyze the physiological and metabolic responses to exercise. Fourier transform infrared spectroscopy has emerged as a powerful tool in this effort, offering the potential to provide unique insights into exercise-related changes at the molecular level. The primary goal of this systematic review is to confirm the viability of utilizing Fourier transform infrared spectroscopy for the analysis of the biochemical changes associated with physical exercise and its potential applications. This systematic review adhered to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and examined studies employing Fourier transform infrared spectroscopy to analyze exercise and physical activity, focusing on a biological sample collection and spectral analysis. Four databases (PubMed, SPORTDiscus, Web of Science, and Scopus) were searched, and inclusion criteria encompassed original English-language studies involving human participants aged 18-50years, a biological sample collection (urine, saliva, and blood), and the use of Fourier transform infrared spectroscopy. The studies were analyzed considering the type of exercise or sport that was investigated, and also the type of spectral analysis conducted. The review encompassed 15 studies that demonstrated the versatility of Fourier transform infrared spectroscopy in assessing various aspects of exercise, including metabolism, cardiovascular responses, and muscular fatigue. The largest study evaluated 57 athletes from several different sports. On average, almost all the studies were performed with around 20 athletes. Notably, the technique's holistic approach allows for a comprehensive analysis of the complex network of metabolites and proteins within the human body. Data analysis methodologies, particularly when coupled with machine learning, show great potential for advancing the field of sports science. Fourier transform infrared spectroscopy emerges as a promising tool for monitoring and enhancing the performance of high-level athletes, preventing overtraining or even over-reaching, and assessing metabolism. Its accuracy, efficiency, and affordability also make it a candidate for broader applications in assessing the health and fitness of the general population. Future research should explore its applicability across diverse exercise modalities and demographic groups, aiming to prescribe exercise plans that consider a multitude of parameters for larger, more intricate exercise cohorts. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) under the ID number CRD42023441965.

Diagnostic electron microscopy in human infectious diseases - Methods and applications.

Diagnostic electron microscopy (EM) is indispensable in all cases of infectious diseases which deserve or profit from the detection of the entire pathogen (i.e. the infectious unit). The focus of its application has shifted during the last decades from routine diagnostics to diagnostics of special cases, emergencies and the investigation of disease pathogenesis. While the focus of application has changed, the methods remain more or less the same. However, since the number of cases for diagnostic EM has declined as the number of laboratories that are able to perform such investigations, the preservation of the present knowledge is important. The aim of this article is to provide a review of the methods and strategies which are useful for diagnostic EM related to infectious diseases in our days. It also addresses weaknesses as well as useful variants or extensions of established methods. The main techniques, negative staining and thin section EM, are described in detail with links to suitable protocols and more recent improvements, such as thin section EM of small volume suspensions. Sample collection, transport and conservation/inactivation are discussed. Strategies of sample examination and requirements for a proper recognition of structures are outlined. Finally, some examples for the actual application of diagnostic EM related to infectious diseases are presented. The outlook section will discuss recent trends in microscopy, such as automated object recognition by machine learning, regarding their potential in supporting diagnostic EM.

Detection of volatile organic compounds in soils (literature review)

Volatile organic compounds (VOC) are major environmental pollutants. Due to their high mobility, they penetrate into all environmental objects, pose an environmental threat and health risks. Getting into the soil, they deteriorate its quality. VOC content requires reliable control. There is presented a review of the literature, including methods of the US Environmental Protection Agency, and regulatory and methodological documents of the Russian Federation regulating methods of selection, storage, preparation and analysis of soil samples for VOC content. The dominant place among methods for monitoring for VOCs belongs to gas chromatography with various types of detectors. For multicomponent analysis of complex objects, gas chromatography with mass selective detection is used due to the wide capabilities provided by the mass detector. A universal mass spectrometry method used in analytical laboratories is electron impact ionization mass spectrometry. For research purposes, modern highly sensitive methods are used – mass spectrometry based on the proton transfer reaction PTR-MS, ion trap mass spectrometry PIT-MS, negative ion ionization mass spectrometry NI-PT-CIMS, time-of-flight mass spectrometry of the transfer reaction proton PTR-TOF-MS. The collection and storage of samples for VOC analysis requires compliance with regulations to prevent both loss of analytes and sample contamination. Sample preparation includes methods such as vacuum and azeotropic distillation, thermal desorption, liquid extraction, various options for static and dynamic headspace analysis.