PEAKTRAMS: An automated computational approach for the simultaneous detection of features in reverse phase and hilic hrms screening

Comparison of chromatograms obtained in reserved phase (RP) liquid chromatography and hydrophilic interaction liquid chromatography (HILIC) can provide valuable information for the identification and confirmation of suspect and non-target compounds. The plausibility of the obtained chromatographic retention times (RTs) in both modes as well as the ψomparison of the MS/MS spectra are strong points to be considered. This work presents the development of a novel automatic approach for the identification of common peaks between RP and HILIC chromatograms. The core of the program is written in R-project while a simple and user friendly graphical user interface (GUI) was built in JAVA. The first step consists of the introduction of the target chromatograms of the same sample (one obtained by RP and one by HILIC) plus the corresponding blank chromatograms. Blank subtraction was performed first using an algorithm to find in each scan the common m/z features (with a given mass accuracy). This algorithm also considers the RTs (a tolerance interval is applied), so the subtraction takes place even with slight drifts in the RTs between target and blank chromatograms. After blank subtraction, two different lists are obtained with the detected peaks in both RP and HILIC modes. Subsequently, m/z values are compared and matches are listed. The developed workflow was validated with solvent standards and with spiked wastewater samples with a mixture of compounds with a wide range of physicochemical properties. Successful results were obtained for 26 out of the 27 evaluated substances, allowing the recording of the corresponding RTs in both RP and HILIC mode

Molecular detection of prostate specific antigen in patients with prostate cancer or benign prostate hyperplasia the first investigation from Iran

Prostate cancer is the second common form of cancer in men. Detection of circulating Prostate Specific Antigen (PSA) transcripts has effectively been used for early diagnosis of prostate cancer cells. This investigation employed a reverse transcriptase polymerase chain reaction (RT-PCR) technique to distinguish the patients with either localized or metastatic prostate cancer (CaP) vs. Benign Prostate Hyperplasia (BPH) and control subjects, as compared with clinical and pathological records. With reservation of ethical issues, blood samples were collected from 60 cases. Based on pathological and clinical findings, 25 patients (20 with localized cancer, 5 with metastatic), 22 with BPH, and 13 healthy (including 3 females) subjects as negative controls, were selected from Shariati, Mehrad, Sina,, Khatam and Atie Hospitals in Tehran, Iran. RT-PCR for a 260 bp PSA transcript was then performed. Clinical and pathological records were used for the assessment and comparison of PSA RT-PCR results. None of the control subjects and BPH (with 7 exceptions) were found positive by RT-PCR (Relative specificity= 72.7). In patients with prostate cancer, 21 out of 25 were found PSA positive (Relative sensitivity= 83.4) and the remaining 3 have been shown to be PSA negative (Positive predictive value= 83.4). All of 5 metastatic patients (100) revealed PSA positive results. Our data reflects the clinical relevance and significance of RT-PCR results as assessed with clinical and pathological examinations. PSA RT-PCR might be used as a powerful means for diagnosis, even when either pathological or clinical findings are negative, and could be employed for further molecular epidemiology surveys

An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model

Over the last century, outbreaks and pandemics have occurred with disturbing regularity, necessitating advance preparation and large-scale, coordinated response. Here, we developed a machine learning predictive model of disease severity and length of hospitalization for COVID-19, which can be utilized as a platform for future unknown viral outbreaks. We combined untargeted metabolomics on plasma data obtained from COVID-19 patients (n = 111) during hospitalization and healthy controls (n = 342), clinical and comorbidity data (n = 508) to build this patient triage platform, which consists of three parts: (i) the clinical decision tree, which amongst other biomarkers showed that patients with increased eosinophils have worse disease prognosis and can serve as a new potential biomarker with high accuracy (AUC = 0.974), (ii) the estimation of patient hospitalization length with ± 5 days error (R2 = 0.9765) and (iii) the prediction of the disease severity and the need of patient transfer to the intensive care unit. We report a significant decrease in serotonin levels in patients who needed positive airway pressure oxygen and/or were intubated. Furthermore, 5-hydroxy tryptophan, allantoin, and glucuronic acid metabolites were increased in COVID-19 patients and collectively they can serve as biomarkers to predict disease progression. The ability to quickly identify which patients will develop life-threatening illness would allow the efficient allocation of medical resources and implementation of the most effective medical interventions. We would advocate that the same approach could be utilized in future viral outbreaks to help hospitals triage patients more effectively and improve patient outcomes while optimizing healthcare resources

The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate! [Commentary]

The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU. The plan is to bring chemical risk assessors and managers together with scientists to accelerate method development and the production of necessary data and knowledge, and to facilitate the transition to next-generation evidence-based risk assessment, a non-toxic environment and the European Green Deal. The NORMAN Network is an independent, well-established and competent network of more than 80 organisations in the field of emerging substances and has enormous potential to contribute to the implementation of the PARC partnership. NORMAN stands ready to provide expert advice to PARC, drawing on its long experience in the development, harmonisation and testing of advanced tools in relation to chemicals of emerging concern and in support of a European Early Warning System to unravel the risks of contaminants of emerging concern (CECs) and close the gap between research and innovation and regulatory processes. In this commentary we highlight the tools developed by NORMAN that we consider most relevant to supporting the PARC initiative: (i) joint data space and cutting-edge research tools for risk assessment of contaminants of emerging concern; (ii) collaborative European framework to improve data quality and comparability; (iii) advanced data analysis tools for a European early warning system and (iv) support to national and European chemical risk assessment thanks to harnessing, combining and sharing evidence and expertise on CECs. By combining the extensive knowledge and experience of the NORMAN network with the financial and policy-related strengths of the PARC initiative, a large step towards the goal of a non-toxic environment can be taken

"Attempt to Detect Mycoplasma and Chlamydia by Culture in the Synovial Fluid of Patients with Arthritis"

The objective was to investigate the presence of Mycoplasma and Chlamydia in the synovial fluid of patients with rheumatoid arthritis (RA) and other chronic arthritides. Samples of synovial fluid (SF) were collected from all patients presenting with an articular effusion. Seventy SF samples were subjected to study for Mycoplasma and cultured on standard media for Mycoplasma. The 70 other SF samples were subjected to study for the presence of Chlamydia and cultivated on cell cultures specially MC coy cell lines. All standard cultures for Mycoplasma and Chlamydia remained negative, consistent with the fact that synovial fluid is sterile, despite of many investigations that have indicated DNA of some bacteria in the SF of patients with arthritis. However, as many other attempts to detect the presence of these fastidious organisms in the joints of patients with such arthritides have failed, the question of their possible roll in the pathogenesis of human rheumatic diseases remains controversial and needs to be re-examined

Wide-scope target and suspect screening methodologies to investigate the occurrence of new psychoactive substances in influent wastewater from Athens

Almost all licit and illicit drugs consumed by the society end up either unchanged or as a mixture of metabolites in the sewage systems. The analysis of influent wastewater samples and the estimation of drug consumption is the field of wastewater-based epidemiology (WBE). A new trend of WBE is the estimation of the consumption of New Psychoactive Substances (NPS), which are legal replacements of established narcotic and psychotropic drugs with slightly modified chemical structures and similar or new effects. To investigate the occurrence of NPS, 30 composite daily influent wastewater samples from the wastewater treatment plant (WWTP) of Athens (Greece) were collected in a four-year sampling campaign (2015–2018). A generic four-sorbent solid-phase extraction (SPE) sample preparation protocol able to retain compounds with wide physicochemical properties was used. Extracts were analyzed by liquid-chromatography coupled to quadrupole-time-of-flight mass spectrometry (LC-QTOF-MS) using target screening for 278 NPS and suspect screening for 451 NPS. Target screening method was validated for a subset of 49 representative NPS and illicit drugs with similar structures with the NPS. 24 NPS and related compounds were detected by target screening and two compounds were tentatively identified based on mass accuracy, prediction of retention time using in-house QSRR prediction models, isotopic pattern and HRMS/MS fragmentation, whereas the excreted mass loads were also calculated. The results indicated an occasional and low occurrence of NPS in wastewater during the week and over the years, whereas the estimation of the exact sources and the evaluation of the patterns in wastewater were critically discussed. © 2019 Elsevier B.V

Molecular Detection of Prostate Specific Antigen in Patients with Prostate Cancer or Benign Prostate Hyperplasia the First Investigation from Iran

Prostate cancer is the second common form of cancer in men. Detection of circulating Prostate Specific Antigen (PSA) transcripts has effectively been used for early diagnosis of prostate cancer cells. This investigation employed a reverse transcriptase polymerase chain reaction (RT-PCR) technique to distinguish the patients with either localized or metastatic prostate cancer (CaP) vs. Benign Prostate Hyperplasia (BPH) and control subjects, as compared with clinical and pathological records. With reservation of ethical issues, blood samples were collected from 60 cases. Based on pathological and clinical findings, 25 patients (20 with localized cancer, 5 with metastatic), 22 with BPH, and 13 healthy (including 3 females) subjects as negative controls, were selected from Shariati, Mehrad, Sina,, Khatam and Atie Hospitals in Tehran, Iran. RT-PCR for a 260 bp PSA transcript was then performed. Clinical and pathological records were used for the assessment and comparison of PSA RT-PCR results. None of the control subjects and BPH (with 7 exceptions) were found positive by RT-PCR (Relative specificity= 72.7%). In patients with prostate cancer, 21 out of 25 were found PSA positive (Relative sensitivity=83.4%) and the remaining 3 have been shown to be PSA negative (Positive predictive value= 83.4%). All of 5 metastatic patients (100%) revealed PSA positive results. Our data reflects the clinical relevance and significance of RT-PCR results as assessed with clinical and pathological examinations. PSA RT-PCR might be used as a powerful means for diagnosis, even when either pathological or clinical findings are negative, and could be employed for further molecular epidemiology surveys

The strength in numbers: comprehensive characterization of house dust using complementary mass spectrometric techniques

Untargeted analysis of a composite house dust sample has been performed as part of a collaborative effort to evaluate the progress in the field of suspect and nontarget screening and build an extensive database of organic indoor environment contaminants. Twenty-one participants reported results that were curated by the organizers of the collaborative trial. In total, nearly 2350 compounds were identified (18%) or tentatively identified (25% at confidence level 2 and 58% at confidence level 3), making the collaborative trial a success. However, a relatively small share (37%) of all compounds were reported by more than one participant, which shows that there is plenty of room for improvement in the field of suspect and nontarget screening. An even a smaller share (5%) of the total number of compounds were detected using both liquid chromatography–mass spectrometry (LC-MS) and gas chromatography–mass spectrometry (GC-MS). Thus, the two MS techniques are highly complementary. Most of the compounds were detected using LC with electrospray ionization (ESI) MS and comprehensive 2D GC (GC×GC) with atmospheric pressure chemical ionization (APCI) and electron ionization (EI), respectively. Collectively, the three techniques accounted for more than 75% of the reported compounds. Glycols, pharmaceuticals, pesticides, and various biogenic compounds dominated among the compounds reported by LC-MS participants, while hydrocarbons, hydrocarbon derivatives, and chlorinated paraffins and chlorinated biphenyls were primarily reported by GC-MS participants. Plastics additives, flavor and fragrances, and personal care products were reported by both LC-MS and GC-MS participants. It was concluded that the use of multiple analytical techniques was required for a comprehensive characterization of house dust contaminants. Further, several recommendations are given for improved suspect and nontarget screening of house dust and other indoor environment samples, including the use of open-source data processing tools. One of the tools allowed provisional identification of almost 500 compounds that had not been reported by participants. [Figure not available: see fulltext.]. © 2019, The Author(s)